Jeffrey Barrick

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Jeffrey E. Barrick is a Professor in the Department of Molecular Biosciences at The University of Texas at Austin. His research uses the tools of genomics, synthetic biology, and molecular biology to study the evolution of microorganisms, including symbionts of insects. Since 2022, Barrick has directed the E. coli Long-Term Evolution Experiment (LTEE), which has been underway since 1988. [1]

Contents

Education and research

Barrick received his undergraduate degree in Chemistry from Caltech in 2001, and he did a Ph.D. in Biochemistry and Biophysics at Yale, [2] working with Ronald Breaker on riboswitches and other regulatory RNA motifs in bacteria. [3] Barrick then did postdoctoral research at Michigan State University, [2] where he worked with Richard Lenski on the LTEE and led the first whole-genome sequencing and analysis of the evolved bacterial samples. [4] An accompanying commentary notes that "The complexity of the relationship between tempo and mode of evolution at the genomic and organismal levels is the cause of some unease, and suggests that caution needs to be exercised in inferring mode of organismal evolution from rates of evolution evident in DNA." [5]

Academic career

Barrick joined the faculty at UT Austin in 2011, [6] becoming full professor in 2024. [7] Since 2012, Barrick has been the faculty mentor for the iGEM synthetic biology student teams at UT Austin. [8] As of August 2024, Barrick has published over 100 scientific papers and has an h-index of 54. [9]

In discussing the LTEE's future in 2015, Lenski, the founding director, proposed that "each successive scientist responsible for the LTEE would, ideally, be young enough that he or she could direct the project for 25 years or so, but senior enough to have been promoted and tenured based on his or her independent achievements in a relevant field (evolutionary biology, genomics, microbiology, etc.)". [10] In 2022, Barrick was named the second director of the LTEE, and the evolving lineages are now being propagated in his lab at UT Austin. [1]

Research findings

Barrick has been a major contributor to the LTEE, including developing the breseq computational pipeline used to analyze whole-genome sequences from that project and other evolution experiments. [11] [12]

Barrick, Lenski, and colleagues identified mutations that allowed a seemingly inferior competitor to eventually prevail over a more-fit lineage in one LTEE population, demonstrating genetic differences in evolvability. [13] Science writer Carl Zimmer compared the findings to a case of "Tortoise and Hare, in a Laboratory Flask". [14] Barrick's team later identified mutations involved in the unexpected evolution of citrate utilization in another population. Zimmer explained that "[Barrick] and his colleagues developed a new method of engineering bacteria in order to identify the mutations that were absolutely essential for full-blown citrate feeding." He went on to say, however, that the relevant mutations "were weirdly few". [15] Barrick's team subsequently discovered that this approach had missed another important mutation involved in citrate use because a later mutation—one involved in refining the new function—overrode the earlier mutation's effect. [16]

In 2015, Barrick was co-recipient of an outstanding-paper award from the Genetics Society of America for a paper on clonal interference and frequency-dependent selection in the LTEE. [17] In 2024, Barrick and collaborators discovered possible instances of de novo gene birth, involving the generation of novel mRNA transcripts and proteins associated with nearby mutations. [18] [19]

For several years, Barrick has also worked with bacterial endosymbionts of honey bees and other arthropods, with the aim of modifying the symbionts for beneficial applications. [20] In 2020, Barrick, Nancy Moran, and colleagues genetically modified Snodgrassella alvi, a bacterial species that lives in the gut of honey bees, so that it induces an RNAi-mediated defense against a parasitic mite that carries a virus that is a major threat to the bees. [21] A commentator noted that this "approach may not only provide a solution to many of the honey bee's woes, it also offers a new functional genomic toolkit with which to dissect the molecular intricacies of honey bees and their societies". [22]

Related Research Articles

<span class="mw-page-title-main">Endosymbiont</span> Organism that lives within the body or cells of another organism

An endosymbiont or endobiont is an organism that lives within the body or cells of another organism. Typically the two organisms are in a mutualistic relationship. Examples are nitrogen-fixing bacteria, which live in the root nodules of legumes, single-cell algae inside reef-building corals, and bacterial endosymbionts that provide essential nutrients to insects.

<span class="mw-page-title-main">Genome</span> All genetic material of an organism

In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA. The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences, and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome.

