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Research Highlights

Geometric Viability Assay: Speeding up antibiotic discovery research

[video:https://www.youtube.com/watch?v=9tAIbpZ_uOw]

Using "Quantum-dot" based antibiotics to clear infection in mice

"on the use of Quatum dot basedantibiotics to reduce intracellular infections in a bone-infection model.

IThe study shows that QD antibiotics are safe and effective in an abcess infection model.

Using "Quantum-dot" based antibiotics to clear biofilms in synergy with traditional antibiotics

of MRSA, Psuedomonas aeruginosa, and Escherichia coli.

Quantum dot antibiotic animal safety and efficacystudy "" shows that specifically-engineeredand light-activated Quantum dot antibiotics can treat infection of MDR bacteria in an in vivo model, and are safe and non-toxic.

. The combination of activation using a deep-tissue-penetrating light source, and selective mechanism of action, produces an effective treatment.

is used to develop antisense molecules that target genes of interest in non-model or genetically intractable spcies, such as MDR clinical isolates of bacteria. This allows us to identify which genes are important for antibtioic tolerance and/or resistance. This process can identify new gene targets in MDR bacteria in less than 5 days.

confirms mechanism of action of Quatum dot antibiotics. We identify genes demonstrate a consistent association with the DNA damage response and deactivation of iron–sulfur clusters.

shows that combining individually fitness-neutral perturbations can compound fitness impacts and sesitize bacteria to antibiotics.

CHAOS Therapy

We reportnovel CHAOS Therapy to Slow down bacterial evolution of antibiotic resistance in paper "" published in Nature Communications Biology.

See media coverage

We report using Quantum dot antibiotics to potentiate antibiotics in highly drug-resistant clinical isolates in paper "" published in Science Advances.

A lot of E. Coli petri dishes

We report a novel Light-Activated Nanotherapy that kills Clinically isolated Multi Drug Resistant Bacteria in manuscript led by Colleen and Sam, "" in Nature Materials!

PO-biofuels

We report a CRISPR gene expression perturbation approach to increase bacterial tolerance to biofuels "" in Frontiers in Bioengineering and Biotechnology!

TA-HCV

We report a new mathematical model fitted to experimental data for predicting intracellular HCV dynamics, "" in Journal of Virology!

TA space

We report transcriptomic signature of E. coli adapted to antibiotics on the International Space Station, in "." Frontiers of Microbiology!

Tolerome

We report the first database that can mine gene expression data sets to identify key players of adaptive resistance in bacteria. "" published in ACS Synthetic Biology.

Diagrams on the experiment

We are pleased to report a new systems bology approach to mine and identify key gene signatures in complex gene expression data sets in our publication "" in mSphere.

Molecules and graphs

We are pleased to report four publications on novel single-molecule sequencing methods in 2017! These publications can be found in,, and.

Description of an experiment along with pictures and diagrams of test tubes

We present a novel application of CRISPR-Cas9 technology for investigating how gene expression governs the adaptive pathways available to bacteria during the evolution of resistance in Peter's paper titled, ""in ACS Synthetic biology!

We report a novel tool for synthetic biology and metabolic engineering by investigating transcriptional interference mechanisms of antisense roadblock and RNA polymerase traffic in a set of convergent promoters, in paper led by Toni, ""in ACS Synthetic biology!

Description of how the antibiotic works

We report a novel gene expression variability based approach to identify important genes involved in bacterial adaptive resistance, in paper led by Keesha, "" in ACS Infectious Diseases!

Antisense Transcription

We report a new mathematical model that describes tunabilty of genetic switch behavior during antisense transcription, in a paper led by Toni, "" in PLoS ONE!

Some cell/molecule diagram in detail

We report a bet-hedging based mechanism of adaptive resistance to PNA based antimicrobials in a paper led by Colleen, "" in ACS Infectious Diseases!

CGTA

We reveal novel nanoelectronic fingerprints for DNA in paper led by Josep, "" in Journal of Physical Chemistry Letters B!

