Research
CEMI’s mission is to enable Caltech researchers to tackle important problems involving microbes in bold and innovative ways. Toward that end, we offer competitive pilot grants once a year (announced at the beginning of the summer and due in the early fall) to allow students or postdocs to explore high-risk interdisciplinary projects for a one-year period. Please click here for a description of how to apply. Here is a list of previous awardees. Here is a list of publications that have resulted from the CEMI pilot grant program.
Labs
CEMI Pilot Projects
| Year | Title | Lead PI |
|---|---|---|
| 2019 | Machine learning for directed evolution | Frances Arnold and Yisong Yue |
| 2019 | High-resolution structure determination of bacterial gas vesicle protein shells | Grant Jensen and Mikhail Shapiro |
| 2019 | Multiplex recombineering for genome scale mutant libraries in diverse bacteria | Dianne Newman and Kaihang Wang |
| 2019 | Towards scalable closed-loop control using conditional guide RNAs | Niles Pierce and Richard Murray |
| 2019 | A high-throughput, biophysics approach to study microbial evolution | Matt Thomson and Rob Phillips |
| 2019 | In situ distribution of ANME-SRB aggregates in seep sea methane seep sediments | David Van Valen and Victoria Orphan |
| 2018 | Structural characterization of UvrC, the essential endonuclease in nucleotide excision repair | Jacqueline Barton |
| 2018 | Photomethanotrophy as a methane sink in the warming Arctic | Woodward Fischer and Christian Frankenburg |
| 2018 | Metabolic coupling in mixed microbial communities of aerobes and anaerobes | Rustem Ismagilov |
| 2018 | Understanding how emulsifiers in food impact the colonic mucus barrier and microbe-host interactions | Rustem Ismagilov and Sarkis Mazmanian |
| 2018 | Understanding carbon flow in the first obligate manganese-oxidizing consortium | Jared Leadbetter |
| 2018 | Electron cryotomography of crystalline cellulose synthesis by Gluconacetobacter hansenii | Elliot Meyerowitz |
| 2018 | Genetic novelty through ancient horizontal gene transfer: would the real arthropod polyketide-synthase please stand up? | Joe Parker |
| 2018 | Deciphering the mechanism that triggers 2 H-enrichment in lipids under oxidative and salt stress | Alex Sessions |
| 2018 | Directed evolution of bacteria-derived gas nanostructures as acoustic reporter genes | Mikhail Shapiro |
| 2018 | Concurrent transcriptomic characterization of host-pathogen populations in chronic skin wounds | Matt Thomson |
| 2018 | The time-resolved proteomic analysis of mazEF-mediated cell stasis and revival in Escherichia coli | David Tirrell |
| 2017 | The role of microbes in the development and aging of primitive animals | Lea Goentoro |
| 2017 | Structural studies of bacterial and archaeal extracellular electron transport components under near-native conditions | Grant Jensen |
| 2017 | Cultivation and analysis of the first chemolithoautotrophic bacteria to utilize Mn(II) as electron donor for growth | Jared Leadbetter |
| 2017 | Novel microbe-mediated neuro-immune interactions in the gastrointestinal tract | Sarkis Mazmanian |
| 2017 | Dynamics and control of metabolically cross-linked microbial consortia | Richard Murray |
| 2017 | Investigation of a novel proteolytic pathway in bacteria and its role in stress survival of the opportunistic pathogen Pseudomonas aeruginosa | Dianne Newman |
| 2017 | Microbial involvement in a beetle-ant symbiosis | Joe Parker |
| 2017 | Understanding nitrogen fixation via electrochemistry | Jonas Peters |
