Systems biology analysis of the EGF MAPK pathway: from structures to data integration

Comunicaciones a congreso

Breathe... Keep Breathing.

I work with short-duration seamless video loops. My work simultaneously depicts and emulates the material composition of time, specifically how action composes time and how time can compose or construct objects. My work is self-reflexive. Self-reflexive means that a product actively considers or examines its own production. In video this means breaking either the illusion of depicted time as real time or the illusion of the depicted image as real space. Video loops are self-reflexive by function. Their periodic recurrence points out the artifact of the medium. The periodic recurrence of video loops also changes the narrative quality of the moving image. Eliminating the beginning and end of videos, making them indefinite, calls the viewer into a suspended narrative. By making that narrative about the material composition of time, I add another layer of reflexivity. A study of the material composition of time also raises the question of the relative metaphysical position of the moment “now” within time. By building this system of inter-connected reflexive relationships around time, I am attempting to create an atmosphere for meditation on and consideration of the self-reflexive nature of our own self-awareness, which philosopher Johann Fichte describes as such: “The self\u27s own positing of itself is thus its own pure activity. The self posits itself, and by virtue of this mere self-assertion it exists; and conversely, the self exists and posits its own existence by virtue of merely existing. It is at once the agent and the product of action; the active, and what the activity brings about; action and deed are one and the same.” (97)* This relationship of our self-awareness to time and to the systems constructed to examine time within time is what fascinates me. I am trying to construct pieces and places that encourage contemplative meditation on that relationship. As a constructed and immersive environment, these video loops are combined and contrasted to add one more layer, one more circle manifest in the physical space of the gallery, to the constructed system. This series of loops and circuits continues when the viewer plugs into the environment and becomes one more dimension of the piece, namely the dimension that defines the piece within the “now”. That definition is locational within time, and the circuit is complete for as long as the viewer’s attention persists. Time is the breath of video. Meditation is an awareness of breath. Breathe… keep breathing. Adviser: Aaron Holz * Fichte, Johann. The Science of Knowledge, trans. Peter Heath and John Lachs (Cambridge: Cambridge, 1982)

Location of Salmonella in poultry fat intended for use in pet food and the influence of fat's physical characteristics on Salmonella prevalence and growth

2016 Fall.Includes bibliographical references.This study was conducted to: (i) utilize fluorescently-tagged Salmonella to assess distribution of Salmonella in a rendered fat matrix; (ii) assess the influence of post-inoculation time and moisture content on distribution of fluorescently-tagged Salmonella in rendered poultry fat; and, (iii) evaluate the impact of post-inoculation time and physical parameters (i.e., impurity level and moisture content) on survival of three Salmonella serotype strains in rendered poultry fat stored at 25˚C or 45˚C. Three studies, designated as Study I(a), I(b) and II were conducted to address the objectives. In Study I(a), a green fluorescent protein (GFP)-expressing strain of Salmonella Typhimurium was used to visually and microbiologically map the organism within warmed (45˚C) poultry fat formulations comprised of a low impurity level (<0.2%) and three moisture contents (low: 0.5%; medium: 2.2%; high: 4.5%). In Study I(b), using the same fat formulations as in Study I(a), survivability of GFP-expressing Salmonella was compared in samples that were either stored at 25˚C or 45˚C. In Study II, survivability of three Salmonella serotype (Enteritidis, Senftenberg, Typhimurium) strains was compared in fat formulations of two impurity levels (0.5%, 1.0%), three moisture contents (low: 0.5-0.7%; medium: 2.1-3.0%; high: 3.9-4.8%) and two temperatures (25˚C, 45˚C). Surviving populations of Salmonella Typhimurium and their location in a rendered fat matrix were achieved for each treatment combination (Study I). For Study I(b) and II, death/survival/growth curves were developed and comparisons among factors of time, temperature and moisture contents were made. In conclusion, the best option for the rendering industry to control Salmonella in poultry fat it is to control multiple factors when storing the final product, more specifically, low impurity poultry fat with low moisture content that is stored at a high temperature (45˚C and above) for a period of time would effectively control Salmonella contamination in poultry fat. Preventing recontamination is another crucial point for the rendering facilities, in that matter, GMP is essential, sanitation conditions that will not allow contamination and biofilm formation should be implemented and validated, as appropriate cleaning with scrubbing in holding bins, storage tanks, floors, walls, trucks, everything that have contact with the product

The depoliticization of public policy.

Political ScienceDoctor of Philosophy (PhD

Breathe... Keep Breathing.

