scholarly journals Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes

2020 ◽  
Author(s):  
Frédéric Bigey ◽  
Diego Segond ◽  
Anne Friedrich ◽  
Stephane Guezenec ◽  
Aurélie Bourgais ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Copy Number ◽  
Population Divergence ◽  
Bread Making ◽  
Number Of Genes ◽  
Maltose Utilization ◽  
Selection For ◽  
Bakery Yeast ◽  
High Level ◽  
First Time

SummaryDespite bread being one of the most historically and culturally important fermented products, its history and influence on the evolution of associated microbial species remains largely unknown. The first evidence of leavened bread dates to the second millenium BCE in Egypt and since, the art of bread-making developed and spread worldwide. Nowadays, leavened bread is made either by using a pure commercial culture of the yeast Saccharomyces cerevisiae or by propagating a sourdough, which is a mix of flour and water spontaneously fermented by yeast and bacteria. We studied the domestication of S. cerevisiae populations originating from industry and sourdough and tested whether these different bread-making processes led to population divergence. We found that the origin of S. cerevisiae bakery strains is polyphyletic with 67 % of strains clustering in two main clades: most commercial strains were tetraploid and clustered with strains having diverse origins, including beer. By contrast, most sourdough strains were diploids and found in a second clade of strains having mosaic genomes and diverse origins including fruits, or clinical and wild environments. When compared to the others, sourdough strains harboured in average a higher copy number of genes involved in maltose utilization, a common sugar produced from dough starch. Overall, a high level of gene flow from multiple contributors was detected. Phenotyping of bakery and non bakery strains further showed that sourdough and industrial bakery populations have undergone human selection for rapidly starting fermentations and for high CO2 production. Interestingly, sourdough strains also showed a better adaptation to a sourdough mimicking environment, suggesting that natural selection occurred as well. In summary, our results revealed that the domestication of bakery yeast populations has been accompanied by dispersion, hybridization and divergent selection through industrial and artisanal bakery processes. In addition, they unveiled for the first time a case of fungus domestication where species divergence occurred through autotetraploidisation.

High-copy-number integration into the ribosomal DNA of Saccharomyces cerevisiae: a new vector for high-level expression

Gene ◽  
1989 ◽  
Vol 79 (2) ◽  
pp. 199-206 ◽  
Author(s):  
Teresa S. Lopes ◽  
Jacobus Klootwijk ◽  
Annemarie E. Veenstra ◽  
Paul C. van der Aar ◽  
Harm van Heerikhuizen ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Dna ◽  
Copy Number ◽  
High Copy Number ◽  
High Level Expression ◽  
High Level

scholarly journals Recombinant Saccharomyces cerevisiae Expressing P450 in Artificial Digestive Systems: a Model for Biodetoxication in the Human Digestive Environment

2003 ◽  
Vol 69 (5) ◽  
pp. 2884-2892 ◽  
Author(s):  
S. Blanquet ◽  
J. P. Meunier ◽  
M. Minekus ◽  
S. Marol-Bonnin ◽  
M. Alric
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Survival Rate ◽  
Gastrointestinal Tract ◽  
Genetically Engineered ◽  
Hydroxylase Activity ◽  
Important Challenge ◽  
Innovative System ◽  
Small Intestinal ◽  
High Level ◽  
First Time

