Past CEMINARs
| Date | Past CEMINARs |
|---|---|
| Wednesday, November 13, 2024 |
“Towards declarative bioengineering” |
| Wednesday, October 16, 2024 |
“Revealing distinct microbial signatures of necrotizing enterocolitis using novel quantitative metagenomic technologies” |
| Thursday, September 26, 2024 |
“Unraveling the role of microbiomes in photosynthetic marine holobionts” |
| Wednesday, September 11, 2024 |
“Building a bioisotopic model of central metabolism and amino acid biosynthesis to merge isotope biogeochemistry and metabolomics” |
| Wednesday, August 14, 2024 |
“Antibody 007: A best-in-class V3-targeting bNAb that utilizes avidity” |
| Wednesday, July 10, 2024 |
“Poking around the twilight zone” |
| Wednesday, June 12, 2024 |
“Directed evolution for the enantio- and diastereodivergent synthesis of spirocycles” |
| Wednesday, May 8, 2024 |
“Development of systemic rAAV tools for regenerative spiny mouse central and peripheral nervous systems” |
| Wednesday, April 10, 2024 |
“Inhibiting the GET pathway in H. sapiens and P. falciparum” |
| Wednesday, March 13, 2024 |
“Droplet sequencing reveals virulence gene clusters in extracellular vesicles from human microbiota” |
| Wednesday, February 14, 2024 |
“Gene-microbiome interactions in mouse models of Parkinson’s disease” |
| Wednesday, January 10, 2024 |
“Cell-selective chemical proteomics enables targeted analysis of a low-abundance organism in a polymicrobial system” |
| Wednesday, December 13, 2023 |
“Human blood-brain barrier receptor-guided evolution of AAVs for brain gene therapy” |
| Wednesday, November 8, 2023 |
“Towards discovering antibodies to target invariant domains in HIV-1” |
| Wednesday, November 1, 2023 |
“Elucidating reaction network in carbon metabolism of soil bacteria: metabolomics-enabled explorations of natural carbon cycling to innovate engineered carbon recycling” |
| Wednesday, October 11, 2023 |
“Crossing the salty divide: the Great Oxidation event, cyanobacterial evolution, and the marine-terrestrial barrier?” |
| September 13, 2023 |
“Spatiotemporal regulation of programmed cell death in Pseudomonas aeruginosa biofilms” |
| August 9, 2023 |
“The role of modulating Drosophila microbiome to promote tissue regeneration” |
| July 12, 2023 |
“Developing a flow-through culturing apparatus for the cultivation of a unique manganese oxidizing biofilm” |
| June 14, 2023 |
“Probing Metabolism in an E. coli-Based Cell-Free System Reveals a Trade-Off between Transcription and Translation” |
| May 10, 2023 |
“How is it killing me?": Using Viral-BONCAT genomics to identify the active viral fraction” |
| April 12, 2023 |
“Structural basis of phage single gene lysis proteins targeting bacterial cell wall biosynthesis” |
| March 8, 2023 |
“Enzymatic nitrogen insertion into aliphatic C–H bonds” |
| February 15, 2023 |
“Structure and function of the Dot/Icm T4SS” |
| February 8, 2023 |
“Chemical and biological discovery in the microbial world” |
| January 30, 2023 |
“Hydra and the big picture: how microbes suppress pathogens, direct development and control the eating behaviour” |
| January 18, 2023 |
“Global analysis of protein degradation in Escherichia coli” |
| December 14, 2022 |
“Development of mosaic nanoparticle vaccines to elicit broadly protective antibody responses” |
| November 9, 2022 |
“Towards a thermally self-regulating living material” |
| October 19, 2022 |
“Gut microbiome shapes mitochondria function in α-syn overexpressing mice” |
| September 14, 2022 |
“Do microbes from cold methane seep sediments prefer sulfur redox intermediates over sulfate?” |
| August 10, 2022 |
“Journey to the center of the nodule: Investigating the ultrastructure of a manganese-oxidizing chemolithoautotrophic co-culture” |
| July 13, 2022 |
“Microbial enrichment method enables high-throughput metagenomic characterization from host-rich samples, including clinical biopsies” |
| June 8, 2022 |
“Lyophilization of LAMP reagents for point-of-sampling wastewater-based epidemiology: A novel system for small, remote and developing system applications” |
| May 11, 2022 |
“The influence of substrate complexity on structure and function of anaerobic marine microbial communities” |
| April 13, 2022, virtual |
“Generation of chimeric organisms through mega-base scale genetic engineering” |
| March 16, 2022, virtual |
“Field-based measurements to quantify controls on the soil methane sink” |
| February 9, 2022, virtual |
“Directed evolution of a tyrosine synthase” |
| January 12, 2022, virtual |
“Role of the microbiome in modulating limb regeneration” Aki Ohdera Goentoro Lab “microPublication Biology: Publishing single experimental results” Daniela Raciti microPublication Biology, Sternberg Lab |
