Difference between revisions of "Microbe Hackers"

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[[File:Alignment.png |400px|thumb|right| Alignment of DNA sequence using Benchling.]]
 
[[File:Alignment.png |400px|thumb|right| Alignment of DNA sequence using Benchling.]]
 
In the Microbe Hackers lab, our research projects are conducted with input from our students.  Our Cyanobacteria project was initiated by advanced undergraduates in 2016 and has continued as a project that our students work on since then.  Other projects were initially conceived by Professor Mishler or Professor Barrick, but have been worked on extensively (and sometimes exclusively!) by undergraduates in the group.  '''Currently, we have four active areas of research.'''  Each of these projects is described below, highlighting recent progress, student accomplishments, and our next steps.  
 
In the Microbe Hackers lab, our research projects are conducted with input from our students.  Our Cyanobacteria project was initiated by advanced undergraduates in 2016 and has continued as a project that our students work on since then.  Other projects were initially conceived by Professor Mishler or Professor Barrick, but have been worked on extensively (and sometimes exclusively!) by undergraduates in the group.  '''Currently, we have four active areas of research.'''  Each of these projects is described below, highlighting recent progress, student accomplishments, and our next steps.  
 
  
 
== Caffeinated Coli ==
 
== Caffeinated Coli ==
[[File:Decaffeination.png |400px|thumb|right| Schematic of how Caffeinated Coli works. The introduced genes allow for demethylation of caffeine, also known as 1,3,7-trimethylxanthine.  This results in the formation of xanthine, which is readily converted into guanine, allowing the cells to grow. Figure from Quandt, et al. 2013; "Caffeinated Coli 1.0"]]
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[[File:Decaffeination.png |400px|thumb|right| Schematic of how Caffeinated Coli works. The introduced genes allow for demethylation of caffeine, also known as 1,3,7-trimethylxanthine.  This results in the formation of xanthine, which is readily converted into guanine, allowing the cells to grow. Figure from Quandt, et al. 2013; "Caffeinated Coli 1.0".]]
The Caffeinated Coli project...
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The Caffeinated Coli project has been part of the Microbe Hackers group since before we existed.  These bacteria have been modified to be "addicted" to caffeine.  If they don't have caffeine, they can't grow!  However, if you give them caffeine, they become active and grow until they metabolize all of the caffeine present. After growing with caffeine, we can count the final number of cells grown to determine how much caffeine was originally present.  This "bioassay" is very accurate, and we have used it to calculate the amount of caffeine in a cup of coffee, a can of coke, or an energy drink.
 +
 
 +
 
 +
The original, "Version 1.0" was pioneered by the UT Austin iGEM team with Professor Barrick.  This story was published in 2013.  Since then, the Microbe Hackers have continued to work on Caffeinated Coli.  Our "Version 2.0" has improved upon the original assay by creating a suite of plasmids that can specifically convert various methylxanthines: caffeine, theophylline, theobromine, etc... into xanthine.  Thus, the bioassay can now determine not just how much caffeine is in your drink, but also how much of each of the other methylxanthines are also present.  In fact, the bioassay is as good as standard chemical methods, such as HPLC.  '''The "Version 2.0" story was submitted for publication at the end of August 2019 and was accepted for publication in September 2019.'''  This paper contains five undergraduate authors: Three alumni now in graduate school and two current Microbe Hackers.
  
