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Nucleic Acid Chemistry and Engineering Unit (Yohei Yokobayashi)

SynBio Journal Club Archive

Past meetings

Winter 2022/2023

Date	Presenter	Paper
November 17	Takeshi	Living material assembly of bacteriogenic protocells https://doi.org/10.1038/s41586-022-05223-w
December 01	Samuel	Mechanistic Insights into the Phase Separation Behavior and Pathway-Directed Information Exchange in all-DNA Droplets https://doi.org/10.1002/anie.202208951
December 15	Marius	Reconstitution of a minimal motility system based on Spiroplasma swimming by two bacterial actins in a synthetic minimal bacterium https://doi.org/10.1126/sciadv.abo7490
January 12	Yoshiki	Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan https://doi.org/10.1038/s43587-022-00340-7
January 26	Stefano	cancelled
February 09	Theo	Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures https://doi.org/10.1021/acssynbio.2c00462
March 02	Bochen	Programmable synthetic biomolecular condensates for cellular control https://doi.org/10.1038/s41589-022-01252-8
March 09	Tomoya	Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan https://doi.org/10.1038/s43587-022-00340-7
March 23	Benjamin	Prediction of designer-recombinases for DNA editing with generative deep learning https://www.nature.com/articles/s41467-022-35614-6
March 30	Amy	A swapped genetic code prevents viral infections and gene transfer https://doi.org/10.1038/s41586-023-05824-z

Spring and Summer 2022 was cancelled due to COVID.

Winter 2021/2022

November 17	Stefano	Designer membraneless organelles sequester native factors for control of cell behavior https://doi.org/10.1038/s41589-021-00840-4
December 01	Marius	Prooxidative chain transfer activity by thiol groups in biological systems https://doi.org/10.1016/j.redox.2020.101628
January 12	Lara	Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods https://doi.org/10.1016/j.cels.2021.08.002
January 26	Takeshi	Multiplex suppression of four quadruplet codons via tRNA directed evolution. https://doi.org/10.1038/s41467-021-25948-y
February 09	Yoshiki	De novo design of modular and tunable protein biosensors https://doi.org/10.1038/s41586-021-03258-z

Summer 2021

Date	Presenter	Paper
May 6	Takeshi	Dual-Colour Imaging of RNAs Using Quencher- and Fluorophore-Binding Proteins
May 20	Yoshiki	A Minimalistic Cyclic Ice-Binding Peptide from Phage Display
June 3	Samuel	Global RNA Profiles Show Target Selectivity and Physiological Effects of Peptide-Delivered Antisense Antibiotics
June 24	Gear	In-ice evolution of RNA polymerase ribozyme activity
July 8	Vyankat	Quadruplex Folding Promotes the Condensation of Linker Histones and DNAs via Liquid-Liquid Phase Separation.

Winter/Spring 2021

Date	Presenter	Paper
January 14	Samuel	Dynamic and Scalable DNA-based Information Storage
January 21	Kamila	Viral Gene Drive in Herpesviruses
January 28	Vyankat	Enzyme-free synthesis of natural phospholipids in water
February 4	Stefano	Computation-guided optimization of split protein systems
February 11	-	National Foundation Day
February 18	Gear	Deep diversification of an AAV capsid protein by machine learning
February 25	Takeshi	Synthetic protein quality control to enhance full-length translation in bacteria
March 4	Yoshiki	Optical control of fast and processive engineered myosins in vitro and in living cells
March 11	Samuel	Stretchable living materials and devices with hydrogel-elastomer hybrids hosting programmed cells
March 18	Kamila	Super-Resolution RNA Imaging Using a Rhodamine-Binding Aptamer with Fast Exchange Kinetics
March 25	Vyankat	Assembly Pathway Selection with DNA Reaction Circuits for Programming Multiple Cell-Cell Interactions
April 1	George Church	Resurrecting Mammoths
April 15	Stefano	Emergence of Function from Single RNA Sequences by Darwinian Evolution
April 22	Kamila	High-Throughput Single-Cell Activity-Based Screening and Sequencing of Antibodies Using Droplet Microfluidics

