scholarly journals Experimental estimation of proteome size for cells and human plasma

2015 ◽  
Vol 61 (2) ◽  
pp. 279-285 ◽  
Author(s):  
S.N. Naryzhny ◽  
V.G. Zgoda ◽  
M.A. Maynskova ◽  
N.L. Ronzhina ◽  
N.V. Belyakova ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Human Plasma ◽  
Single Molecule ◽  
Human Cell ◽  
Theoretical Point ◽  
Yeast Saccharomyces Cerevisiae ◽  
Single Molecule Level ◽  
E Coli ◽  
Cell Hepg2 ◽  
Insufficient Sensitivity

Huge range of concentrations of different protein and insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. In our investigations, we tried to evaluate the size of different proteomes (cells and plasma). The approach used is based on detection of protein spots in 2-DE after staining by protein dyes with different sensitivities. The function representing the dependence of the number of protein spots on sensitivity of protein dyes was generated. Next, by extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) it was calculated that a single human cell (HepG2) may contain minimum 70000 proteoforms, and plasma – 1.5 mln. Utilization of this approach to other, smaller proteomes showed the competency of this extrapolation. For instance, the size of mycoplasma (Acholeplasma laidlawii) was estimated in 1100 proteoforms, yeast (Saccharomyces cerevisiae) - 40000, E. coli – 6200, P. furiosus – 3400. In hepatocytes, the amount of proteoforms was the same as in HepG2 – 70000. Significance of obtained data is in possibilities to estimating the proteome organization and planning next steps in its study.

scholarly journals Real-Time 3D Imaging at the Single Molecule Level of Signal Transduction in Saccharomyces CerevisiÆ Responding to Environmental Changes

2016 ◽  
Vol 110 (3) ◽  
pp. 145a
Author(s):  
Erik G. Hedlund ◽  
Sviatlana Shashkova ◽  
Adam J.M. Wollman ◽  
Stefan Hohmann ◽  
Mark C. Leake
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signal Transduction ◽  
Real Time ◽  
Single Molecule ◽  
3D Imaging ◽  
Environmental Changes ◽  
Single Molecule Level

scholarly journals An Electron Microscopic Study of the Effect of (Saccharomyces cerevisiae) on the Ability of E. coli 0157:H7 to Attach and Efface Healthy Young Broilers

2019 ◽  
pp. 1-15
Author(s):  
M. S. Shathele Abdullah ◽  
Sharif M. Hassan ◽  
A. A. Alaqil
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Pathogenic Bacteria ◽  
Control Diet ◽  
Inhibitory Effect ◽  
Positive Control ◽  
Bacterial Attachment ◽  
Productive Performance ◽  
Electron Microscopic ◽  
Yeast Saccharomyces Cerevisiae ◽  
E Coli

The present study was carried out to determine the influence of dietary probiotic source feed (fungal-yeast; Saccharomyces cerevisiae) on the ability of E. coli 0157:H7 to attach and efface healthy young broilers at different feeding periods (7, 10, 14, 21, and 28 days of age). There were reductions in bacterial attachment of broilers fed various yeast levels. Twenty one days post-challenging about 87% of the (G1); positive control, chicks fed control diet containing 0.00% baker yeast and challenged with E. coli 0157:H7, showed both cecal attachment and effacement. On the other hand  37% of the (G2); chicks fed control diet containing 0.75% baker yeast and challenged with E. coli 0157:H7, showed cecal attachment. And only 16% of the (G3); chicks fed control diet containing 1.00% baker yeast and challenged with E. coli 0157:H7  showed cecal attachment. The results of this study suggest adding yeast at 1.0% into broilers diets causing a significant (P<0.005) decrease in bacterial attachment and may enhance the productive performance and nutrients utilization via the inhibitory effect of yeast against pathogenic bacteria E. coli 0157:H7.

scholarly journals Bayesian inference and comparison of stochastic transcription elongation models

2018 ◽  
Author(s):  
Jordan Douglas ◽  
Richard Kingston ◽  
Alexei J. Drummond
Keyword(s):  
Bayesian Inference ◽  
Markov Process ◽  
Single Molecule ◽  
Continuous Time ◽  
Transcription Elongation ◽  
Rna Polymerases ◽  
Partial Equilibrium ◽  
Single Molecule Level ◽  
Bayesian Techniques ◽  
E Coli

