Synthetic Biology Teams

• Team Switch; Xi -- In vivo selection of aptazyme and other riboregulators (Near-term priorities)
• Team OptimiRNA; Tony -- Functional miRNA selection (Near-term priorities)
• Team Antibody; Randy, Kris, Paulina, Clint -- Light-modulated antibodies (Near-term priorities)
• Team Prediction; Randy, Kris, Paulina, Casey -- Dezymer-mediated predictions of protein specificities (Near-term priorities)
• Team Plastic; Daniel M. -- Extruding enzymes in plastics (Near-term priorities)
• Team SA; Matt, Wayne -- Emulsion selections with biotin analogues (Near-term priorities)
• Team Orthog; Randy, Kris, Paulina -- Orthogonal amino acid insertion based on tryptophanyl tRNA synthetase (Near-term priorities)
• Team ITS; Eric -- Emulsion selections of polymerase control regions (Near-term priorities)
• Team Autogene; Eric -- Emulsion selections of polymerase enzymes Near-term priorities)
• Team Flp; Eric -- Emulsion selections of recombinases (Near-term priorities)
• Team GFP; Ram -- Screening yeast GFP fusion library for localization Near-term priorities
• Team Amorphous; Zack, Michael W. -- Amorphous computation (Near-term priorities)

Anatomy of A Group Meeting (stolen from www.phdcomics.com without permission, but Jorge would probably okay it.)

[edit] Therapeutics Sub-Group

The recognition of tumor and other cell types is important for the development of diagnostics and therapeutics. Directed evolution can be used to generate reagents that can identify particular cell types, even if the particular biomarker being recognized is unknown, and deliver therapeutic or other molecules to those cells. We have so far focused on the development of aptamer reagents for the recognition of tumor cells, and the use of these aptamer reagents to deliver siRNAs to cells. Ultimately, we believe that we can carry out selections in animal models. Such experiments may lead to the development of 'diapeutics,' therapeutic nucleic acids that also provide a readout of the physiological state of an organism. It should also be possible to engineer development using delivered nucleic acids.

[edit] Technician Sub-Group

[edit] Technology Sub-Group

• Presentations

[edit] Synthetic Biology Sub-Group

It should be possible to engineer living systems at any of a variety of levels. In particular, we are interested in creating self-replicating, self-evolving systems, and in engineering autonomous genetic circuits that can modulate metabolism and physiology. Along the way, we will need to create various components that can be modularly assembled into the larger systems. Various directed evolution methods can be used to create the components and the systems, but emulsion technologies may be amongst the most powerful. The assembly of circuits and systems can either be in vitro or in vivo, and will likely involve the engineering and re-engineering of subsystems, such as translation, signal transduction, and metabolism. We will also need to come up with new software to program our creations, which will require efforts in amorphous computation. Interestingly, the whole notion of synthetic biology also encompasses origins of life research. In many ways, origins was the ultimate biotechnology project.

• Presentations

[edit] Undergraduate Sub-Group

• Presentations
  

[edit] Available projects (Rotation and FRI)

• Assay binding or internalization of anti-cell or anti-receptor aptamers (Jessica; Rotation or FRI; requires tissue culture experience).

• Examine cross-linking of aptamers containing modified nucleotides such as 4-SU or 8-N3A (Gwen; Rotation or FRI).

• Use anti-cell aptamers to introduce miRNAs into cells and examine phenotype changes (Dmitriy; Rotation; requires tissue culture experience).

• Introduce a PSMA expression construct into a lentiviral vector, stably transform it into a eukaryotic cell line, and verify stable expression (Xi; Rotation; requires tissue culture experience).

• Apply anti-cell or anti-receptor aptamers to cells. Determine changes in gene expression using microarray technologies (Dmitriy and EJC; Rotation or FRI; requires tissue culture experience).

• Prepare mutant HIV-1 RTs (Arti; Rotation or FRI).

• Immunoprecipitate and characterize the activities of Ade4 punctates from yeast (Ram; Rotation; collaboration with Marcotte; not concurrent with other projects Ram may supervise). User:Ramm

• High-throughput insertion of Group II introns into bacteria such as Geobacter (Ram; Rotation; collaboration with Lambowitz; not concurrent with other projects Ram may supervise).

• Evolve Qbeta replicase circuit (Eric; Rotation; not concurrent with other projects Eric may supervise).

• Adapt Group II intron to an emulsion selection (Eric; Rotation; collaboration with Lambowitz; not concurrent with other projects Eric may supervise).

