Beth's Midterm Proposal

TITLE
The Role of Toxin-Antitoxin Gene Pairs in Cell Death/Cell Survival in Escherichia coli


ABSTRACT
Toxin-antitoxin pairs are pairs of genes that encode the information necessary for the generation of a toxin and an antitoxin. Within a healthy cell, toxin and antitoxin proteins are simultaneously produced, and bind together to form a complex that is harmless to the cell; however, in an abnormal cell, the toxin protein accumulates, disrupting normal cellular functions and ultimately causing cell death. For this reason, toxin-antitoxin pairs have been implicated as key components of programmed cell death mechanisms and the plasmid addiction system (a mechanism in which a cell dies if it does not receive a copy of a small, circular piece of DNA called a plasmid). Understanding the basic mechanisms underlying programmed cell death and plasmid addiction is an important step in gaining insight into disorders/diseases caused by uncontrolled cell proliferation like cancer, and may yield important molecular tools for initiating death in specific, undesired cells in laboratory experiments.

The aim of this project is to generate a miniature database documentary about toxin-antitoxin pairs, and more specifically toxin-antitoxin pairs in the bacterium Escherichia coli. This will be a referential and educational tool that includes a review of toxin-antitoxin pair literature, as well progress on toxin-antitoxin pair research being conducted in the Finkel laboratory at the University of Southern California.


PROJECT GOAL
The primary goal of this multimedia project is to generate a miniature database of information regarding toxin-antitoxin pairs in Escherichia coli. This will be an interactive project that can be used as either a source of reference for people conducting research on toxin-antitoxin pairs in E. coli, or an educational experience for people, both in the general public and in other scientific fields, that have an interest in learning about toxin-antitoxin pairs.

To accomplish this goal, the information contained within this project will be made accessible to both the lay person and the professional researcher: a researcher can browse through the project, looking at current information and research about toxin-antitoxin pairs and bypassing explanations and images that describe basic knowledge (e.g. transcription and translation), while a lay person can browse through the project, bringing up annotations (textual and/or visual) that explain concepts they do not know or understand.


RESEARCH GOALS / METHODLOGY
The specific aim of this research project is to conduct an extensive literature review of toxin-antitoxin pairs in the bacterium Escherichia coli. This project will be comprised of five major components: (1) general information about toxin-antitoxin pairs, (2) toxin-antitoxin pairs in E. coli, (3) proposed theories for the role of toxin-antitoxin pairs in E. coli death and/or survival, (4) potential applications of toxin-antitoxin pair research, (5) progress with research that I am conducting in the laboratory.

The first component of this project will present a broad overview of toxin-antitoxin pairs – the background information. It will begin with two basic concepts that are crucially important to toxin-antitoxin pair action, programmed cell death and plasmid addiction (a mechanism in which a cell dies if it does not receive a copy of a circular piece of extra-genomic DNA called a plasmid). The discussion will continue with the identification of toxin-antitoxin pairs on bacterial genomes, what they are, how they are thought to act, and their potential significance for cell death or survival.

The second component of this project will concentrate on the main focus of this project, toxin-antitoxin pairs on the E. coli genome. This section will include information about each of the toxin-antitoxin pairs identified in E. coli, their locations on the E. coli genome, their putative modes of action, and other pertinent information.
The third section will be focused on the major theories regarding the purposes of these toxin-antitoxin pairs in E. coli. The theories proposed by the two major camps of toxin-antitoxin pair research, the Gerdes laboratory and the Engelberg-Kulka laboratory, will be discussed here, as well as the theory proposed by the Finkel laboratory.

The fourth, and final section of the literature review, will be concerned with the potential applications of toxin-antitoxin pair research. Understanding the mechanisms of toxin-antitoxin pairs is a major step forward in understanding programmed cell death mechanisms, and possibly the mechanisms underlying the termination of programmed cell death abnormal proliferation of cells (e.g. cancer). Additionally, toxin-antitoxin pairs have the potentially of being a very useful molecular technique that can be used to terminate certain, unwanted cells in controlled experiments.

The final component of this project will be concerned with my own research. This section will consist primarily of the protocols and processes that are involved in my research, with a little bit of data. Realistically, there will be little data to present, as current research endeavors are focused on the generation of mutant E. coli strains required for the study of toxin-antitoxin pairs.


PROJECT FORMAT AND JUSTIFICATION
Data presentation is one of the most important aspects of the scientific process, regardless of whether the project is a literature review or laboratory-based research. The publication of papers and the presentation of works at conferences and symposiums allow researchers to present their findings to the scientific community, as well as the general public. This generates a forum for the discussion and exchange of ideas, which is inherently important to scientific progress.

There are three primary modes of presentation in scientific disciplines: paper publications, oral presentations, and poster presentations. Despite the inherently scholastic nature of science, which demands careful note-taking, attention to detail, and the analysis and interpretation of data, there are many aspects of science that are better explained through images, especially for lay audiences or those unfamiliar with the research topic. These components include physical, chemical, or physiological mechanisms, experimental procedures, and data. For instance, it is much easier to understand how a neurotoxin can cause paralysis via a schematic drawing or an animation, than it is to read a dense passage detailing each step in the process. Likewise, it is much easier to understand data presented as a graph than as a list of numbers.

For this reason, the multimedia format of this project will be a database documentary. It is critically important to maintain a textual, scholarly component in the presentation of this project because of the scientific nature of the research: at the core of this project is a literature review of toxin-antitoxin pairs in the bacterium Escherichia coli, and secondarily, data collected from ongoing research. However, there are multiple components of this project that are far better served by visual aids: pictures, animations, interviews, etc. A database documentary will allow for the incorporation of both scholastic and multimedia components, as well as allow the audience to explore and learn about toxin-antitoxin pairs in E. coli at their leisure and personal level of understanding.