scholarly journals Functional analyses of PAU genes in Saccharomyces cerevisiae

Microbiology ◽  
2009 ◽  
Vol 155 (12) ◽  
pp. 4036-4049 ◽  
Author(s):  
Zongli Luo ◽  
Hennie J. J. van Vuuren
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Pairwise Comparison ◽  
Expression Data ◽  
Coding Regions ◽  
Response To Stress ◽  
Flanking Sequences ◽  
The Stability ◽  
The Individual ◽  
Functional Analyses ◽  
Subtelomeric Regions

PAU genes constitute the largest gene family in Saccharomyces cerevisiae, with 24 members mostly located in the subtelomeric regions of chromosomes. Little information is available about PAU genes, other than expression data for some members. In this study, we systematically compared the sequences of all 24 members, examined the expression of PAU3, PAU5, DAN2, PAU17 and PAU20 in response to stresses, and investigated the stability of all Pau proteins. The chromosomal localization, synteny and sequence analyses revealed that PAU genes could have been amplified by segmental and retroposition duplication through mechanisms of chromosomal end translocation and Ty-associated recombination. The coding sequences diverged through nucleotide substitution and insertion/deletion of one to four codons, thus causing changes in amino acids, truncation or extension of Pau proteins. Pairwise comparison of non-coding regions revealed little homology in flanking sequences of some members. All 24 PAU promoters contain a TATA box, and 22 PAU promoters contain at least one copy of the anaerobic response element and the aerobic repression motif. Differential expression was observed among PAU3, PAU5, PAU17, PAU20 and DAN2 in response to stress, with PAU5 having the highest capacity to be induced by anaerobic conditions, low temperature and wine fermentations. Furthermore, Pau proteins with 124 aa were less stable than those with 120 or 122 aa. Our results indicate that duplicated PAU genes have been evolving, and the individual Pau proteins might possess specific roles for the adaptation of S. cerevisiae to certain environmental stresses.

scholarly journals The use of simplicial analysis to adjust cognitive structure

2020 ◽  
Vol 15 (90) ◽  
pp. 119-129
Author(s):  
Valentina A. Marenko ◽  
◽  
Vyacheslav E. Lozhnikov ◽  
Keyword(s):  
Cognitive Dissonance ◽  
Simulation Experiment ◽  
Cognitive Model ◽  
Cognitive Structure ◽  
Pairwise Comparison ◽  
Detailed Structure ◽  
And Performance ◽  
The Stability ◽  
Object Of Study ◽  
The Individual

Description of a new method of researching objects in the form of a set of information tasks is the goal of the work. A simplicial analysis of the cognitive structure of the object of study is included in the method. Several stages have a method. The set of basic factors is revealed at the first stage. Pairwise comparison of factors is carried out. The formation of the cognitive model in the form of an adjacency matrix of the 1st level of the hierarchy is done. Factors for the formation of the 2nd level of the hierarchy are grouped. The combination of components in the cognitive structure of the 3rd level of the hierarchy is carried out. Detailing the components of the 3rd level of the hierarchy is presented at the 4th level. A series of simulation experiments is conducted to test the stability of the detailed structure of the cognitive model. The implicit relationship between the underlying factors are studied. The method was tested on the example of the cognitive model "lifestyle" of students. The components "living conditions", "cognitive dissonance", and "performance" are grouped at the second level of the hierarchy. A simulation experiment was conducted. The presence of pulse resonance in the detailed structure of the 4th level of the hierarchy is established. Simplicial analysis is done. The ordering of the elements its purpose is. The simulation experiment was made after simplicial analysis. The result now corresponds to the theory. The influence of cognitive dissonance of the individual on the "activity" was revealed. The "activity" factor affects cognitive dissonance, among other things. To identify significant factors, detection of hidden trends and the implementation of measures of social control, this method need.

Implications of Person Fluctuation for the Stability and Validity of Test Scores

Methodology ◽  
2006 ◽  
Vol 2 (4) ◽  
pp. 142-148 ◽  
Author(s):  
Pere J. Ferrando
Keyword(s):  
Item Response ◽  
Test Scores ◽  
Temporal Stability ◽  
Person Fit ◽  
Item Parameters ◽  
Individual Trait ◽  
The Stability ◽  
The Individual ◽  
Different Levels ◽  
Fluctuation Model

In the IRT person-fluctuation model, the individual trait levels fluctuate within a single test administration whereas the items have fixed locations. This article studies the relations between the person and item parameters of this model and two central properties of item and test scores: temporal stability and external validity. For temporal stability, formulas are derived for predicting and interpreting item response changes in a test-retest situation on the basis of the individual fluctuations. As for validity, formulas are derived for obtaining disattenuated estimates and for predicting changes in validity in groups with different levels of fluctuation. These latter formulas are related to previous research in the person-fit domain. The results obtained and the relations discussed are illustrated with an empirical example.