Constrictor molecule

New Metabolic Flux Analysis tool CONSTRICTOR is available on

Our lab designs and reports a new FBA tool called CONSTRICTOR, in a paper led by Keesha, "" in PLoS ONE!

Sam's paper"" is published in The Journal of Physical Chemistry Letters!

Our mathematical modeling paper on "" accepted in Antiviral Therapy!

Anushree's paper on "" is published in PNAS!

Lab web 2

Welcome

Our research group uses a combination of interdisciplinary approaches including synthetic biology, systems biology, microbiology, synthetic chemistry, and nanoengineering to address the key global challenge involving antimicrobial resistance. We aim at developing strategies for rationally engineering next-generation smart antimicrobials that can eliminate multi-drug resistant superbugs, with the ultimate goal of creating therapies that can evade evolution of drug-resistance in microbes. To this end, we are also interested in investigating the non-genetic mechanisms responsible for antimicrobial tolerance/resistance to devise strategies that can one day prevent evolution of drug resistance. Using synthetic biology tools we are also interested in designing, constructing and engineering modular synthetic genetic devices based on less-explored naturally occurring mechanisms, for both understanding fundamentally how nature works as well as built devices for potential biotechnological applications.

Featured by Engineering

[video:https://youtu.be/VcXuTGNphPY]

--by Chase Purdy, Quartz

For years, scientists at the University of Colorado have sought to defuse the destructive powers of a pernicious bacteria that often sneaks into the human body through tainted food.Turns out, one of the most effective ways to beatE. coliis to sow chaos. ()

Lab invents CHAOS Therapy to Slow down the bacterial evolutionof antibiotic resistance

How to stop an antibiotic-resistant superbug

-- ByTrent Knoss,University of Colorado press release

A genetic disruption strategy developed by University of Colorado Boulder researchers effectively stymies the evolution of antibiotic-resistant bacteria such asE. coli, giving scientists a crucial leg up in the ongoing battle against deadly superbugs. (Read more)

-by, Denver Post and Boulder Daily Camera

Kryptonite for superbugs could be on the horizon, as a result of research led by University of Colorado researchers that hinders the progress of antibiotic-resistant superbugs such asE.coli... ()

Anushree speaks at the Institute of Systems Biology's Future of Health Symposium

[video:https://youtu.be/wB5Q9gqMMcw]

Session 3: Prevention and TherapyAnushree Chatterjee, PhD | University of Colorado at Boulder "From Synthetic Biology to Nanobiotechnology: Rational Antimicrobial Engineering Approaches for Combating Multidrug-Resistant Pathogens"

[video:https://youtu.be/VSE2RRv4JEc]

--Lab Research Featured by Hamodia

A WATERSHED IN RESEARCH STUDIES

Trailblazing research studies of diverse approaches, recently published in peer-reviewed science journals, are poised to combat antibiotic resistance. Hamodia interviewed these leading researchers, each at the helm of his study.Assistant Professors Prashant Nagpal and Anushree Chatterjee of the Department of Chemical and Biological Engineering in the University of Colorado Boulder, whose studies were published in the science journalsNature MaterialsandScience Advances.“Our approach is a two-pronged strategy to fight antibiotic-drug resistance..... ()

MSN, Newsweek, Science News, CIDRAP features our work on potentiating drug-resistant clinical bacteria to antibiotics

[video:https://youtu.be/qBCrZCmgZos]

Boulder, Colorado—Light-activated nanoparticles, also known as quantum dots, can provide a crucial boost in effectiveness for antibiotic treatments used to combat drug-resistant superbugs such asE.coliandSalmonella, new Boulder research shows......

Todd Neff for UC Health- DENVER, CO. Science can border on science fiction. Designing swarms of infinitesimal semiconductors that, shined with green light, turn standard oxygen into a superoxide that makes life hell for drug-resistant bacteria – that qualifies.....

[video:https://youtu.be/6xGn-z6B_uM]

Boulder, Colorado—Scientists have been creating antibiotics to kill deadly bacteria for nearly 80 years. Unfortunately, the bacteria that cause disease can adapt so quickly, some have evolved into superbugs that are resistant to all antibiotics, and making new drugs is a long, expensive, involved process....