  
Let's modify its genome and then throw in a genetic device that allows it to live off of caffeinePrevious research by our students can be found covering the [http://pubs.acs.org/doi/abs/10.1021/sb4000146 creation of caffeinated coli] and its use by [http://2014.igem.org/Team:Austin_Texas/human_practices our students in Austin] and further ongoing research on applying the system to [http://2015.igem.org/Team:Austin_UTexas/Project/Caffeine complex beverages].  This work is currently being written up for submission to a scientific journal.  All of the authors are either current or former Microbe Hackers.
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We are now working on "Version 3.0" of the bioassay, attempting to approve assay sensitivity and growth conditions, while demonstrating its usage on a wider array of samples, including environmental and biological samplesThese experiments are being conducted by current Microbe Hackers.  '''Two of our current students, Mina K. and David G., will present their research at the annual [https://sites.cns.utexas.edu/mbssg/fall-undergraduate-research-symposium Fall Undergraduate Research Symposium] here at UT Austin on September 28th.'''  Previous research can be found covering the [http://pubs.acs.org/doi/abs/10.1021/sb4000146 creation of caffeinated coli], its use by [http://2014.igem.org/Team:Austin_Texas/human_practices our students in Austin], and an initial Version 2.0 attempt as part of iGEM 2015 in [http://2015.igem.org/Team:Austin_UTexas/Project/Caffeine complex beverages].
  
 
== Cyanobacteria ==
 
== Cyanobacteria ==

Revision as of 13:52, 19 September 2019

Contents

Welcome to the Microbe Hackers!

Note: This website has been optimized for laptop displays, and may look a bit odd on mobile devices or larger monitors.

Class photo from Spring 2019, our fifth cohort of students.


The Microbe Hackers is a very active and exciting undergraduate teaching and research lab at the University of Texas at Austin. We are part of the Freshman Research Initiative (the FRI program). We conduct research in the field of synthetic biology during the academic year as well as the summer. On our page below, you will find information about our research projects, our course curriculum, and what it means to be a "Microbe Hacker" and a member of the FRI program overall.


In this FRI stream, we do research in the vast and emerging field of synthetic biology. We genetically engineer bacteria for a purpose of our choosing. Information about our projects can be found below. Briefly, in order to modify or engineer our bacteria for some of the applications below, we must work with "genetic devices" (DNA sequences) and specific technology and techniques that are used in research across many disciplines: synthetic biology, molecular biology, microbiology, cell biology, and many more.

Where else would everyone be, but in the lab? Spring 2018 Microbe Hackers.


Students in our group have presented their research at symposiums on campus, conferences across the country, published blog posts and research articles, and have gone on to graduate programs in the health professions and business school, medical school, and PhD programs. Others have taken their experience and pivoted, using the time with us to develop vital skills for 21st century job markets. Many of these students, maybe even most, joined us with little to NO previous lab experience.


Are you a future Microbe Hacker?

If you are interested in research, are looking for a challenge, and you think synthetic biology is something interesting, then YES!

You sound like the perfect Microbe Hacker! Being a Microbe Hacker is about doing research, but more importantly, about developing your potential and preparing you for whatever awaits you in the future.


For more information regarding joining the Microbe Hackers, please read below in the "open house" section.




Stream Research

Alignment of DNA sequence using Benchling.

In the Microbe Hackers lab, our research projects are conducted with input from our students. Our Cyanobacteria project was initiated by advanced undergraduates in 2016 and has continued as a project that our students work on since then. Other projects were initially conceived by Professor Mishler or Professor Barrick, but have been worked on extensively (and sometimes exclusively!) by undergraduates in the group. Currently, we have four active areas of research. Each of these projects is described below, highlighting recent progress, student accomplishments, and our next steps.

Caffeinated Coli

Schematic of how Caffeinated Coli works. The introduced genes allow for demethylation of caffeine, also known as 1,3,7-trimethylxanthine. This results in the formation of xanthine, which is readily converted into guanine, allowing the cells to grow. Figure from Quandt, et al. 2013; "Caffeinated Coli 1.0".

The Caffeinated Coli project has been part of the Microbe Hackers group since before we existed. These bacteria have been modified to be "addicted" to caffeine. If they don't have caffeine, they can't grow! However, if you give them caffeine, they become active and grow until they metabolize all of the caffeine present. After growing with caffeine, we can count the final number of cells grown to determine how much caffeine was originally present. This "bioassay" is very accurate, and we have used it to calculate the amount of caffeine in a cup of coffee, a can of coke, or an energy drink.