AbstractTranscription elongation can be modelled as a three step process, involving polymerase translocation, NTP binding, and nucleotide incorporation into the nascent mRNA. This cycle of events can be simulated at the single-molecule level as a continuous-time Markov process using parameters derived from single-molecule experiments. Previously developed models differ in the way they are parameterised, and in their incorporation of partial equilibrium approximations.We have formulated a hierarchical network comprised of 12 sequence-dependent transcription elongation models. The simplest model has two parameters and assumes that both translocation and NTP binding can be modelled as equilibrium processes. The most complex model has six parameters makes no partial equilibrium assumptions. We systematically compared the ability of these models to explain published force-velocity data, using approximate Bayesian computation. This analysis was performed using data for the RNA polymerase complexes ofE. coli, S. cerevisiaeand Bacteriophage T7.Our analysis indicates that the polymerases differ significantly in their translocation rates, with the rates in T7 pol being fast compared toE. coliRNAP andS. cerevisiaepol II. Different models are applicable in different cases. We also show that all three RNA polymerases have an energetic preference for the posttranslocated state over the pretranslocated state. A Bayesian inference and model selection framework, like the one presented in this publication, should be routinely applicable to the interrogation of single-molecule datasets.Author summaryTranscription is a critical biological process which occurs in all living organisms. It involves copying the organism’s genetic material into messenger RNA (mRNA) which directs protein synthesis on the ribosome. Transcription is performed by RNA polymerases which have been extensively studied using both ensemble and single-molecule techniques (see reviews: [1, 2]). Single-molecule data provides unique insights into the molecular behaviour of RNA polymerases. Transcription at the single-molecule level can be computationally simulated as a continuous-time Markov process and the model outputs compared with experimental data. In this study we use Bayesian techniques to perform a systematic comparison of 12 stochastic models of transcriptional elongation. We demonstrate how equilibrium approximations can strengthen or weaken the model, and show how Bayesian techniques can identify necessary or unnecessary model parameters. We describe a framework to a) simulate, b) perform inference on, and c) compare models of transcription elongation.

Teaching nutritional biochemistry: an experimental approach using yeast

2012 ◽  
Vol 36 (4) ◽  
pp. 313-318
Author(s):  
Manuel Alonso ◽  
Carlos A. Stella
Keyword(s):  
High School ◽  
Saccharomyces Cerevisiae ◽  
Human Cell ◽  
College Freshmen ◽  
Experimental Approach ◽  
System Model ◽  
Science Students ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cell Nutrition ◽  
Approach To Teaching

In this report, we present a practical approach to teaching several topics in nutrition to science students at the high school and college freshmen levels. This approach uses baker's yeast ( Saccharomyces cerevisiae ) as a biological system model. The diameters of yeast colonies, which vary according to the nutrients present in the medium, can be observed, compared, and used to teach metabolic requirements. The experiments described in this report show simple macroscopic evidence of submicroscopic nutritional events. This can serve as a useful base for an analogy of heterotrophic human cell nutrition.

scholarly journals Effect of the use of Yarrowia lipolytica and Saccharomyces cerevisiae yeast with a probiotic in the diet of turkeys on their gut microbiota and immunity

2020 ◽  
Vol 65 (No. 4) ◽  
pp. 174-182
Author(s):  
A Czech ◽  
I Sembratowicz ◽  
G Zieba
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gut Microbiota ◽  
Beneficial Effect ◽  
Yarrowia Lipolytica ◽  
Control Group ◽  
Yeast Saccharomyces Cerevisiae ◽  
E Coli ◽  
Combined Use ◽  
Number Of Microorganisms ◽  
Fodder Yeast

An experiment was carried out to determine whether the yeast species Yarrowia lipolytica added to compound feeds for turkeys would have a more beneficial effect on their immunity and gut microflora composition than the commonly used species Saccharomyces cerevisiae. An additional aim of the study was to test whether the addition of a probiotic (Bacillus licheniformis and Bacillus subtilis) to the feed containing Yarrowia lipolytica or Saccharomyces cerevisiae yeast would enhance their effect. The experiment was carried out on growing turkey hens aged 7 to 112 days and randomly divided into six groups (each n = 80). The birds in the control group (C) and group P were fed standard feeds, but group P additionally received a probiotic. Groups Y and YP received the feed containing the Yarrowia lipolytica fodder yeast, and the probiotic for the YP group. Similarly, in groups S and SP, the turkeys received the feed with the Saccharomyces cerevisiae fodder yeast, and the probiotic was additionally added to the feed for the SP group. Yarrowia lipolytica yeast can be an alternative to the commonly used yeast Saccharomyces cerevisiae in turkey feeds. Yarrowia lipolytica favourably influenced the intestinal microbiota (reduced the number of microorganisms – P &lt; 0.001, fungi – P &lt; 0.001, and coliforms – P &lt; 0.001, including E. coli), and stimulated erythropoiesis (increased Hb content – P = 0.049 and RBC count – P = 0.027; increased Ht – P &lt; 0.001) and immune mechanisms (increased the %pc – P = 0.021, NBT value – P = 0.013 and lysozyme content – P = 0.013; decreased IgM concentration – P = 0.049). The combined use of a probiotic with yeast, particularly Yarrowia lipolytica, has a more beneficial effect on the gut microbiota than the use of Yarrowia lipolytica alone. The combined use of a probiotic with a yeast, particularly Yarrowia lipolytica, has a more beneficial effect on the gut microbiota than the use of Yarrowia lipolytica alone.

