publications

2024

1. Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia

   Abhinav Pujar, Amit Pathania, Corbin Hopper, Amir Pandi, Cristian Ruiz Calderón, Matthias Függer, Thomas Nowak, and Manish Kushwaha

   Nucleic Acids Research, Dec 2024

2023

1. Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides

   Amir Pandi, David Adam, Amir Zare, Van Tuan Trinh, Stefan L Schaefer, Marie Burt, Björn Klabunde, Elizaveta Bobkova, Manish Kushwaha, Yeganeh Foroughijabbari, and  others

   Nature Communications, Dec 2023

2022

1. Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts

   Angelo Cardoso Batista, Antoine Levrier, Paul Soudier, Peter L Voyvodic, Tatjana Achmedov, Tristan Reif-Trauttmansdorff, Angelique DeVisch, Martin Cohen-Gonsaud, Jean-Loup Faulon, Chase L Beisel, and  others

   ACS synthetic biology, Dec 2022
2. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

   Joan Hérisson, Thomas Duigou, Melchior Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, Gizem Buldum, Olivier Telle, Yorgo El Moubayed, Pablo Carbonell, Neil Swainston, and  others

   Nature Communications, Dec 2022
3. Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates

   Mahnaz Sabeti Azad, Angelo Cardoso Batista, Jean-Loup Faulon, Chase L Beisel, Jerome Bonnet, and Manish Kushwaha

   Journal of visualized experiments: JoVE, Dec 2022
4. PeroxiHUB: A Modular Cell-Free Biosensing Platform Using H 2 O 2 as Signal Integrator

   Paul Soudier, Ana Zúñiga, Thomas Duigou, Peter L Voyvodic, Kenza Bazi-Kabbaj, Manish Kushwaha, Julie A Vendrell, Jerome Solassol, Jerome Bonnet, and Jean-Loup Faulon

   ACS synthetic biology, Dec 2022
5. Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima

   Paul Soudier, Daniel Rodriguez Pinzon, Tristan Reif-Trauttmansdorff, Hassan Hijazi, Maëva Cherrière, Cátia Goncalves Pereira, Doriane Blaise, Maxime Pispisa, Angelyne Saint-Julien, William Hamlet, and  others

   Synthetic and systems biotechnology, Dec 2022
6. Cell-Free Biosensors and AI Integration

   Paul Soudier, Léon Faure, Manish Kushwaha, and Jean-Loup Faulon

   Methods in molecular biology (Clifton, NJ), Dec 2022
7. A synthetic communication system uncovers extracellular immunity that self-limits bacteriophage transmission

   Amit Pathania, Corbin Hopper, Amir Pandi, Matthias Függer, Thomas Nowak, and Manish Kushwaha

   bioRxiv, Dec 2022

   Abs

   Understanding how delivery and exchange of genetic information by bacteriophages shapes bacterial populations is important for designing applications for phage therapy, biocontrol, and microbiome engineering. Here, we present a synthetic intercellular communication system that repurposes phage M13 for genetic exchange between Escherichia coli cells and build mathematical models of the communication behaviour. Our models, based on Chemical Reaction Networks, capture the growth burden, cell density, and growth phase dependence of phage secretion and infection kinetics and predict the stochasticity characterising phage-bacterial interactions at low numbers. In co-cultures of phage sender and receiver cells, resource sharing and selection pressure determine the choice of horizontal versus vertical phage transmission. Surprisingly, we discover that a phage-encoded immunity factor confers extracellular protection to uninfected bacteria, reducing infection rates by 70%. In a simulated gut environment, this novel “self-jamming” mechanism enables the phage to farm uninfected bacteria for future infections, increasing the overall success of both M13 and E. coli. The synthetic system developed here lays the groundwork for implementing population level controls in engineered bacterial communities, using phage signals for communication.Competing Interest StatementThe authors have declared no competing interest.

