The subtype I-F CRISPR–Cas system influences pathogenicity island retention in Pectobacterium atrosepticum via crRNA generation and Csy complex formation

2013 ◽  
Vol 41 (6) ◽  
pp. 1468-1474 ◽  
Author(s):  
Corinna Richter ◽  
Peter C. Fineran
Keyword(s):  
Complex Formation ◽  
Large Scale ◽  
Protein Complexes ◽  
Acquired Resistance ◽  
Mobile Genetic Elements ◽  
Bacterial Evolution ◽  
Pectobacterium Atrosepticum ◽  
Crispr System ◽  
Wide Range ◽  
Associated Proteins

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and Cas (CRISPR-associated) proteins confer acquired resistance against mobile genetic elements in a wide range of bacteria and archaea. The phytopathogen Pectobacterium atrosepticum SCRI1043 encodes a single subtype I-F CRISPR system, which is composed of three CRISPR arrays and the cas operon encoding Cas1, Cas3 (a Cas2–Cas3 fusion), Csy1, Csy2, Csy3 and Cas6f (Csy4). The CRISPR arrays are transcribed into pre-crRNA (CRISPR RNA) and then processed by Cas6f to generate crRNAs. Furthermore, the formation of Cas protein complexes has been implicated in both the interference and acquisition stages of defence. In the present paper, we discuss the development of tightly controlled ‘programmable’ CRISPR arrays as tools to investigate CRISPR–Cas function and the effects of chromosomal targeting. Finally, we address how chromosomal targeting by CRISPR–Cas can cause large-scale genome deletions, which can ultimately influence bacterial evolution and pathogenicity.

scholarly journals Classification of protein–protein association rates based on biophysical informatics

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kalyani Dhusia ◽  
Yinghao Wu
Keyword(s):  
Large Scale ◽  
Cross Validation ◽  
Protein Complexes ◽  
Dynamic Properties ◽  
Conformational Dynamics ◽  
Classification Model ◽  
Coarse Grained ◽  
Modeling Framework ◽  
Validation Data ◽  
Wide Range

Abstract Background Proteins form various complexes to carry out their versatile functions in cells. The dynamic properties of protein complex formation are mainly characterized by the association rates which measures how fast these complexes can be formed. It was experimentally observed that the association rates span an extremely wide range with over ten orders of magnitudes. Identification of association rates within this spectrum for specific protein complexes is therefore essential for us to understand their functional roles. Results To tackle this problem, we integrate physics-based coarse-grained simulations into a neural-network-based classification model to estimate the range of association rates for protein complexes in a large-scale benchmark set. The cross-validation results show that, when an optimal threshold was selected, we can reach the best performance with specificity, precision, sensitivity and overall accuracy all higher than 70%. The quality of our cross-validation data has also been testified by further statistical analysis. Additionally, given an independent testing set, we can successfully predict the group of association rates for eight protein complexes out of ten. Finally, the analysis of failed cases suggests the future implementation of conformational dynamics into simulation can further improve model. Conclusions In summary, this study demonstrated that a new modeling framework that combines biophysical simulations with bioinformatics approaches is able to identify protein–protein interactions with low association rates from those with higher association rates. This method thereby can serve as a useful addition to a collection of existing experimental approaches that measure biomolecular recognition.

scholarly journals Evolution of the D. melanogaster chromatin landscape and its associated proteins

2018 ◽  
Author(s):  
Elise Parey ◽  
Anton Crombach
Keyword(s):  
Protein Complexes ◽  
Replication Timing ◽  
Fruit Fly ◽  
Biochemical Properties ◽  
Polycomb Group ◽  
A Genome ◽  
Wide Range ◽  
Associated Proteins ◽  
Binary Division ◽  
Inference Methods

AbstractIn the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit fly D. melanogaster chromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the emergence of the different chromatin types. Our results indicate that the two euchromatic types, YELLOW and RED, were one single activating type that split early in eukaryotic history. Next, we provide evidence that GREEN-associated proteins are involved in a centromere drive and expanded in a lineage-specific way in D. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.

scholarly journals PWWP INTERACTOR OF POLYCOMBS (PWO1) links PcG-mediated gene repression to the nuclear lamina inArabidopsis

