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 publications that have resulted from the CEMI pilot grant program
Labs
CEMI Pilot Projects
Number of projects: 106
Year | Title | Lead PI | Grant Recipient |
---|---|---|---|
2023 | Elucidating the biodegradation of dimethylsilanediol by soil microbes | Frances Arnold | Ryen O'Meara |
2023 | Structural studies on Runella zeae prokaryotic Argonaute protein | Tsui-Fen Chou | Kate Radford |
2023 | Reoptimizing plant microbiomes through exudate engineering | Gözde Demirer | Chiara Berruto |
2023 | Exploration of the aging Parkinson’s microbiome | Rustem Ismagilov | Natalie Wu-Woods |
2023 | An integrated-omics approach to assess carbon fluxes in soil microbiomes under drought stress | Smruthi Karthikeyan | Grace Solini |
2023 | Cell-free systems as a universal platform for phage production | Richard Murray | Yan Zhang |
2023 | Quantifying the basal power requirement during microbial energy-limitation in the lab | Dianne Newman | John Ciemniecki |
2023 | Aerobic short-chain alkane oxidation with novel particulate Cu-monooxygenases on carbonates at methane seeps | Victoria Orphan | Magdalena Mayr |
2023 | Understanding the responses of bacteria growth dynamics to the host environment | Ned Ruby | Liu Yang |
2023 | Toward injectable sub-mm wireless living electronic sensors | Mikhail Shapiro | Josh Chen |
2023 | Multiplex generation of chimeric bacterial strains via conjugation and CRISPR-associated transposons | Kaihang Wang | Tomasz Gawda |
2022 | Feasibility of mapping all DNA within each bacterial cell from a microbial community | Rustem Ismagilov | Matt Ratanapanichkich |
2022 | Identification of determinants of lithotrophic manganese oxidation via heterologous expression of a random Manganitrophus-genome library | Jared Leadbetter and Dianne Newman | Lydia Varesio |
2022 | A living voltmeter: Protein chimeras quantifying transmembrane electron transfer | Karthish Manthiram | James Wang |
2022 | ‘Re-wilding’ the microbiome of laboratory mice promotes sociability | Sarkis Mazmanian and Mikhail Shapiro | Jessica Griffiths and Claire Rabut |
2022 | Snapshot of host-microbe interactions in the squid-vibrio system | Margaret McFall-Ngai and Lior Pachter | Vera Beilinson |
2022 | Model-based design of microbial self-assembly response to environmental conditions | Richard Murray and Victoria Orphan | Alex Johnson and Ayush Pandey |
2022 | Formulating a defined medium to study chronic wound infections | Dianne Newman | Chelsey VanDrisse |
2022 | Targeted sequencing of ANME-3 genomes from enrichment cultures and FACS | Victoria Orphan | Philip Woods |
2022 | Quantifying stochastic geometry and physiology in polymicrobial communities | Rob Phillips and Dianne Newman | Gabe Salmon |
2022 | Studying the spatiotemporal dynamics of native gut microbes with acoustic reporter genes | Mikhail Shapiro and Sarkis Mazmanian | Whee-Soo Kim |
2022 | Constructing synthetic large DNA molecules with toehold assisted DNA assembly | Kaihang Wang | Noah Robinson and Jeongsoo Hur |
2022 | Megabase DNA insertion in Agrobacterium tumefaciens for plant genome engineering | Kaihang Wang | Raymond Zhang and Charles Sanfiorenzo |
2022 | Recoded bacteria strain as predator release factory | Kaihang Wang | Jolena Zhou |
2021 | Searching for traces of microbial life in exceptionally well-preserved Paleoarchean black cherts from South Africa | Joe Kirschvink, George Rossman, and John Eiler | Noah Tashbook |
2021 | Interaction between programmable nuclease defense systems: Argonaute proteins and CRISPR-Cas | Alexei Aravin | Anton Kuzmenko |
2021 | Interaction between programmable nuclease defense systems: Argonaute proteins and CRISPR-Cas | Alexei Aravin | Anton Kuzmenko |
2021 | Mechanistic studies of a bacterial arsenic efflux system with implications for bioremediation | Bil Clemons, Dianne Newman and Doug Rees | Shivansh Mahajan |
2021 | A minimal gene cassette for probing magnetosome biomineralization | Ryan Hadt and Doug Rees | Christian Totoiu |
2021 | Mathematically rigorous quantitative microbiome analysis tools | Rustem Ismagilov and Matt Thomson | Matt Cooper and Jialong Jiang |
2021 | Identification and characterization of proteins involved in symbiosis in the entomopathogenic nematode Steinernema hermaphroditum | Paul Sternberg | Chieh-Hsiang Tan and Mengyi Cao |
2020 | Teasing out the structural and evolutionary origins of the Get3 family | William Clemons | Shyam Saladi |
2020 | Microbes underlie regenerative capacity in a poorly regenerative jellyfish model | Lea Goentoro | Aki Ohdera and Zevin Condiotte |
2020 | Culture-free detection of functional bacteriophage-host interactions in the mouse cecum by single-cell isolation and genome sequencing | Rustem Ismagilov | Eric Liaw |
