BØPosphere – February 2023

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bioRxiv : the preprint server for biology

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.

2023-02-21

PubMed:36865326; DOI:10.1101/2023.02.20.529291

Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson

Affiliations

In realms of genes, a dance unfolds,
Transcriptome’s whispers, proteome’s codes,
From data’s depths, insights arise,
Modules connect, a wondrous surprise,
In bacterial rhythms, their secrets enfold.

Proteome’s canvas, where modules entwine,
Transcriptome’s palette, a creation defined.
Known rules in genes’ orchestration play,
With module variations, their secrets display.
Transcript’s insight, proteome’s fate enshrined.

Metabolic engineering

Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals.

2023-02-03

PubMed:36738854; DOI:10.1016/j.ymben.2023.01.012

Rebecca M Lennen¹, Hyun Gyu Lim², Kristian Jensen¹, Elsayed T Mohammed¹, Patrick V Phaneuf¹, Myung Hyun Noh², Sailesh Malla¹, Rosa A Börner¹, Ksenia Chekina¹, Emre Özdemir¹, Ida Bonde¹, Anna Koza¹, Jérôme Maury¹, Lasse E Pedersen¹, Lars Y Schöning¹, Nikolaus Sonnenschein¹, Bernhard O Palsson³, Alex T Nielsen¹, Morten O A Sommer¹, Markus J Herrgård⁴, Adam M Feist⁵

Affiliations

The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr. #0412, La Jolla, CA, 92093-0412, USA
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr. #0412, La Jolla, CA, 92093-0412, USA
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; BioInnovation Institute, Ole Maaløes Vej 3, 2830, Copenhagen, Denmark.
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr. #0412, La Jolla, CA, 92093-0412, USA.

In strains that biomanufacture with glee,
Chemical tolerance holds the key,
Evolved with finesse,
11 toxic challenges, they progress,
A symphony of adaptation, clear to see.

Over 200 genomes sequenced, mechanisms in sight,
Challenged by chemicals, a courageous fight,
Membrane mutations rise,
Toxicity defies,
E. coli’s dance, survival takes flight.

Osmotic stress and mutations align,
Tolerance blooms, a response so divine,
Structurally akin,
A tradeoff might begin,
A roadmap of resilience, a tale to enshrine.

FBA-classic

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Communications biology

Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation.

2023-02-10

PubMed:36765199; DOI:10.1038/s42003-023-04540-8

Sanjeev Dahal¹, Alina Renz², Andreas Dräger², Laurence Yang³

Affiliations

Department of Chemical Engineering, Queen’s University, Kingston, Canada
Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany
Department of Chemical Engineering, Queen’s University, Kingston, Canada.

We’ve detected a paper from Communications Biology that cites a retracted paper post-retraction.

Citing paper: https://doi.org/10.1038/s42003-023-04540-8…
Retracted paper:

2023-04-09

One of the most threatening hospital germs that can cause serious #infectiousdiseases is 𝘗𝘴𝘦𝘶𝘥𝘰𝘮𝘰𝘯𝘢𝘴 𝘢𝘦𝘳𝘶𝘨𝘪𝘯𝘰𝘴𝘢. Its now published, most comprehensive and accurate computer model to date should support fighting it – despite its antibiotic resistance.

2023-02-10

bioRxiv

Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

2023-02-27

DOI:10.1101/2023.02.26.530115

B. Vezina, S. C. Watts, J. Hawkey, H. B. Cooper, L. M. Judd, A. Jenney, J. M. Monk, K. E. Holt, K. L. Wyres

Affiliations

Monash University

metabolic-engineering

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New biotechnology

Automating the design-build-test-learn cycle towards next-generation bacterial cell factories.

2023-02-01

PubMed:36736693; DOI:10.1016/j.nbt.2023.01.002

Nicolás Gurdo¹, Daniel C Volke¹, Douglas McCloskey¹, Pablo Iván Nikel²

Affiliations

The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark.

Check the latest article by @NicolasGurdo, @Daniel__Volke & Douglas McCloskey on #automation of the #SynBio #DBTL cycle—the way forward to #bioproduction & #bioeconomy #OpenAccess @ElsevierConnect @LabNikel @DTUBiosustain

2023-02-12

human-health

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Lancet (London, England)

Cell-free fetal DNA for genetic evaluation in Copenhagen Pregnancy Loss Study (COPL): a prospective cohort study.

2023-02-02

PubMed:36739882; DOI:10.1016/S0140-6736(22)02610-1

Tanja Schlaikjær Hartwig¹, Louise Ambye², Jennifer R Gruhn³, Jesper Friis Petersen⁴, Tine Wrønding⁵, Letizia Amato⁶, Andrew Chi-Ho Chan³, Boyang Ji⁷, Maiken Hemme Bro-Jørgensen², Lene Werge², Mette Marie Babiel Schmidt Petersen⁵, Clara Brinkmann⁵, Julie Birch Petersen⁵, Morten Dunø⁸, Iben Bache⁸, Markus J Herrgård⁷, Finn Stener Jørgensen⁹, Eva R Hoffmann³, Henriette Svarre Nielsen¹⁰, COPL consortium

Affiliations

Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Hvidovre Hospitals NIPT Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
Hvidovre Hospitals NIPT Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Obstetrics and Gynaecology, Copenhagen University Hospital-North Zealand, Hillerød, Denmark; Department of Obstetrics and Gynaecology, Copenhagen University Hospital Herlev, Herlev, Denmark
Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; BioInnovation Institute, Copenhagen, Denmark
BioInnovation Institute, Copenhagen, Denmark
Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
Hvidovre Hospitals NIPT Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Fetal Medicine Unit, Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

bioRxiv

Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses

2023-02-07

DOI:10.1101/2023.02.07.527430

C. J. Moore, C. Holstege, J. Papin

Affiliations

University of Virginia

AI

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bioRxiv

Deep learning-based codon optimization with large-scale synonymous variant datasets enables generalized tunable protein expression

2023-02-12

DOI:10.1101/2023.02.11.528149

D. A. Constant, J. M. Gutierrez, A. V. Sastry, R. Viazzo, N. R. Smith, J. Hossain, D. A. Spencer, H. Carter, A. B. Ventura, M. T. M. Louie, C. Kohnert, R. Consbruck, J. Bennett, K. A. Crawford, J. M. Sutton, A. Morrison, A. K. Steiger, K. A. Jackson, J. T. Stanton, S. Abdulhaqq, G. Hannum, J. Meier, M. Weinstock, M. Gander

Affiliations

Absci

First, we used #AI to optimize an antibody’s binding affinity and Naturalness score.

Then we used it to build novel antibodies.

Now we’ve turned AI towards codon optimization.

Read our latest preprint @biorxivpreprint
https://biorxiv.org/content/10.1101/2023.02.11.528149v1…
#AI #generativeAi

2023-02-14

BØPosphere – February 2023

kedalionlabs.com

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