<span class="mw-page-title-main">Mutation</span> Alteration in the nucleotide sequence of a genome

In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA, which then may undergo error-prone repair, cause an error during other forms of repair, or cause an error during replication. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.

Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.

<span class="mw-page-title-main">Pseudogene</span> Functionless relative of a gene

Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by gene duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are usually identified when genome sequence analysis finds gene-like sequences that lack regulatory sequences needed for transcription or translation, or whose coding sequences are obviously defective due to frameshifts or premature stop codons. Pseudogenes are a type of junk DNA.

<span class="mw-page-title-main">Molecular genetics</span> Scientific study of genes at the molecular level

Molecular genetics is a branch of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens. 

Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics. Evolution may be observed in the laboratory as individuals/populations adapt to new environmental conditions by natural selection.

In population genetics and population ecology, population size is a countable quantity representing the number of individual organisms in a population. Population size is directly associated with amount of genetic drift, and is the underlying cause of effects like population bottlenecks and the founder effect. Genetic drift is the major source of decrease of genetic diversity within populations which drives fixation and can potentially lead to speciation events.

<span class="mw-page-title-main">Conserved sequence</span> Similar DNA, RNA or protein sequences within genomes or among species

In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.

<span class="mw-page-title-main">Richard Lenski</span> American evolutionary biologist

Richard E. Lenski is an American evolutionary biologist, the John A. Hannah Distinguished Professor of Microbial Ecology at Michigan State University. He is a member of the National Academy of Sciences and a MacArthur Fellow. Lenski is best known for his still ongoing 36-year-old long-term E. coli evolution experiment, which has been instrumental in understanding the core processes of evolution, including mutation rates, clonal interference, antibiotic resistance, the evolution of novel traits, and speciation. He is also well known for his pioneering work in studying evolution digitally using self-replicating organisms called Avida.

Dr. Charles A. Ofria is a Professor in the Department of Computer Science and Engineering at Michigan State University, the director of the Digital Evolution (DEvo) Lab there, and Director of the BEACON Center for the Study of Evolution in Action. He is the son of the late Charles Ofria, who developed the first fully integrated shop management program for the automotive repair industry. Ofria attended Stuyvesant High School and graduated from Ward Melville High School in 1991. He obtained a B.S. in Computer Science, Pure Mathematics, and Applied Mathematics from Stony Brook University in 1994, and a Ph.D. in Computation and Neural Systems from the California Institute of Technology in 1999. Ofria's research focuses on the interplay between computer science and Darwinian evolution.

<i>E. coli</i> long-term evolution experiment Scientific study

The E. coli long-term evolution experiment (LTEE) is an ongoing study in experimental evolution begun by Richard Lenski at the University of California, Irvine, carried on by Lenski and colleagues at Michigan State University, and currently overseen by Jeffrey Barrick at the University of Texas at Austin. It has been tracking genetic changes in 12 initially identical populations of asexual Escherichia coli bacteria since 24 February 1988. Lenski performed the 10,000th transfer of the experiment on March 13, 2017. The populations reached over 73,000 generations in early 2020, shortly before being frozen because of the COVID-19 pandemic. In September 2020, the LTEE experiment was resumed using the frozen stocks. When the populations reached 75,000 generations, the LTEE was transferred from the Lenski lab to the Barrick lab. In August 2024, the LTEE populations passed 80,000 generations in the Barrick lab.

Gene Ezia Robinson is an American entomologist, Director of the Carl R. Woese Institute for Genomic Biology and National Academy of Sciences member. He pioneered the application of genomics to the study of social behavior and led the effort to sequence the honey bee genome. On February 10, 2009, his research was famously featured in an episode of The Colbert Report whose eponymous host referred to the honey Dr. Robinson sent him as "pharmaceutical-grade hive jive".

Nancy A. Moran is an American evolutionary biologist and entomologist, University of Texas Leslie Surginer Endowed Professor, and co-founder of the Yale Microbial Diversity Institute. Since 2005, she has been a member of the United States National Academy of Sciences. Her seminal research has focused on the pea aphid, Acyrthosiphon pisum and its bacterial symbionts including Buchnera (bacterium). In 2013, she returned to the University of Texas at Austin, where she continues to conduct research on bacterial symbionts in aphids, bees, and other insect species. She has also expanded the scale of her research to bacterial evolution as a whole. She believes that a good understanding of genetic drift and random chance could prevent misunderstandings surrounding evolution. Her current research goal focuses on complexity in life-histories and symbiosis between hosts and microbes, including the microbiota of insects.

Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of eukaryotes. Bacterial genomes can range in size anywhere from about 130 kbp to over 14 Mbp. A study that included, but was not limited to, 478 bacterial genomes, concluded that as genome size increases, the number of genes increases at a disproportionately slower rate in eukaryotes than in non-eukaryotes. Thus, the proportion of non-coding DNA goes up with genome size more quickly in non-bacteria than in bacteria. This is consistent with the fact that most eukaryotic nuclear DNA is non-gene coding, while the majority of prokaryotic, viral, and organellar genes are coding. Right now, we have genome sequences from 50 different bacterial phyla and 11 different archaeal phyla. Second-generation sequencing has yielded many draft genomes ; third-generation sequencing might eventually yield a complete genome in a few hours. The genome sequences reveal much diversity in bacteria. Analysis of over 2000 Escherichia coli genomes reveals an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Genome sequences show that parasitic bacteria have 500–1200 genes, free-living bacteria have 1500–7500 genes, and archaea have 1500–2700 genes. A striking discovery by Cole et al. described massive amounts of gene decay when comparing Leprosy bacillus to ancestral bacteria. Studies have since shown that several bacteria have smaller genome sizes than their ancestors did. Over the years, researchers have proposed several theories to explain the general trend of bacterial genome decay and the relatively small size of bacterial genomes. Compelling evidence indicates that the apparent degradation of bacterial genomes is owed to a deletional bias.

<span class="mw-page-title-main">Minimal genome</span> Concept in genetics

The minimal genome is a concept which can be defined as the set of genes sufficient for life to exist and propagate under nutrient-rich and stress-free conditions. Alternatively, it can also be defined as the gene set supporting life on an axenic cell culture in rich media, and it is thought what makes up the minimal genome will depend on the environmental conditions that the organism inhabits.

<span class="mw-page-title-main">Zachary Blount</span> American evolutionary biologist

Zachary D. Blount is an American evolutionary biologist best known for his work on the evolution of a key innovation, aerobic growth on citrate, in one of the twelve populations of the E. coli long-term evolution experiment. Blount is a research assistant professor working with Richard Lenski at Michigan State University. He was previously a postdoctoral research assistant for Lenski, and was a visiting assistant professor of biology at Kenyon College from 2018 to 2019.

<span class="mw-page-title-main">Jose V. Lopez</span> American-Filipino molecular biologist

Jose V. Lopez is an American-Filipino Molecular Biologist. He has been a faculty member and Professor of Biology at Nova Southeastern University (NSU) in Dania Beach, Florida, since 2007. Lopez has contributed as a co-founder of the Global Invertebrate Genomics Alliance (GIGA), a community of scientists. He has also participated in the "Porifera—Tree of Life," "Earth Microbiome," and Earth BioGenome projects.

<span class="mw-page-title-main">Heather Hendrickson</span> American-born New Zealand-based microbiologist

Heather Hendrickson is a microbiologist and an Associate Professor in the School of Biological Sciences at the University of Canterbury in Christchurch, New Zealand. She previously worked at Massey University, Auckland, New Zealand. Her research is focussed on the evolution of bacterial cell shape, and the discovery of bacteriophages that can attack antibiotic-resistant bacteria and the bee disease American foulbrood.

<i>Snodgrassella alvi</i> Species of bacterium

Snodgrassella alvi is a species of Gram-negative bacteria within the Neisseriaceae and was previously the only known species of the genus Snodgrassella. It was isolated and scientifically described in 2012 by Waldan K. Kwong and Nancy A. Moran, who named the bacteria after the American entomologist Robert Evans Snodgrass.