ABC News

[video:https://www.thedenverchannel.com/news/local-news/cu-researchers-use-light-activated-nanoparticles-used-to-kill-antibiotic-resistant-superbugs]

In the ever-escalating evolutionary battle with drug-resistant bacteria, humans may soon have a leg up thanks to adaptive, light-activated nanotherapy developed by researchers at the University of Colorado Boulder.

Antibiotic-resistant bacteria such as Salmonella,E. Coliand Staphylococcus infect some 2 million people and kill at least 23,000 people in the United States each year. Efforts to thwart these so-called “superbugs” have consistently fallen short due to the bacteria’s ability to rapidly adapt and develop immunity to common antibiotics such as penicillin.

New research from -Boulder, however, suggests that the solution to this big global problem might be to think small—very small.

Inpublished today in the journalNatureMaterials, researchers at the Department of Chemical and Biological Engineering and the BioFrontiers Institute describe new light-activated therapeutic nanoparticles known as “quantum dots.” The dots, which are about 20,000 times smaller than a human hair and resemble the tiny semiconductors used in consumer electronics, successfully killed 92 percent of drug-resistant bacterial cells in a lab-grown culture.....

News

  • Shane and Yuchen's paper "" published inChemBioChem. Congratulations!

  • Christian's paper ""accepted in Nature Microbiology. Congratulations!

  • Check out how to use the Geometric Viabilty Assay for speeding up your microbiology research using the link provided.

  • [video:https://www.youtube.com/watch?v=9tAIbpZ_uOw]

  • Yuchen's paperpublished in ChemSuSChem. Congratulations!

  • Christian awarded NIHK99 Pathway to Independence award! Congratulations!

  • Fateh and Yangming complete a successul summer internship in the Chatterjee lab!

  • abc

  • Welcome Fateh to the lab for antibitic research! Thanks to support fromMitacs Globalink Research Award Abroad.

  • Safety and biodistribution study for COVID targeting direct-acting antiviral is now published in !

  • CongratulationsCory for winningthe Advanced Light Source (ALS) Doctoral Fellowship at Berkeley Lab!

  • Congratulations Christian on being awarded the Fall 2022 PAC Research/Outreach Grant!

  • "on the use of QD antibiotics to reduce intracellular infections in a bone-infection model is published in Nanoscale Advances!

  • Christian Meyer joins lab as a post-doc. He brings his expertise in biophysics, drug-drug interactions, as well as novel high-througput methods to measure bacterial viability! Welcome!

  • Nolan O'Connor defends Ph.D. and becomes Dr. O'Connor! Congratulations!!

  • Colleen McCollum defends Ph.D. and becomes Dr. McCollum! Congratulations!!

    pic

  • Kristen Eller defends Ph.D. and becomes Dr. Kristen Eller! Congratulations!!

  • Peter andKristen's paper on "" published inNature Communications Biology.

  • "," an international collaborative effort to develop treatment against SARS-CoV2 published in Cell Reports.

  • "Therapeutics in less than a week." Our Nature Comm Biology paper got selected for an article in. Congrats Kristen! Check it out !

  • FAST paper recieves press:|||||||| Boulder|| | | | | | |

  • Tom Aunins becomes Dr. Thomas Aunins and graduates with a Ph.D. Congratulations!! Thanks for all the great work and best of luck for the next chapter of your career!

  • "Feeling the need for speed (for new therapeutic modalities). Outsmarting evolving microbes." Check out our new paper on translation of Quantum dot antibiotics:Colleen R. McCollum,John R. Bertram,Prashant Nagpal,and Anushree Chatterjee* (2021).. ACS Applied Materials & Interfaces (In press).

