25 Yeast Genetic Strain and Plasmid Collections

Author(s):  
Karl-Dieter Entian ◽  
Peter Kötter
Keyword(s):  
Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1569-1579 ◽  
Author(s):  
Michael L Rolfsmeier ◽  
Michael J Dixon ◽  
Luis Pessoa-Brandão ◽  
Richard Pelletier ◽  
Juan José Miret ◽  
...  

Abstract Trinucleotide repeat (TNR) instability in humans is governed by unique cis-elements. One element is a threshold, or minimal repeat length, conferring frequent mutations. Since thresholds have not been directly demonstrated in model systems, their molecular nature remains uncertain. Another element is sequence specificity. Unstable TNR sequences are almost always CNG, whose hairpin-forming ability is thought to promote instability by inhibiting DNA repair. To understand these cis-elements further, TNR expansions and contractions were monitored by yeast genetic assays. A threshold of ∼15–17 repeats was observed for CTG expansions and contractions, indicating that thresholds function in organisms besides humans. Mutants lacking the flap endonuclease Rad27p showed little change in the expansion threshold, suggesting that this element is not altered by the presence or absence of flap processing. CNG or GNC sequences yielded frequent mutations, whereas A-T rich sequences were substantially more stable. This sequence analysis further supports a hairpin-mediated mechanism of TNR instability. Expansions and contractions occurred at comparable rates for CTG tract lengths between 15 and 25 repeats, indicating that expansions can comprise a significant fraction of mutations in yeast. These results indicate that several unique cis-elements of human TNR instability are functional in yeast.


2021 ◽  
pp. 101033
Author(s):  
Bo Zhang ◽  
Xue Zhang ◽  
M. Wes Schilling ◽  
Xiaofei Li ◽  
George T. Tabler ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joseph H. Collins ◽  
Kevin W. Keating ◽  
Trent R. Jones ◽  
Shravani Balaji ◽  
Celeste B. Marsan ◽  
...  

AbstractYeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow—it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.


Genetics ◽  
1987 ◽  
Vol 115 (2) ◽  
pp. 247-253
Author(s):  
Lenore Neigeborn ◽  
Marian Carlson

ABSTRACT We have selected 210 mutants able to grow on sucrose in the presence of 2-deoxyglucose. We identified recessive mutations in three major complementation groups that cause constitutive (glucose-insensitive) secreted invertase synthesis. Two groups comprise alleles of the previously identified HXK2 and REG1 genes, and the third group was designated cid1 (constitutive invertase derepression). The effect of cid1 on SUC2 expression is mediated by the SUC2 upstream regulatory region, as judged by the constitutive expression of a SUC2-LEU2-lacZ fusion in which the LEU2 promoter is under control of SUC2 upstream sequences. A cid1 mutation also causes glucose-insensitive expression of maltase. The previously isolated constitutive mutation ssn6 is epistatic to cid1, reg1 and hxk2 for very high level constitutive invertase expression. Mutations in SNF genes that prevent derepression of invertase are epistatic to cid1, reg1 and hxk2; we have previously shown that ssn6 has different epistasis relationships with snf mutations. The constitutive mutation tup1 was found to resemble ssn6 in its genetic interactions with snf mutations. These findings suggest that CID1, REG1 and HXK2 are functionally distinct from SSN6 and TUP1.


Author(s):  
FS Montagna ◽  
G Garcia ◽  
IA Nääs ◽  
NDS Lima ◽  
FR Caldara
Keyword(s):  

2019 ◽  
Vol 3 (2) ◽  
Author(s):  
M. E. Von Staden ◽  
M. D. Byron ◽  
T. R. Jarvis ◽  
X. Zhang ◽  
C. A. Crist ◽  
...  

