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Principal Investigator (PI)
Principal Investigator (PI)
Dr. Nicholas C. Butzin ("But-ZEEN”)
Dr. Nicholas C. Butzin ("But-ZEEN”)
Associate Professor of Synthetic Biology
Department of Biology and Microbiology.
Affiliated Assistant Professor,
Department of Chemistry and Biochemistry.
Co-Director, 3D Microfabrication Shared Facility (3MSF). 3MSF link.
South Dakota State University (SDSU), Brookings, SD.
Start date: August, 2017
Brief Biography
Dr. Butzin joined the Department of Biology and Microbiology at South Dakota State University in 2017 as an Assistant Professor. He previously was a Research Scientist and postdoc in the Department of Physics, Virginia Tech, and a postdoc in the Department of Molecular & Cell Biology, University of Connecticut. The Butzin lab explores microbial systems using an evolutionary perspective and a synthetic biology approach. His goal is to understand the principles behind robustness in both natural and synthetic microbial systems. He is particularly interested in how individual cells cope with constant fluctuations in natural environments and limited enzymatic resources. Although his lab has several ongoing projects ranging from the development of new robust synthetic circuits to the study of antibiotic resistance and biofilms, all projects utilize synthetic biology to understand natural phenomena or to develop products for industrial and medical applications. His lab uses mathematical and computational approaches along with wet-lab experiments to probe and develop a more comprehensive understanding of the mechanisms that generate cellular plasticity and robustness.
Current Work
I am broadly interested in molecular microbial physiology and evolution, which I have studied in the past using traditional microbiology, molecular biology, and bioinformatic tools. However, these methods limit the analysis to one aspect of the cell (e.g. gene or protein, one pathway, etc.). To overcome these limitations, we employ the more holistic approach of Synthetic and Systems Biology. Current work utilizes several organisms including Escherichia coli, Mycoplasma, and a few thermophiles. We utilize these organisms and synthetic systems to study persistence, synthetic ecologies, bottlenecks, cellular response to stress, and other phenomena. We use both mathematical and computational methods alongside wet-lab experiments to probe and develop a more comprehensive understanding of the mechanisms that generate and maintain bacterial robustness. This combination of approaches encompasses several disciplines: microbiology, molecular and cell biology, engineering, physics, biophysics, and bioinformatics. Much of our work involves using cutting-edge techniques such as microfluidic devices and machine learning algorithms.
Research Interests
Metabolic engineering and synthetic biology.
Molecular microbial physiology and evolution.
Natural and synthetic microbial networks: oscillators, biosensors, etc.
Robustness and fitness of microbial life and biological systems: antibiotic resistance, tolerance, and persistence; microbial adaptation; microbial ecology.
Life at the extreme (extremophilic organisms) and the origin of cellular life.
Graduate Students
Graduate Students
Ruqayyah Amaratunga
Ruqayyah Amaratunga
PhD student
Department of Biology and Microbiology
South Dakota State University
Start date: Fall 2020
Current Work
My primary research is to engineer genetic oscillator in Escherichia coli which is fast, robust and persistent, with tunable oscillatory periods.
Research Interests
Bacterial pathogenesis, Synthetic biology and Cancer biology.
Hobbies
Reading
Links
Sudeshna Roy
Sudeshna Roy
PhD candidate
Department of Biology and Microbiology
South Dakota State University
Start date: Spring 2021
Current Work
My primary research goal is to evolve the bacteria to use rare amino acid.
I am also working on find out the molecular mechanism used by bacteria to revive from their metabolically repressed state (such as persister and VBNC state).
RNA-sequencing,, microscopic data-analysis etc.
Hobbies
Playing piano, listening to music, reading, traveling
Links
Manisha Guha
Manisha Guha
PhD candidate
Department of Biology and Microbiology
South Dakota State University
Start date: Fall 2021
Current Work
My primary research goal is to uncover the cellular mechanisms that prime a subpopulation of bacteria to tolerate lethal doses of antibiotics in Priestia megaterium for prolonged periods.
Research Interests
Synthetic Biology, Space Biology.
