scholarly journals Population dynamics analysis of Saccharomyces cerevisiae deletion library during fed-batch cultivation using Bar-seq

2020 ◽  
Author(s):  
Maren Wehrs ◽  
Mitchell G. Thompson ◽  
Deepanwita Banerjee ◽  
Jan-Philip Prahl ◽  
Carolina A. Barcelos ◽  
...  
Keyword(s):  
Stress Responses ◽  
Large Scale ◽  
Glycogen Synthase ◽  
Batch Cultivation ◽  
Population Diversity ◽  
Fed Batch ◽  
Industrial Fermentation ◽  
Biological Stress ◽  
Yeast Deletion Library ◽  
Deletion Library

AbstractTo understand the genetic basis of changes in strain physiology during industrial fermentation, and the corresponding roles these genes play in strain performance, we employed a barcoded yeast deletion library to assess genome-wide strain fitness across a simulated industrial fermentation regime. Our results demonstrate the utility of Bar-seq to assess fermentation associated stresses in yeast populations under industrial conditions. We find that mutant population diversity is maintained through multiple seed trains, enabling for large scale fermentation selective pressures to act upon the community. We identify specific deletion mutants that were enriched in all processes, independent of the cultivation conditions, which include MCK1, RIM11, MRK1, and YGK3 that encode homologues of mammalian glycogen synthase kinase 3 (GSK-3). Further, we show that significant changes in the population diversity during fed-batch cultivations reflect the presence of significant external stresses, such as the accumulation of the fermentative byproduct ethanol. The mutants that were lost during the time of most extreme population selection suggest that specific biological processes may be required to cope with these specific stresses. Overall our work highlights a promising avenue to identify genetic loci and biological stress responses required for fitness under industrial conditions.

scholarly journals Versatile Physiological Functions of Plant GSK3-Like Kinases

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 697
Author(s):  
Juan Mao ◽  
Wenxin Li ◽  
Jing Liu ◽  
Jianming Li
Keyword(s):  
Stress Responses ◽  
Glycogen Synthase ◽  
Plant Stress ◽  
Normal Growth ◽  
Growth Conditions ◽  
Genetic Studies ◽  
Physiological Functions ◽  
Environmental Signals ◽  
Plant Stress Responses ◽  
Diverse Plant

The plant glycogen synthase kinase 3 (GSK3)-like kinases are highly conserved protein serine/threonine kinases that are grouped into four subfamilies. Similar to their mammalian homologs, these kinases are constitutively active under normal growth conditions but become inactivated in response to diverse developmental and environmental signals. Since their initial discoveries in the early 1990s, many biochemical and genetic studies were performed to investigate their physiological functions in various plant species. These studies have demonstrated that the plant GSK3-like kinases are multifunctional kinases involved not only in a wide variety of plant growth and developmental processes but also in diverse plant stress responses. Here we summarize our current understanding of the versatile physiological functions of the plant GSK3-like kinases along with their confirmed and potential substrates.

scholarly journals Efficacy and Underlying Mechanism of Acupuncture in the Treatment of Posttraumatic Stress Disorder: A Systematic Review of Animal Studies

2021 ◽  
Vol 10 (8) ◽  
pp. 1575
Author(s):  
Chan-Young Kwon ◽  
Boram Lee ◽  
Sang-Ho Kim
Keyword(s):  
Posttraumatic Stress Disorder ◽  
Posttraumatic Stress ◽  
Stress Responses ◽  
Methodological Quality ◽  
Animal Studies ◽  
Large Scale ◽  
Stress Disorder ◽  
Spatial Learning And Memory ◽  
Expectancy Effects ◽  
Therapeutic Mechanisms

Acupuncture is a nonpharmacological intervention that can be useful in the clinical management of posttraumatic stress disorder (PTSD), especially in situations with a lack of medical resources, including large-scale PTSD events such as disasters. Some clinical studies have reported the clinical effect of acupuncture in improving PTSD symptoms, but the underlying therapeutic mechanism has yet to be explored. Therefore, this review summarized the underlying therapeutic mechanisms of acupuncture in animal PTSD models. A comprehensive search was conducted in 14 electronic databases, and two independent researchers performed study selection, data extraction, and the methodological quality assessment. Twenty-four relevant studies were included in this review and summarized according to the proposed main mechanisms. In behavioral evaluation, acupuncture, including manual acupuncture and electro-acupuncture, reduced anxiety and fear responses and weakened fear conditioning, improved sleep architecture, reduced depressive symptoms, and alleviated disturbance of spatial learning and memory of PTSD animal models. The therapeutic mechanisms of acupuncture proposed in the included studies could be classified into two categories: (1) regulation of stress responses in the neuroendocrine system and (2) promotion of neuroprotection, neurogenesis, and synaptic plasticity in several brain areas. However, the methodological quality of the included animal studies was not high enough to produce robust evidence. In addition, mechanistic studies on specific aspects of acupuncture that may affect PTSD, including expectancy effects, in human PTSD subjects are also needed.