Autumn 2020

Date	Presenter	Paper
September 10	Stefano	A protein functionalization platform based on selective reactions at methionine residues
September 17	Vyankat	Cell- and Polymerase- Selective Labeling of Cellular RNA with 2'-Azidocytidine
September 24	Takeshi	Acoustic Biosensors for Ultrasound Imaging of Enzyme Activity
October 1	Kamila	Characterization and Mitigation of Gene Expression Burden in Mammalian Cells
October 8	Gear	Electrogenetic Cellular Insulin Release for Real-Time Glycemic Control in Type-1 Diabetic Mice
October 15	Yoshiki	Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase
October 22	cancelled
October 29	Samuel	Maximizing Transcription of Nucleic Acids with Efficient T7 Promoters
November 5	Vyankat	Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging
November 12	Stefano	Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities
November 19	cancelled
November 26	Takeshi	Reversible Membrane Deformations by Straight DNA Origami Filaments
December 3	Kamila	Rapid (30-second), equipment-free purification of nucleic acids using easy-to-make dipsticks
December 10	Gear	Automation in the Life Science Laboratory
December 17	Yoshiki	Label as you fold: methyltransferase-assisted functionalization of DNA nanostructures

Summer 2020:

Date	Presenter	Paper
May 21	Samuel	Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria
May 28	Stefano	Protein Engineers Turned Evolutionists (1) (2)
June 4	Vyankat	Allosteric Regulation of DNAzyme Activities through Intrastrand Transformation Induced by Cu(II)-Mediated Artificial Base Pairing
June 11	Takeshi	Conditionally Replicative Adenovirus Controlled by the Stabilization System of AU-Rich Elements Containing mRNA
June 18	Shiv	Genome-scale Transcriptional Dynamics and Environmental Biosensing
June 25	cancelled
July 2	Kamila	Cell-Free Protein Synthesis as a Prototyping Platform for Mammalian Synthetic Biology
July 9	Gear	Hidden Specificity in an Apparently Nonspecific RNA-Binding Protein
July 16	cancelled
July 30	Samuel	Sequence-based Engineering of Dynamic Functions of Micrometer-sized DNA droplets
August 6	Yoshiki	Designer Protein Assemblies with Tunable Phase Diagrams in Living Cells

Spring 2020:

Date	Presenter	Paper
January 16	Takeshi	PERSIA for Direct Fluorescence Measurements of Transcription, Translation, and Enzyme Activity in Cell-Free Systems
January 30	Yumi	Conditional control of RNA-guided nucleic acid cleavage and gene editing
February 6	Gear	Isothermal digital detection of microRNAs using background-free molecular circuit
February 13	Kamila	Design of Protein Logic Gate System Operating on Lipid Membranes
February 20	Yoshiki	Reengineering a tRNA Methyltransferase to Covalently Capture New RNA Substrates
February 28	Samuel	Codon usage influences fitness through RNA toxicity
March 5	Stefano	Machine learning-assisted directed protein evolution with combinatorial libraries
March 12	Vyankat	Functional DNA Regulated CRISPR-Cas12a Sensors for Point-of-Care Diagnostics of Non-Nucleic-Acid Targets
March 19	Shiv	Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space
March 26	Takeshi	Application of Cell-Free Systems in Education (1) (2) (3)
April 2	Yumi	Decorating bacteria with self-assembled synthetic receptors
April 9	Gear	Synthetic Sequence Entanglement Augments Stability and Containment of Genetic Information in Cells
April 16	Kamila	Sci-fate characterizes the dynamics of gene expression in single cells
April 30	Yoshiki	Engineering Methyllysine Readers and Writers for Allele-Specific Regulation of Protein-Protein Interactions