  • Dana's paper on "Light-Activated Quantum Dot Potentiation of Antibiotics to Treat Drug-Resistant Bacterial Biofilms" published in Nanoscale Advances
  • Shane recieves NSF GRFP Honorable mention! Congrats!
  • "Feel the need for speed?" FAST Antimicrobials in less than one week. Kristen's paper on "" published inCommunications Biology
  • Nolan's paper "" published inACS Synthetic Biology
  • Colleen's paper on Quantum dot antibiotic animal safety and efficacystudy "" published in ACS Biomaterials Science & Engineering
  • Tom and Keesha's paper on "" published in PNAS
  • Lab recieves funding from to create technology to mitigate the effects of space radiation as part of an interdisciplinary team led by CSU
  • Lab featured on
  • Lab collaborates on LDRD project with Sandia National Laboratory
  • Lab recieves funding from The to support COVID-19 research
  • Lab supports COVID-19 International Research Team () insearch of therapeutic solutions against SARS-CoV2
  • ARMOR releases podcast series on Spotify:
  • Lab featured onOn E Podcast: The Anti-Microbial Resistance Mediation Outreach Program (ARMOR)
  • Lab outreach effort ARMOR featured on cover of E Engineering Magazine
  • Lee defends Ph. D. thesis virtually and becomes Dr. Korshoj! Many congratulations on a job welldone!
  • We are proud to present the first seminar by Dr. John Aunins on Feb 10th, 2020!! The seminar will be livestreamed globally.
  • ARC1
  • Lab recieves NIH Division of Microbiology and Infectious Diseases (DMID) contract for studying efficacy of QD antibiotics in animal models.
  • Super FAST response to disease outbreaks:Lab featured as Leading Edge in Engineering Magazine Fall 2019 edition.
  • Toni and Nolan's paper onpublished in ACS Synthetic Biology.
  • Lab receives a $2.25M led by the
  • Lab receives funding from Vastbiome Inc. to study gut bacteria.
  • Anushree recieves Provost Faculty Achievement Award
  • Lab issued two patents:and
  • Tom's paper on "," published inACS Biomaterials Science and Engineering.
  • Dr. Sadhana Sharma joins lab as aresearch assistant professor/senior postodoctoral fellow.Welcome!
  • Two of Max's papers published.paper published in Angewandte Chemie andin ACS Biomaterials and Engineering!
  • Anushree receives Outstanding Junior Faculty Award from ChBE!
  • ARMOR program in full flow!Read more:
  • Congrats to high school student Anudeep Golla for winning 2nd out of around 60 projects in Computational Biology catgory at ISEF! He won $$ and was chosen to have an asteroid named after him!
  • Antimicrobial Resistance Mediation OutReach (ARMOR) Program Boulder Chapter official website launched! See link. Check out our outreach events!
  • Lab undergraduate researcher Vismaya Bachu wins Silver Medal Award from the College of Engineering! Congratulations!! :) Vismaya will be heading to Johns Hopkins medical school this fall.
  • REU student Suxuen Yew from Kansas University joins lab for summer research. Welcome!
  • New Postdoc Job posting: See here
  • Lab receives funding from and Lab VentureChallenge!
  • Anushree wins Lab Venture challenge award for developing novel nucleic acid therapiesagainst Multi-drug resistant bacteria.
  • Lab developsa
  • : Science Buffs blog about CHAOS Therapy
  • CHAOS paper receives significant media press:University of Colorado press release,,, ,,, and more.
  • Toni successfully defends his Ph. D. and becomes Dr. Antoni E. Bordoy! Many congratulations!!
  • Peter's paper "" published in Frontiers in Biotechnology and Bioengineering. Congrats!
  • Peter successfully defends his Ph. D. and becomes Dr. Peter Otoupal! Peter will move on to his new post-doc position at Sandia National Lab starting in August. Many congratulations Peter!
  • Peter's paper "" is published in Nature Communications Biology! Congrats!
  • Anushree nominated as "Rising Stars" by the journal Frontiers of Chemistry!
  • Peter wins Excellence in Graduate student research award from ChBE department. Congrats!