scholarly journals Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome

2017 ◽  
Vol 114 (40) ◽  
pp. 10630-10635 ◽  
Author(s):  
Jacob S. Lewis ◽  
Lisanne M. Spenkelink ◽  
Grant D. Schauer ◽  
Flynn R. Hill ◽  
Roxanna E. Georgescu ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Single Molecule ◽  
Average Rate ◽  
Clamp Loader ◽  
Minichromosome Maintenance ◽  
Single Molecule Level ◽  
Fork Protection Complex ◽  
Important Player ◽  
Leading Strand

The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ε DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1–Tof1–Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication.

PREPARASI DEINOCOCCUS RADIODURANS DAN KHAMIR DALAM MATERIAL KECAP L-DRYING SEBAGAI BAHAN UJI PROFISIENSI

2016 ◽  
Vol 13 (1) ◽  
pp. 93
Author(s):  
Titin Yulinery ◽  
Ratih M.Dewi
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Deinococcus Radiodurans ◽  
Test Preparation ◽  
Quality Parameters ◽  
Soy Sauce ◽  
Yeast Saccharomyces Cerevisiae ◽  
Microbiological Test ◽  
Bacterial Contaminants ◽  
Minimum Number ◽  
Important Quality

Tes kemampuan adalah salah satu kegiatan penting dalam pengendalian mutu dan jaminan kualitas mikrobiologi laboratorium untuk mengukur kompetensi analis dan analisis uji profisiensi membutuhkan persiapan Model mikroorganisme adalah kualitas standar dan validitas. Mikrobiologi uji kualitas produk kedelai utama diarahkan pada kehadiran Saccharomyces cerevisiae ragi (S. cerevisiae), S. Bailli, S. rouxii dankontaminan bakteri seperti Bacillus dan Deinococcus. Jenis ragi dan bakteri yang terlibat dalam proses dan dapat menjadi salah satu parameter kualitas penting dalam persiapan yang dihasilkan. Jumlah dan viabilitas bakteri dan ragi menjadi parameter utama dalam proses persiapan bahan uji. Jumlah tersebut adalah jumlah minimum yang berlaku dapat dianalisis. Jumlah ini harus dibawah 10 CFU diperlukan untuk menunjukkan tingkat hygienitas proses dan tingkat minimal kontaminasi. Viabilitas bakteri dan bahan tes ragi persiapan untuk tes kemahiran kecap yang diawetkan dengan L-pengeringan adalah teknik Deinococcus radiodurans (D. radiodurans) 16 tahun, 58 tahun S. cerevisiae, dan S. roxii 13 tahun. kata kunci: Viabilitas, Deinococcus, khamir, L-pengeringan, Proficiency AbstractProficiency test is one of the important activities in quality control and quality assurance microbiology laboratory for measuring the competence of analysts and analysis Proficiency test requires a model microorganism preparations are standardized quality and validity. Microbiological test of the quality of the main soy products aimed at thepresence of yeast Saccharomyces cerevisiae (S. cerevisiae), S. bailli, S. rouxii and bacterial contaminants such as Bacillus and Deinococcus. Types of yeasts and bacteria involved in the process and can be one of the important quality parameters in the preparation produced. The number and viability of bacteria and yeasts become themain parameters in the process of test preparation materials. The amount in question is the minimum number that is valid can be analyzed. This amount must be below 10 CFU required to indicate the level of hygienitas process and the minimum level of contamination. Viability of bacteria and yeast test preparation materials for proficiencytest of soy sauce that preserved by L-drying technique is Deinococcus radiodurans ( D. radiodurans ) 16 years, 58 years S. cerevisiae, and S. roxii 13 years. key words : Viability, Deinococcus, Khamir, L-drying, Proficiency

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