Arnold World May 2023

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bioRxiv

Self-driving laboratories to autonomously navigate the protein fitness landscape

2023-05-20

DOI:10.1101/2023.05.20.541582

J. T. Rapp, B. J. Bremer, P. A. Romero

Affiliations

UW-Madison

I think the “self-driving labs” preprint, where 4 autonomous agents independently designed proteins w/ high Tms, may contradict this. All 4 had different sequence->fitness mappings due to insufficient data, but still succeeded in their design objective.

2023-06-07

As seen on the @ml4proteins seminar a few weeks back. Check their YouTube channel to see Jacob dive into this topic more!

2023-05-22

In labs where science’s threads align,
Proteins, novel, bright stars to shine,
SAMPLE, the autonomous guide,
In protein landscapes doth ride,
A dance of progress, design.

From chemistry’s bond to life’s cure,
SAMPLE’s prowess shines brilliantly pure,
Through sequences it roams,
New functions it hones,
Proteins with talents, so sure.

bioRxiv

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

2023-05-11

DOI:10.1101/2023.05.11.540424

J. Yang, J. Ducharme, K. E. Johnston, F.-Z. Li, Y. Yue, F. H. Arnold

Affiliations

California Institute of Technology

Jason Yang’s @jsunn_y paper on designing combinatorial libraries for #machinelearning guided #proteinengineering #directedevolution #MLDE is out on biorxiv. Putting tools out!

2023-05-22

A tunable method for optimizing degenerate codon libraries that sample protein variants that are likely to have both high fitness and high diversity.

@jsunn_y Julie Ducharme @kadinaj @francescazfl @yisongyue @francesarnold
https://biorxiv.org/content/10.1101/2023.05.11.540424v1…

2023-05-22

evolutionary-engineering–proteins

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Sheng wu gong cheng xue bao = Chinese journal of biotechnology

[Commentary: polymer binding modules accelerate enzymatic degradation of poly(ethylene terephthalate)].

2023-05-22

PubMed:37212219; DOI:10.13345/j.cjb.221033

Yi Lu¹, Ruizhi Han¹, Ulrich Schwaneberg¹, Yu Ji¹

Affiliations

Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Germany

Journal of the American Chemical Society

Redox-Paired Alkene Difunctionalization Enables Skeletally Divergent Synthesis.

2023-05-23

PubMed:37220422; DOI:10.1021/jacs.3c03274

Hui-Qi Ni¹, Malkanthi K Karunananda¹, Tian Zeng¹, Shenghua Yang¹, Zhen Liu¹, K N Houk², Peng Liu³, Keary M Engle¹

Affiliations

Department of Chemistry, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States

The final version of @NiHuiqi’s study is now online @J_A_C_S.

the “Everything Everywhere All at Once” reaction

2023-05-24

Advanced materials (Deerfield Beach, Fla.)

Fluoride-Catalyzed Siloxane Exchange as a Robust Dynamic Chemistry for High-Performance Vitrimers.

2023-05-16

PubMed:37191236; DOI:10.1002/adma.202303280

Chase Tretbar¹, Jordan Castro¹, Kosuke Yokoyama¹, Zhibin Guan¹

Affiliations

Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA

Accounts of chemical research

FhuA: From Iron-Transporting Transmembrane Protein to Versatile Scaffolds through Protein Engineering.

2023-05-16

PubMed:37191525; DOI:10.1021/acs.accounts.3c00060

Daniel F Sauer¹, Ulrich Markel¹, Johannes Schiffels¹, Jun Okuda², Ulrich Schwaneberg¹

Affiliations

Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany

It is finally online! The summary of our work with FhuA, a transmembrane protein, which is used in various research areas (#biocatalysis #artificialmetalloenzymes #nanobiotechnology). @ACSPublications #AccChemRes

2023-05-19

Cell systems

In vitro continuous protein evolution empowered by machine learning and automation.

2023-05-18

PubMed:37224814; DOI:10.1016/j.cels.2023.04.006

Tianhao Yu¹, Aashutosh Girish Boob², Nilmani Singh³, Yufeng Su⁴, Huimin Zhao⁵

Affiliations

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA; NSF Molecule Maker Lab Institute, Urbana, IL, USA
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
NSF Molecule Maker Lab Institute, Urbana, IL, USA; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA; NSF Molecule Maker Lab Institute, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Excited to share our recent perspective for closed-loop in vitro continuous protein evolution framework leveraging the best of both worlds, ML and automation, and provide a brief overview of the recent developments in the field.

2023-05-24

evolution-physiology

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Fish & shellfish immunology

Isolation and characterization of single domain antibodies from banded houndshark (Triakis scyllium) targeting SARS-CoV-2 spike RBD protein.

2023-05-09

PubMed:37169112; DOI:10.1016/j.fsi.2023.108807

Woo Sung Kim¹, Hee Do Chae¹, Inji Jung², Won-Kyu Lee³, Woo Jun Lee⁴, Jisun Lee², Yejin Gong¹, Dohyun Lee³, Byeong-Won Kim³, Jin-Koo Kim⁴, Jaehyeon Hwang⁵, Dae-Hyuk Kweon⁵, Sang Taek Jung⁶, Jung-Hyun Na⁷

Affiliations

Department of Pharmaceutical Engineering, Sangji University, Wonju, 26339, Republic of Korea
Department of Biomedical Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
New Drug Development Center, Osong Medical Innovation Foundation (Kbiohealth), Cheongju, 28160, Republic of Korea
Department of Marine Biology, Pukyong National University, Busan, 48513, Republic of Korea
Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
Department of Biomedical Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
Department of Pharmaceutical Engineering, Sangji University, Wonju, 26339, Republic of Korea; Research Institute of Korean Medicine, Sangji University, Wonju, 26339, Republic of Korea.

Scientific reports

RNA ligase ribozymes with a small catalytic core.

2023-05-26

PubMed:37237056; DOI:10.1038/s41598-023-35584-9

Yoko Nomura¹, Yohei Yokobayashi²

Affiliations

Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.

synbio-meteng

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bioRxiv

Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides

2023-05-09

DOI:10.1101/2023.05.07.539759

S. Mishra, A. Deewan, H. Zhao, C. Rao

Affiliations

University of Illinois at Urbana Champaign

Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides https://biorxiv.org/cgi/content/short/2023.05.07.539759v1… #bioRxiv

2023-05-09

bioRxiv

A landing pad system for multicopy gene integration in Issatchenkia orientalis

2023-05-21

DOI:10.1101/2023.05.21.541627

Z. Fatma, S.-I. Tan, A. G. Boob, H. Zhao

Affiliations

University of Illinois at Urbana-Champaign

human-physiology

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bioRxiv

Acoustically-Targeted Measurement of Transgene Expression in the Brain

2023-05-24

DOI:10.1101/2023.05.23.541868

J. P. Seo, J. S. Trippett, Z. Huang, R. Wang, S. Lee, J. O. Szablowski

Affiliations

Rice University

What if you could point to a brain region and measure c-Fos, or assess the success of gene delivery? We combined synthetic markers with focused ultrasound to enable site-specific measurement of gene expression in the brain. More in the preprint:
https://biorxiv.org/content/10.1101/2023.05.23.541868v1…

2023-05-25

kedalionlabs.com

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