| 2017 | Conditional guide RNAs for scalable biological control | Niles Pierce |
| 2016 | Selective killing of latently infected CD4+ T-cells by conditionally replicating viruses that detect HIV transcripts | Pamela Bjorkman |
| 2016 | Transmission of viruses through fine particles (PM2.5) | Michael Hoffmann |
| 2016 | Structural studies of bacterial and archaeal extracellular electron transport components under near-native conditions | Grant Jensen |
| 2016 | The cell biology of starvation: Polyphosphate granule dynamics in Pseudomonas aeruginosa | Suliana Manley |
| 2016 | Life on lava flows: Which microbes grow on volcanic deposits and why? | Victoria Orphan |
| 2016 | Genomic rearrangements and the origins of immunity | Rob Phillips |
| 2015 | Sequence-level prediction and control of integral membrane protein expression | William Clemons |
| 2015 | A rapid approach to characterize spatial patterns of microbial colonization of host tissue | Rustem Ismagilov |
| 2015 | How widespread among bacteria is the ability to sporulate | Grant Jensen |
| 2015 | Symbiosis within a symbiosis: Cultivation and characterization of a novel, protozoan-associated deltaproteobacterial acetogen from termite guts | Jared Leadbetter |
| 2015 | Microbiome-based autism treatment through gut barrier repair | Sarkis Mazmanian |
| 2015 | Do different hopanoid types facilitate active transport of organic solutes? | Dianne Newman |
| 2015 | Characterization of protein responsible for extracellular electron transport in Euryarchaeota | Victoria Orphan |
| 2015 | Unveiling the nutritional capabilities of heterotrophic deep-sea bacterial symbionts using NanoSIMS | Victoria Orphan |
| 2015 | The proteomic response of Staphylococcus aureus to the innate immune system in vivo | David Tirrell |
| 2014 | Evolution and structural analysis of microbial rhodopsin based sensors | Frances Arnold |
| 2014 | In situ "sequencing" by FISH (seqFISH) for cell ID and transcription profiling | Long Cai |
| 2014 | Using optogenetic tools to manipulate the membrane potential of pathogens | Viviana Gradinaru |
| 2014 | Uncovering serotonergic members of the human microbiota | Rustem Ismagilov |
| 2014 | Microfluidic isolation of microbes that inactivate nematode signaling molecules | Rustem Ismagilov |
| 2014 | Substrate coordination to the active site cofactor of nitrogenase | Jonas Peters |
| 2014 | Mapping biological magnetism at the nanoscale: Bringing a key technology to Caltech CEMI | Mikhail Shapiro |
| 2014 | Detection of nematode-induced transcripts in the nematophagous fungus A. oligospora using Fluorescence in situ hybridization | Paul Sternberg |
| 2014 | Site-specific labeling of bacterial proteins in-situ using N-Myristoyltransferase for correlated, cryogenic Stochastic Optical Reconstruction Microscopy (cryo-STORM) | David Tirrell |
| 2013 | DNA signaling among proteins with 4Fe-4S clusters | Jacqueline Barton |
| 2013 | Mechanosensitive channels: Their role in photosynthetic cell biology | Ian Booth |
| 2013 | Imaging chromosome conformation in single bacteria cells | Long Cai |
| 2013 | Constructing mutants of Saccharomyces cerevisiae with CRISPR/CAS9 and characterization of genes involved in mutagenesis | Judith Campbell |
| 2013 | Evolution of photosynthesis in cyanobacteria | Woodward Fischer |
| 2013 | An integrated MEMS device for use as a microbial monitoring system in wastewater treatment | Michael Hoffmann |
| 2013 | Structure and organization of the bacterial chromosome | Grant Jensen |
| 2013 | A novel probiotic therapy for Parkinson's disease in animal models | Sarkis Mazmanian |
