scholarly journals BIoInfoRmatIonal analySIS of YersiniapseudotuberculosisIP32953 CRISPR/CaSSyStem

2016 ◽  
Vol 1 (5) ◽  
pp. 64-67 ◽  
Author(s):  
Степаненко ◽  
Liliya Stepanenko ◽  
Парамонов ◽  
Aleksey Paramonov ◽  
Колбасеева ◽  
...  
Keyword(s):  
Yersinia Pseudotuberculosis ◽  
Search Algorithm ◽  
System Structure ◽  
Online Tool ◽  
Close Proximity ◽  
Search Tool ◽  
Cas Genes ◽  
Modelling Methods ◽  
Salmonella Phage ◽  
Blastn Search

The results of this study include Yersinia pseudotuberculosis CRISPR/Cas system structure analysis. CRISPR/Cas system is a specific adaptive protection against heterogeneous genetic elements. The object of research was the complete genome of Y. pseudotuberculosis IP32953 (NC_006155). CRISPR/Cas system screening was performed by program modelling methods MacSyFinder ver. 1.0.2. CRISPR loci screening and analyzing were carried out by program package: CRISPR Recognition tool (CRT), CRISPI: a CRISPR Interactive database, CRISPRFinder, and PilerCR. Spacer sequences were used in order to find protospacers in ACLAME, GenBank-Phage and RefSeq-Plasmid databases by BLASTn search algorithm. Protospacer sequences could be found in genomes of phages, plasmids and bacteria. In last case complete genomes of bacteria were analyzed by online-tool PHAST: PHAge Search Tool. Y. pseudotuberculosis IP329353 has CRISPR/Cas system that consists of one sequence of cas-genes and three loci. These loci are far away from each other. Locus YP1 is situated in close proximity to cas-genes. Protospacers were found in genomes of Y. pseudotuberculosis PB1/+, Y. intermedia Y228, Y. similis str. 228, Salmonella phage, Enterobacteria phage, Y. pseudotuberculosis IP32953 plasmid pYV and plasmid of Y. pseudotuberculosis IP31758. Thus, the combination of four program methods allows finding CRISPR/Cas system more precisely. Spacer sequences could be used for protospacer screening.

scholarly journals T4-like Bacteriophages Isolated from Pig Stools Infect Yersinia pseudotuberculosis and Yersinia pestis Using LPS and OmpF as Receptors

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 296
Author(s):  
Mabruka Salem ◽  
Maria I. Pajunen ◽  
Jin Woo Jun ◽  
Mikael Skurnik
Keyword(s):  
Yersinia Pseudotuberculosis ◽  
Host Recognition ◽  
Tail Fiber ◽  
Long Tail ◽  
Phage T4 ◽  
One Step ◽  
In Trans ◽  
Step Growth ◽  
Resistant Strains ◽  
Salmonella Phage

The Yersinia bacteriophages fPS-2, fPS-65, and fPS-90, isolated from pig stools, have long contractile tails and elongated heads, and they belong to genus Tequatroviruses in the order Caudovirales. The phages exhibited relatively wide host ranges among Yersinia pseudotuberculosis and related species. One-step growth curve experiments revealed that the phages have latent periods of 50–80 min with burst sizes of 44–65 virions per infected cell. The phage genomes consist of circularly permuted dsDNA of 169,060, 167,058, and 167,132 bp in size, respectively, with a G + C content 35.3%. The number of predicted genes range from 267 to 271. The phage genomes are 84–92% identical to each other and ca 85% identical to phage T4. The phage receptors were identified by whole genome sequencing of spontaneous phage-resistant mutants. The phage-resistant strains had mutations in the ompF, galU, hldD, or hldE genes. OmpF is a porin, and the other genes encode lipopolysaccharide (LPS) biosynthetic enzymes. The ompF, galU, and hldE mutants were successfully complemented in trans with respective wild-type genes. The host recognition was assigned to long tail fiber tip protein Gp38, analogous to that of T-even phages such as Salmonella phage S16, specifically to the distal β-helices connecting loops.

scholarly journals COMPARATIVE ANALYSIS OF CRISPR-CAS SYSTEM STRUCTURES OF YERSINIA PSEUDOTUBERCULOSIS IP32953 AND IP31758