2017 ◽  
Author(s):  
Pawel Mikulski ◽  
Mareike L. Hohenstatt ◽  
Sara Farrona ◽  
Cezary Smaczniak ◽  
Kerstin Kaufmann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Target Genes ◽  
Protein Complexes ◽  
Nuclear Lamina ◽  
Polycomb Group ◽  
Gene Repression ◽  
Polycomb Repressive Complex 2 ◽  
Peripheral Protein ◽  
Wide Range ◽  
Associated Proteins

AbstractPolycomb group (PcG) proteins facilitate chromatin-mediated gene repression through the modification of histone tails in a wide range of eukaryotes, including plants and animals. One of the PcG protein complexes, Polycomb Repressive Complex 2 (PRC2), promotes repressive chromatin formation via tri-methylation of lysine-27 on histone H3 (H3K27me3). The animal PRC2 is implicated in impacting subnuclear distribution of chromatin as its complex components and H3K27me3 are functionally connected with the nuclear lamina (NL) - a peripheral protein mesh that resides underneath the inner nuclear membrane (INM) and consists of lamins and lamina-associated proteins. In contrast to animals, NL in plants has an atypical structure and its association with PRC2-mediated gene repression is largely unknown. Here, we present a connection between lamin-like protein, CROWDED NUCLEI 1 (CRWN1), and a novel PRC2-associated component, PWWP INTERACTOR OF POLYCOMBS 1 (PWO1), inArabidopsis thaliana. We show that PWO1 and CRWN1 proteins associate physically with each other, act in the same pathway to maintain nuclear morphology and control expression of similar set of target genes. Moreover, we demonstrate that PWO1 proteins form speckle-like foci located partially at the subnuclear periphery inNicotiana benthamianaandArabidopsis thaliana. Ultimately, as CRWN1 and PWO1 are plant-specific, our results argue that plants developed an equivalent, rather than homologous, mechanism of linking PRC2-mediated chromatin repression and nuclear lamina.

Electron microscopy study of reactively sputter-deposited Ti/N films on silicon

1992 ◽  
Vol 50 (2) ◽  
pp. 1362-1363
Author(s):  
V. C. Kannan ◽  
A. K. Singh ◽  
R. B. Irwin ◽  
S. Chittipeddi ◽  
F. D. Nkansah ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Large Scale ◽  
Hexagonal Phase ◽  
Microscopy Study ◽  
Electron Microscopy Study ◽  
Process Conditions ◽  
Tin Films ◽  
Wide Range ◽  
Fcc Phase ◽  
Circuits Vlsi

Titanium nitride (TiN) films have historically been used as diffusion barrier between silicon and aluminum, as an adhesion layer for tungsten deposition and as an interconnect material etc. Recently, the role of TiN films as contact barriers in very large scale silicon integrated circuits (VLSI) has been extensively studied. TiN films have resistivities on the order of 20μ Ω-cm which is much lower than that of titanium (nearly 66μ Ω-cm). Deposited TiN films show resistivities which vary from 20 to 100μ Ω-cm depending upon the type of deposition and process conditions. TiNx is known to have a NaCl type crystal structure for a wide range of compositions. Change in color from metallic luster to gold reflects the stabilization of the TiNx (FCC) phase over the close packed Ti(N) hexagonal phase. It was found that TiN (1:1) ideal composition with the FCC (NaCl-type) structure gives the best electrical property.

Chaperonin as the normal controls and pathological anti-stress response in the human reproductive system

2016 ◽  
pp. 126-129
Author(s):  
M. Makarenko ◽  
◽  
D. Hovsyeyev ◽  
L. Sydoryk ◽  
◽  
...  
Keyword(s):  
Reproductive System ◽  
Stress Proteins ◽  
Physiological Stress ◽  
Protein Complexes ◽  
Reproductive Function ◽  
Intercellular Signaling ◽  
Toll Like Receptors ◽  
Wide Range ◽  
Protein Functions ◽  
And Function