scholarly journals Development and Characterization of Two Types of Surface Displayed Levansucrases for Levan Biosynthesis

Catalysts ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 757
Author(s):  
Huiyi Shang ◽  
Danni Yang ◽  
Dairong Qiao ◽  
Hui Xu ◽  
Yi Cao
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Molecular Weight ◽  
Large Scale ◽  
Surface Display ◽  
Yeast Surface Display ◽  
Fusion Partner ◽  
Whole Cell ◽  
Food Industries ◽  
Yeast Surface ◽  
The Stability

Levan has wide applications in chemical, cosmetic, pharmaceutical and food industries. The free levansucrase is usually used in the biosynthesis of levan, but the poor reusability and low stability of free levansucrase have limited its large-scale use. To address this problem, the surface-displayed levansucrase in Saccharomyces cerevisiae were generated and evaluated in this study. The levansucrase from Zymomonas mobilis was displayed on the cell surface of Saccharomyces cerevisiae EBY100 using a various yeast surface display platform. The N-terminal fusion partner is based on a-agglutinin, and the C-terminal one is Flo1p. The yield of levan produced by these two whole-cell biocatalysts reaches 26 g/L and 34 g/L in 24 h, respectively. Meanwhile, the stability of the surface-displayed levansucrases is significantly enhanced. After six reuses, these two biocatalysts retained over 50% and 60% of their initial activities, respectively. Furthermore, the molecular weight and polydispersity test of the products suggested that the whole-cell biocatalyst of levansucrase displayed by Flo1p has more potentials in the production of levan with low molecular weight which is critical in certain applications. In conclusion, our method not only enable the possibility to reuse the enzyme, but also improves the stability of the enzyme.

Examining sharp restart in a Monte Carlo method for the linearized Poisson–Boltzmann equation

2020 ◽  
Vol 26 (3) ◽  
pp. 223-244
Author(s):  
W. John Thrasher ◽  
Michael Mascagni
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Algorithm ◽  
Significant Bias ◽  
Poisson Boltzmann ◽  
Electrostatic Free Energy ◽  
Poisson Boltzmann Equation ◽  
The Stability ◽  
Potential Methods ◽  
The Individual

AbstractIt has been shown that when using a Monte Carlo algorithm to estimate the electrostatic free energy of a biomolecule in a solution, individual random walks can become entrapped in the geometry. We examine a proposed solution, using a sharp restart during the Walk-on-Subdomains step, in more detail. We show that the point at which this solution introduces significant bias is related to properties intrinsic to the molecule being examined. We also examine two potential methods of generating a sharp restart point and show that they both cause no significant bias in the examined molecules and increase the stability of the run times of the individual walks.

The great Chinese surprise: the rupture with the United States is real and is happening

2020 ◽  
Vol 96 (2) ◽  
pp. 419-437
Author(s):  
Xiangfeng Yang
Keyword(s):  
United States ◽  
The United States ◽  
Donald Trump ◽  
Ample Evidence ◽  
Pendulum Swing ◽  
The Us ◽  
Methodological Problems ◽  
Trade War ◽  
The Stability ◽  
The Individual

Abstract Ample evidence exists that China was caught off guard by the Trump administration's onslaught of punishing acts—the trade war being a prime, but far from the only, example. This article, in addition to contextualizing their earlier optimism about the relations with the United States under President Trump, examines why Chinese leaders and analysts were surprised by the turn of events. It argues that three main factors contributed to the lapse of judgment. First, Chinese officials and analysts grossly misunderstood Donald Trump the individual. By overemphasizing his pragmatism while downplaying his unpredictability, they ended up underprepared for the policies he unleashed. Second, some ingrained Chinese beliefs, manifested in the analogies of the pendulum swing and the ‘bickering couple’, as well as the narrative of the ‘ballast’, lulled officials and scholars into undue optimism about the stability of the broader relationship. Third, analytical and methodological problems as well as political considerations prevented them from fully grasping the strategic shift against China in the US.

scholarly journals Temporal Stability and Biodiversity of Two Complex Antilisterial Cheese-Ripening Microbial Consortia