The original, "Version 1.0" was pioneered by the UT Austin iGEM team with Professor Barrick. This story was published in 2013. Since then, the Microbe Hackers have continued to work on Caffeinated Coli. Our "Version 2.0" has improved upon the original assay by creating a suite of plasmids that can specifically convert various methylxanthines: caffeine, theophylline, theobromine, etc... into xanthine. Thus, the bioassay can now determine not just how much caffeine is in your drink, but also how much of each of the other methylxanthines are also present. In fact, the bioassay is as good as standard chemical methods, such as HPLC. The "Version 2.0" story was submitted for publication at the end of August 2019 and was accepted for publication in September 2019. This paper contains five undergraduate authors: Three alumni now in graduate school and two current Microbe Hackers.


We are now working on "Version 3.0" of the bioassay, attempting to approve assay sensitivity and growth conditions, while demonstrating its usage on a wider array of samples, including environmental and biological samples. These experiments are being conducted by current Microbe Hackers. Two of our current students, Mina K. and David G., will present their research at the annual Fall Undergraduate Research Symposium here at UT Austin on September 28th. Previous research can be found covering the creation of caffeinated coli, its use by our students in Austin, and an initial Version 2.0 attempt as part of iGEM 2015 in complex beverages.

Cyanobacteria

The Cyanobacteria project...

These bacteria are photosynthetic algae. We attempt to isolate them from the amazing "UTEX" facility that collects algae from around the world. We also attempt to genetically engineer them. This is challenging for several reasons, and an active area of interest.


Broad Host Range Kit

The Broad Host Range Kit (BHR Kit) project...

Give it a genetic device that codes for a green fluorescent protein!

Or, maybe a different color. In Microbe Hackers, you work with these genetically engineered bacteria and you engineer your own bacteria, learning the techniques that will allow you to partake in more comprehensive projects that may span not only your time in Microbe Hackers, but also the time of past and future students. Virtually every organism that you work with was created by a previous Microbe Hacker.


Evolutionary Stability

The Evolutionary Stability (EvoStab) project...

Studying DNA sequence elements that are more prone to mutation, and determining these rates. This data will allow synthetic biologists and other scientists to design "more stable" DNA sequences. This is important for the field of synthetic biology. It is only tangentially related to human disease and we do not actively explore these connections. Some of this research was presented as our 2015 iGEM team project.


No Longer Active Research Projects

Agar plate of E. coli containing different genetic devices created by our Microbe Hackers.
Currently, we have several active research areas:
Image of recapitulated Kombucha with cellulose pellicle using in lab strains. Image by Matthew Hooper (FRI/iGEM2016 student).
  1. Kombucha -NOT ACTIVE- This is a "brewed beverage", that is made by yeast and bacteria. We are attempting to isolate and genetically engineer these organisms in hopes of creating a "designer kombucha". This was our 2016 iGEM team project and is still active.
  2. Broad Host Range Plasmid Kit - This is a relatively new project that is part of our 2017 iGEM team project. This project emerged as a potential answer to some of our earlier difficulties working with "non-model" bacteria, such as cyanobacteria, the bacteria in Kombucha and many other bacteria.


Additionally, over the past few years several projects have wrapped up or have been merged into other projects. We are also considering starting a new project or two in 2020, but we won't know for sure until sometime in 2020.

Course Related Information

Growth of Oscillatoria lutea over 8 days. Work done by Grace Long, undergraduate researcher with the Microbe Hackers and iGEM team member (2016).

Microbe Hackers is the "synthetic biology" research stream. However, our experiments and research can also be broadly classified as molecular biology, genetic engineering, and microbiology. In terms of concepts covered, we deal a lot with genetics, molecular biology, and microbiology. A lot of our course material overlaps with genetics and some overlaps with introductory biology. So, if you take genetics after our stream, then you can hopefully use a lot of what you learn in this FRI stream when you take genetics. And if you are currently taking genetics, then hopefully it will make your semesters with us easier.

