Faculty

Carrine E. Blank

Carrine E. Blank

Ph.D., University of California, Berkeley; Integrative Biology, 2002

Office: CHCB 109a
Email: carrine.blank@umontana.edu

Personal Website
Curriculum Vitae

Current Position

Research Assistant Professor

Education

PhD 2002; University of California, Berkeley; Integrative Biology

BSc 1992; University of Washington, Seattle; Microbiology and Immunology

BSc 1992; University of Washington, Seattle; Cell and Molecular Biology

Research Interests

Microbial Evolution/Bioinformatics:

My collaborative research uses cutting-edge natural language processing, ontologies, and phylogenomics to study the large-scale evolution of microbial phenotypes through deep evolutionary time.  Project themes include:

  1. Using phylogenetic comparative analysis to study the evolution of phenotypic traits in the prokaryotes.
  2. Using an ontology of prokaryotic phenotypes to advance data integration of phenotypes and genotypes.
  3. Developing natural language processing tools for extracting phenotypic data from microbial taxonomic descriptions.
  4. Microbial phylogenomics; identifying core phylogenies and lateral transfer events defining the ecological niches.

Green Algal Biotechnology:

Our patented technology uses a new naturally-occurring source of organic nitrogen (chitin) which is a carbon-neutral, low-cost waste-product of the shellfish industry.  Our technology efficiently removes phosphorus from water (to levels below 12 ppb, or 12 micrograms per liter) using algae and without adding any nitrogen back into the water.   We are actively working and publishing in the following areas:

  1. demonstrating enhanced value-added products in the resulting algal biomass (enhanced carotenoid pigment and biofuel content of the biomass)
  2. demonstrating efficient phosphorus removal kinetics from wastewaters (including pulp and paper mill and Buchu Mercaptan production water) 
  3. demonstrating efficient phosphorus removal kinetics from phosphorus-impacted natural bodies of water
  4. evaluating the economics, greenhouse gas footprint, and sustainability of this new technology, and
  5. evaluating feedstock requirements (wastestreams of the crustacean shellfish and pulp mill industries)

Geomicrobiology:

The goal of this project is to study how microbial phenotype evolution has influenced the evolution of Earth's biogeochemical cycles through time.

  1. Correlating microbial evolutionary events with changes in the Earth’s climate and biogeochemical cycles.
  2. Reconstructing the evolution of carbon, nitrogen, and sulfur microbial biogeochemical cycles through deep time using phylogenomics and explicit trait/character evolution.

Projects

Invited participant for 2018 Explorer of Taxon Concepts and Authors Project Workshop, lead by Hong Cui (Univ. of Arizona).  Held January 11-12,2018 in Tucson, AZ.

Invited speaker for the Sixth Annual Workshop of the Clinical and Translational Science Ontology Group.  Talk title: "The MicrO ontology; enabling the acquisition of higher-order knowledge of phenotypes from prokaryotic taxonomic descriptions and the construction of very large character matrices".  Held October 25-26, 2017 in Ann Arbor, MI.

Invited speaker/presenter for the scientific workshop "Trees, traits and functions: semantics for comparative biology".  Talk title: "Use of natural language processing algorithms, ontologies, and phylogenomic trees to automate and accelerate phenotypic trait evolutionary studies for prokaryotes".  Other presenters included Paula Mabee, Paul Thomas, Martin Ramirez, with Todd Vision and Hilmar Lapp (organizers).  Sponsored by the Society of Systematic Biologists, held in conjunction with the Evolution 2017 Meeting Jun 23-27, 2017, in Portland, OR.

Invited participant for the scientific workshop "Arbor Summit 2017", held Apr 19-20, 2017, University of Utah Scientific Computing and Imaging Institute.

Lead organizer of the scientific workshop "Advancing Prokaryotic Data Layer Integration: The Future of Connecting Genotypes to Phenotypes in Prokaryotes".  Co-organized with Lisa R Moore and Robert W. Thacker.  Held Oct 21-23, 2016, in Chicago, IL.  Funded by the NSF and FuturePhy: A Conference and Workshop Series on the Future of Phylogenetics; https://futurephy.org.

The following research projects are available for interested students (please contact Dr. Blank for more information):

  • High through-put study of microbial evolution and character evolution.
  • Genomics and biochemistry of chitin metabolism in the cyanobacteria and eukaryotic microalgae.
  • Bioplastics from cyanobacteria.
  • Biofuel production in microalgae.
  • Wastewater treatment for the green chemical industry using algae.
  • Pulp and paper mill wastewater treatment using algae.
  • Evolution of microbial traits on the Precambrian Earth.
  • Connecting microbial evolution with climate change records of the past.

Selected Publications

Bioinformatics Software/Scripts

MicrO: An ontology (formal, hierarchical, logical network) of prokaryotic phenotypic terms/traits.  Constructed in OWL Protégé; following OBO Foundry principles.  Imports terms from 19 other ontologies and contains >22,000 logical axioms connecting entities and processes across multiple ontologies to increase higher-order knowledge of traits).  Version 1.5 is available at https://github.com/carrineblank/MicrO.