2003 ◽  
Vol 69 (7) ◽  
pp. 4012-4018 ◽  
Author(s):  
Ariel Maoz ◽  
Ralf Mayr ◽  
Siegfried Scherer
Keyword(s):  
Species Composition ◽  
Bacterial Species ◽  
Temporal Stability ◽  
Individual Characteristics ◽  
Microbial Consortia ◽  
Cheese Ripening ◽  
Safe Food ◽  
The Stability ◽  
The Individual ◽  
First Time

ABSTRACT The temporal stability and diversity of bacterial species composition as well as the antilisterial potential of two different, complex, and undefined microbial consortia from red-smear soft cheeses were investigated. Samples were collected twice, at 6-month intervals, from each of two food producers, and a total of 400 bacterial isolates were identified by Fourier-transform infrared spectroscopy and 16S ribosomal DNA sequence analysis. Coryneform bacteria represented the majority of the isolates, with certain species being predominant. In addition, Marinolactobacillus psychrotolerans, Halomonas venusta, Halomonas variabilis, Halomonas sp. (106 to 107 CFU per g of smear), and an unknown, gram-positive bacterium (107 to 108 CFU per g of smear) are described for the first time in such a consortium. The species composition of one consortium was quite stable over 6 months, but the other consortium revealed less diversity of coryneform species as well as less stability. While the first consortium had a stable, extraordinarily high antilisterial potential in situ, the antilisterial activity of the second consortium was lower and decreased with time. The cause for the antilisterial activity of the two consortia remained unknown but is not due to the secretion of soluble, inhibitory substances by the individual components of the consortium. Our data indicate that the stability over time and a potential antilisterial activity are individual characteristics of the ripening consortia which can be monitored and used for safe food production without artificial preservatives.

DESIGN OF ADAPTIVE FUZZY SLIDING MODE CONTROL FOR NONLINEAR SYSTEMS

1999 ◽  
Vol 07 (05) ◽  
pp. 463-474 ◽  
Author(s):  
JEN-YANG CHEN
Keyword(s):  
Sliding Mode ◽  
Membership Functions ◽  
System Specification ◽  
Pendulum System ◽  
Control Rules ◽  
Inverted Pendulum System ◽  
Equivalent Control ◽  
Fuzzy Sliding Mode ◽  
The Stability ◽  
The Individual

In this paper, a fuzzy sliding mode controller (FSMC), which is synthesized by a collection of linguistic control rules whose membership functions of THEN-part is adapted, is proposed. Both the membership functions of IF-part and THEN-part are arranged symmetrically and distributed equally in the individual universe of discourse. In particular, the membership functions of the THEN-part can be adapted via one parameter adaptation to meet the required system specification. The proposed direct adaptive FSMC can be synthesized through the following stages. First, the control rules are constructed according to the concepts of SMC, and the fuzzy sets whose membership functions are symmetrically covered in state space. Then, the derived adaptive law is used to adjust the membership functions of the THEN-part. The FSMC is employed to approximate the equivalent control of SMC without knowing the mathematical model of the controlled system. Third, a hitting control is developed to guarantee the stability of the control system. Finally, we apply this FSMC to control a nonlinear inverted pendulum system for confirming the validity of the proposed approach.

Two separate regions of the extrachromosomal ribosomal deoxyribonucleic acid of Tetrahymena thermophila enable autonomous replication of plasmids in Saccharomyces cerevisiae

1981 ◽  
Vol 1 (6) ◽  
pp. 535-543
Author(s):  
G B Kiss ◽  
A A Amin ◽  
R E Pearlman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
High Frequency ◽  
Deoxyribonucleic Acid ◽  
Tetrahymena Thermophila ◽  
The Other ◽  
Yeast Cells ◽  
Origin Of Replication ◽  
Autonomous Replication ◽  
Coding Regions ◽  
Dna Fragment

Plasmids containing the nontranscribed central and terminal, but not the coding, regions of the extrachromosomal ribosomal deoxyribonucleic acid (rDNA) of Tetrahymena thermophila are capable of autonomous replication in Saccharomyces cerevisiae. These plasmids transform S. cerevisiae at high frequency; transformants are unstable in the absence of selection, and plasmids identical to those used for transformation were isolated from the transformed yeast cells. One plasmid contains a 1.85-kilobase Tetrahymena DNA fragment which includes the origin of bidirectional replication of the extrachromosomal rDNA. The other region of Tetrahymena rDNA allowing autonomous replication of plasmids in S. cerevisiae is a 650-base pair, adenine plus thymine-rich segment from the rDNA terminus. Neither of these Tetrahymena fragments shares obvious sequence homology with the origin of replication of the S. cerevisiae 2-microns circle plasmid or with ars1, an S. cerevisiae chromosomal replicator.

