Synthetic Biology

Cell-free protein synthesis as a method to rapidly screen machine learning-directed protease variants

1. Ella Lucille Thornton
2. Jeremy T. Boyle
3. Nadanai Laohakunakorn
4. Lynne Regan

Reviewed by Arcadia Science

A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine

1. Deruilin Liu
2. Demin Xu
3. Liuxin Shi
4. Jiayuan Zhang
5. Kewei Bi
6. Bei Luo
7. Chen Liu
8. Yuxiang Li
9. Guangyi Fan
10. Wen Wang
11. Zhi Ping

• Curated by GigaByte

  Editors Assessment:

  DNA has huge potential as a data storage medium because of its incredibly high storage density and stability. This work addresses the potential of modified bases, specifically 5-methylcytosine (5mC), in enhancing DNA data storage systems. This paper introduces a transcoding scheme named R+, which incorporates this modified 5mC base to increase information density beyond the standard limits. By encoding various file types into DNA sequences of between 1.3 to 1.6 kb in size, this method achieves an average recovery rate of 98.97% (with reference), validating the effectiveness of the method. On top of a wet-lab protocol (hosted in protocols.io) for the experimental validation of the transcoding scheme, it also includes open source code for in-silico simulation tests. Peer review scruitinising the protocols and validation are reusable and provide convincing results. As nanopore sequencing has enabled reading of these modified bases, it is timely making them applicable as extra letters in the molecular alphabet for DNA data storage

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Dynamical mechanisms of growth-feedback effects on adaptive gene circuits

1. Ling-Wei Kong
2. Wenjia Shi
3. Xiao-Jun Tian
4. Ying-Cheng Lai

• Curated by eLife

  eLife Assessment

  The paper presents valuable computational findings on how growth feedback affects the performance of synthetic gene circuits designed for adaptive responses. By systematically analyzing over four hundred circuit topologies, the authors provide solid evidence for their conclusions on failure mechanisms and design features that enhance robustness against growth dynamics. While the study's significance and rigor are somewhat constrained by its reliance on previously published network topologies, these results are highly relevant for advancing the engineering of gene circuits in various applications.

Reviewed by eLife

Spheroplasted cells: a game changer for DNA delivery to diatoms

1. E.J.L. Walker
2. M. Pampuch
3. L. Deng.
4. Y. Li
5. G. Tran
6. T. Mock
7. B.J. Karas

Reviewed by Arcadia Science

Mapping targetable sites on the human surfaceome for the design of novel binders

1. Petra E. M. Balbi
2. Ahmed Sadek
3. Anthony Marchand
4. Ta-Yi Yu
5. Jovan Damjanovic
6. Sandrine Georgeon
7. Joseph Schmidt
8. Simone Fulle
9. Che Yang
10. Hamed Khakzad
11. Bruno E. Correia

Reviewed by Arcadia Science

Chai-1: Decoding the molecular interactions of life

1. Chai Discovery
2. Jacques Boitreaud
3. Jack Dent
4. Matthew McPartlon
5. Joshua Meier
6. Vinicius Reis
7. Alex Rogozhnikov
8. Kevin Wu

Reviewed by PREreview

A molecular proximity sensor based on an engineered, dual-component guide RNA

1. Junhong Choi
2. Wei Chen
3. Hanna Liao
4. Xiaoyi Li
5. Jay Shendure

• Curated by eLife

  eLife Assessment

  This important manuscript describes a creative approach using dual-component gRNAs to create a new class of molecular proximity sensors for genome editing. The authors demonstrate that this tool can be coupled with several different gene editing effectors, showing convincingly that the tool functions as intended. This study not only introduces a first-of-its kind approach, but through careful measurements also enables future further development of the technology.

Reviewed by eLife

De novo-designed minibinders expand the synthetic biology sensing repertoire

1. Zara Y Weinberg
2. Sarah S Soliman
3. Matthew S Kim
4. Devan H Shah
5. Irene P Chen
6. Melanie Ott
7. Wendell A Lim
8. Hana El-Samad

• Curated by eLife

  eLife Assessment

  This study presents a useful investigation of the use of small, de novo-designed protein binding domains (mini-binders) against the Spike protein of SARS-CoV-2 and EGFR, as ligand binding domains on two classes of synthetic receptors, second-generation synNotch (SNIPR) and CAR. The methods and evidence supporting the focused claims are solid. This work will be of interest to synthetic biologists and cell engineers as a starting point to map out the rules for receptor engineering based on mini-binders and ultimately to advance them in biomedical applications.

Reviewed by eLife

A synthetic method to assay polycystin channel biophysics

1. Megan Larmore
2. Orhi Esarte Palomero
3. Neha Kamat
4. Paul G DeCaen

• Curated by eLife

  eLife Assessment

  The authors have developed a valuable approach that employs cell-free expression to reconstitute ion channels into giant unilamellar vesicles for biophysical characterisation. The work is convincing and will be of particular interest to those studying ion channels that primarily occur in organelles and are therefore not amenable to be studied by more traditional methods.

Reviewed by eLife

Light-driven synchronization of optogenetic clocks

1. Maria Cristina Cannarsa
2. Filippo Liguori
3. Nicola Pellicciotta
4. Giacomo Frangipane
5. Roberto Di Leonardo

• Curated by eLife

  eLife assessment

  This study presents a light-entrainable synthetic oscillator in bacteria, the optorepressilator. The authors develop a toolbox using optogenetics that makes the cellular oscillator easily controllable. This toolbox is valuable, contributing both to bioengineering and to the understanding of biological dynamical systems. The comparison with a mathematical model, population, and single-cell measurements demonstrate convincingly that the planned system was achieved and is suitable to control and study biological oscillators.

Reviewed by eLife