scholarly journals Classification of CRISPR/Cas system and its application in tomato breeding

2022 ◽  
Author(s):  
Abira Chaudhuri ◽  
Koushik Halder ◽  
Asis Datta
Keyword(s):  
Protein Composition ◽  
Base Editing ◽  
Detailed Classification ◽  
Target Dna ◽  
Class 1 ◽  
Mechanisms Of Adaptation ◽  
Tomato Breeding ◽  
Primary Focus ◽  
Target Rna

AbstractRemarkable diversity in the domain of genome loci architecture, structure of effector complex, array of protein composition, mechanisms of adaptation along with difference in pre-crRNA processing and interference have led to a vast scope of detailed classification in bacterial and archaeal CRISPR/Cas systems, their intrinsic weapon of adaptive immunity. Two classes: Class 1 and Class 2, several types and subtypes have been identified so far. While the evolution of the effector complexes of Class 2 is assigned solely to mobile genetic elements, the origin of Class 1 effector molecules is still in a haze. Majority of the types target DNA except type VI, which have been found to target RNA exclusively. Cas9, the single effector protein, has been the primary focus of CRISPR-mediated genome editing revolution and is an integral part of Class 2 (type II) system. The present review focuses on the different CRISPR types in depth and the application of CRISPR/Cas9 for epigenome modification, targeted base editing and improving traits such as abiotic and biotic stress tolerance, yield and nutritional aspects of tomato breeding.

scholarly journals Precise adenine base editors that exhibit minimized cytosine catalysis

2020 ◽  
Author(s):  
You Kyeong Jeong ◽  
SeokHoon Lee ◽  
Gue-Ho Hwang ◽  
Sung-Ah Hong ◽  
Se-eun Park ◽  
...  
Keyword(s):  
Synergistic Effect ◽  
Adenosine Deaminase ◽  
Rna Editing ◽  
The Other ◽  
Cytosine Deamination ◽  
Base Editing ◽  
Target Dna ◽  
Editing Activity ◽  
Target Rna ◽  
Adenine Base

Abstract Adenine base editors (ABEs) promise specific A-to-G conversions at genomic sites of interest. However, ABEs also induce cytosine deamination at the target DNA site and exhibit transcriptome-wide off-target RNA editing. To alleviate the ABE-mediated cytosine editing activity, here we engineered the commonly-used version of adenosine deaminase, TadA7.10, to contain rationally designed mutations. We ultimately found that ABE7.10 with a D108Q mutation in TadA7.10 exhibited greatly reduced cytosine deamination activity, and conversely, ABE7.10 containing a P48R mutation displayed increased cytosine deamination activity rather than adenine editing. We found that the D108Q mutation also reduces cytosine deamination activity in two recently-developed versions of ABE, ABE8e and ABE8s, and has a synergistic effect with V106W, a key mutation that reduces off-target RNA editing. On the other hand, by incorporating the P48R mutation into ABE7.10, we demonstrated TC-specific base editing tools that enable either TC-to-TT or TC-to-TG conversions, broadening the utility of base editors.

scholarly journals Coaxial Access for Microcatheter Stabilization During Aneurysm Coiling: 2-Dimensional Operative Video

2021 ◽  
Author(s):  
Miri Kim ◽  
Rachyl Shanker ◽  
Anthony Kam ◽  
Matthew Reynolds ◽  
Joseph C Serrone
Keyword(s):  
Artery Aneurysm ◽  
Anterior Communicating Artery ◽  
Distal Catheter ◽  
Anterior Communicating Artery Aneurysm ◽  
Class 1 ◽  
Previously Treated ◽  
Aneurysm Occlusion ◽  
Intracranial Circulation ◽  
Aneurysm Coiling

Abstract Coaxial support is a fundamental technique utilized by neurointerventionalists to optimize distal catheter control within the intracranial circulation. Here we present a 41-yr-old woman with a previously coiled ruptured anterior communicating artery aneurysm with progressive recurrence harboring tortuous internal carotid anatomy to demonstrate the utility of coaxial support. Raymond-Roy classification of initial aneurysm coiling of class 1 resulted as class 3b over the 21 mo from initial treatment.1 The patient consented to stent-assisted coiling for retreatment of this aneurysm. Coaxial support was advanced as distally as possible in the proximal vasculature to improve catheter control, reducing dead space within which the microcatheter could move, decreasing angulations within proximal vasculature, limiting the movement of the native vessels, and providing a surface of lower friction than the endothelium. As the risk of recurrent subarachnoid hemorrhage in previously treated coiled aneurysms approaches 3%, retreatment occurs in 16.4% within 6 yr2 and in 17.4% of patients within 10 yr.3 Rerupture is slightly higher in patients who underwent coiling vs clipping, with the rerupture risk inversely proportional to the degree of aneurysm occlusion,4 further substantiating that coaxial support provides technical advantage in selected patients where additional microcatheter control is necessary for optimal occlusion. Pitfalls of this technique include vasospasm and vascular injury, which can be ameliorated by pretreatment of the circulation with vasodilators to prevent catheter-induced vasospasm. This case and model demonstration illustrates the technique of coaxial access in the stent-assisted coiling of a recurrent anterior communicating artery aneurysm and identification and management of catheter-induced vasospasm.