2018 ◽  
Vol 3 (5) ◽  
pp. 54-59
Author(s):  
N. P. Peretolchina ◽  
A. Y. Borisenko ◽  
Yu. P. Dzhioev ◽  
V. I. Zlobin
Keyword(s):  
Public Health ◽  
Yersinia Pseudotuberculosis ◽  
Medical Science ◽  
Protein Structures ◽  
Far East ◽  
Database Search ◽  
Online Tools ◽  
Complete Genomes ◽  
Nucleotide Database ◽  
Cas Genes

Background. Pseudotuberculosis is still relevant problem in medical science and public health of Russia and other countries. Typing of Y. рseudotuberculosis strains by their CRISPR systems is a perspective tool for monitoring of Yersinia populations as was shown in Y. pestis.Aims. Here we describe and compare CRISPR-Cas systems of Yersinia pseudotuberculosis strains IP32953 and IP31758 causing classic pseudotuberculosis and Far-East scarlet-like fever (FESLF) respectively.Materials and methods. Complete genomes of Y. pseudotuberculosis IP329353 and IP31758 (NC_006155 and NC_009708 respectively) were obtained from NCBI Nucleotide Database. Search; identification; and analysis of CRISPR systems were carried out by online-tools CRISPROne; CRISPRDetect; and CRISPRTarget.Results and discussion. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953 by the combination of program methods. CRISPR-Cas system of this strain consist of array YP1 located near cas-genes; arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific marks of analyzed strains.Conclusions. We suggest that acquisition of certain spacers may play a role in evolution and divergence of Y. pseudotuberculosis strains.

scholarly journals In silico comparative analysis of crispr-cas system structures of Yersinia pseudotuberculosis causing different clinical manifestations of pseudotuberculosis

2019 ◽  
Vol 11 (2) ◽  
pp. 80-87
Author(s):  
N. P. Peretolchina ◽  
Yu. P. Dzhioev ◽  
A. Yu. Borisenko ◽  
L. A. Stepanenko ◽  
E. A. Voskresenskaya ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Yersinia Pseudotuberculosis ◽  
Protein Structures ◽  
Clinical Manifestations ◽  
Systemic Infection ◽  
Complete Genomes ◽  
Nucleotide Database ◽  
Cas Genes ◽  
Species Variability ◽  
Cas Proteins

The aim of this research was to analyze and compare CRIPSR loci and cas-proteins of Yersinia pseudotuberculosis strains isolated in different territories from patients with various clinical manifestations of pseudotuberculosis.Materials and Methods. Complete genomes of Y. pseudotuberculosis IP329353 (NC_006155) and IP31758 (NC_009708) were obtained from NCBI Nucleotide Database. Strains were isolated from patients with gastroenteritis and systemic infection respectively. Search, identification, and analysis of CRISPR systems were carried out by onlinetools CRISPROne, CRISPRDetect, and CRISPRTarget.Results. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953: array YP1 located near cas-genes, arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers.Conclusion. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific molecular marks of analyzed strains during the study of intra-species variability and evolution of Y. pseudotuberculosis.

scholarly journals Unraveling neutrophil–Yersinia interactions during tissue infection

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1046 ◽  
Author(s):  
Joan Mecsas
Keyword(s):  
Yersinia Pseudotuberculosis ◽  
Signal Transduction Pathway ◽  
Effector Proteins ◽  
Tissue Infection ◽  
Host Cells ◽  
Serum Factors ◽  
Bacterial Adhesins ◽  
Animal Pathogens ◽  
Close Proximity ◽  
Type 3

The human and animal pathogens Yersinia pestis, which causes bubonic and pneumonic plague, and Yersinia pseudotuberculosis and Yersinia enterocolitica, which cause gastroenteritis, share a type 3 secretion system which injects effector proteins, Yops, into host cells. This system is critical for virulence of all three pathogens in tissue infection. Neutrophils are rapidly recruited to infected sites and all three pathogens frequently interact with and inject Yops into these cells during tissue infection. Host receptors, serum factors, and bacterial adhesins appear to collaborate to promote neutrophil–Yersinia interactions in tissues. The ability of neutrophils to control infection is mixed depending on the stage of infection and points to the efficiency of Yops and other bacterial factors to mitigate bactericidal effects of neutrophils. Yersinia in close proximity to neutrophils has higher levels of expression from yop promoters, and neutrophils in close proximity to Yersinia express higher levels of pro-survival genes than migrating neutrophils. In infected tissues, YopM increases neutrophil survival and YopH targets a SKAP2/SLP-76 signal transduction pathway. Yet the full impact of these and other Yops and other Yersinia factors on neutrophils in infected tissues has yet to be understood.