scholarly journals Optimization of Synthetic Media Composition for Kluyveromyces marxianus Fed-Batch Cultivation

Fermentation ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 62
Author(s):  
Konstantins Dubencovs ◽  
Janis Liepins ◽  
Arturs Suleiko ◽  
Anastasija Suleiko ◽  
Reinis Vangravs ◽  
...  
Keyword(s):  
Kluyveromyces Marxianus ◽  
Reaction Medium ◽  
Value Added ◽  
Batch Cultivation ◽  
Batch Processes ◽  
Biomass Growth ◽  
High Cell ◽  
Media Composition ◽  
Fed Batch ◽  
Fed Batch Cultivation

The Kluyveromyces marxianus yeast recently has gained considerable attention due to its applicability in high-value-added product manufacturing. In order to intensify the biosynthesis rate of a target product, reaching high biomass concentrations in the reaction medium is mandatory. Fed-batch processes are an attractive and efficient way how to achieve high cell densities. However, depending on the physiology of the particular microbial strain, an optimal media composition should be used to avoid by-product synthesis and, subsequently, a decrease in overall process effi-ciency. Thus, the aim of the present study was to optimise the synthetic growth medium and feeding solution compositions (in terms of carbon, nitrogen, phosphorous, magnesium, and calcium concentrations) for high cell density K. marxianus fed‑batch cultivations. Additionally, the biomass yields from the vitamin mixture and other macro/microelements were identified. A model predictive control algorithm was successfully applied for a fed-batch cultivation control. Biomass growth and substrate consumption kinetics were compared with the mathematical model predictions. Finally, 2‑phenylethanol biosynthesis was induced and its productivity was estimated. The determined optimal macronutrient ratio for K. marxianus biomass growth was identified as C:N:P = 1:0.07:0.011. The maximal attained yeast biomass concentration was close to 70 g·L-1 and the 2-PE biosynthesis rate was 0.372 g·L−1·h−1, with a yield of 74% from 2-phenylalanine.

scholarly journals Glucose-Limited Fed-Batch Cultivation Strategy to Mimic Large-Scale Effects in Escherichia coli Linked to Accumulation of Non-Canonical Branched-Chain Amino Acids by Combination of Pyruvate Pulses and Dissolved Oxygen Limitation

2021 ◽  
Vol 9 (6) ◽  
pp. 1110
Author(s):  
Ángel Córcoles García ◽  
Peter Hauptmann ◽  
Peter Neubauer
Keyword(s):  
Amino Acids ◽  
Dissolved Oxygen ◽  
Large Scale ◽  
Scale Effects ◽  
Branched Chain Amino Acids ◽  
Oxygen Limitation ◽  
Fed Batch ◽  
Fermentation Products ◽  
Cultivation Strategy ◽  
Branched Chain

Insufficient mixing in large-scale bioreactors provokes gradient zones of substrate, dissolved oxygen (DO), pH, and other parameters. E. coli responds to a high glucose, low oxygen feeding zone with the accumulation of mixed acid fermentation products, especially formate, but also with the synthesis of non-canonical amino acids, such as norvaline, norleucine and β-methylnorleucine. These amino acids can be mis-incorporated into recombinant products, which causes a problem for pharmaceutical production whose solution is not trivial. While these effects can also be observed in scale down bioreactor systems, these are challenging to operate. Especially the high-throughput screening of clone libraries is not easy, as fed-batch cultivations would need to be controlled via repeated glucose pulses with simultaneous oxygen limitation, as has been demonstrated in well controlled robotic systems. Here we show that not only glucose pulses in combination with oxygen limitation can provoke the synthesis of these non-canonical branched-chain amino acids (ncBCAA), but also that pyruvate pulses produce the same effect. Therefore, we combined the enzyme-based glucose delivery method Enbase® in a PALL24 mini-bioreactor system and combined repeated pyruvate pulses with simultaneous reduction of the aeration rate. These cultivation conditions produced an increase in the non-canonical branched chain amino acids norvaline and norleucine in both the intracellular soluble protein and inclusion body fractions with mini-proinsulin as an example product, and this effect was verified in a 15 L stirred tank bioreactor (STR). To our opinion this cultivation strategy is easy to apply for the screening of strain libraries under standard laboratory conditions if no complex robotic and well controlled parallel cultivation devices are available.

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