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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.

CEMI Oscar's
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.

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