Events
CEMINAR
The most important community-oriented activity we sponsor is CEMINAR, a monthly seminar series where students and postdocs in the CEMI program present their work. Usually 2 individuals present 20-25 min talks (+ 5 min questions) to fill the hour, but on rare occasions we invite an outside speaker. CEMINAR is primarily designed to provide CEMI students and postdocs with an opportunity to practice giving a formal talk to a friendly Caltech audience. Numerous collaborations have been sparked between labs at Caltech thanks to creative connections made during these seminars.
CEMINAR - formerly MicroMorning
4:00-5:00pm Virtual Talks
Wednesday, February 10, 2021 at 4:00pm
Meeting ID: 840 2017 8938
Password: microbes
"Machine learning-assisted directed evolution"
Bruce Wittman
Arnold Lab
Directed evolution of proteins often involves a single-step greedy optimization in which the mutation in the highest-fitness variant identified in each round of single-site mutagenesis is fixed. Because the effects of a mutation can depend on the presence or absence of other mutations, the efficiency of a single-step greedy walk is influenced by the order in which beneficial mutations are identified—the process is path-dependent. This talk details the investigation and optimization of a path-independent machine learning-assisted directed evolution (MLDE) protocol that allows in silico screening of full combinatorial libraries. When applied to an epistatic fitness landscape, the final protocol achieved the global fitness maximum up to 77-fold more frequently than single-step greedy optimization.
"Words Matter: Using ontologies to systematically model biology"
Kimberly Van Auken
Sternberg Lab
Biological knowledgebases such as WormBase, a founding member of the Alliance of Genome Resources, are tasked with curating experimental data from the life sciences literature in both human-readable and computationally amenable forms. One of the major challenges facing biocurators is modeling and annotating experimental data in a systematic way so that information is standardized and thus maximally useful for subsequent analyses. Ontologies, controlled vocabularies that formalize entities, concepts, and the relations between them, are a key component of biocuration. In this talk, I’ll introduce the ontologies we use at WormBase and the Alliance to curate the life sciences literature and introduce an exciting new project we’re undertaking with the Gene Ontology Consortium to create causal models (known as GO-CAMs) of biological systems.
| Date | Past MicroMornings |
|---|---|
| January 13, 2021, virtual |
“Time-resolved proteomic analysis of toxin-mediated growth arrest in Escherichia coli” Elliot Mackrell Tirrell Lab “Single-cell phenotypic analysis and digital molecular detection linkable by a hydrogel bead-based platform” Yanzhe Zhu Hoffman Lab and Orphan Lab |
| December 9, 2020, virtual |
“Biomass degradation by copper enzymes” Jieun Shin Gray Lab “In situ structural study of the ATPases in the Legionella pneumophila type IV secretion system” Yuxi Liu Jensen Lab |
| November 11, 2020, virtual |
“Microbial succession and dynamics in meromictic Mono Lake, California” Alexandra Phillips Sessions Lab “Transparent soil microcosms to advance soil and sediment microbial ecology” Kriti Sharma Orphan Lab |
| October 14, 2020, virtual |
“Early impacts of climate change on a microbial mat ecosystem” Usha Lingappa Fischer Lab “Gut microbiota composition regulates sugar-seeking behaviors in mice” James Ousey Mazmanian Lab |
| September 9, 2020, virtual |
“Carbon monoxide: Chemotherapeutic applications” Miguel Nicolás Pinto Barton Lab “An introduction to biochemical circuit modeling with the synthetic biology tools suite” William Poole Murray Lab |
| August 12, 2020, virtual |
“Novel viral capsid engineering and new research avenues in non-human primates” Miggy Chuapoco Gradinaru Lab “Directed evolution of a genetically encoded contrast agent for ultrasound” Robert Hurt Shapiro Lab |
| July 8, 2020, virtual |
“Scalable, continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities” Ella Watkins-Dulaney Arnold Lab “Structural evidence for nitrogenase metallocluster modularity” Trixia M. Buscagan Rees Lab |
