Difference: ResearchInterests (59 vs. 60)

Revision 602025-03-20 - JeffreyBarrick

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  Barrick Lab :: Research
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+Listen to an introduction to our research: Studying Evolution and Engineering Bee Guts (EBRC in Translation Podcast)
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+Listen to an introduction to our synthetic biology research:
Studying Evolution and Engineering Bee Guts (EBRC in Translation Podcast)
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+Watch a public seminar on our microbial evolution research at UT Tyler 2024 Darwin Day:
The Long-Term Evolution Experiment: Watching Bacteria Evolve for More Than Three Decades
   Evolving and Engineering Insect Symbionts 
  Honey Bees: Functional Genomics and Protecting Pollinator Health
   Aphids: Understanding the Evolution of Endosymbionts and Pest Control
 
   Improving the Reliability of Synthetic Biology
   Dynamics of Microbial Genome Evolution 
  The E. coli Long-Term Evolution Experiment (LTEE)
   Evolution and Engineering of Naturally Transformable Bacteria 
   Evolution and Ecology of Bartonella Parasites in the Negev Desert
 
 


See also: Previous Research Projects
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+ Evolving and Engineering Insect Symbionts
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+ Evolving and Engineering Insect Symbionts
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+Many insects have more consequential associations with bacteria than we have with the human microbiome. We create genetic tools to study these bacterial symbionts and engineer their interactions with insects. We also use experimental evolution to examine how new symbionts arise and how interactions within a microbiome and between microbes and their hosts can change. These projects are highly collaborative and have also involved researchers from the Moran Lab, the Ellington Lab, the Davies Lab, and other research groups.
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+Many insects have more consequential associations with bacteria than we have with the human microbiome. We create genetic tools to study these bacterial symbionts and engineer their interactions with insects. We also use experimental evolution to examine how new symbionts arise and how interactions within a microbiome and between microbes and their hosts can change. These projects are highly collaborative and have also involved researchers from the Moran Lab, the Davies Lab, the Ellington Lab and other research groups.
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+ Current Funding: ARO MURI, NSF EDGE, ERDC     Past Funding: DARPA BRICS, DARPA Insect Allies
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+ Current Funding: ARO MURI, NSF EDGE, USDA NIFA     Past Funding: DARPA BRICS, DARPA Insect Allies, ERDC
  Overview Publication 
 Elston et al. (2022) Trends in Microbiology  PMID: 34103228
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+ Honey Bees: Functional Genomics and Protecting Pollinator Health
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+ Honey Bees: Functional Genomics and Protecting Pollinator Health
 Engineered symbionts kill honey bee parasites 
Bees are ecologically and economically important pollinators. We created a bee microbiome toolkit (BTK) for engineering bacteria that colonize the guts of honey bees (Apis mellifera) and bumble bees (Bombus species). We recently showed that we can engineer the bacterium Snodgrassella alvi to implement effective symbiont-mediated RNAi. This system can be used for the targeted knockdown of bee genes to study their functions. For example, we have used it to alter honey bee feeding behavior. We have also shown that these engineered symbionts can be used to protect honey bees from viral pathogens and arthropod parasites that imperil the health of hives.
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+ Current Researchers: Zuberi Ashraf, Kathleen Sotelo, Kadena Cope, PJ Lariviere, Lucio Navarro, Dennis Mishler
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+ Current Researchers: Zuberi Ashraf, Kadena Cope, Korin Jones, Kathleen Sotelo, PJ Lariviere, Lucio Navarro, Dennis Mishler
  News: Bacteria Engineered to Protect Bees from Pests and Pathogens