Vibration Fault Diagnosis for Hydroelectric Generating Units Based on the Modified Cuckoo Search Algorithm and Evidence Theory

2019 ◽  
Vol 13 (3) ◽  
pp. 281-288
Author(s):  
Jiatang Cheng ◽  
Li Ai ◽  
Yan Xiong
Keyword(s):  
Neural Network ◽  
Fault Diagnosis ◽  
Bp Neural Network ◽  
Search Algorithm ◽  
Evidence Theory ◽  
Cuckoo Search ◽  
Cuckoo Search Algorithm ◽  
System Structure ◽  
Hybrid Scheme ◽  
Independent Evidence

Background: In view of the complex system structure and uncertain factors in the fault diagnosis of hydroelectric generating units (HGU), it is a difficult problem to design the diagnosis method rationally. Objective: An attempt is made to employ multi-source feature information to improve the accuracy of fault diagnosis, and the effectiveness of the proposed scheme is verified by using a diagnostic example. Methods: Through the research on recent papers and patents related to fault diagnosis of the HGU, a hybrid scheme based on the modified cuckoo search algorithm, back-propagation (BP) neural network and evidence theory are proposed. For this modified version named cuckoo search with fitness information (CSF), the step factor is adaptively tuned using the fitness value. Next, three diagnostic models based on BP neural network trained by CSF are used for primary diagnosis. These diagnostic results are then used as the independent evidence, and the fusion decision is made by using evidence theory. Results: Experimental results show that CSF algorithm is better than the original cuckoo search (CS) and its three variants, and the hybrid method has the highest diagnostic accuracy. Conclusion: The proposed hybrid scheme has strong robustness and fault tolerance, and can effectively classify the vibration faults of hydroelectric generating units

Efficient RNA structure comparison algorithms

2017 ◽  
Vol 15 (06) ◽  
pp. 1740009 ◽  
Author(s):  
Abdullah N. Arslan ◽  
Jithendar Anandan ◽  
Eric Fry ◽  
Keith Monschke ◽  
Nitin Ganneboina ◽  
...  
Keyword(s):  
Rna Structure ◽  
Search Algorithm ◽  
Suffix Array ◽  
Rna Structures ◽  
Structure Comparison ◽  
Structure Representation ◽  
Substructure Search ◽  
Common Substructure ◽  
Search Tool ◽  
Comparison Algorithms

Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonoverlapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan ). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.

The Adaptive Stochastic Resonance Signal Detection System Based on the Multi-Point Random Search Algorithm

2013 ◽  
Vol 339 ◽  
pp. 409-415
Author(s):  
Shui Lin Tu ◽  
Zheng Yang Wu ◽  
Zhen Yi Wu
Keyword(s):  
Signal Detection ◽  
Stochastic Resonance ◽  
Search Algorithm ◽  
Detection System ◽  
Signal To Noise Ratio ◽  
Random Search ◽  
System Structure ◽  
Bistable System ◽  
Weak Signal ◽  
Random Search Algorithm

A model of adaptive stochastic resonance system based on the multi-point random search algorithm is proposed, and a weak signal detection system of adaptive stochastic resonance is established on the LabVIEW development platform. In this detection system, the typical nonlinear bistable system is used as the core of signal processing, and the system output signal-to-noise ratio is chosen as the optimizing objective function. The system structure parameters can be adjusted adaptively by using the multi-point random search algorithm, on which the optimal state of stochastic resonance of the system can be remained and the frequency of the weak signal can be obtained. Influences of the system parameters and the Gaussian noise on the stochastic resonance can be detected by this system. Experimental results show that this detection system is efficient, and has potential applications.