ABSTRACT The use of genetically engineered microorganisms such as bacteria or yeasts as live vehicles to carry out bioconversion directly in the digestive environment is an important challenge for the development of innovative biodrugs. A system that mimics the human gastrointestinal tract was combined with a computer simulation to evaluate the survival rate and cinnamate 4-hydroxylase activity of a recombinant model of Saccharomyces cerevisiae expressing the plant P450 73A1. The yeasts showed a high level of resistance to gastric and small intestinal secretions (survival rate after 4 h of digestion, 95.6% ± 10.1% [n = 4]) but were more sensitive to the colonic conditions (survival rate after 4 h of incubation, 35.9% ± 2.7% [n = 3]). For the first time, the ability of recombinant S. cerevisiae to carry out a bioconversion reaction has been demonstrated throughout the gastrointestinal tract. In the gastric-small intestinal system, 41.0% ± 5.8% (n = 3) of the ingested trans-cinnamic acid was converted into p-coumaric acid after 4 h of digestion, as well as 8.9% ± 1.6% (n = 3) in the stomach, 13.8% ± 3.3% (n = 3) in the duodenum, 11.8% ± 3.4% (n = 3) in the jejunum, and 6.5% ± 1.0% (n = 3) in the ileum. In the large intestinal system, cinnamate 4-hydroxylase activity was detected but was too weak to be quantified. These results suggest that S. cerevisiae may afford a useful host for the development of biodrugs and may provide an innovative system for the prevention or treatment of diseases that escape classical drug action. In particular, yeasts may provide a suitable vector for biodetoxication in the digestive environment.

Training Decay Selection for Usability Validation

2016 ◽  
Vol 5 (1) ◽  
pp. 76-83
Author(s):  
Shannon E. Clark
Keyword(s):  
Medical Device ◽  
Medical Devices ◽  
Validation Studies ◽  
Future Research ◽  
Medical Device Manufacturers ◽  
Selection For ◽  
The Moment ◽  
High Level ◽  
First Time ◽  
Validation Testing

When conducting usability validation testing, representative users must use the device in the expected conditions of use in the field. There is usually a period of time—days or weeks—between the point in time a user is trained, and the moment they use the device for the first time. For this reason, the FDA acknowledges the need for “training decay” as part of usability validation testing, but manufacturers face challenges simulating real-time decays. In response to challenges associated with lags of days or weeks between training and usability validation testing, medical device manufacturers typically simulate shortened training decay periods. This paper discusses the theory behind the shapes of various training decay curves and the variables that drive differences between training decay curves. The author proposes to use a task-based approach for defining training decay curves in usability validation studies and sets out generalized training decay curves at a high level. Future research could reveal detailed and generalizable training decay curves. Identifying generalizable training decay curves could standardize the usability testing required for medical devices, and ultimately improve use error identification while avoiding an undue toll on manufacturer resources.

High-level secretion of correctly processed β-lactamase from Saccharomyces cerevisiae using a high-copy-number secretion vector

Gene ◽  
1994 ◽  
Vol 142 (1) ◽  
pp. 113-117 ◽  
Author(s):  
L.A. Castelli ◽  
C.J. Mardon ◽  
P.M. Strike ◽  
A.A. Azad ◽  
I.G. Macreadie
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Copy Number ◽  
High Copy Number ◽  
Secretion Vector ◽  
High Level

A Confrontation between Two Doctrines: The Birth of Struggle for Hegemony in Hebrew Children's Literature during the 1930s and 1940s

2008 ◽  
Vol 1 (2) ◽  
pp. 139-155 ◽  
Author(s):  
YAEL DARR
Keyword(s):  
Children's Literature ◽  
Educational System ◽  
Single Channel ◽  
Children’S Literature ◽  
The Political ◽  
Literary Creation ◽  
History Of ◽  
High Level ◽  
First Time ◽  
Literary Quality

This article describes a crucial and fundamental stage in the transformation of Hebrew children's literature, during the late 1930s and 1940s, from a single channel of expression to a multi-layered polyphony of models and voices. It claims that for the first time in the history of Hebrew children's literature there took place a doctrinal confrontation between two groups of taste-makers. The article outlines the pedagogical and ideological designs of traditionalist Zionist educators, and suggests how these were challenged by a group of prominent writers of adult poetry, members of the Modernist movement. These writers, it is argued, advocated autonomous literary creation, and insisted on a high level of literary quality. Their intervention not only dramatically changed the repertoire of Hebrew children's literature, but also the rules of literary discourse. The article suggests that, through the Modernists’ polemical efforts, Hebrew children's literature was able to free itself from its position as an apparatus controlled by the political-educational system and to become a dynamic and multi-layered field.