Our course material also attempts to cover the most recent news in the field of synthetic biology and how it affects society. This includes CRISPR and the issues dealing with genetic engineering in humans, GMO foods, and how should cutting edge technology be communicated to the public in a way that inspires open dialogue and respect. In 2019, we have discussed in depth CRISPR babies and GMO mosquitoes, among other topics.


For Spring 2020

  • The Lecture portion of this FRI stream should be listed as Mondays 3pm - 5pm. Only ~1 hr of this will be used for lecture. The other hour will be used as a discussion/review/technique time hour for students who want to receive extra exposure to concepts or to the lab prior to beginning that week's lab.
  • The Lab portion of this FRI stream will be determined during the first week of class based on student schedules. You will have a 4 hour lab period that meets once a week during the first part of the course. Later, you will be able to schedule your own lab time.
  • There will also be a weekly discussion time. Attendance is strongly suggested, but not required. You are recommended to sign up for a discussion time prior to your lab time each week!


  • The stream can be taken for: CH204 credit.

NOTE: For Spring 2020 you must take the course for CH204 credit. You can take our second semester course for BIO206L or CH369K/BIO377 credit in the fall. Thus, if you stay with the stream for a full year, you can cover both your CH204 and BIO206L required courses through FRI, which means you do research for two semesters instead of the standard (boring?) intro labs.

If you have other questions, please contact Dr. Mishler. My contact information can be found on the FRI website page that brought you here.

Fall 2019 Open House

If you are interested in hearing about these topics or some of the projects that we have in the research lab, visit us during the Fall 2019 open house or contact Dr. Mishler.

Our Fall 2019 Open House consists of a tour of the lab that lasts approximately 30 minutes. During this tour a mentor and Dr. Mishler will introduce you to the stream, some of the research we conduct, and answer questions. Each tour starts promptly at the time indicated. Please show up 5 minutes early and wait in the hallway near the lab door.

NOTE: You must sign up for a tour using this link: Sign up link. Tour wills consist of no more than 15 students at once.

You will be asked to sign in before the tour starts. If your name is not on the list of attendees, you will be asked to come back later. Please sign up well in advance, if you are interested in our stream.

Spring 2016 Class Photo

NOTE - Include other information: Trivia as well as course photos.

Class photo from Spring 2016

iGEM Competition

iGEM 2018 Team  : NEEDS TO BE UPDATED. NOT CURRENT

The 2018 iGEM team application period is NOT currently open.

Please see this iGEM 2018 Application. Our iGEM team is composed solely of UT Austin undergraduates. These students develop a new project each year, and work on it from Spring to Fall under the guidance of UT professors and graduate students. At the end of this timeline, representatives go to Boston and present their research at an international meeting. Applications are due in "fall", and the new members are selected by the end of the semester.

If you are a freshman, see below for info on joining the iGEM team.

The Microbe Hackers FRI stream also feeds directly into the UT Austin iGEM team, which is led by Professor Mishler and Professor Barrick. Students who conduct research with us during the year, and especially in the summer, are able to participate in the annual project. Every fall, a handful of students are selected to represent UT Austin at this international academic event that features hundreds of teams from around the world, 90% of which are comprised solely of undergraduates conducting research in synthetic biology. Below is a photo of our 2016 and 2015 teams in Boston.

NOTE: The next application period will open in the near future. If you are interested, please see last year's application (above) for details regarding this year's likely expectations.

Previous iGEM teams

Here are our team pages from 2018, 2017, 2016, 2015, and 2014.


FRI students at iGEM2017 in Boston. The five Microbe Hackers are shown with their poster in the background.


FRI students at iGEM2016 in Boston. The five Microbe Hackers are shown with their banner and Professor Mishler.
FRI students at the annual iGEM conference on synthetic biology in Boston. The students presented their research at the end of September to an international audience. The six students in the back row were Microbe Hackers in 2015, and some have continued on as mentors or researchers. The three students in front are high school students from LASA, a local Austin high school that also had an iGEM team in 2015.