BØPosphere – April 2023 – Biowall Project

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Proceedings of the National Academy of Sciences of the United States of America

Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks.

2023-04-03

PubMed:37011218; DOI:10.1073/pnas.2218835120

Edward Alexander Catoiu¹, Patrick Phaneuf², Jonathan Monk³, Bernhard O Palsson¹

Affiliations

Department of Bioengineering, University of California, San Diego, La Jolla, CA 92101
The Novo Nordisk Foundation (NNF) Center for Biosustainability, The Technical University of Denmark, Kongens Lyngby 2800, Denmark
Avellino Lab, Menlo Park, CA 94025

This is fascinating. Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks

2023-04-11

In the realm where genetics ignite,
Alleleome’s tapestry of colours unite,
Amino acid sequences in wild strains, they define,
Variations across genes, a grand design.
Nature’s palette of evolution, vibrant and bright.

Conserved and enriched in a genome’s embrace,
Protein’s function, in its rightful place,
Laboratory’s touch, mutations arise,
Severe substitutions, a daring surprise,
A journey of changes, in evolution’s grace.

With allelic diversity, a window to see,
Bacterial wonders, in sequences free,
Synthetic pathways, a boundless explore,
Unveiling nature’s secrets, at the core,
In the realm of strains, evolution’s spree.

Trends in biotechnology

From observational to actionable: rethinking omics in biologics production.

2023-04-14

PubMed:37062598; DOI:10.1016/j.tibtech.2023.03.009

Helen O Masson¹, Karen Julie la Cour Karottki², Jasmine Tat³, Hooman Hefzi⁴, Nathan E Lewis⁵

Affiliations

Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Amgen Inc., Thousand Oaks, CA, USA
Biogen, Inc., Cambridge, MA, USA.
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

In biotech, omics’ on the rise,
Expanding with success, no surprise.
From academia’s reach,
To industry’s breach,
Omic experiments, a sought-after prize.

Discovery science, it does excel,
In academia’s research, it’s swell.
But in biomanufacture,
A different nature,
To unlock actionable insights, we must dwell.

Deliberate selection is key,
When choosing the omics strategy.
With forethought in place,
And analysis space,
Maximize value, and insights we’ll see.

Designing omic experiments with care,
Considerations, we must be aware.
Systems biology in play,
To enhance the way,
Actionable insights we can prepare.

In mammalian biologics, the aim,
To optimize production, a game.
With omics as our guide,
We’ll uncover and stride,
Towards solutions that industry can claim.

FBA-classic

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PLoS computational biology

Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies.

2023-04-26

PubMed:37099624; DOI:10.1371/journal.pcbi.1011076

Deborah A Powers¹, Matthew L Jenior², Glynis L Kolling², Jason A Papin¹

Affiliations

Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, Virginia, United States of America

Some great work from @debapowers with support from @mattagenomics and @kolling_g. #PLOSCompBio: Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies

2023-05-16

bioRxiv

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

2023-04-20

DOI:10.1101/2023.04.19.537435

T. W. H. Backman, C. Schenk, T. Radivojevic, D. Ando, J. Singh, J. J. Czajka, Z. Costello, J. D. Keasling, Y. Tang, E. Akhmatskaya, H. Garcia Martin

Affiliations

Lawrence Berkeley National Laboratory

physiology

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bioRxiv

Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples

2023-04-30

DOI:10.1101/2023.04.28.538731

H. M. Baghdassarian, D. Dimitrov, E. Armingol, J. Saez-Rodriguez, N. E. Lewis

Affiliations

1/ New protocol paper for #CellCellCommunication! Our manuscript presents a pipeline for robust and generalizable cell-cell communication analysis of complex single-cell datasets, combining the best of LIANA & Tensor-cell2cell! #CompBio #SingleCell
https://doi.org/10.1101/2023.04.28.538731…

2023-05-02

metabolic-engineering

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Journal of the American Chemical Society

Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase.

2023-04-14

PubMed:37057992; DOI:10.1021/jacs.2c11027

Elias Englund¹, Matthias Schmidt¹, Alberto A Nava², Anna Lechner³, Kai Deng¹, Renee Jocic¹, Yingxin Lin⁴, Jacob Roberts², Veronica T Benites¹, Ramu Kakumanu¹, Jennifer W Gin¹, Yan Chen¹, Yuzhong Liu³, Christopher J Petzold¹, Edward E K Baidoo¹, Trent R Northen¹, Paul D Adams¹, Leonard Katz¹, Satoshi Yuzawa¹, Jay D Keasling¹

Affiliations

Joint BioEnergy Institute, Emeryville, California 94608, United States
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States

Great news! Our latest research on polyketide synthase engineering has just been published in @J_A_C_S. Our work presents innovative methods for synthesizing unnatural polyketides with important implications for novel drug and biomaterial discovery.

2023-04-14

non-microbe-hosts

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STAR protocols

GlycoMME, a Markov modeling platform for studying N-glycosylation biosynthesis from glycomics data.

2023-04-21

PubMed:37086409; DOI:10.1016/j.xpro.2023.102244

Chenguang Liang¹, Austin W T Chiang², Nathan E Lewis³

Affiliations

Department of Pediatrics, University of California, San Diego, La Jolla, San Diego, CA 92130, USA; Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92130, USA
Department of Pediatrics, University of California, San Diego, La Jolla, San Diego, CA 92130, USA.
Department of Pediatrics, University of California, San Diego, La Jolla, San Diego, CA 92130, USA; Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92130, USA.

Markov model

BØPosphere – April 2023

kedalionlabs.com

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