Different kinds of physiological stress cause mass changes in the cells, including the changes in the structure and function of the protein complexes and in separate molecules. The protein functions is determined by its folding (the spatial conclusion), which depends on the functioning of proteins of thermal shock- molecular chaperons (HSPs) or depends on the stress proteins, that are high-conservative; specialized proteins that are responsible for the correct proteinaceous folding. The family of the molecular chaperones/ chaperonins/ Hsp60 has a special place due to the its unique properties of activating the signaling cascades through the system of Toll-like receptors; it also stimulates the cells to produce anti- inflammatory cytokines, defensins, molecules of cell adhesion and the molecules of MHC; it functions as the intercellular signaling molecule. The pathological role of Hsp60 is established in a wide range of illnesses, from diabetes to atherosclerosis, where Hsp60 takes part in the regulation of both apoptosis and the autoimmune processes. The presence of the HSPs was found in different tissues that are related to the reproductive system. Key words: molecular chaperons (HSPs), Toll-like receptors, reproductive function, natural auto antibody.

THE SOME QUESTIONS OF AUTONOMOUS MOTION AND MANAGEMENT OF LAND-MOBILE ROBOTIC COMPLEXES FOR UKRAINIAN GROUND FORCESE

2019 ◽  
pp. 53-58
Author(s):  
О. Кravchuk ◽  
V. Symonenkov ◽  
I. Symonenkova ◽  
O. Hryhorev
Keyword(s):  
Large Scale ◽  
Armed Forces ◽  
Distributed Information ◽  
Wide Range ◽  
Highly Effective ◽  
Information Management Systems ◽  
Robotic Devices ◽  
Principles And Standards ◽  
And Control ◽  
The Eu

Today, more than forty countries of the world are engaged in the development of military-purpose robots. A number of unique mobile robots with a wide range of capabilities are already being used by combat and intelligence units of the Armed forces of the developed world countries to conduct battlefield intelligence and support tactical groups. At present, the issue of using the latest information technology in the field of military robotics is thoroughly investigated, and the creation of highly effective information management systems in the land-mobile robotic complexes has acquired a new phase associated with the use of distributed information and sensory systems and consists in the transition from application of separate sensors and devices to the construction of modular information subsystems, which provide the availability of various data sources and complex methods of information processing. The purpose of the article is to investigate the ways to increase the autonomy of the land-mobile robotic complexes using in a non-deterministic conditions of modern combat. Relevance of researches is connected with the necessity of creation of highly effective information and control systems in the perspective robotic means for the needs of Land Forces of Ukraine. The development of the Armed Forces of Ukraine management system based on the criteria adopted by the EU and NATO member states is one of the main directions of increasing the effectiveness of the use of forces (forces), which involves achieving the principles and standards necessary for Ukraine to become a member of the EU and NATO. The inherent features of achieving these criteria will be the transition to a reduction of tasks of the combined-arms units and the large-scale use of high-precision weapons and land remote-controlled robotic devices. According to the views of the leading specialists in the field of robotics, the automation of information subsystems and components of the land-mobile robotic complexes can increase safety, reliability, error-tolerance and the effectiveness of the use of robotic means by standardizing the necessary actions with minimal human intervention, that is, a significant increase in the autonomy of the land-mobile robotic complexes for the needs of Land Forces of Ukraine.

Stirring and aeration system for the upgrading of small waste water treatment plants

1994 ◽  
Vol 29 (12) ◽  
pp. 149-156 ◽  
Author(s):  
Marcus Höfken ◽  
Katharina Zähringer ◽  
Franz Bischof
Keyword(s):  
Waste Water ◽  
Water Treatment ◽  
Large Scale ◽  
Waste Water Treatment ◽  
Water Treatment Plants ◽  
Waste Water Treatment Plants ◽  
Basic Fluid ◽  
Aeration System ◽  
Technical Realization ◽  
Wide Range

A novel agitating system has been developed which allows for individual or combined operation of stirring and aeration processes. Basic fluid mechanical considerations led to the innovative hyperboloid design of the stirrer body, which ensures high efficiencies in the stirring and the aeration mode, gentle circulation with low shear forces, excellent controllability, and a wide range of applications. This paper presents the basic considerations which led to the operating principle, the technical realization of the system and experimental results in a large-scale plant. The characteristics of the system and the differences to other stirring and aeration systems are illustrated. Details of the technical realization are shown, which conform to the specific demands of applications in the biological treatment of waste water. Special regard is given to applications in the upgrading of small compact waste water treatment plants.