scholarly journals Cytosine and adenine deaminase base-editors induce broad and nonspecific changes in gene expression and splicing

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jiao Fan ◽  
Yige Ding ◽  
Chao Ren ◽  
Ziguo Song ◽  
Jie Yuan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Double Strand Breaks ◽  
Great Promise ◽  
Single Nucleotide ◽  
Strand Breaks ◽  
Dna Base ◽  
Target Dna ◽  
Single Nucleotide Variations ◽  
Adenine Deaminase ◽  
Target Rna

AbstractCytosine or adenine base editors (CBEs or ABEs) hold great promise in therapeutic applications because they enable the precise conversion of targeted base changes without generating of double-strand breaks. However, both CBEs and ABEs induce substantial off-target DNA editing, and extensive off-target RNA single nucleotide variations in transfected cells. Therefore, the potential effects of deaminases induced by DNA base editors are of great importance for their clinical applicability. Here, the transcriptome-wide deaminase effects on gene expression and splicing is examined. Differentially expressed genes (DEGs) and differential alternative splicing (DAS) events, induced by base editors, are identified. Both CBEs and ABEs generated thousands of DEGs and hundreds of DAS events. For engineered CBEs or ABEs, base editor-induced variants had little effect on the elimination of DEGs and DAS events. Interestingly, more DEGs and DAS events are observed as a result of over expressions of cytosine and adenine deaminases. This study reveals a previously overlooked aspect of deaminase effects in transcriptome-wide gene expression and splicing, and underscores the need to fully characterize such effects of deaminase enzymes in base editor platforms.

scholarly journals BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
András Tálas ◽  
Dorottya A. Simon ◽  
Péter I. Kulcsár ◽  
Éva Varga ◽  
Sarah L. Krausz ◽  
...  
Keyword(s):  
High Throughput ◽  
Genome Engineering ◽  
Sequence Context ◽  
Base Editing ◽  
Target Dna ◽  
Dna Strands ◽  
Deaminase Domain ◽  
Target Effects ◽  
Target Sets

AbstractAdenine and cytosine base editors (ABE, CBE) allow for precision genome engineering. Here, Base Editor Activity Reporter (BEAR), a plasmid-based fluorescent tool is introduced, which can be applied to report on ABE and CBE editing in a virtually unrestricted sequence context or to label base edited cells for enrichment. Using BEAR-enrichment, we increase the yield of base editing performed by nuclease inactive base editors to the level of the nickase versions while maintaining significantly lower indel background. Furthermore, by exploiting the semi-high-throughput potential of BEAR, we examine whether increased fidelity SpCas9 variants can be used to decrease SpCas9-dependent off-target effects of ABE and CBE. Comparing them on the same target sets reveals that CBE remains active on sequences, where increased fidelity mutations and/or mismatches decrease the activity of ABE. Our results suggest that the deaminase domain of ABE is less effective to act on rather transiently separated target DNA strands, than that of CBE explaining its lower mismatch tolerance.

scholarly journals Analysis and Classification of Mitigation Tools against Cyberattacks in COVID-19 Era

2021 ◽  
Vol 2021 ◽  
pp. 1-21
Author(s):  
George Iakovakis ◽  
Constantinos-Giovanni Xarhoulacos ◽  
Konstantinos Giovas ◽  
Dimitris Gritzalis
Keyword(s):  
Computer Networks ◽  
Risk Mitigation ◽  
Security Risks ◽  
Work From Home ◽  
Detailed Classification ◽  
Threat Intelligence ◽  
One Step ◽  
Automated Tools ◽  
Cyber Threat Intelligence

The COVID-19 outbreak has forced businesses to shift to an unprecedented “work from home” company environment. While this provides advantages for employees and businesses, it also leads to a multitude of shortcomings, most prevalent of which is the emergence of additional security risks. Previous to the outbreak, company computer networks were mainly confined within its facilities. The pandemic has now caused this network to “spread thin,” as the majority of employees work remotely. This has opened up a variety of new vulnerabilities, as workers’ cyber protection is not the same at home as it is in office. Although the effects of the virus are now subsiding, working remotely has embedded itself as the new normal. Thus, it is imperative for company management to take the necessary steps to ensure business continuity and be prepared to deal with an increased number of cyber threats. In our research, we provide a detailed classification for a group of tools which will facilitate risk mitigation and prevention. We also provide a selection of automated tools such as vulnerability scanners, monitoring and logging tools, and antivirus software. We outline each tool using tables, to show useful information such as advantages, disadvantages, scalability, cost, and other characteristics. Additionally, we implement decision trees for each category of tools, in an attempt to assist in navigating the large amount of information presented in this paper. Our objective is to provide a multifaceted taxonomy and analysis of mitigation tools, which will support companies in their endeavor to protect their computer networks. Our contribution can also help companies to have some type of cyber threat intelligence so as to put themselves one step ahead of cyber criminals.

scholarly journals A STATE OF ART AND PROSPECTS OF USED PNEUMATIC TIRES MANAGEMENT (REVIEW)