ObjectivesThe woody breast (WB) myopathy has caused economic losses in excess of $200 million annually to the poultry industry due to undesirable textural attributes and decreased functionality. This hardened muscle is also associated with other undesirable traits, such as white striping. This research was conducted to evaluate the impact of WB severity and genetic strain on consumer acceptability and sensory attributes of baked and fried broiler breast meat and elucidate the consumer acceptability of tumble-marinated, fajita meat made from broilers with normal (NOR), moderate (MOD) and severe (SEV) WB meat.Materials and MethodsFor descriptive analysis (n = 7 panelists, 10 panels) on baked and fried chicken, 3 × 5 factorial arrangements within randomized complete block designs with four replications were utilized to evaluate three severities of woody breast and the five different genetic strains that are most commonly used in the poultry industry. When significant differences (P < 0.05) occurred among treatments, Duncan’s multiple range test was utilized to separate treatment means. For consumer acceptability of baked chicken (n = 123 panelists), fried chicken (n = 125 panelists), and fajita meat (n = 127 panelists), randomized complete block designs with two replications were used to determine the impact of strain and severity on acceptability.ResultsFor baked chicken, SEV breasts were chewier, juicier, crunchier, and more cohesive (P < 0.05) than NOR and MOD breast samples. For fried chicken, SEV breasts were less tender and chewier (P < 0.05) than NOR breasts. In addition, SEV breasts were more cohesive and juicier, but less mushy (P < 0.05) than NOR and MOD breasts. For fried chicken samples, SEV breasts were crunchier (P < 0.05) than MOD breasts, which were crunchier (P < 0.05) than NOR breasts. The texture and overall acceptability of NOR baked breasts and fajita meat were preferred by consumers (P < 0.05) over SEV breasts. In contrast, the SEV breasts were preferred (P < 0.05) over the NOR breast meat for the fried chicken formulation. No differences existed (P > 0.05) in acceptability among genetic strains in baked or fried chicken breasts. The baked chicken consumer panelists were divided into 7 distinct clusters based on their sensory evaluation ratings. Cluster analysis indicated that 49% of panelists preferred NOR breast fillets, 21% preferred SEV, and 30% had no preference between NOR and WB (MOD, SEV) samples. The fried chicken consumer panelists were divided into 5 clusters, of which 65% preferred WB (MOD, SEV) over NOR, 29% preferred strain B over strain A, and 11% preferred strain A over strain B. The fajita chicken meat consumer panelists were divided into 5 clusters, of which 75% of panelists liked NOR breast samples, 72% liked MOD samples, and 45% liked SEV samples.ConclusionResults indicated that WB severity had a greater impact on sensory attributes and consumer acceptability than genetic strain. Higher WB severity created an undesirable texture that negatively impacted the acceptability of baked meat. However, the increased crunchiness and cohesiveness due to woodiness had a positive impact on the fried chicken acceptability. Results indicated that a large percentage of consumers rated baked, fried, and fajita samples as acceptable regardless of whether NOR or WB (MOD, SEV) meat was used, but some consumers did not like baked or fajita meat that was made from SEV WB meat.


2020 ◽  
Author(s):  
Marianyela Petrizzelli ◽  
Dominique de Vienne ◽  
Thibault Nidelet ◽  
Camille Noûs ◽  
Christine Dillmann

The relationship between different levels of integration is a key feature for understanding the genotype-phenotype map.Here, we describe a novel method of integrated data analysis that incorporates protein abundance data into constraint-based modeling to elucidate the biological mechanisms underlying phenotypic variation. Specifically, we studied yeast genetic diversity at three levels of phenotypic complexity in a population of yeast obtained by pairwise crosses of eleven strains belonging to two species, Saccha-romyces cerevisiae and S. uvarum. The data included protein abundances, integrated traits (life-history/fermentation) and computational estimates of metabolic fluxes.Results highlighted that the negative correlation between production traits such as population carrying capacity (K) and traits associated with growth and fermentation rates (Jmax) is explained by a differential usage of energy production pathways: a high K was associated with high TCA fluxes, while a high Jmax was associated with high glycolytic fluxes. Enrichment analysis of protein sets confirmed our results.This powerful approach allowed us to identify the molecular and metabolic bases of integrated trait variation, and therefore has a broad applicability domain.


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