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

scholarly journals Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1341-1351 ◽  
Author(s):  
I King Jordan ◽  
John F McDonald
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Negative Selection ◽  
Sequence Variation ◽  
Size Variation ◽  
Sequence Comparisons ◽  
Ty Elements ◽  
Ty Element ◽  
Amino Acid Sequence Variation ◽  
Element Evolution ◽  
High Level

Abstract The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.

scholarly journals Transcriptome Analysis Reveals a Promotion of Carotenoid Production by Copper Ions in Recombinant Saccharomyces cerevisiae

2021 ◽  
Vol 9 (2) ◽  
pp. 233
Author(s):  
Buli Su ◽  
Anzhang Li ◽  
Ming-Rong Deng ◽  
Honghui Zhu
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptome Analysis ◽  
Gene Expression Analysis ◽  
Target Genes ◽  
Copper Ions ◽  
Carotenoid Production ◽  
Carotenoid Accumulation ◽  
Nutritional Components ◽  
Differential Gene ◽  
First Time

We previously constructed a Saccharomyces cerevisiae carotenoid producer BL03-D-4 which produced much more carotenoid in YPM (modified YPD) media than YPD media. In this study, the impacts of nutritional components on carotenoid accumulation of BL03-D-4 were investigated. When using YPM media, the carotenoid yield was increased 10-fold compared to using the YPD media. To elucidate the hidden mechanism, a transcriptome analysis was performed and showed that 464 genes changed significantly in YPM media. Furthermore, inspired by the differential gene expression analysis which indicated that ADY2, HES1, and CUP1 showed the most remarkable changes, we found that the improvement of carotenoid accumulation in YPM media was mainly due to the copper ions, since supplementation of 0.08 mM CuSO4 in YPD media could increase carotenoid yield 9.2-fold. Reverse engineering of target genes was performed and carotenoid yield could be increased 6.4-fold in YPD media through overexpression of ACE1. The present study revealed for the first time the prominent promotion of carotenoid yield by copper ions in engineered S. cerevisiae and provided a new target ACE1 for genetic engineering of S. cerevisiae for the bioproduction of carotenoids.

scholarly journals Aberrant Expression of TLR2, TLR7, TLR9, Splicing Variants of TLR4 and MYD88 in Chronic Lymphocytic Leukemia Patients

2021 ◽  
Vol 10 (4) ◽  
pp. 867
Author(s):  
Katarzyna Skorka ◽  
Paulina Wlasiuk ◽  
Agnieszka Karczmarczyk ◽  
Krzysztof Giannopoulos
Keyword(s):  
Bone Marrow ◽  
Chronic Lymphocytic Leukemia ◽  
Cytotoxic T Cells ◽  
Lymphocytic Leukemia ◽  
Aberrant Expression ◽  
Downstream Signaling ◽  
Splicing Variants ◽  
High Level ◽  
Time To First Treatment ◽  
First Time

Functional toll-like receptors (TLRs) could modulate anti-tumor effects by activating inflammatory cytokines and the cytotoxic T-cells response. However, excessive TLR expression could promote tumor progression, since TLR-induced inflammation might stimulate cancer cells expansion into the microenvironment. Myd88 is involved in activation NF-κB through TLRs downstream signaling, hence in the current study we provided, for the first time, a complex characterization of expression of TLR2, TLR4, TLR7, TLR9, and MYD88 as well as their splicing forms in two distinct compartments of the microenvironment of chronic lymphocytic leukemia (CLL): peripheral blood and bone marrow. We found correlations between MYD88 and TLRs expressions in both compartments, indicating their relevant cooperation in CLL. The MYD88 expression was higher in CLL patients compared to healthy volunteers (HVs) (0.1780 vs. 0.128, p < 0.0001). The TLRs expression was aberrant in CLL compared to HVs. Analysis of survival curves revealed a shorter time to first treatment in the group of patients with low level of TLR4(3) expression compared to high level of TLR4(3) expression in bone marrow (13 months vs. 48 months, p = 0.0207). We suggest that TLRs expression is differentially regulated in CLL but is similarly shared between two distinct compartments of the microenvironment.

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