| June 10, 2020, virtual |
“Colonization patterns of the small intestine by the synergistic E. coli and Bacteroides/Parabacteroides spp. community” Roberta Poceviciute Ismagilov Lab “Single-cell phenotypic analysis and digital molecular detection linked by a hydrogel bead-based platform” Yanzhe Zhu Hoffmann Lab |
| May 13, 2020, virtual |
“Collateral benefits of slaying your own demons: An ecophysiological perspective on antibiotic tolerance and resistance” Lucas A. Meirelles and Elena K. Perry Newman Lab “Anaerobic chitin degradation in bio-electrochemical cells” Yamini Jangir Orphan Lab |
| March 11, 2020 |
“Proof of concept serine integrase based continuous event logging in E. coli” Andrey Shur Murray Lab “Genetically programmable microbial assembly” Bradley Silverman Tirrell Lab |
| February 12, 2020 |
“Rhodium complex conjugates: DNA damage and cell-selective cytotoxicity” Adela Nano Barton Lab “Structural studies of membrane and peripheral proteins in the peptidoglycan-synthesis pathway” Anna Karen Orta Clemons Lab |
| January 8, 2020 |
“Evolution of adeno-associated viral capsids to target different cell types of the central nervous system” Sripriya Ravindra Kumar Gradinaru Lab “Straightening out the kinks: structural insights into the transport cycle of a bacterial ABC exporter” Chengcheng Fan Rees Lab |
| December 11, 2019 |
“Cellular transformation for anaerobic N2 fixation” Fabai Wu Orphan Lab “Engineered protein degradation for the proteomic analysis of a transient and probabilistic cell state” Elliot Mackrell Tirrell Lab |
| November 13, 2019 |
“Nitrene transfer catalyzed by a non-heme iron enzyme and enhanced by non-native small-molecule ligands” Nathaniel Goldberg Arnold Lab “The cellular determinants for the biosynthesis of crystalline cellulose ribbons in the Gluconacetobacter genus” William Nicolas Jensen Lab |
| October 9, 2019 |
“How did evolution affect carbon-fixing metabolisms?” Renée Wang Fischer Lab “Microbial metabolites and neuroinflammation in Parkinson’s disease” Reem Abdel-Haq Mazmanian Lab |
| September 11, 2019 |
“3D imaging for the quantitative discovery of spatial patterns in the microbiota of the intestinal mucosa” Octavio Mondragón-Palomino Ismagilov Lab “Deep sea oases: Correlating biogeochemistry and (microbial) ecology at a Costa Rica methane seep” Mike Zott Peters Lab |
| August 14, 2019 |
“Energy conservation by manganese oxidizing bacteria” Hang Yu Leadbetter Lab “The biology and chemistry of ammonia oxidation” Sean Mullin Orphan Lab |
| July 10, 2019 |
“Exploring the roles of a [4Fe4S] cluster coordinated by UvrC” Rebekah Silva Barton Lab “Non-invasive control of cellular localization in vivo assisted by magnetic particles” Marjorie Buss Shapiro Lab |
| June 12, 2019 |
“Evolution of enzymes in aerobic respiration and denitrification – discovery of functional diversity using molecular phylogeny and a neural network algorithm” Ranjani Murali Orphan Lab “Reconstituting NETosis in vitro: A bacteria killing adventure” Suzy Beeler Phillips Lab |
| May 22, 2019 |
“Quorum sensing selectivity and the potential for interspecies crosstalk” Samantha Wellington University of Washington “Extracellular DNA promotes efficient extracellular electron transfer by pyocyanin in Pseudomonas aeruginosa biofilms” Scott Saunders Newman Lab |
| April 10, 2019 | “Tailored superabsorbent polymer beads for environmental microbial pathogen concentration in low-resource settings” Xunyi (Alison) Wu Hoffmann Lab “Structural and functional characterization of the Neisseria meningitidis ABC methionine transporter system” Naima Sharaf Rees Lab |
| March 13, 2019 | “Enzymatic labeling of bacterial proteins for live-cell super-resolution imaging” Samuel Ho Tirrell Lab “A tunable integrase differentiation circuit improves output of burdensome functions” Rory Williams Murray Lab |
| February 13, 2019 | “Does evolution care about bits: Information as currency in nature’s stock market” Manuel Razo-Mejia Phillips Lab “Binding to tail-anchored proteins in the GET pathway” Michelle Fry Clemons Lab |
