A Fermentation State Marker Rule Design Task in Metabolic Engineering.

Egils Stalidzans, Reinis Muiznieks, Konstantins Dubencovs, Elina Sile, Kristaps Berzins, Arturs Suleiko, Juris Vanags

Abstract read

In one paragraph

Article in Bioengineering (Basel, Switzerland), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Egils StalidzansInstitute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia.ORCID 0000-0001-6063-0184

Reinis MuiznieksInstitute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia.ORCID 0000-0003-3432-4321

Konstantins DubencovsBioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia.

Elina SileBioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia.ORCID 0000-0002-4199-1352

Kristaps BerzinsInstitute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia.

Arturs SuleikoBioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia.

Juris VanagsBioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia.

Funding

European Regional Development Fund No. 1.1.1.1/20/A/137

6 · The paper itself

Abstract

There are several ways in which mathematical modeling is used in fermentation control, but mechanistic mathematical genome-scale models of metabolism within the cell have not been applied or implemented so far. As part of the metabolic engineering task setting, we propose that metabolite fluxes and/or biomass growth rate be used to search for a fermentation steady state marker rule. During fermentation, the bioreactor control system can automatically detect the desired steady state using a logical marker rule. The marker rule identification can be also integrated with the production growth coupling approach, as presented in this study. A design of strain with marker rule is demonstrated on genome scale metabolic model

Indexed as

genome scale metabolic modelgrowth couplingmarker rulemetabolic engineeringproduction envelope

Identifiers

PMID38136018

DOI10.3390/bioengineering10121427

PMCPMC10740952

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.