MicroPIE: extracts phenotypic characters from prokaryotic taxonomic descriptions and outputs a character spreadsheet which can then be converted into a character matrix.  Constructed in collaboration with colleagues at the University of Arizona and University of Southern Maine.  MicroPIE v. 0.1.0 is available at https://github.com/biosemantics/micropie2.

MicroPIEDigester: perl script that converts raw phenotypic character information generated by MicroPIE, coding it into characters and character states.  Extracts discrete and continuous character types, and outputs nexus files. In the process of character coding, it uses the standard vocabulary and synonyms of terms established in MicrO to ontologize chacters, release v. 1.5 is available at https://github.com/carrineblank/MicroPIEDigester.

SortMicrobe: perl script that searches through large phenotypic datasets of discrete and continuous characters, created/captured using natural language processing and coded using MicroPIEDigester, for particular taxa that fit within user-designated criteria.  Designed for use by the biotech sector to identify prokaryotic taxa that have desirable phenotypes applicable to applied research objectives. (Proprietary script has not been released.)

Electronically Published Data Packages

Uyeda JC, Harmon LJ, Blank CE.  2016.  Data from: A comprehensive study of cyanobacterial morphological and ecological evolutionary dynamics through deep geologic time.  PLoS ONE.  MorphoBank project P2525.

Blank CE.  2014.  Data from: Origin and early evolution of photosynthetic eukaryotes in freshwater environments – reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution.  J Phycology.  MorphoBank project P1097.

Blank CE. 2013. Data from: Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time. Archaea: An International Microbiological Journal doi:10.5061/dryad.j87v8.

Blank CE.  2013.  Data from: An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating. Journal of Molecular Evolution doi:10.5061/dryad.30j63.

Blank CE.  2013.  Data from: Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen. Geobiology doi:10.5061/dryad.11vj2.

Blank CE.  2013.  Data from: Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life. Geobiology doi:10.5061/dryad.71r61.

Publications

Blank CE, Cui H, Mao J, Moore LR, Thacker RW, Walls RL.  2018.  Accelerating the large-scale study of prokaryotic phenotypes and niche space evolution through time using the MicrO ontology, MicroPIE, and MicroPIEDigester software. In: Thessen, AE (Ed.) Application of Semantic Technologies in Biodiversity Science. Studies on the Semantic Web, IOS Press/AKA Verlag. To appear.  [Submitted 4/6/2017, in press.]

Mao J, Moore LR, Blank CE, Wu EH-H, Ackerman M, Renade S, Cui H.  2016.  Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources.  BMC Bioinformatics, 17:528.  doi 10.1186/s12859-016-1396-8.

Uyeda JC, Harmon LJ, Blank CE.  2016.  A comprehensive study of cyanobacterial morphological and ecological evolutionary dynamics through deep geologic time.  PLoS ONE, http://dx.doi.org/10.1371/journal.pone.0162539.

Blank CE, Cui H, Moore LR, Walls RL.  2016.  MicrO: An Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions, Journal of Biomedical Semantics 7:18.  DOI:10.1186/s13326-016-0060-6.

Blank CE, Hinman NW.  2016.  Cyanobacterial and algal growth on chitin as a source of nitrogen; ecological, evolutionary, and biotechnological implications. Algal Research 15(2016):152-163. DOI: 10.1016/j.algal.2016.02.014.

Blank CE, Parks RW, Hinman NW.  2016.  Chitin: a potential new alternative nitrogen source for the tertiary, algal-based treatment of pulp and paper mill wastewater.  Journal of Applied Phycology.  DOI: 10.007/s10811-016-0808-5.

Blank CE.  2013.  Origin and early evolution of photosynthetic eukaryotes in freshwater environments – reinterpreting Proterozoic paleobiology and biogeochemical processes in light of trait evolution.  Journal of Phycology 49(6):1040-1055.  DOI: 10.1111/jpy.12111.

Blank CE.  2013.  Phylogenetic distribution of compatible solute synthesis genes support a freshwater origin for Cyanobacteria. Journal of Phycology 49(5):880-895. DOI: 10.1111/jpy.12098.

Gammons CH, Pape BL, Parker SR, Poulson SR, Blank CE.  2013.  Geochemistry, water balance, and stable isotopes of a “clean” pit lake at an abandoned tungsten mine, Montana, USA.    Applied Geochemistry, 36:57-69. http://dx.doi.org/10.1016/j.apgeochem.2013.06.011.

Burleigh JG, Alphonse K, Alverson A, Bik H, Blank CE et al.  2013. Next generation phenomics for the tree of life. PLoS Currents - Tree of Life.  doi: 10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733.

Blank CE. 2012.   Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of Archaea through deep time.  Archaea  doi:10.1155/2012/843539.

Blank CE.  2011.  An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating. Journal of Molecular Evolution, 73(3), 188-208.

Blank CE and Sánchez-Baracaldo P.  2010.  Timing of morphological and ecological innovations in the Cyanobacteria – A key to understanding the rise in atmospheric oxygen.  Geobiology, 8(1), 1-23.

