Saturday, October 21, 2006, 06:06 PM
Brad is beginning his 5th year as a graduate student in the Ellington Lab. Prior to this, he worked as a research technician on a project to develop nucleic acid taggant technologies for tracking solid and liquid substances. He graduated from Indiana University in Bloomington where he received his B.S. in Microbiology and worked in Jeff Palmer's lab elucidating the phylogenetic relationships of Pelargonium species.
His main area of focus is predicting conformational changes in functional nucleic acids for the design and application of biosensors. One aspect this work has been to design computationally tractable algorithms to construct and select molecular beacon switches from known aptamer sequences. Targets of these aptamers include angiogenesis inducers (VegF, bFGF, Angiogenin, PDGF and MEK1) which are known to accompany solid tumor growth. Biosensors developed from this method could be used to noninvasively detect the presence of tumors in vivo. While computation plays a large role in the design, he also experimentally validates many of the computational predictions. The major impact of the work is that if researchers can in fact segue from 'in vitro' to 'in silico' selection and back again it will vastly decrease the time and effort necessary for the development of sensitive and specific biosensors.
Monday, August 7, 2006, 12:33 PM
Dat Vo, Ellington Lab Researcher, worked part-time in the Ellington laboratory as an undergraduate and then began full-time work in the Ellington lab after graduation. He shared some thoughts about what it's like to work in the Ellington Lab as a researcher.
Dat:
At UT, I received my Bachelor of Science in Biochemistry in 12/ 2004. After graduation, I worked in the Ellington lab, focusing on the design of RNA-based genetic regulatory elements. In an effort to engineer RNA-based genetic regulatory elements as potential gene therapies, we have chosen to use tools pioneered by our group in allosteric ribozymes, catalytic polynucleotides whose function is modulated by an effector such as a small molecule, oligonucleotides, or proteins making it a good candidate for the design of regulatory elements. In addition to using allosteric ribozymes as a means to regulate the delivery of nucleic acid-based regulatory elements, we have coupled it with an emerging technology in RNA interference. Since its recent discovery in model organisms, it has been shown to be a powerful tool for the study of biology and is a viable candidate for use in gene therapy; because of its vast potential, we have chosen RNAi technology as our nucleic acid-based therapy of choice.
To this end, the overall goal of our system and efforts is to create an effective control of gene silencing under induction from an external effector. RNA silencing has been shown to be an effective tool for stable and efficient gene suppression. However, constitutive and undesired gene silencing highly affect other endogenous systems especially those essential to cell survival, cell cycle regulation, and cell development. The prospect of dose-dependent and time-dependent silencing from allosteric ribozyme delivered-gene silencing to remedy the downfall of constitutive gene silencing is highly applicable and useful for the development of RNAi-based therapeutics. A major application of controllable RNA interference is when partial gene silencing, especially when a cell shows distinct phenotypes as a result of the level of a gene or when lethality from a complete gene suppression is a concern, or a temporal desire for gene silencing is preferred. Our hope from our engineering is to produce a system that allows for the facile and finely-tuned control of gene silencing.
In the fall of 2006, I will begin studies at The University of Texas Health Sciences Center at San Antonio, training in both the basic and clinical sciences in an MD/PhD program with the ultimate goal in bridging the gap between bench discoveries and clinical practices.
Wednesday, July 19, 2006, 11:45 AM
I received my B.A. studying Biology and Biochemistry from the University of Texas in 2001. I studied evolutionary biology in the lab of Jim Bull for two years during that time.
I received my Ph. D. in May 2006 from the University of Texas, studying under Andy Ellington and will be joining the Voigt lab as a post-doc in August 2006. My primary interests include the forward design and programming of novel cellular behaviors (synthetic biology) using genetic regulation strategies at both the canonical protein/DNA interaction level (e.g. controlling POPS; Endy, Nature, 2005) and at the level of riboregulation (e.g. Bayer and Smolke, Nature Biotechnology 2005). I have been heavily involved with a synthetic biology group here at UT over the last two years which has designed and built a "bacterial photography" system in which a community of E.coli act as a biological film capable of capturing and permanently recapitulating any light image.
