The Brazelton Lab Git Hub contains several software repositories that we have written and continually update as appropriate. We appreciate any contributions to any of our software projects. A short description of each repo follows:

 

bio_utils

 

bio_utils is a generic, Python-based bioinformatics library. It aims to be a faster, more vanilla, less monolithic version of BioPython while having a broader scope and more up-to-date than screed.

 

metameta

 

metameta is a package containing software for analyzing metatranscriptomic data mapped onto metagenomic data. It is currently in need of a re-work and is largely non-useful in its current state.

 

seq_qc

 

seq_qc is a package containing several Python programs to process and filter short read data. Several of these scripts probably improve upon previous, similar tools like prinseq-lite and trimmomatic (data pending).

 

workflow_scripts

 

workflow_scripts repo contains scripts mentioned in our publicly available protocols so that anyone can fully replicate and perform said protocols.

  • Principle Investigatortop ↑


  • Dr. William Brazelton

    Brazelton photoAssistant Professor of Biology

    Microbial Extremist

    Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Postdoctoral Researcherstop ↑


  • Dr. Katrina Twing

    Katrina photoDr. Twing is a postdoctoral researcher with interests in microbial ecology in extreme environments. Her PhD work at Michigan State University focused on identifying diversity and metabolic potential of microorganisms within the continental serpentinite environment. She was a ship-board scientist on IODP Expedition 357: Atlantis Massif Serpentinization and Life, where she helped collect drill core samples from the hard-rock subseafloor adjacent to the Lost City Hydrothermal Field. Dr. Twing's postdoctoral research focuses on identifying the metabolic potential and activity of microorganism within hard rock cores from the Atlantis Massif using 'omics approaches.

    Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Graduate Studentstop ↑


  • Shahrzad Motamedi

    Sheri websiteShahrzad Motamedi is an EEOB graduate student in the Brazelton Lab. Shahrzad is attempting to extract DNA from low-biomass carbonate rocks from cold geysers near Green River, Utah. In addition to this, she is doing some culture-dependent studies on water samples from the geysers. She would like to determine what microorganisms are living there and the kinds of metabolisms that are used by the community that allow them to become adapted to their environment. Also, she is going to work on the rock samples from the Lost City site in the Atlantic Ocean that will be collected in the upcoming Fall. Her research interests are microbial ecology in extreme environments, origin and evolution of life on earth, and life and habitability of Mars.

    Email: This email address is being protected from spambots. You need JavaScript enabled to view it., This email address is being protected from spambots. You need JavaScript enabled to view it.
    Phone: (801) 558-1611


  • Julia McGonigle

    JuliaPicJulia McGonigle is a PhD student of the MCEB program. She is currently working on developing a technique to trace carbon cycling in methanogens using Raman spectroscopy. Her research interests include biology of extreme environments, exobiology, nutrient cycling, and microbial metabolism.

    Email: This email address is being protected from spambots. You need JavaScript enabled to view it.


  • Christopher Thornton

    ChrispicChris is a PhD student in the EEOB program. His research is centered around the use of bioinformatics to investigate communities of microbes in their natural habitats. A project that he is currently involved with makes use of genomic and metagenomic techniques to investigate the influence of human and agricultural waste on antimicrobial concentrations and the presence of antimicrobial resistance determinants in watersheds.

    Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Technicianstop ↑


  • Lizethe Pendleton

    LizethepicLizethe is a Biology Major in her fourth year at the University of Utah. She is currently working with DNA extractions and PCR procedures in the Brazelton Lab. A native to Utah, she enjoys the beauty of this great state in ways that include exploding targets, shooting, river rafting, canoeing, reading, and spending time with family and friends. Her interests in the scientific world include Astronomy, Biology, Geology, and Astrobiology. She hopes to one day become a Marine Biologist or Zoologist.

  • Former Lab Memberstop ↑


  • Alex Hyer

    alexhyerAlex is attending the SLSTP program at the NASA Ames Research Center after which he will be attending graduate school at LSU.


  • Cody Dangerfield

    Cody web photoCody is currently attending graduate school at Utah State University where he will be focusing on tree-ring growth, stable isotopes, and ecophysiology of redwood trees in response to disturbance and climate.

 

 

 

 

 


  • Emily Dart

    Emilypic

    Emily is currently attending graduate school at Clark University.


  • LeAundra Jeffs

    leaundra website LeAundra is currently attending graduate school at the University of Deleware.


  • August Longino

    Augustpic

    August is currently attending medical school at the University of Washington.


  • Mac Pierce

    MacpicMac currently works at the University of Hong Kong.

Research Presentations

A recording of Dr. Brazelton presenting an overview of current research in the lab at a NASA Astrobiology Early Career Seminar.

 

Slides for Dr. Brazelton's presentation, "Introduction to Serpentinite-Hosted Microbial Ecosystems", presented at the Deep Carbon Observatory's "Deep Life" meeting in Lisbon, May 2015. 

 

Slides for Dr. Brazelton's presentation on the importance of microbial ecology and metagenomics in astrobiology, presented at the NASA Astrobiology Conference (AbSciCon) in Chicago, June 2015. 

 

BIOL 3960/5960 Microbial Ecosystems

taught Spring 2015, will be next taught either in Fall 2016 or Spring 2017 under course number BIOL 3270/5270

Syllabus

Canvas course page

List of assigned readings

Slides for lectures available on figshare

 

Microbes Fueled by the Earth:

A major research focus of the Brazelton lab is the study of bacteria and archaea who inhabit rock-hosted environments influenced by a process known as serpentinization. These environments host a set of extreme environmental conditions characterized by high concentrations of hydrogen gas, methane, and other simple organic compounds that are attractive food and energy sources for microbes. Serpentinization has been occurring on Earth ever since it became cool enough to have liquid water, and it is also expected to occur on other planets, such as Mars. Therefore, the lessons we learn by studying the weird archaea and bacteria associated with serpentinization are likely to help us understand the origin, distribution, and evolution of life in the solar system.

What is Serpentinization?

researchheaderSerpentinization is the closest thing to a free lunch that the universe provides. The word 'serpentinization' refers to a complex suite of poorly understood geochemical reactions that occur when rocks from the Earth's mantle are uplifted to the surface. The mantle rocks are oxidized and hydrated by the wet, oxidized conditions at the surface, resulting in the production of water with high pH and high concentrations of hydrogen gas. These reactions occur exothermically (meaning spontaneously), and the elevated levels of hydrogen gas lead to the abiotic synthesis of simple organic compounds. In other words, the consequence of making a rock wet results in the production of hydrogen gas (which is a great fuel for microbial activity) and organic compounds (which everybody likes to eat). The types of rocks involved in the process are possibly even more prevalent beyond Earth, so there is potential for serpentinization activity almost anywhere in the universe where rocks encounter liquid water.

 

The Brazelton lab is associated with the Rock-Powered Life team, a member of the NASA Astrobiology Institute.

Rock Powered Life sponsored by NASA Astrobiology

 

Funding to the lab is also provided by the National Science Foundation, the Center for Dark Energy Biosphere Investigations, and the Deep Carbon Observatory.

Explore specific research projects by clicking on the links in the Research Projects menu or by browsing the map below.

 

You can also learn more about the type of research done in the Brazelton lab by checking out the content at the Education page.

 

View Brazelton Lab Site Map as a full screen map

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