Blank, CE.  2009.  Not so old Archaea – The antiquity of biogeochemical processes in the archaeal domain of life.  Geobiology, 7(5), 495-514.

Blank CE.  2009.  Phylogenomic dating - A method of constraining the age of microbial taxa that lack a conventional fossil record.  Astrobiology, 9(2):173-192.

Blank CE.  2009.  Phylogenomic dating – The relative antiquity of archaeal metabolic and physiological traits.  Astrobiology, 9(2):192-220.

Blank CE.  2008.  Phylogenomic dating and the relative ancestry of prokaryotic metabolisms.  In: "From Fossils to Astrobiology", edited by M. Walsh and J. Seckbach, Springer-Verlag.

Tenesch AC, Dietrich A, Cady SL, Blank CE, and Hinman NW.  2008. Silica deposition on cells in environmentally defined experimental solutions.  Geochimica et Cosmochimica Acta 72(12):A940.

Huntress WT, Noonan NE, Atreya SK, Blank CE, et al.,  2007.  Grading NASA’s Solar System Exploration Program; A Midterm Review.  National Research Council Committee on Assessing NASA’s Solar System Exploration Program.

Sánchez-Baracaldo P, Hayes PK, and Blank CE.  2005.  Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach.  Geobiology, 3(3):145-165.

Blank CE.  2004.  Evolutionary timing of the origins of mesophilic sulfate reduction and oxygenic photosynthesis: A phylogenomic dating approach.  Geobiology, 2(1):1-20.

Blank CE, Cady SL, and Pace NR.  2002.  Microbial composition of silica-depositing thermal springs throughout Yellowstone National Park.  Applied and Environmental Microbiology, 68(10):5123-5135.

Leigh JA, Kessler PS, and Blank CE.  1998.  Regulation of nif gene transcription in Methanococcus maripaludis, In: “Biological Nitrogen Fixation for the 21st Century”, C. Elmerich, A. Kondorosi, and W. E. Newton, eds., pp. 115-116.

Kessler PS, Blank CE, and Leigh JA.  1998.  The nif gene operon of the methanogenic archaeon Methanococcus maripaludisJournal of Bacteriology, 180(6):1504-1511.

Cohen-Kupiec R, Blank CE, and Leigh JA.  1997.  Transcriptional regulation in Archaea: In vivo demonstration of a repressor binding site in a methanogen.  Proceedings of the National Academy of Sciences USA, 94:1316-1320.

Cattolico RA, Hariharan T, Johnson P, Blank C, and Kurtz H.  1996.  Evolutionary variations in phosphoribulokinase among autotrophic organisms.  Journal of Phycology, 32(3):SUPPL. 10.

Blank CE, Kessler PS, and Leigh JA.  1995.  Genetics in methanogens: transposon insertion mutagenesis of a Methanococcus maripaludis nifH gene.  Journal of Bacteriology, 177:5773-7.

Honors

2014 Luigi Provasoli Award, awarded by the Phycological Society of America.

2006 Nominated to participate in the German-American Kavli Frontiers of Science Symposium [sponsored by US National Academy of Sciences and the Alexander von Humboldt Foundation.]

Specialized Skills

Patent Pending: Process of Treating Buchu Mercaptan Production Wastewater Using Microalgae and Chitin as a Nitrogen Source.  Serial number 15/611,046 (filed 6/1/2017). 

Patent: Process of Treating Buchu Mercaptan Production Wastewater Using Microalgae and Chitin as a Nitrogen Source.  United States Patent Number 9,688,557, issued 6/27/2017 (filed 8/4/2015).

Divisional Patent: Production of Cyanobacterial or Algal Biomass Using Chitin As a Nitrogen Source (covering wastewater treatment claims for pulp and paper mill wastewater).  United States Patent Number 9,102,552, issued 8/11/2015 (filed 2/14/2014).

Patent: Production of Cyanobacterial or Algal Biomass Using Chitin As a Nitrogen Source.  United States Patent Number 8,673,619, issued 3/18/2014 (filed 3/26/2012).  Submitted as an International Patent, Application No. PCT/US12/30620 (filed 3/26/2012).

Provisional Patent: Photosynthetic Degradation of Chitin Using Cyanobacteria or Algae for Biomass or Biofuel Production.  Serial No. 61/467,869 (filed 3/25/2011).

Teaching Experience

At University of Montana:

Intro to Physical Geology: Spring 2012, Winter 2012, Fall 2011, Winter 2010, Fall 2010

At Washington University:

Controversies in Astrobiology: Fall 2006, Spring 2005, Spring 2003

Intro to Astrobiology: Spring 2006, Spring 2004

Microbes in the Environment: Fall 2003, Fall 2005

Topics in the Geosciences - History of Science: Spring 2006

Topics in the Geosciences - Microbial Evolution: Spring 2005

Seminar in Population Biology - Tree of Life: Spring 2005

Professional Experience

2007-present Research Assistant Professor, University of Montana, Geosciences Dept.

2010-2012 Adjunct Assistant Professor; University of Montana, Geosciences Dept.

2002-2007 Assistant Professor, Washington University, Dept. Earth and Planetary Sciences