2020 | The mechanics of microbial rainbows: optomechanical properties of iridescent biofilms | Julia Kornfield | Priya Chittur |
2020 | Engineering probiotics that sense and regulate inflammation | Richard Murray and Sarkis Mazmanian | Richard Murray and Sarkis Mazmanian |
2020 | Experimental and theoretical approaches to studying the physiology of single cells in structured environments | Dianne Newman and Rob Phillips | Avi Flamholz |
2020 | High-throughput enrichment and physiological study of microbial metabolic symbioses of the Asgard Archaea | Victoria Orphan | Yanzhe Zhu |
2020 | Horizontal transmission of an insect primary endosymbiont | Joe Parker | Sheila Kitchen |
2020 | Isotopic fingerprinting of serine to probe carbon flows in phytoplankton | Alex Sessions and John Eiler | Elise Wilkes |
2020 | Time-resolved, state-selective proteomic interrogation of P. aeruginosa & S. aureus co-culture dynamics | Dave Tirrell | Grace Wang |
2020 | Designing orthogonal transcription and translation memory circuits | Kaihang Wang and Richard Murray | Bryan Gerber and Matthieu Kratz |
2019 | Machine learning for directed evolution | Frances Arnold and Yisong Yue | Bruce Wittmann |
2019 | High-resolution structure determination of bacterial gas vesicle protein shells | Grant Jensen and Mikhail Shapiro | Lauren Metskas |
2019 | Multiplex recombineering for genome scale mutant libraries in diverse bacteria | Dianne Newman and Kaihang Wang | Scott Saunders |
2019 | Towards scalable closed-loop control using conditional guide RNAs | Niles Pierce and Richard Murray | Jining Huang |
2019 | In situ distribution of ANME-SRB aggregates in seep sea methane seep sediments | David Van Valen and Victoria Orphan | Haley Sapers |
2018 | Structural characterization of UvrC, the essential endonuclease in nucleotide excision repair | Jacqueline Barton | Rebekah Silva |
2018 | Photomethanotrophy as a methane sink in the warming Arctic | Woodward Fischer and Christian Frankenburg | Woodward Fischer and Christian Frankenberg |
2018 | Metabolic coupling in mixed microbial communities of aerobes and anaerobes | Rustem Ismagilov | Tahmineh Khazaei |
2018 | Understanding carbon flow in the first obligate manganese-oxidizing consortium | Jared Leadbetter | Hank Yu |
2018 | Electron cryotomography of crystalline cellulose synthesis by Gluconacetobacter hansenii | Elliot Meyerowitz | William Nicolas |
2018 | Genetic novelty through ancient horizontal gene transfer: would the real arthropod polyketide-synthase please stand up? | Joe Parker | Adrian Brueckner |
2018 | Deciphering the mechanism that triggers 2 H-enrichment in lipids under oxidative and salt stress | Alex Sessions | Reto Wijker |
2018 | Directed evolution of bacteria-derived gas nanostructures as acoustic reporter genes | Mikhail Shapiro | Robert Hurt |
2018 | Concurrent transcriptomic characterization of host-pathogen populations in chronic skin wounds | Matt Thomson | Sisi Chen |
2018 | The time-resolved proteomic analysis of mazEF-mediated cell stasis and revival in Escherichia coli | David Tirrell | Elliot Mackrell |
2017 | The role of microbes in the development and aging of primitive animals | Lea Goentoro | David Gold |
2017 | Structural studies of bacterial and archaeal extracellular electron transport components under near-native conditions | Grant Jensen | Poorna Subramanian |
2017 | Cultivation and analysis of the first chemolithoautotrophic bacteria to utilize Mn(II) as electron donor for growth | Jared Leadbetter | Jared Leadbetter |
2017 | Novel microbe-mediated neuro-immune interactions in the gastrointestinal tract | Sarkis Mazmanian | Bryan Yoo |
2017 | Dynamics and control of metabolically cross-linked microbial consortia | Richard Murray | Rory Williams |
2017 | Investigation of a novel proteolytic pathway in bacteria and its role in stress survival of the opportunistic pathogen Pseudomonas aeruginosa | Dianne Newman | David Basta |
2017 | Microbial involvement in a beetle-ant symbiosis | Joe Parker | Joe Parker |
2017 | Understanding nitrogen fixation via electrochemistry | Jonas Peters | Matthew Chalkley |
2017 | Conditional guide RNAs for scalable biological control | Niles Pierce | Mikhail Hanewich-Hollatz |
2016 | Selective killing of latently infected CD4+ T-cells by conditionally replicating viruses that detect HIV transcripts | Pamela Bjorkman | Magnus Hoffmann |
2016 | Transmission of viruses through fine particles (PM2.5) | Michael Hoffmann | Lijie (Sara) Li |
2016 | Structural studies of bacterial and archaeal extracellular electron transport components under near-native conditions | Grant Jensen | Poorna Subramanian |