2021

1. Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs

   Jacob Beal, Geoff S Baldwin, Natalie G Farny, Markus Gershater, Traci Haddock-Angelli, Russell Buckley-Taylor, Ari Dwijayanti, Daisuke Kiga, Meagan Lizarazo, John Marken, and  others

   PloS one, Dec 2021
2. Optimising protein synthesis in cell-free systems, a review

   Angelo C Batista, Paul Soudier, Manish Kushwaha, and Jean-Loup Faulon

   Engineering Biology, Dec 2021
3. Reaching Agreement in Competitive Microbial Systems

   Victoria Andaur, Janna Burman, Matthias Függer, Manish Kushwaha, Bilal Manssouri, Thomas Nowak, and Joel Rybicki

   Dec 2021

2020

1. Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics

   Roberto Galizi, John N Duncan, William Rostain, Charlotte M Quinn, Marko Storch, Manish Kushwaha, and Alfonso Jaramillo

   The CRISPR journal, Dec 2020
2. Digital circuit design for biological and silicon computers

   Matthias Függer, Manish Kushwaha, and Thomas Nowak

   Advances in Synthetic Biology, Dec 2020

2019

1. Metabolic perceptrons for neural computing in biological systems

   Amir Pandi, Mathilde Koch, Peter L Voyvodic, Paul Soudier, Jerome Bonnet, Manish Kushwaha, and Jean-Loup Faulon

   Nature communications, Dec 2019
2. Dynamic colocalization of 2 simultaneously active VSG expression sites within a single expression-site body in Trypanosoma brucei

   James Budzak, Louise E Kerry, Aris Aristodemou, Belinda S Hall, Kathrin Witmer, Manish Kushwaha, Carys Davies, Megan L Povelones, Jacquelyn R McDonald, Aakash Sur, and  others

   Proceedings of the National Academy of Sciences of the United States of America, Dec 2019

2018

1. Quantification of bacterial fluorescence using independent calibrants

   Jacob Beal, Traci Haddock-Angelli, Geoff Baldwin, Markus Gershater, Ari Dwijayanti, Marko Storch, Kim Mora, Meagan Lizarazo, Randy Rettberg, and  others

   PloS one, Dec 2018

2016

1. Using RNA as Molecular Code for Programming Cellular Function

   Manish Kushwaha, William Rostain, Satya Prakash, John N Duncan, and Alfonso Jaramillo

   ACS synthetic biology, Dec 2016
2. Functionalization of an Antisense Small RNA

   Guillermo Rodrigo, Satya Prakash, Teresa Cordero, Manish Kushwaha, and Alfonso Jaramillo

   Journal of molecular biology, Dec 2016

2015

1. A portable expression resource for engineering cross-species genetic circuits and pathways

   Manish Kushwaha, and Howard M Salis

   Nature communications, Dec 2015
2. Identification of the ISWI Chromatin Remodeling Complex of the Early Branching Eukaryote Trypanosoma brucei

   Tara Stanne, Mani Shankar Narayanan, Sophie Ridewood, Alexandra Ling, Kathrin Witmer, Manish Kushwaha, Simone Wiesler, Bill Wickstead, Jennifer Wood, and Gloria Rudenko

   The Journal of biological chemistry, Dec 2015

2014

1. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

   Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook, Matthew Guido, and Howard M Salis

   Molecular systems biology, Dec 2014

2011

1. TbISWI regulates multiple polymerase I (Pol I)-transcribed loci and is present at Pol II transcription boundaries in Trypanosoma brucei

   Tara M Stanne, Manish Kushwaha, Matthew Wand, Jesse E Taylor, and Gloria Rudenko

   Eukaryotic cell, Dec 2011
2. NLP is a novel transcription regulator involved in VSG expression site control in Trypanosoma brucei

   Mani Shankar Narayanan, Manish Kushwaha, Klaus Ersfeld, Alexander Fullbrook, Tara M Stanne, and Gloria Rudenko

   Nucleic acids research, Dec 2011

2010

1. TbISWI and its role in transcriptional control in Trypanosoma brucei

   Manish Kushwaha

   Oxford University, UK, Dec 2010

2006

1. Computational analysis of Entamoeba histolytica genome-Exploring junk DNA for hidden messages

   MANISH KUSHWAHA

   JAWAHARLAL NEHRU UNIVERSITY NEW DELHI, Dec 2006