Thin structure of heterogeneous and multiphase fluid flows

2012 ◽  
Vol 9 (1) ◽  
pp. 175-180
Author(s):  
Yu.D. Chashechkin
Keyword(s):  
Large Scale ◽  
Fundamental System ◽  
Fluid Flows ◽  
Regular Solutions ◽  
Flow Models ◽  
Group Methods ◽  
Wide Range ◽  
Thin Structure ◽  
Multiphase Fluid ◽  
Complete Solutions

According to the results of visualization of streams, the existence of structures in a wide range of scales is noted: from galactic to micron. The use of a fundamental system of equations is substantiated based on the results of comparing symmetries of various flow models with the usage of theoretical group methods. Complete solutions of the system are found by the methods of the singular perturbations theory with a condition of compatibility, which determines the characteristic equation. A comparison of complete solutions with experimental data shows that regular solutions characterize large-scale components of the flow, a rich family of singular solutions describes formation of the thin media structure. Examples of calculations and observations of stratified, rotating and multiphase media are given. The requirements for the technique of an adequate experiment are discussed.

Integrative Data Analysis from a Unifying Research Synthesis Perspective

2018 ◽  
Author(s):  
Eun-Young Mun ◽  
Anne E. Ray
Keyword(s):  
Data Analysis ◽  
Large Scale ◽  
Research Synthesis ◽  
Alcohol Intervention ◽  
Data Set ◽  
Integrative Data Analysis ◽  
Level Data ◽  
Model Complex ◽  
Wide Range ◽  
Individual Participant

Integrative data analysis (IDA) is a promising new approach in psychological research and has been well received in the field of alcohol research. This chapter provides a larger unifying research synthesis framework for IDA. Major advantages of IDA of individual participant-level data include better and more flexible ways to examine subgroups, model complex relationships, deal with methodological and clinical heterogeneity, and examine infrequently occurring behaviors. However, between-study heterogeneity in measures, designs, and samples and systematic study-level missing data are significant barriers to IDA and, more broadly, to large-scale research synthesis. Based on the authors’ experience working on the Project INTEGRATE data set, which combined individual participant-level data from 24 independent college brief alcohol intervention studies, it is also recognized that IDA investigations require a wide range of expertise and considerable resources and that some minimum standards for reporting IDA studies may be needed to improve transparency and quality of evidence.

Quantum Optomechanics and Nanomechanics

2020 ◽  
Keyword(s):  
Gravitational Wave ◽  
Summer School ◽  
Large Scale ◽  
Quantum Noise ◽  
Foundations Of Quantum Mechanics ◽  
Wide Range ◽  
Measurement Laser ◽  
Quantum Limits ◽  
Quantum Optomechanics ◽  
Quantum Ground State

The Les Houches Summer School 2015 covered the emerging fields of cavity optomechanics and quantum nanomechanics. Optomechanics is flourishing and its concepts and techniques are now applied to a wide range of topics. Modern quantum optomechanics was born in the late 70s in the framework of gravitational wave interferometry, initially focusing on the quantum limits of displacement measurements. Carlton Caves, Vladimir Braginsky, and others realized that the sensitivity of the anticipated large-scale gravitational-wave interferometers (GWI) was fundamentally limited by the quantum fluctuations of the measurement laser beam. After tremendous experimental progress, the sensitivity of the upcoming next generation of GWI will effectively be limited by quantum noise. In this way, quantum-optomechanical effects will directly affect the operation of what is arguably the world’s most impressive precision experiment. However, optomechanics has also gained a life of its own with a focus on the quantum aspects of moving mirrors. Laser light can be used to cool mechanical resonators well below the temperature of their environment. After proof-of-principle demonstrations of this cooling in 2006, a number of systems were used as the field gradually merged with its condensed matter cousin (nanomechanical systems) to try to reach the mechanical quantum ground state, eventually demonstrated in 2010 by pure cryogenic techniques and a year later by a combination of cryogenic and radiation-pressure cooling. The book covers all aspects—historical, theoretical, experimental—of the field, with its applications to quantum measurement, foundations of quantum mechanics and quantum information. Essential reading for any researcher in the field.

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