Links
Roha Razzaq
Roha Razzaq
PhD student
Department of Biology and Microbiology
South Dakota State University
Start date: Fall 2022
Current Work
My research is centered on antibiotic discovery, especially targeting bacterial proteases that play a critical role in bacterial survival and pathogenicity.
Research Interests
Microbiology, Genomics, Bioinformatics and Computational Biology
Hobbies
Traveling, watching movies and novel reading.
Links
Suchi Parvin Biki
Suchi Parvin Biki
PhD student
Department of Biology and Microbiology
South Dakota State University
Start date: Fall 2023
Current Work
My primary research is to screen promoters for identifying expression of upregulated genes in E. coli persisters.
I am also working on exploration of epigenetic inheritance in E. coli to endure sub-MIC levels of antibiotics.
Research Interests
Genetic engineering, 3D Printing, Microfluidics
Links
Sheetalpreet Kaur
Sheetalpreet Kaur
PhD student
Department of Biology and Microbiology
South Dakota State University
Start date: Fall 2023
Current Work
My primary research is to investigate the biological significance of the orphan genes in bacteria and developing strategies to study proteins with no known homology. My goal is to uncover novel protein functions and pathways that may not be detectable through traditional comparative methods.
Research Interests
Vaccinology, Microbiome, Medical microbiology
Links
Michelle Steyn
Michelle Steyn
PhD student
Department of Biology and Microbiology
South Dakota State University
Start date: Summer 2025
Current Work
My primary research is to identify if inherent phenotypic heterogeneity in bacterial cells have any advantage to the population under stress.
Research Interests
Mycology, Microbiology, Cancer Biology
Links
Undergraduate Students
Undergraduate Students
Jacob Spreng
Jacob Spreng
Undergraduate Student
Major in Human Biology, Minor in Chemistry
Start date: Spring 2023
Current Work
Making knockout mutants using the CRISPR-Cas9 system to study the role of uncharacterized genes in bacterial persistence.
Research Interests
Antibiotic resistance, gene knockouts, gut microbiome
Hobbies
Lifting, volunteering, and traveling
New undergrads (to be updated)
New undergrads (to be updated)
- Hunter Lemer 2023 Fa - Present
- Hunter Lemer 2023 Fa - Present
- Derek Follett 2022 Sum - Present
- Derek Follett 2022 Sum - Present
- Levi McKinley 2024 Sum - Present
- Levi McKinley 2024 Sum - Present
- Jackson Dorsett 2024 Sum - Present
- Jackson Dorsett 2024 Sum - Present
- Jared Volesky 2024 Sum - Present
- Jared Volesky 2024 Sum - Present
- Aidan Donelan 2024 Sp - Present
- Aidan Donelan 2024 Sp - Present
- Derek Follett 2022 Sum - Present
- Derek Follett 2022 Sum - Present
Former graduate students
Former graduate students
Elise Schweer, MS
Elise Schweer, MS
Fall 2022 - Fall 2024
Work
Making knockout mutants using CRISPR-Cas9 system.
Creating microfluidic device using 3D Printing.
Research Interests
3D Printing, Microfluidics, Antibiotic Tolerance
Publications Links
Hobbies
Playing piano, Reading, Cooking, Walking
K M Taufiqur Rahman, PhD
K M Taufiqur Rahman, PhD
Fall 2020 - Spring 2024
Work
3D printing, Lab-on-a-chip, Microscopic Image Analysis, NGS data analysis
Python, R and Linux command line
Research Interests
Synthetic Biology, Microfluidics, Bacterial pathogenesis, Computational Biology and Bioinformatics
Hobbies
Creative writing, Reading, Traveling
Links
Position after graduation: Scientist IV Global MSAT at Boehringer Ingelheim.
Mohammed Salahuddin, MS
Mohammed Salahuddin, MS
Spring 2021 - Summer 2023
Work
Probing the regulatory mechanisms behind proteolytic queueing and crosstalk.
RNA-sequencing, Mass-spec, microscopic data-analysis.