 Representative Publications 

 Lariviere et al. (2023) Nature Protocols  PMID: 36460809
  Leonard et al. (2020) Science  PMID: 32001655
  Leonard et al. (2018) ACS Synthetic Biology PMID: 29608282
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+ Aphids: Understanding the Evolution of Endosymbionts
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+ Aphids: Understanding the Evolution of Endosymbionts and Pest Control
   GFP-tagged symbiont colonizing the aphid gut
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+Aphids are plant pests and model systems for studying bacteria-insect symbioses. We have developed tools for engineering strains of Serratia symbiotica that colonize the aphid gut. We are now using these tools to unravel how these strains, which can be pathogenic to their hosts, are related to strains of S. symbiotica that live within insect cells, are inherited across aphid generations, and can benefit their aphid hosts. We have showed that cultured S. symbiotica strains are capable of maternal transmission within aphids, suggesting that they possess a latent capacity to evolve a long-term symbiotic relationship with their hosts. We are also exploring applications of these engineered bacteria related to pest control.
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+Aphids are plant pests and model systems for studying bacteria-insect symbioses. We have developed tools for engineering strains of Serratia symbiotica that colonize the aphid gut. We are now using these tools to unravel how these strains, which can be pathogenic to their hosts, are related to strains of S. symbiotica that live within insect cells, are inherited across aphid generations, and can benefit their aphid hosts. We have showed that cultured S. symbiotica strains are capable of maternal transmission within aphids, suggesting that they possess a latent capacity to evolve a long-term symbiotic relationship with their hosts. We are also exploring applications of these engineered bacteria related to pest control, especially through symbiont-mediated RNAi.
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+ Current Researchers: Anthony VanDieren
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+ Current Researchers: Anthony VanDieren, Lucio Navarro
  News: Turning Plant Pests into Helpers

 Representative Publications 

 Elston et al. (2023) PeerJ PMID:  36874963
  Elston et al. (2020) Applied and Environmental Microbiology PMID: 33277267
  Perreau et al. (2020) mBio PMID: 35012344
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+ Leafhoppers: Evolution and Biochemistry of Natural Nanoparticles 


 
  Leafhopper and SEM image of brochosomes on its wing 

Leafhoppers produce unique nanostructures, called brochosomes, that they anoint onto their wings and sometimes eggs. Brochosomes have interesting materials properties, including superhydrophobicity and omnidirectional antireflectivity. We are characterizing natural variation in brochosome structures and performing comparative genomics to understand the molecular components that make up these structures, how they evolved, and their biological functions. We are also working towards genetically engineering symbionts of leafhoppers to create new tools for studying brochosomes and potentially enhancing their properties for various applications.


 News: Tiny Insects Provide Inspiration for New Biomaterials
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+ Improving the Reliability of Synthetic Biology
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+ Improving the Reliability of Synthetic Biology
 Evolutionary half-lives of biological devices 


Synthetic biology applies engineering principles to create living systems with predictable and useful behaviors from collections of standardized genetic parts. However, living systems – unlike mechanical devices – inevitably evolve when their DNA sequences accumulate copying errors, often resulting in "broken" cells that no longer function as they were programmed. We are addressing this challenge by better characterizing how engineered cells evolve and using this information to design DNA sequences and host cells that are more robust against unwanted evolution. Also, precisely defining the function, extent, and provenance of genetic parts can be complicated because variation in these parts can arise from engineering or intentional evolution. This work includes: (1) developing "negative design" software to alert researchers to genetically unstable and unintentionally burdensome DNA designs; (2) using experimental evolution and engineering to create "antimutator" variants of host organisms that have lower-than-natural mutation rates; and (3) developing databases and software tools for improved annotation of engineered DNA sequences and common variants of those sequences.
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+ Current Researchers: Cameron Roots
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+ Current Researchers: Dennis Mishler, Cameron Roots
  Representative Publications
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+ Radde et al. (2024) Nature Communications PMID: 39048554
  Roots & Barrick (2024) Synthetic Biology PMID: 39722801
  McGuffie & Barrick (2021) Nucleic Acids Research PMID: 34019636
  Deatherage et al. (2018) Nucleic Acids Research PMID: 30137492
  Jack et al. (2015) ACS Synthetic Biology PMID:26096262
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+ Renda et al. (2014) Molecular Biosystems  PMID:24556867
  Current Funding: NIH R01;      Past Funding: NSF CAREER, DARPA BRICS, DARPA Insect Allies
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+ Dynamics of Microbial Genome Evolution
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+ Dynamics of Microbial Genome Evolution
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+ The E. coli Long-Term Evolution Experiment (LTEE)
 Accumulation of mutations in population Ara-1 of the LTEE over 20,000 generations of evolution
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+We develop the breseq computational pipeline for identifying mutations in laboratory-evolved microbial genomes from next-generation sequencing data. We have used this tool to extensively study rates of genome evolution in the 30-year Lenski long-term evolution experiment (LTEE) with E. coli. We continue to develop breseq so that it can be used for more additional applications related to strain engineering and medicine. For example, we are interested in how tracking rare variants within populations of microorganisms can anticipate further evolutionary trajectories and how this information might be used to better diagnose and treat disease.
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+We develop the breseq computational pipeline for identifying mutations in laboratory-evolved microbial genomes from next-generation sequencing data. We have used this tool to extensively study rates of genome evolution in the >35-year Lenski long-term evolution experiment (LTEE) with E. coli. We continue to develop breseq and related computational pipelines so that it can be used for more additional applications related to strain engineering and medicine. For example, we are interested in how tracking rare variants within populations of microorganisms can anticipate further evolutionary trajectories and how this information might be used to better diagnose and treat disease. We also have other ongoing projects related to understanding the mechanisms and dynamics of bacterial evolution and ecology in the LTEE using other high-throughput and systems biology approaches.
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+ Current Researchers: Ira Zibbu, Pranesh Rao, Alexa Morton
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+ Current Researchers: Alexa Morton, Pranesh Rao,  Ira Zibbu
  News: Legendary bacterial evolution experiment enters new era