References

  1. 1 2 Callaway, Ewen (June 14, 2022). "Legendary bacterial evolution experiment enters new era". Nature. 606 (7915): 634–635. Bibcode:2022Natur.606..634C. doi: 10.1038/d41586-022-01620-3 . PMID   35701611 – via www.nature.com.
  2. 1 2 "Jeffrey E. Barrick | Department of Molecular Biosciences". molecularbiosci.utexas.edu. Retrieved 2024-08-25.
  3. ↑ "| The Breaker Lab". breaker.yale.edu.
  4. ↑ Barrick, Jeffrey E.; Yu, Dong Su; Yoon, Sung Ho; Jeong, Haeyoung; Oh, Tae Kwang; Schneider, Dominique; Lenski, Richard E.; Kim, Jihyun F. (October 26, 2009). "Genome evolution and adaptation in a long-term experiment with Escherichia coli". Nature. 461 (7268): 1243–1247. Bibcode:2009Natur.461.1243B. doi:10.1038/nature08480. PMID   19838166 – via www.nature.com.
  5. ↑ Rainey, PB (28 October 2009). "Arrhythmia of tempo and mode". Nature. 461 (7268): 1219–1221. doi:10.1038/4611219a. PMID   19865158.
  6. ↑ "Dr. Jeffrey E. Barrick Joins Faculty". cm.utexas.edu.
  7. ↑ "BARRICK, JEFFREY E - Molecular Biosciences - CNS Directory". ils.utexas.edu.
  8. ↑ "The University of Texas at Austin :: iGEM Team". barricklab.org.
  9. ↑ Google scholar page for Jeffrey E. Barrick
  10. ↑ Fox, JW; Lenski, RE (June 23, 2015). "From Here to Eternity—The Theory and Practice of a Really Long Experiment". PLOS Biology. 13 (6): e1002185. doi: 10.1371/journal.pbio.1002185 . PMID   26102073.
  11. ↑ breseq on Biowulf: High Performance Computing at the NIH
  12. ↑ Tenaillon, Olivier; Barrick, Jeffrey E.; Ribeck, Noah; Deatherage, Daniel E.; Blanchard, Jeffrey L.; Dasgupta, Aurko; Wu, Gabriel C.; Wielgoss, Sébastien; Cruveiller, Stéphane; Médigue, Claudine; Schneider, Dominique; Lenski, Richard E. (August 26, 2016). "Tempo and mode of genome evolution in a 50,000-generation experiment". Nature. 536 (7615): 165–170. Bibcode:2016Natur.536..165T. doi:10.1038/nature18959. PMC   4988878 . PMID   27479321.
  13. ↑ Coghlan, A (17 March 2011). "Steady beats flashy in evolution death match". New Scientist.
  14. ↑ Zimmer, C (21 March 2011). "Tortoise and Hare, in a Laboratory Flask". The New York Times .
  15. ↑ Zimmer, Carl (January 6, 2014). "Evolution Hidden in Plain Sight".
  16. ↑ Kliebenstein, DJ (December 15, 2015). "Metabolism: Evolution retraces its steps to advance". eLife. 4: e12386. doi: 10.7554/eLife.12386 . PMC   4749388 . PMID   26670654.
  17. ↑ "Centennial Awards honor outstanding GENETICS articles". EurekAlert!.
  18. ↑ uz-Zaman, Md Hassan; D’Alton, Simon; Barrick, Jeffrey E.; Ochman, Howard (May 7, 2024). "Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli". PLOS Biology. 22 (5): e3002418. doi: 10.1371/journal.pbio.3002418 . PMC   11101190 . PMID   38713714.
  19. ↑ Van Oss, Stephen Branden; Carvunis, Anne-Ruxandra (May 23, 2019). "De novo gene birth". PLOS Genetics. 15 (5): e1008160. doi: 10.1371/journal.pgen.1008160 . PMC   6542195 . PMID   31120894.
  20. ↑ "Bacteria Engineered to Protect Bees from Pests and Pathogens | Department of Molecular Biosciences". molecularbiosci.utexas.edu.
  21. ↑ Leonard, Sean P.; Powell, J. Elijah; Perutka, Jiri; Geng, Peng; Heckmann, Luke C.; Horak, Richard D.; Davies, Bryan W.; Ellington, Andrew D.; Barrick, Jeffrey E.; Moran, Nancy A. (31 January 2020). "Engineered symbionts activate honey bee immunity and limit pathogens". Science. 367 (6477): 573–576. Bibcode:2020Sci...367..573L. doi:10.1126/science.aax9039. PMC   7556694 . PMID   32001655.
  22. ↑ Paxton, RJ (31 January 2020). "A microbiome silver bullet for honey bees". Science. 367 (6477): 504–506. Bibcode:2020Sci...367..504P. doi:10.1126/science.aba6135. PMID   32001639.
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