Hobbies
Watching TV shows, Listening to music, Reading, Traveling
Position after graduation: Research Scientist at Charles River Laboratories, Shrewsbury, MA.
Hazera Khatun Koly, MS
Hazera Khatun Koly, MS
Spring 2021 - Spring 2023
Department of Chemistry and Biochemistry
South Dakota State University
Work
Novel antibiotic discovery targeting bacterial proteases.
Research Interests
Molecular Biology, Bioinformatics, Computational Biology, and Cancer Biology
Hobbies
Cooking, Traveling, Reading, Youtube content creation
Position after graduation: Associate Scientist at Northeast Biolabs.
Tahmina Hossain, PhD
Tahmina Hossain, PhD
Fall 2018 - Fall 2022
Work
Discovery of antibiotic primed cells in E. coli.
Demonstration of antibiotic persistence in Syn 3B.
Links
Position after graduation: Postdoctoral fellow at Pfizer.
Prajakta Jadhav, PhD
Prajakta Jadhav, PhD
Fall 2018 - Spring 2022
Work
Engineering novel protein degradation tags for bacterial synthetic oscillator.
Position after graduation: Scientist at Arzeda, Seattle.
Tanim Islam, MS
Tanim Islam, MS
Spring 2020 - Spring 2022
Position after graduation: PhD at Oklahoma State University.
Lukas Stanley Nelson, MS
Lukas Stanley Nelson, MS
Spring 2021- Spring 2022
Position after graduation: Teacher at Jefferson High School, Sioux Falls, SD.
Heather S. Deter, PhD
Heather S. Deter, PhD
Fall 2017 - Summer 2020
Links
Deter Email, Google Scholar, Twitter: @h_deter, GitHub: hdeter
Position after graduation: Postdoctoral Research Associate, University of Illinois at Urbana-Champaign.
Current position: Assistant Professor of Biology, Concordia University Chicago.
Alawiah Hussain Abualrahi, MS
Alawiah Hussain Abualrahi, MS
Fall 2017 - Fall 2019
Position after graduation: QC Microbiologist at Dammam Pharma (SPIMACO).
Former POSTDOCS
Former POSTDOCS
Dr. Arantxa Urchueguía Fornes
Dr. Arantxa Urchueguía Fornes
Tenure
Spring 2022 - Fall 2022
Publication link
Position after Butzin lab: Scientist and Study coordinator at Fisabio, a public health institute in Valencia, Spain.
Dr. Santosh Rathan Paul Bandlamudi
Dr. Santosh Rathan Paul Bandlamudi
Tenure
Fall 2021- Fall 2022
Position after Butzin lab: Postdoctoral Research Scientist in condensed matter physics at South Dakota School of Mines.
Former undergraduates
Former undergraduates
Kaden Westergaard
Kaden Westergaard
2023 Sp - 2024 Sp, graduated with BS
Hattie Shaffer
Hattie Shaffer
2023 Sp - 2024 Sp, graduated with BS
Majors in Human Biology and Microbiology, Minor in Chemistry
Start date: Spring 2023
Work
Making knockout mutants using the CRISPR-Cas9 system to study the role of uncharacterized genes in bacterial persistence.
Research Interests
Antibiotic resistance, tolerance, and persistence
Hobbies
Running, reading, cooking, hanging out with friends, and activities outside
Emma Jensen
Emma Jensen
2022 Sp - 2024 Sp, graduated with BS
Major in Human Biology, Minor in Chemistry
Work
Exploring bacterial evolution by incorporating unnatural amino acids in E. coli
Syn-Bio REU (synthetic biology research experience for undergraduates) awardee, summer 2022.
Research Interests
Microscopy
Hobbies
Painting, swimming, and ceramics
Isaac Kovash
Isaac Kovash
2022 Sp - 2024 Sp, graduated with BS
Major in Human Biology, Minor in Chemistry
Work
Making knockout mutants using the CRISPR-Cas9 system to study the role of uncharacterized genes in bacterial persistence.
