SynBio Journal Club Archive

Past meetings

Winter 2022/2023

Date Presenter Paper
November 17 Takeshi

Living material assembly of bacteriogenic protocells

December 01 Samuel

Mechanistic Insights into the Phase Separation Behavior and Pathway-Directed Information Exchange in all-DNA Droplets
December 15 Marius

Reconstitution of a minimal motility system based on Spiroplasma swimming by two bacterial actins in a synthetic minimal bacterium 

January 12 Yoshiki Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan
January 26 Stefano cancelled
February 09 Theo

Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures

March 02 Bochen

Programmable synthetic biomolecular condensates for cellular control

March 09 Tomoya

Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan

March 23 Benjamin

Prediction of designer-recombinases for DNA editing with generative deep learning

March 30 Amy

A swapped genetic code prevents viral infections and gene transfer


Spring and Summer 2022 was cancelled due to COVID.


Winter 2021/2022

November 17


Designer membraneless organelles sequester
native factors for control of cell behavior

December 01


Prooxidative chain transfer activity by thiol groups in biological systems

January 12


Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods  

January 26


Multiplex suppression of four quadruplet codons via tRNA directed evolution.

February 09


De novo design of modular and tunable protein biosensors


Summer 2021 




May 6


Dual-Colour Imaging of RNAs Using Quencher- and Fluorophore-Binding Proteins

May 20


A Minimalistic Cyclic Ice-Binding Peptide from Phage Display

June 3


Global RNA Profiles Show Target Selectivity and Physiological Effects of Peptide-Delivered Antisense Antibiotics

June 24


In-ice evolution of RNA polymerase ribozyme activity

July 8


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


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
April 30  Yoshiki Engineering Methyllysine Readers and Writers for Allele-Specific Regulation of Protein-Protein Interactions