| January 9, 2019 | “Discovery of bacteria oxidizing manganese for energy” Hank Yu Leadbetter Lab “Transcriptional regulation during slow growth in Pseudomonas aeruginosa” Megan Bergkessel Newman Lab |
| December 12, 2018 | “Repurposing cytochrome P450 for biocatalytic silicon oxidation” Kari Hernandez Arnold Lab “Measuring cell envelope damage after 15 min β-lactam exposure in N. gonorrhoeae to enable phenotypic diagnostics” Emily Savela Ismagilov Lab |
| November 14, 2018 | “Manganese oxidation by Cyanobacteria and the evolution of photosystem II” Usha Lingappa Fischer Lab “Untargeted metabolomic analysis of O-acyltransferase genes in C. elegans” Sarah Cohen Sternberg Lab |
| October 10, 2018 | “Evolution in action: The diversity of the bacterial flagellar motor” Mohammed Kaplan Jensen Lab “When microbes are not our friends: Understanding how RAG binding site sequence influences the production of the antibodies that protect us” Soichi Hirokawa Phillips Lab |
| September 12, 2018 | “3D Microfluidic solutions for waterborne pathogen analysis” Yanzhe Zhu Hoffmann Lab “Oxidative stress leads to D-enrichment in microbial lipids” Reto Wijker Sessions Lab |
| August 8, 2018 | “Nitric oxide modulates DNA repair enzyme redox activity through [Fe4S4] cluster nitrosylation” Levi Ekanger Barton Lab “SlipChip method for total single-cell RNAseq applicable to bacteria” Eugenia Khorosheva Ismagilov Lab |
| July 11, 2018 | “Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase” Rusty Lewis Arnold Lab “Genetic tools to study and interrogate enteric nervous system” Bryan Yoo Mazmanian Lab |
| June 13, 2018 | “Mössbauer spectroscopy as a tool in bioinorganic chemistry” Matthew Chalkley Peters Lab “Ultraparamagnetic iron mineralization for non-invasive imaging and magnetic capture of engineered microbes” Pradeep Ramesh Shapiro Lab |
| May 9, 2018 | “Taking control of the flagellar motor” Davi Ortega Jensen Lab “Visualizing microbial colonization 4850’ underground” Haley Sapers Orphan Lab |
| April 11, 2018 | "A redox role for the [4Fe4S] cluster of yeast DNA polymerase δ" Phillip Bartels Barton Lab "Functional responses of Pseudomonas aeruginosa during energy-limited growth arrest" David Basta Newman Lab |
| March 14, 2018 | “L-form bacteria: from the origins of life to recurrent infection” Professor Jeff Errington Director of the Centre for Bacterial Cell Biology, Newcastle University, England |
| February 14, 2018 | “From insult to injury: mapping survival under osmotic shock to mechanosensitive channel number” Griffin Chure Phillips Lab “Engineered protein degradation for time-resolved proteomics” Elliot Mackrell Tirrell Lab |
| January 10, 2018 | “GETting tail-anchored proteins to the ER membrane” Michelle Fry Clemons Lab "Study of cellular structures in-situ using a combination of focussed ion beam milling and electron cryotomography" Shrawan Kumar Mageswaran Jensen Lab |
| December 13, 2017 | “Diverse engineered heme proteins enable stereodivergent cyclopropanation of unactivated alkenes” Anders Knight Arnold Lab “Hole hopping in P450: protective mechanisms against oxidative damage” Brian C. Sanders Gray Lab |
| November 8, 2017 | “Indigenous gut bacteria utilize immunoglobulin A for mucosal colonization” Greg Donaldson Mazmanian Lab “Silica precipitation mediated by ANME-SRB aggregates” Kyle Metcalfe Orphan Lab |
| October 11, 2017 | “Analysis and modeling of nucleoids seen by electron-cryo-tomography” Andrew Jewett Jensen Lab “Decoding the regulatory genome in E. coli” Nathan Belliveau Phillips Lab |
Social Events
In addition to MicroMorning, CEMI sponsors three social events during the academic year:
Poster Sessions (virtual CEMI poster session coming Fall 2020): All CEMI labs present one or more posters on their lab’s research. This helps incoming/current students and postdocs remain up-to-date on that latest research projects going on across the campus. One attractive feature of Caltech is that students admitted in any graduate program are welcome to rotate in any lab (as long as the lab is taking students), so this poster session can open up new interests and areas for exploration. It also can spawn new collaborations between labs.