 Representative Publications 

 Deatherage & Barrick et al. (2021) Cell Systems PMID: 34536379
  Zhang et al. (2019) Nature Communications PMID: 31863068
  Deatherage et al. (2017) PNAS PMID: 28202733
  Deatherage and Barrick (2014) Methods Mol in Molecular Biology PMID:24838886
  Barrick and Lenski (2013) Nature Reviews Genetics. PMID:24166031
 

 Funding: NSF LTREB, UT-CNS SPARK, NSF EEID, NASA     Past Funding: NSF K99/R00


 Evolution and Engineering of Naturally Transformable Bacteria 


 
 
Insertion sequences (red) deleted in the transposon-free strain Acinetobacter baylyi ADP1-ISx 


Naturally competent bacteria have expanded evolutionary potential because they can readily acquire new DNA from their environment. We are using experimental evolution of the model organism Acinetobacter baylyi ADP1 to understand how horizontally acquired genes and mobile genetic elements become domesticated after their incorporation into a new genome and the broader effects of gene acquisition on the rest of the genome. We are also studying the role of chemical specificity in determining the fate of acquired DNA as either nutrition or genetic information. These bacteria also provide an improved platform for studying microbial genome engineering due to the ease of reconstructing mutations and introducing new genes. We are investigating sources of genetic instability in ADP1 and engineering a clean genome version of this strain by deleting transposable elements and prophages. This will promote the use of ADP1 in synthetic biology by reducing rates of mutations that lead to inactivation of introduced genes. Further, we are using ADP1 as a platform to understand the limits to streamlining bacterial genomes and identifying adaptations to overcome the fitness costs of reduced genomes.

 Current Researchers: Isaac Gifford, Meghna Vergis

 Representative Publications
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+ Gifford et al. (2020) PLoS Genetics PMID:32232367
  Suárez et al. (2020) Nucleic Acids Research PMID:32232367 
  Suárez et al. (2017) Applied and Environmental Microbiology PMID:28667117 
  Renda et al. (2015) Journal of Bacteriology PMID:25512307 
 

 Funding: NSF, UT-CNS SPARK     Past Funding: Welch Foundation, NSF CAREER
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+ Evolution and Ecology of Bartonella Parasites in the Negev Desert 


 
 
Diverse Bartonella vectored by fleas infect multiple gerbil species in the Negev Desert
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+Bartonella are diverse blood-borne parasites that can cause zoonotic infections of humans. The Hawlena Lab studies Bartonella species that circulate in gerbil populations in the Negev Desert in southwestern Israel. In these natural wildlife communities, multiple species of Bartonella infect and co-infect multiple host species, making it a dynamic system for studying host-parasite interactions. Our laboratory collaborates on projects characterizing how the genomes of these Bartonella evolve within and over multiple infection cycles in wild and lab-reared rodents. Our lab is particularly interested in mechanisms for genome evolvability utilized by these bacteria to escape host immune responses, including simple-sequence repeat contingency loci, gene accordions, and recombination during co-infections.

 Current Researchers: Isaac Gifford

 Representative Publications 

 Rodríguez‑Pastor et al. (2024) PLoS Pathogens PMID: 39348417 
  Rodríguez‑Pastor et al. (2022) Molecular Ecology Resources PMID:35599628 
 

 Funding: BSF     Past Funding: NSF EEID
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