  • Will Cordell wins Marilyn and Howard L. Anseth Outstanding Undergraduate Research Award and Outstanding Undergraduate Research Awards ‐Gold medal. Congrats!
  • Kristen and Tom recieve NSF GRFP Honorable mentions. Congrats!
  • Anushree receives ACS Infectious Diseases Young Investigator Award!
  • Anushree becomes Associate Editor of Frontiers in Bioengineering and Biotechnology.
  • BBC features our Quantum dot antibiotic research!
  • Tom's paper" published in Journal of Virology. Congrats Tom!
  • Tom's paper "" is published in Frontiers in Microbiology. Congrats Tom!
  • University of Colorado Health features our research to combat antibiotic resistance!
  • Peter wins third place in Stars symposium. Congrats!
  • Lee's paper on "" published in JACS. Congratulations!
  • Keesha's paper on "" published in ACS Syn Bio. Congratulations!
  • Our potentiating antibiotics paper in Science Advances receives press coverage including
  • Colleen's paper on "" published in Science Advances. Congratulations!
  • Sepideh's paper "" published in ACS Nano. Congratulations!
  • Colleen moves on to her new post-doc position at Sandia National Lab at Livermore. Congratulations and all the best!
  • Anushree receives grant funding from National Science Foundation!
  • Colleen successfully defends her Ph.D., and becomes Dr. Courtney!! Congratulations!!
  • Colleen recieves Max Peters Outstanding Graduate Student Award. Congratulations!
  • Keesha successfully defends her Ph.D. and becomes Dr. Erickson! Keesha moves on to pursue postdoctoral research at Los Alamos National Laboratory. Congratulations and all the best!!
  • Anushree recieves DARPA Young Faculty Award!
  • Lee wins . Congratulations!
  • Keesha's paper on "Transcriptome level signatures in gene expression and gene expression variability during bacterial adaptive evolutionpublished in mSphere. Congrats!
  • Voice of America features our Quantum Dot Antibiotic work in article, ""
  • Colleen won 2nd place at the 9th Annual Bionanotechnology Graduate Student Award Session at AIChE. Her award talk was titled “Photoexcited Quantum Dots Potentiate Antibiotic Activity in Multidrug-Resistant Bacteria”. Congrats Colleen!
  • Lee's paper titled "" published in Small. Congrats Lee!
  • Colleen wins Best Poster Award from theBiochemical Engineering Journaland the AIChE Food, Pharmaceutical and Bioengineering Division for her work titled, "Sequence Specific Antisense Inhibitors of Non-Traditional Antibiotic Pathways." Congrats Colleen!
  • Anushree recognized as one of the most highly prolific authors for!
  • Sam Goodman defends his Ph.D. and moves on to a postdoctoral fellow position at the National Academy of Sciences. Congrats Sam!
  • Peter's paper on "" is published in ACS Synthetic Biology. Congrats Peter!
  • Lab's Quantum dot antibiotic research featured by reporter Shelley Schlender on 88.5 FM KGNU Science Show "How on Earth." See
  • Hear
  • Toni's paper on "" is published in ACS Synthetic Biology.CongratsToni!
  • Quantum dot antibiotic work highlighted in MRS Bulletin!
  • See
  • Quantum dot antibiotic work featured in France's Tech 24 TV show!
  • See
  • Vismaya and Pallavi recieve UROP awards to pursue research. Congrats!
  • Keesha recieves NSF-EAPSI Fellowship to conduct collaborative research. Congrats Keesha!
  • Lee recieves GAANN fellowship. Congrats!
  • Our Light Activated Nanotherapy featured in ABC's Denver Channel 7 News!
  • Sepideh and Sajida join lab as postdoctoral fellows. Welcome!
  • New graduate students Lee, Partha join Chatterjee Lab. Welcome!
  • Keesha wins Dean's Graduate Student Research Grant for discovery of novel drug targets for treating MDR infections. Congrats!
  • Anushree presents five talks on synthetic biology, antimicrobial adaptive resistance, and strategies for novel therapeutics for MDR bacterial infections at AIChE 2015 conference.
  • Our paper featured in the !