I am also interested in the quantitative characteristics of natural mechanisms of gene regulation and expression. Uncontrollable fluctuations in gene expression in populations of genetically identical individuals can lead to quantifiably diverse (even opposite) phenotypes within that population. It is becoming more and more obvious that biology, being evolutionarily adept as it is, has taken advantage of the noise inherent in gene expression to encode complex population level behaviors using simple genetic level specifications. For example, the virus HIV encodes a genetic amplifier in its genome, wherein a protein product of a gene results in higher transcription levels of that gene. Upon infection of a host cell, the levels of that protein product usually tend about some mean. Uncontrollable fluctuations below that mean at some critical time point result in the HIV genomes in that invaded cell going lysogenic. Fluctuations above that mean at some critical time point result in the HIV genomes in that cell going lytic. There are fitness advantages to such a bifuracted reproductive strategy, and this virus has used noise as opposed to hard-wired genetic to encode this behavior. Clearly, noise can sometimes be detrimental to cellular survival, and in certain instances biology has evolved ways to insulate, buffer or engineer away noise in gene expression as well.
Wednesday, May 24, 2006, 12:44 PM
Allysia Matthews, Ellington Lab Researcher, graduated from the University of Texas at Austin and then began working in the lab full-time as a laboratory technician. She shared some thoughts about what it's like to work in the Ellington Lab as a researcher.
Allysia:
"I began working in the Ellington Lab 4 years ago. During my time here I have been part of a variety of projects that have enhanced my abilities as a scientist. My most recent projects have involved HIV-1 inhibition and the variation of microRNA expression under different stress conditions. With the HIV-1 inhibition project, I have been investigating the inhibitory effects of L-canavanine, a structural analogue of L-arginine and a compound found in Sutherlandia frutescens (an immune boosting medicinal plant used to treat HIV/AIDS in parts of Africa) (paper in progress). I am also working to create microRNA expression profiles of HIV-infected vs. non-infected cells using microarray technology. Our ultimate goal is to look at the microRNA expression profiles of a wide variety of viral infections, including avian influenza."
"I graduated from UT with a BS in Biochemistry two years ago and since that time I have been working as a full-time technician. During this time I have had the opportunity to learn about the administrative side to running a lab, while continuing my bench work. I have treasured my time here and am grateful for the experience it has given me. I will be leaving the lab at the end of June to attend Weill Graduate School in New York, NY, where I will work towards my PhD in Immunology. The knowledge that I gained during my time in the Ellington Lab was instrumental in allowing me to pursue this next stage in my life. From here, I hope to build on this knowledge and have a rewarding scientific career."
Tuesday, May 23, 2006, 10:03 AM
Patrick Goertz, Ellington Lab Undergraduate Researcher, recently graduated from the University of Texas at Austin with a degree in Molecular Biology and Chemistry. He shared some thoughts about what it's like to work in the Ellington Lab as an undergraduate.
Patrick:
"I am currently working on improving existing aptamer utility by extending the aptamer sequence to include a new, unevolved nucleic acid segment. The new construct is re-evolved by in vitro selection. We have been developing this method to improve nucleic acid binders (i.e. aptamers) against HIV reverse transcriptase. The preliminary results have been very promising. The project recently received the Ambion Award for Excellence in RNA Research when presented at a poster conference on the UT campus."
"I have been in the lab for three years. I joined at the end of my freshman year after attending a seminar given by Dr. Ellington. I greatly enjoy the freedom given to researchers in the lab. As an undergraduate, I never expected to be allowed to work independently in a research environment. In the Ellington lab, I was given my own project and allowed to make decisions regarding its execution within the first few months of joining. The experiences in the lab had an incalculable impact on my undergraduate experience. The techniques and methods learned in the lab reinforced the concepts of the courses that I undertook."
The Ellington lab will miss Patrick, and we wish him the best!
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