Isolation and transcriptional characterization of three genes which function at start, the controlling event of the Saccharomyces cerevisiae cell division cycle: CDC36, CDC37, and CDC39

1983 ◽  
Vol 3 (5) ◽  
pp. 881-891
Author(s):  
H J Breter ◽  
J Ferguson ◽  
T A Peterson ◽  
S I Reed
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Division ◽  
Dna Sequences ◽  
Shuttle Vector ◽  
Control Process ◽  
Haploid Cell ◽  
Loop Analysis ◽  
Mrna Species ◽  
Coding Regions ◽  
Plasmid Library

The genes CDC36, CDC37, and CDC39, thought to function in the cell division control process in Saccharomyces cerevisiae, were isolated from a recombinant plasmid library prepared by partial digestion of S. cerevisiae genomic DNA with Sau3A and insertion into the S. cerevisiae-Escherichia coli shuttle vector YRp7. In each case, S. cerevisiae DNA sequences were identified which could complement mutant alleles of the gene in question and which could direct integration of a plasmid at the chromosomal location known to correspond to that gene. Complementing DNA segments were subcloned to remove extraneous coding regions. The coding regions corresponding to CDC36, CDC37, and CDC39 were then identified and localized by R-loop analysis. The estimated sizes of the three coding regions were 615, 1,400, and 2,700 base pairs, respectively. Transcriptional orientation of the coding regions was established by using M13 vectors to prepare strand-specific probes followed by hybridization to blots of electrophoresed S. cerevisiae mRNA. The intracellular steady-state abundance of the mRNA species corresponding to the genes was estimated by comparing hybridization signals on RNA blots to that of a previously determined standard, the cell cycle start gene CDC28. The quantities calculated for the three mRNA species were low, ranging from 1.5 +/- 1 copies per haploid cell for the CDC36 mRNA to 3.1 +/- 1.5 and 4.6 +/- 2 copies per haploid cell for the CDC37 and CDC39 mRNAs, respectively. The CDC28 mRNA had been previously estimated at 7.0 +/- 2 copies per cell.

scholarly journals Levitation of non-magnetizable droplet inside ferrofluid

2018 ◽  
Vol 857 ◽  
pp. 398-448 ◽  
Author(s):  
Chamkor Singh ◽  
Arup K. Das ◽  
Prasanta K. Das
Keyword(s):  
Magnetic Field ◽  
Steady State ◽  
Viscosity Ratio ◽  
Temporal Dynamics ◽  
Liquid Droplet ◽  
Droplet Surface ◽  
Two Dimensions ◽  
Projection Algorithm ◽  
The Stability ◽  
The Individual

The central theme of this work is that a stable levitation of a denser non-magnetizable liquid droplet, against gravity, inside a relatively lighter ferrofluid – a system barely considered in ferrohydrodynamics – is possible, and exhibits unique interfacial features; the stability of the levitation trajectory, however, is subject to an appropriate magnetic field modulation. We explore the shapes and the temporal dynamics of a plane non-magnetizable droplet levitating inside a ferrofluid against gravity due to a spatially complex, but systematically generated, magnetic field in two dimensions. The coupled set of Maxwell’s magnetostatic equations and the flow dynamic equations is integrated computationally, utilizing a conservative finite-volume-based second-order pressure projection algorithm combined with the front-tracking algorithm for the advection of the interface of the droplet. The dynamics of the droplet is studied under both the constant ferrofluid magnetic permeability assumption as well as for more realistic field-dependent permeability described by Langevin’s nonlinear magnetization model. Due to the non-homogeneous nature of the magnetic field, unique shapes of the droplet during its levitation, and at its steady state, are realized. The complete spatio-temporal response of the droplet is a function of the Laplace number $La$ , the magnetic Laplace number $La_{m}$ and the Galilei number $Ga$ ; through detailed simulations we separate out the individual roles played by these non-dimensional parameters. The effect of the viscosity ratio, the stability of the levitation path and the possibility of existence of multiple stable equilibrium states is investigated. We find, for certain conditions on the viscosity ratio, that there can be developments of cusps and singularities at the droplet surface; we also observe this phenomenon experimentally and compare with the simulations. Our simulations closely replicate the singular projection on the surface of the levitating droplet. Finally, we present a dynamical model for the vertical trajectory of the droplet. This model reveals a condition for the onset of levitation and the relation for the equilibrium levitation height. The linearization of the model around the steady state captures that the nature of the equilibrium point goes under a transition from being a spiral to a node depending upon the control parameters, which essentially means that the temporal route to the equilibrium can be either monotonic or undulating. The analytical model for the droplet trajectory is in close agreement with the detailed simulations.

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