Effects of Vincristine on Endothelial Microtubules in the Spinal Cord

1976 ◽  
Vol 34 ◽  
pp. 58-59
Author(s):  
John L. Beggs ◽  
John D. Waggener ◽  
Wanda Miller
Keyword(s):  
Spinal Cord ◽  
Biological Activity ◽  
Horseradish Peroxidase ◽  
Transport Mechanism ◽  
Vasogenic Edema ◽  
Vesicular Transport ◽  
Close Proximity

Microtubules (MT) are versatile organelles participating in a wide variety of biological activity. MT involvement in the movement and transport of cytoplasmic components has been well documented. In the course of our study on trauma-induced vasogenic edema in the spinal cord we have concluded that endothelial vesicles contribute to the edema process. Using horseradish peroxidase as a vascular tracer, labeled endothelial vesicles were present in all situations expected if a vesicular transport mechanism was in operation. Frequently,labeled vesicles coalesced to form channels that appeared to traverse the endothelium. The presence of MT in close proximity to labeled vesicles sugg ested that MT may play a role in vesicular activity.

Experiments with a scanning tunneling microscope (STM) mounted in a scanning electron microscope (SEM)

1986 ◽  
Vol 44 ◽  
pp. 636-639
Author(s):  
Oliver C. Wells ◽  
Mark E. Welland
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Mechanical Stability ◽  
Tunneling Current ◽  
Feedback System ◽  
Scanning Tunneling ◽  
Surface Profiling ◽  
Close Proximity ◽  
Metal Tip ◽  
Scanning Electron

Scanning tunneling microscopes (STM) exist in two versions. In both of these, a pointed metal tip is scanned in close proximity to the specimen surface by means of three piezos. The distance of the tip from the sample is controlled by a feedback system to give a constant tunneling current between the tip and the sample. In the low-end STM, the system has a mechanical stability and a noise level to give a vertical resolution of between 0.1 nm and 1.0 nm. The atomic resolution STM can show individual atoms on the surface of the specimen.A low-end STM has been put into the specimen chamber of a scanning electron microscope (SEM). The first objective was to investigate technological problems such as surface profiling. The second objective was for exploratory studies. This second objective has already been achieved by showing that the STM can be used to study trapping sites in SiO2.

Ultrastructure and Senescence in an Achloroplastic Mutant of Hordeum vulgare L. cv. Dyan

1992 ◽  
Vol 50 (1) ◽  
pp. 844-845
Author(s):  
R.H.M. Cross ◽  
C.E.J. Botha ◽  
A.K. Cowan ◽  
B.J. Hartley
Keyword(s):  
Cell Wall ◽  
Hordeum Vulgare ◽  
Leaf Tissue ◽  
Ultrastructural Changes ◽  
Hordeum Vulgare L ◽  
Mesophyll Cells ◽  
Lethal Mutant ◽  
Cytoplasmic Matrix ◽  
Close Proximity ◽  
Pinocytotic Vesicles

Senescence is an ordered degenerative process leading to death of individual cells, organs and organisms. The detection of a conditional lethal mutant (achloroplastic) of Hordeum vulgare has enabled us to investigate ultrastructural changes occurring in leaf tissue during foliar senescence.Examination of the tonoplast structure in six and 14 day-old mutant tissue revealed a progressive degeneration and disappearance of the membrane, apparently starting by day six in the vicinity of the mitochondria associated with the degenerating proplastid (Fig. 1.) where neither of the plastid membrane leaflets is evident (arrows, Fig. 1.). At this stage there was evidence that the mitochondrial membranes were undergoing retrogressive changes, coupled with disorganization of cristae (Fig. 2.). Proplastids (P) lack definitive prolamellar bodies. The cytoplasmic matrix is largely agranular, with few endoplasmic reticulum (ER) cisternae or polyribosomal aggregates. Interestingly, large numbers of actively-budding dictysomes, associated with pinocytotic vesicles, were observed in close proximity to the plasmalemma of mesophyll cells (Fig. 3.). By day 14 however, mesophyll cells showed almost complete breakdown of subcellular organelle structure (Fig. 4.), and further evidence for the breakdown of the tonoplast. The final stage of senescence is characterized by the solubilization of the cell wall due to expression and activity of polygalacturonase and/or cellulose. The presence of dictyosomes with associated pinocytotic vesicles formed from the mature face, in close proximity to both the plasmalemma and the cell wall, would appear to support the model proposed by Christopherson for the secretion of cellulase. This pathway of synthesis is typical for secretory glycoproteins.

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