| 2013 | X-ray absorption spectroscopic studies of nitrogen fixation | Douglas Rees |
| 2012 | Argonaute proteins in bacteria: A glimpse into the ancient non-coding RNA world | Alexei Aravin |
| 2012 | Characterization of a novel membrane protein-targeting pathway in photosynthetic bacteria | William Clemons |
| 2012 | Understanding the physiological roles of subpopulations in clonal bacterial communities | Michael Elowitz |
| 2012 | Evolution and mechanism of type VI secretion-related nanomachines | Grant Jensen |
| 2012 | Diverse studies in microbial diversity | Jared Leadbetter |
| 2012 | Probing microbial energetics with microcalorimetry: The environmental and energetic meaning of heat production | Victoria Orphan |
| 2012 | Quantitative dissection of iron-mediated gene regulation in Pseudomonas aeruginosa | Rob Phillips |
Pilot Grant Recipients
| Funding | Lead PI | Recipient |
|---|---|---|
| 2017 | Lea Goentoro | David Gold |
| 2017 | Grant Jensen | Poorna Subramanian |
| 2017 | Jared Leadbetter | Jared Leadbetter |
| 2017 | Sarkis Mazmanian | Bryan Yoo |
| 2017 | Richard Murray | Rory Williams |
| 2017 | Dianne Newman | David Basta |
| 2017 | Joe Parker | Joe Parker |
| 2017 | Jonas Peters | Matthew Chalkley |
| 2017 | Niles Pierce | Mikhail Hanewich-Hollatz |
| 2016 | Pamela Bjorkman | Magnus Hoffmann |
| 2016 | Michael Hoffmann | Lijie (Sara) Li |
| 2016 | Grant Jensen | Poorna Subramanian |
| 2016 | Suliana Manley | Lisa Racki |
| 2016 | Victoria Orphan | Ranjani Murali |
| 2016 | Rob Phillips | Soichi Hirokawa |
| 2015 | William Clemons | Stephen Marshall |
| 2015 | Rustem Ismagilov | Antti Lignell and Octavio Mondragon-Palomino |
| 2015 | Grant Jensen | Davi Ortega and Will DePas |
| 2015 | Jared Leadbetter | Ella Yanay |
| 2015 | Sarkis Mazmanian | Brittany Needham |
| 2015 | Dianne Newman | Gargi Kulkarni |
| 2015 | Victoria Orphan | Grayson Chadwick |
| 2015 | Victoria Orphan | Shana Goffredi |
| 2015 | David Tirrell | Shannon Stone |
| 2014 | Frances Arnold | Austin Rice |
| 2014 | Long Cai | Timur Zhiyentayev |
| 2014 | Viviana Gradinaru | Sripriya Ravindra Kumar and Ruth Lee |
| 2014 | Rustem Ismagilov | Elaine Hsiao |
| 2014 | Rustem Ismagilov | Liang Ma |
| 2014 | Jonas Peters | Jon Rittle |
| 2014 | Mikhail Shapiro | Pradeep Ramesh |
| 2014 | Paul Sternberg | Yen-Ping Hsueh and Ting-Fan He |
| 2014 | David Tirrell | Samuel Ho |
| 2013 | Jacqueline Barton | Michael Grodick |
| 2013 | Ian Booth | Vojtech Prazak |
| 2013 | Long Cai | Timur Zhiyentayev |
| 2013 | Judith Campbell | Martin Budd |
| 2013 | Woodward Fischer | James Hemp and Jena Johnson |
| 2013 | Michael Hoffmann | Penvipha Satsanarukkit |
| 2013 | Grant Jensen | Yi-Wei Chang |
| 2013 | Sarkis Mazmanian | Catherine (Katie) Schretter |
| 2013 | Douglas Rees | Limei Zhang |
| 2012 | Alexei Aravin | Ivan Olovnikov |
| 2012 | William Clemons | Vijay Somalinga |
| 2012 | Michael Elowitz | Adam Rosenthal |
| 2012 | Grant Jensen | Martin Pilhofer |
| 2012 | Jared Leadbetter | N/A - Supplies |
| 2012 | Victoria Orphan | Jeff Marlow |
| 2012 | Rob Phillips | James Boedicker |
How to Apply for a Pilot Grant
We have a limited pool of resources to advance novel, collaborative pilot projects conducted by students or postdocs. Research awards support stipend and tuition (students) or salary and benefits (post-doctoral fellows) for 1 year (starting in fall to be spent within the academic year). Candidates from any Division at Caltech may apply. Contact the CEMI administrator with questions.