Winter Lectures and Evening Gala (early January): To celebrate the start of the calendar year, we invite a keynote speaker from outside Caltech to give a seminar, plus a few shorter talks by assistant professors or postdocs at Caltech and other local universities. These “Winter Lectures” are open to anyone interested. As a companion event, we hold a formal gathering for a limited number of CEMI sponsors, faculty, and students and postdocs currently being supported by CEMI grants. The evening’s entertainment is organized by a different CEMI lab each year, and the evening culminates with a presentation of the “CEMI Oscars” (we are close to Hollywood, after all…), roasting CEMI members for notable achievements in the past year, all in good fun.
| Date | Past Lectures |
|---|---|
| January 10, 2020 |
Sydney Glassman (UCR) “A tale of two megafires: building towards generalizable traits of fire fungi” Margaret McFall-Ngai (U. Hawaii) “Host-symbiont molecular dialogue drives the onset and maturation of the daily rhythm” Nick Shikuma (San Diego State) “A tail of phage and tubeworms: how bacteria stimulate animal metamorphosis” Kaihang Wang (Caltech) “Genome synthesis: tools and implementations” |
| January 11, 2019 |
Carol Gross (UCSF) “Predictive analysis of ECF sigma function across the bacterial kingdom” Elaine Hsiao (UCLA) “Host microbiome interactions through the serotonergic system” Chang Liu (UCI) “Continuous mutagenesis and evolution in vivo” Joe Parker (Caltech) “Convergent evolution of a social symbiosis” |
| January 5, 2018 | James Boedicker (USC) “The regulation and consequences of gene transfer in extracellular vesicles” Roy Kishony (Technion) “Tracing and reversing antibiotic resistance” Mikhail Shapiro (Caltech) “Proteins, sound waves and heat: imaging and controlling the function of microbes in mammalian hosts” Katrine Whiteson (UCI) “Metabolites, germs and people: eavesdropping on microbial communities in the Cystic Fibrosis airways” |
| December 9, 2016 | Martin Ackermann (ETH) “Collective functionality in bacterial groups” Kevin Foster (Oxford) “Cooperation and competition in microbes: from model systems to the microbiome” Alexis Pasulka (Caltech, Orphan Lab) “Nanoscale isotopic and microscopic investigations of marine viruses” Lisa Racki (Caltech, Newman Lab) “Cell biology of starvation: polyphosphate granules biogenesis in Pseudomonas aeruginosa” |
| January 29, 2016 | Frances Arnold (Caltech) “Innovation by evolution: expanding the enzyme universe” Michael Wagner (University of Vienna) “Nitrification revisited with single cell tools” |
Spring Happy Hour (early April): In recognition of the fact that sometimes the most inspired ideas come when we least expect them, we promote casual conversation between all members of the CEMI community supplemented with drinks and food at the start of the spring term (no posters required!).
Workshops
CEMI occasionally supports training courses at Caltech that provide members of the CEMI community with an opportunity for intensive training in a particular area. Any member of the CEMI community is welcome to suggest a topic for a workshop. Please contact the CEMI administrator if you have an idea.
| Year | Topic |
|---|---|
| 2014 | A Scientific Presentation Skills Workshop was held June 24 through August 19, 2014 on campus to help students and postdocs with public speaking and scientific presentation skills. |
| 2013 | A Bioinformatics Workshop was held Sept 16 through Sept 20, 2013 on campus. Instructors: Titus Brown and Rob Knight. |