• Adapt quorum sensing to an emulsion (Matt; Rotation).

[edit] Ellington Lab Organization

[edit] Administration and Responsibilities

The Ellington lab has always functioned as a semi-organic entity, with roles filled from the bottom up rather than the top down. This of course conforms to Andy's hands-off style, but this style is changing somewhat.

Currently we have what resembles a ‘council of elders’ to guide lab business. The Technicians’ sub-group meets on Tuesday mornings at 9:30 in MBB 3.304. The lab’s representatives include Amos Yan, Angel Syrett, Jessica Ebright, Ana Roberts, Gwen Stovall, and Brad Hall. Supriya Pai attends as our ‘animal rights’ representative. Much of the real work of the lab is borne on the backs of our excellent technicians, Jessica Ebright, Ana Roberts, Paulina Duglosz, and Anthony Paolini. They have their own ways of doing things.

In order to keep everything running we all have Lab Jobs, and a basic way of doing things (Basic Ellington Lab SOP). If you're a new lab member, you may find the following useful: New Member FAQs

• Lab Tech Info
• Lab Jobs (including lab cleanup)
• Basic Ellington Lab SOP

[edit] Operations Infrastructure

Research can be broken down to some basics: get money from grants, do research and spend the money, write papers to justify getting more money. In the best of all worlds, come up with discoveries or products along the way.

However, to abet this process at least some administration is required. You have to order and maintain things, including equipment, to do experiments, and experiments should be carried out according to some set of relatively standardized protocols. In executing these protocols, your safety remains paramount.

Because of the information rich nature of what we do, databases and computation are essential. We maintain an oligonucleotide database, and we need to maintain a database of sequences. These databases will be explicitly connected to oligonucleotides and sequences in publications and theses.

Once you think you have something worth saying to the world, there are procedures and tips for how we Write and communicate manuscripts.

• Administration
  • Andy's Calendar
• Purchasing
• Equipment
• Protocols and SOP's
• Safety
• Databases (including oligonucleotides and pools)
• Computing Resources
• Papers
• Archival

[edit] Beyond the Lab

The Ellington lab maintains associations with and / or guides the development of other entities. We are attempting to enhance interactions with clinical partners via the Division of Biomedical Sciences. In addition, we are trying to advance a number of Facilities to support our mission. The Texas Institute for Drug and Diagnostics Development (TI-3D) and the Center for Systems and Synthetic Biology (CSSB) serve as overarching ORUs for these Facilities. Amongst the Facilities that are supported are the High-Throughput Screenin Facility (HTSF) of the TI-3D, which fronts assays using compound libraries, and the UT Microarray Core Facility of the CSSB, which provides excellent array services. In addition, we are trying to streamline the acquisition and education of human resources (i.e., wetware), mainly via the Freshman Research Initiative.

The Ellington lab coordinates with other entities via Eun Jeong Cho (UTMCF, HTSF), Brad Hall (FRI), Alisha Hall (CSSB), and David Parr (CSSB, computation).

• Division of Biomedical Sciences
• CSSB
• TI-3D
• Freshman Research Initiative
  • CNS FRI Page
  • FRI Wiki

[edit] Lab Members

Researchers in the Ellington lab are highly independent. They run their own projects, their own collaborations, and in many instances their own grants. When necessary, students take short sabbaticals and learn techniques in other labs.

The lab as a whole is and will likely remain a very organic entity. Students and other researchers find their own level within the laboratory. There is somewhat less top-down guidance than the norm, in part because researchers who can set their own direction are prized and researchers frequently help each other more effectively than could the PI. The role of the PI is to provide strategic direction, to come up with fun ideas, and to try to ensure funding, although these goals are also the joint responsibility of lab members. Almost all students will end up directly contributing to the writing of one or more grants during their tenure.

• Lab Member Contact Info
• Lab Users' Pages
• Research Blog
• Lab Artifacts
• Andy's Geopolitical rants
• Further Ranting
• Contests

[edit] Help

• Editing Help Page
• Less Detailed but Potentially Useful Help Page
• Abbreviations - Commonly used abbreviations in Ellingtonia

• To view a journal article from home cut and paste the following proxy address before the .pdf address:

http://ezproxy.lib.utexas.edu/login?url=

Example: The article "Ligand recognition determinants of guanine riboswitches" in NAR has the following link

http://nar.oxfordjournals.org/cgi/content/full/gkm572v1

It would get changed to