| December 8, 2021, virtual |
“Trade-offs in the dynamics of biomolecular sensing systems, Part I: Lag phase as a link between regulatory architecture and population behavior” John Marken Murray Lab “Trade-offs in the dynamics of biomolecular sensing systems, Part II: Developing a theoretical framework for sensing via a molecular switch” Gabe Salmon Phillips Lab |
| November 10, 2021, virtual |
“Structure of the Tight adherence (Tad) pilus nanomachinery in Caulobacter crescentus via cryo-ET” Rachel Rosenzweig Jensen Lab “Peering into the nitrogen-fixing cell: Cryoelectron-tomography of Azotobacter vinelandii” Rebeccah Warmack Rees Lab |
| October 13, 2021, virtual |
“Contribution of an Autism genetic risk factor to gut dysfunction in mice” Jessica Griffiths Mazmanian Lab “Cell-selective chemo-proteomic interrogation reveals novel interspecies interactions in the CF (Cystic Fibrosis) lung microbiome” Zimu (Grace) Wang Tirrell Lab |
| September 8, 2021, virtual |
“The Tetrahymena thermophila gene network landscape, revisited” Lev Tsypin Newman Lab “Evidence for sustained growth and broad nitrogen utilization under dark conditions in the microalga Picocystis sp. strain ML” Shaelyn Silverman Sessions Lab |
| August 11, 2021, virtual |
“Optomechanical properties of iridescent biofilms” Priya Chittur Kornfield Lab “Understanding translationally-mediated cellular adaptation” Rodney Tollerson II Orphan Lab |
| July 14, 2021, virtual |
“Membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system enables rapid and extraction-free SARS-CoV-2 quantification in milliliters of environmental waters” Jing Li Hoffmann Lab “Fantastic gas vesicles and how to make them” Mengtong (Tom) Duan Shapiro Lab |
| June 9, 2021, virtual |
“Quantitative microbiome profiling of the human small-intestine” Jacob Barlow Ismagilov Lab “Addressing evolutionary stability of engineered functions through tunable and redundant integrase mediated differentiation” Rory Williams Murray Lab |
| May 12, 2021, virtual |
First annual CEMI spring Celebration of Science on May 12, 2021 at 4PM. The hour-long science program featured short lightning talks from CEMI graduate students and postdocs, followed by time to talk with the speakers and socialize with our CEMI colleagues. |
| April 14, 2021, virtual |
“Concerted proton-electron transfer mediators for nitrogen fixation” Pablo Garrido-Barros Peters Lab “ORBIT: Easy oligo-based genetics for E. coli and beyond” Scott Saunders Phillips Lab |
| March 10, 2021, virtual |
“Investigations into a unique paralog of Get3 conserved in plants and photosynthetic bacteria” Alex Barbato Clemons Lab “Designing an orthogonal transcription and translation memory circuit” Bryan Gerber Wang Lab |
| February 10, 2021, virtual |
“Machine learning-assisted directed evolution” Bruce Wittman Arnold Lab “Words Matter: Using ontologies to systematically model biology” Kimberly Van Auken Sternberg Lab |
| 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 |
Past Symposium Lectures
| Date | Past Lectures |
|---|---|
| March 8, 2024 |
Joseph Pogliano (Professor, Department of Molecular Biology, UC San Diego Annette Rowe (Assistant Professor, Department of Biological Sciences, University of Cincinnati) Rustem Ismagilov (Professor, Division of Chemistry and Chemical Engineering, Caltech) Jason Stajich (Professor, Department of Microbiology and Plant Pathology, UC Riverside) |
| April 7, 2023 |
Lisa Racki, Scripps Research Institute Department of Integrative structural and computational biology Julia Schwartzman, Assistant professor, USC Department of Biological Sciences Bil Clemons, Professor of biochemistry, Division of Chemistry and Chemical Engineering, Caltech KEYNOTE: Christa Schleper, Professor, University of Vienna, Archaea Biology and Ecogenomics Division |
| April 8, 2022 |
Anne Dekas (Stanford) “A single-cell view of microbial activity and its intracommunity heterogeneity in two extreme marine habitats: the deep sea and coastal evaporitic brines” Dr. Manuel Razo-Mejia (Stanford) “The physics of bacteria's decision making” Professor Lea Goentoro (Caltech) “Can microbes help induce limb regeneration?” Professor Kerwyn ‘KC’ Huang (Stanford) KEYNOTE: “Growing up in the new microbiology: integrating physics, chemistry, and biology to understand microbial ecosystems” |
| 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” |
Past Workshops
| Year | Topic |
|---|---|
| 2024 | We hosted a ½ day bioinformatics workshop on November 8th, 2024 with the KBase team for students, postdocs, and faculty who are currently using or have an interest in microbial genomic and metagenomic data analysis. |
| 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. |