Optimizing our CRISPR-Cas9 system
Research Interests
Antibiotic persistence and genetics
Hobbies
Reading, playing soccer, and watching movies
Jordyn Post
Jordyn Post
2023 Sp - 2024 Sp, graduated with BS
Major in Human Biology, Minor in Chemistry
Work
Making knockout mutants using the CRISPR-Cas9 system to study the role of uncharacterized genes in bacterial persistence.
Research Interests
Antibiotic resistance, women's health, physiology
Hobbies
Running, playing piano, and spending time with my family and dog
Tatum Gregston
Tatum Gregston
Undergraduate Research Capstone (spring 2022) entitled 'Using CRISPR Cas9 Lambda Red Homologous Recombination System to Make lon and sspB Gene Knockouts in E. coli'
Graduated spring 2023
Thomas Ebrahem
Thomas Ebrahem
2021 Fa - 2023 Fa, graduated with BS
Major in Human Biology
Undergraduate Honor Medallion Winners: 05/05/23
Left: Dr. Nicholas C. Butzin
Right: Thomas Ebrahem
Takrim Rimon
Takrim Rimon
Undergraduate Research Assistant: fall 2021 to fall 2022
Graduated fall 2022
Left: Dr. Nicholas C. Butzin
Right: Takrim Rimon
Katherine A. Erickson
Katherine A. Erickson
Undergraduate Capstone project (spring 2021) entitled, 'Evolving the Cells to Use Alternative Amino Acids'
Undergraduate Honor Medallion Winners: 05/06/22
Graduated: spring 2022
Drew Westerman
Drew Westerman
Syn-Bio REU (synthetic biology research experience for undergraduates) awardee, summer 2021.
Undergraduate Research Assistant: spring 2021, fall 2021, and spring 2022.
Undergraduate Honor Medallion Winners: 05/06/22.
Graduated: spring 2022.
Eliza Peters
Eliza Peters
Undergraduate Research Capstone (Spring 2019) entitled, 'Evolving the Minimal Cell (Mycoplasma mycoides JCVI-Syn3B) to Survive Stress
Undergraduate Research Assistant: fall 2020 to spring 2022
Syn-Bio REU (synthetic biology research experience for undergraduates) awardee, summer 2021.
Major: Human Biology
Undergraduate Honor Medallion Winners: 05/06/22.
Publication Link: 2021
Hobbies: Travel, running, soccer, and watching movies.
Graduated: spring 2022
Courtney Cameron
Courtney Cameron
Undergraduate Research Capstone (Spring 2019) entitled, 'Examination of the Relationship of Proteolytic Queueing and Persistence in Escherichia coli Treated with Ciprofloxacin'
Major: Microbiology and Biotechnology
Minors: Chemistry
Publications Link: 2019
Hobbies: Drawing, Baking, Puzzles, and Crafting
Undergraduate Research Assistant: spring 2018 Sp to spring 2021
Graduated: spring 2021
Chase Flickema
Chase Flickema
FAST REEU Program: Summer 2019
Undergraduate Research Capstone (fall 2019) entitled, 'Assay in the degradation of Toxins in TA systems within Escherichia coli'
Undergraduate Research Assistant: Spring 2020 to spring 2021
Hobbies: Biking, photography, videography, puzzles, soccer, and movie watching
Graduated spring 2021.
Major: Microbiology
Minor: Chemistry
Position of graduation: SAb Biotherapeutics: Link
Caroline Kincade
Caroline Kincade
Undergraduate in the FAST REEU program in 2018
Graduated Spring, 2019
Andrew Christiansen
Andrew Christiansen
Undergraduate Capstone (Summer 2020 - Fall 2020) entitled, 'Protein Engineering at the Whole-Cell Level'
Graduated spring 2021.
Major: Human Biology
Mitch Lack
Mitch Lack
Undergraduate Capstone (spring 2020 - fall 2020) entitled, 'Development of the Methodology to Screen for New Antimicrobial Peptides Engineered from Toxic Microbial Proteins'
Graduated spring 2021
Major: Human Biology
Disclaimer: This is website is maintained by Dr. Nicholas C. Butzin. Information presented here does not represent official views or opinions of South Dakota State University or any other association that Dr. Butzin is connected with.
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