I work with short-duration seamless video loops. My work simultaneously depicts and emulates the material composition of time, specifically how action composes time and how time can compose or construct objects. My work is self-reflexive. Self-reflexive means that a product actively considers or examines its own production. In video this means breaking either the illusion of depicted time as real time or the illusion of the depicted image as real space. Video loops are self-reflexive by function. Their periodic recurrence points out the artifact of the medium. The periodic recurrence of video loops also changes the narrative quality of the moving image. Eliminating the beginning and end of videos, making them indefinite, calls the viewer into a suspended narrative. By making that narrative about the material composition of time, I add another layer of reflexivity. A study of the material composition of time also raises the question of the relative metaphysical position of the moment “now” within time. By building this system of inter-connected reflexive relationships around time, I am attempting to create an atmosphere for meditation on and consideration of the self-reflexive nature of our own self-awareness, which philosopher Johann Fichte describes as such: “The self\u27s own positing of itself is thus its own pure activity. The self posits itself, and by virtue of this mere self-assertion it exists; and conversely, the self exists and posits its own existence by virtue of merely existing. It is at once the agent and the product of action; the active, and what the activity brings about; action and deed are one and the same.” (97)* This relationship of our self-awareness to time and to the systems constructed to examine time within time is what fascinates me. I am trying to construct pieces and places that encourage contemplative meditation on that relationship. As a constructed and immersive environment, these video loops are combined and contrasted to add one more layer, one more circle manifest in the physical space of the gallery, to the constructed system. This series of loops and circuits continues when the viewer plugs into the environment and becomes one more dimension of the piece, namely the dimension that defines the piece within the “now”. That definition is locational within time, and the circuit is complete for as long as the viewer’s attention persists. Time is the breath of video. Meditation is an awareness of breath. Breathe… keep breathing. Adviser: Aaron Holz * Fichte, Johann. The Science of Knowledge, trans. Peter Heath and John Lachs (Cambridge: Cambridge, 1982)

Combining Gene-Disease Associations with Single-Cell Gene Expression Data Provides Anatomy-Specific Subnetworks in Age-Related Macular Degeneration

Background: Age-related macular degeneration (AMD) is the most common cause of visual impairment in the developed world. Despite some treatment options for late AMD, there is no intervention that blocks early AMD proceeding to the late and blinding forms. This is partly due to the lack of precise drug targets, despite great advances in genetics, epidemiology, and protein-protein interaction (PPI) networks proposed to be driving the disease pathology. A systems approach to narrow down PPI networks to specific protein drug targets would provide new therapeutic options. Materials and Methods: In this study we analyzed single cell RNAseq (RNA sequencing) datasets of 17 cell types present in choroidal, retinal pigment epithelium (RPE), and neural retina (NR) tissues to explore if a more granular analysis incorporating different cell types exposes more specific pathways and relationships. Furthermore, we developed a novel and systematic gene ontology database (SysGO) to explore if a subcellular classification of processes will further enhance the understanding of the pathogenesis of this complex disorder and its comorbidities with other age-related diseases. Results: We found that 57% of the AMD (risk) genes are among the top 25% expressed genes in ∼1 of the 17 choroidal/RPE/NR cell types, and 9% were among the top 1% of expressed genes. Using SysGO, we identified an enrichment of AMD genes in cell membrane and extracellular anatomical locations, and we found both functional enrichments (e.g., cell adhesion) and cell types (e.g., fibroblasts, microglia) not previously associated with AMD pathogenesis. We reconstructed PPI networks among the top expressed AMD genes for all 17 choroidal/RPE/NR cell types, which provides molecular and anatomical definitions of AMD phenotypes that can guide therapeutic approaches to target this complex disease. Conclusion: We provide mechanism-based AMD endophenotypes that can be exploited in vitro, using computational models and for drug discovery/repurposing

Ribosome recycling: An essential process of protein synthesis

A preponderance of textbooks outlines cellular protein synthesis (translation) in three basic steps: initiation, elongation, and termination. However, researchers in the field of translation accept that a vital fourth step exists; this fourth step is called ribosome recycling. Ribosome recycling occurs after the nascent polypeptide has been released during the termination step. Despite the release of the polypeptide, ribosomes remain bound to the mRNA and tRNA. It is only during the fourth step of translation that ribosomes are ultimately released from the mRNA, split into subunits, and are free to bind new mRNA, thus the term ribosome recycling. This step is essential to the viability of cells. In bacteria, it is catalyzed by two proteins, elongation factor G and ribosome recycling factor, a near perfect structural mimic of tRNA. Eukaryotic organelles such as mitochondria and chloroplasts possess ribosome recycling factor and elongation factor G homologues, but the nature of ribosome recycling in eukaryotic cytoplasm is still under investigation. In this review, the discovery of ribosome recycling and the basic mechanisms involved are discussed so that textbook writers and teachers can include this vital step, which is just as important as the three conventional steps, in sections dealing with protein synthesis