2016 | The cell biology of starvation: Polyphosphate granule dynamics in Pseudomonas aeruginosa | Suliana Manley | Lisa Racki |
2016 | Life on lava flows: Which microbes grow on volcanic deposits and why? | Victoria Orphan | Ranjani Murali |
2016 | Genomic rearrangements and the origins of immunity | Rob Phillips | Soichi Hirokawa |
2015 | Sequence-level prediction and control of integral membrane protein expression | William Clemons | Stephen Marshall |
2015 | A rapid approach to characterize spatial patterns of microbial colonization of host tissue | Rustem Ismagilov | Antti Lignell and Octavio Mondragon-Palomino |
2015 | How widespread among bacteria is the ability to sporulate | Grant Jensen | Davi Ortega and Will DePas |
2015 | Symbiosis within a symbiosis: Cultivation and characterization of a novel, protozoan-associated deltaproteobacterial acetogen from termite guts | Jared Leadbetter | Ella Yanay |
2015 | Microbiome-based autism treatment through gut barrier repair | Sarkis Mazmanian | Brittany Needham |
2015 | Do different hopanoid types facilitate active transport of organic solutes? | Dianne Newman | Gargi Kulkarni |
2015 | Characterization of protein responsible for extracellular electron transport in Euryarchaeota | Victoria Orphan | Grayson Chadwick |
2015 | Unveiling the nutritional capabilities of heterotrophic deep-sea bacterial symbionts using NanoSIMS | Victoria Orphan | Shana Goffredi |
2015 | The proteomic response of Staphylococcus aureus to the innate immune system in vivo | David Tirrell | Shannon Stone |
2014 | Evolution and structural analysis of microbial rhodopsin based sensors | Frances Arnold | Austin Rice |
2014 | In situ "sequencing" by FISH (seqFISH) for cell ID and transcription profiling | Long Cai | Timur Zhiyentayev |
2014 | Using optogenetic tools to manipulate the membrane potential of pathogens | Viviana Gradinaru | Sripriya Ravindra Kumar and Ruth Lee |
2014 | Uncovering serotonergic members of the human microbiota | Rustem Ismagilov | Elaine Hsiao |
2014 | Microfluidic isolation of microbes that inactivate nematode signaling molecules | Rustem Ismagilov | Liang Ma |
2014 | Substrate coordination to the active site cofactor of nitrogenase | Jonas Peters | Jon Rittle |
2014 | Mapping biological magnetism at the nanoscale: Bringing a key technology to Caltech CEMI | Mikhail Shapiro | Pradeep Ramesh |
2014 | Detection of nematode-induced transcripts in the nematophagous fungus A. oligospora using Fluorescence in situ hybridization | Paul Sternberg | Yen-Ping Hsueh and Ting-Fan He |
2014 | Site-specific labeling of bacterial proteins in-situ using N-Myristoyltransferase for correlated, cryogenic Stochastic Optical Reconstruction Microscopy (cryo-STORM) | David Tirrell | Samuel Ho |
2013 | DNA signaling among proteins with 4Fe-4S clusters | Jacqueline Barton | Michael Grodick |
2013 | Mechanosensitive channels: Their role in photosynthetic cell biology | Ian Booth | Vojtech Prazak |
2013 | Imaging chromosome conformation in single bacteria cells | Long Cai | Timur Zhiyentayev |
2013 | Constructing mutants of Saccharomyces cerevisiae with CRISPR/CAS9 and characterization of genes involved in mutagenesis | Judith Campbell | Martin Budd |
2013 | Evolution of photosynthesis in cyanobacteria | Woodward Fischer | James Hemp and Jena Johnson |
2013 | An integrated MEMS device for use as a microbial monitoring system in wastewater treatment | Michael Hoffmann | Penvipha Satsanarukkit |
2013 | Structure and organization of the bacterial chromosome | Grant Jensen | Yi-Wei Chang |
2013 | A novel probiotic therapy for Parkinson's disease in animal models | Sarkis Mazmanian | Catherine (Katie) Schretter |
2013 | X-ray absorption spectroscopic studies of nitrogen fixation | Douglas Rees | Limei Zhang |
2012 | Argonaute proteins in bacteria: A glimpse into the ancient non-coding RNA world | Alexei Aravin | Ivan Olovnikov |
2012 | Characterization of a novel membrane protein-targeting pathway in photosynthetic bacteria | William Clemons | Vijay Somalinga |
2012 | Understanding the physiological roles of subpopulations in clonal bacterial communities | Michael Elowitz | Adam Rosenthal |
2012 | Evolution and mechanism of type VI secretion-related nanomachines | Grant Jensen | Martin Pilhofer |
2012 | Diverse studies in microbial diversity | Jared Leadbetter | N/A - Supplies |
2012 | Probing microbial energetics with microcalorimetry: The environmental and energetic meaning of heat production | Victoria Orphan | Jeff Marlow |
2012 | Quantitative dissection of iron-mediated gene regulation in Pseudomonas aeruginosa | 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.