2021 ◽  
pp. 63-83
Author(s):  
I.O. Mikulionok
Keyword(s):  
Critical Analysis ◽  
Raw Materials ◽  
Chemical Processing ◽  
Detailed Classification ◽  
The World ◽  
Intended Use ◽  
State Of Art ◽  
Frag Ments ◽  
Pneumatic Tires

The basic data on the volume of production of pneumatic tires in the world and in Ukraine are presented. The need to improve the ways of handling pneumatic tires that have lost their con-sumer properties (worn out tires as a result of their intended use and tires rejected as a result of passing quality control during their manufacture) is shown as one of the most dangerous for the environment and promising in terms of using their properties. A detailed classification of methods for handling worn out and defective tires is proposed and a critical analysis of each of them is given. Particular attention is paid to the methods of utilization of tires, in particular, recycling, which makes it possible to efficiently use the secondary raw materials obtained from tires directly for their intended purpose. The features of physical, physicochemical and chemical processing methods, in particular combustion, gasification, pyrolysis of tires and their frag-ments, as well as the prospects for their decomposition under the influence of environmental factors, in particular microorganisms, are also considered. The main ways of solving the prob-lem of tires that have lost their consumer properties in Ukraine are proposed. Bibl. 88, Fig. 2.

scholarly journals Pattern Recognition by Hierarchical Feature Extraction

2003 ◽  
Vol 15 (3) ◽  
pp. 278-285
Author(s):  
Daigo Misaki ◽  
◽  
Shigeru Aomura ◽  
Noriyuki Aoyama
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Pattern Recognition ◽  
Feature Extraction ◽  
Input Data ◽  
Local Features ◽  
Detailed Classification

We discuss effective pattern recognition for contour images by hierarchical feature extraction. When pattern recognition is done for an unlimited object, it is effective to see the object in a perspective manner at the beginning and next to see in detail. General features are used for rough classification and local features are used for a more detailed classification. D-P matching is applied for classification of a typical contour image of individual class, which contains selected points called ""landmark""s, and rough classification is done. Features between these landmarks are analyzed and used as input data of neural networks for more detailed classification. We apply this to an illustrated referenced book of insects in which much information is classified hierarchically to verify the proposed method. By introducing landmarks, a neural network can be used effectively for pattern recognition of contour images.

scholarly journals A Classification of Baire Class 1 Functions

1990 ◽  
Vol 318 (1) ◽  
pp. 209 ◽  
Author(s):  
A. S. Kechris ◽  
A. Louveau
Keyword(s):  
Baire Class ◽  
Class 1

Melanoma Detection by Meta-Heuristically-Optimized MLP Parameters Using Non-Dermatoscopy Images

2021 ◽  
Vol 12 (4) ◽  
pp. 177-200
Author(s):  
Soumen Mukherjee ◽  
Arunabha Adhikari ◽  
Madhusudan Roy
Keyword(s):  
Particle Swarm Optimization ◽  
Simulated Annealing ◽  
Skin Lesion ◽  
Multilayer Perceptron ◽  
Binary Classification ◽  
Ranking Algorithm ◽  
Swarm Optimization ◽  
Melanoma Detection ◽  
Class 1

This paper represents a scheme of melanoma detection using handcrafted feature set with meta-heuristically optimized multilayer perceptron (MLP) parameters. Features including shape, color, and texture are extracted from camera images of skin lesion collected from University of Waterloo database. The features are used in two different ways for binary classification of the data into benign and malignant class. 1) The extracted features are ranked on their relevance using ReleifF ranking algorithm and also converted into PCA components and ranked according to their variance. Best result is obtained with 50 best ranked raw features with accuracy of 87.1%. 2) All 1,888 features are fed to an MLP with two hidden layers, with number of neurons optimized by two different metaheuristic algorithms, namely particle swarm optimization (PSO) and simulated annealing (SA) separately. The latter method is found to be more efficient, and an accuracy of 88.38%, sensitivity of 92.22%, and specificity of 83.07% are achieved by PSO, which is better in comparison with the latest research on this dataset.

Congenital and Pediatric Glaucomas, by Robert N. Shaffer, M.D., F.A.C.S. and Daniel I. Weiss, M.D. St. Louis: C. V. Mosby Company, 1970, 221 pp., $20.50

PEDIATRICS ◽  
1971 ◽  
Vol 47 (6) ◽  
pp. 1103-1104
Author(s):  
David S. Walton
Keyword(s):  
Final Section ◽  
Clinical Signs ◽  
Diagnostic Techniques ◽  
Operative Techniques ◽  
Concise Review ◽  
Detailed Classification ◽  
Methods Of Treatment

The authors begin their presentation–in this, the first textbook I know of devoted entirely to pediatric glaucomas–with a detailed classification of glaucomas in childhood. This is followed by a discussion of diagnostic techniques and the important clinical signs encountered in the pediatric glaucomas. A description of the conditions assoiated with childhood glaucomas follows, including a concise review of their distinguishing ocular features, with additional comments on treatment. The final section deals with methods of treatment; appropriate emphasis is given to the operative techniques used in performing a goniotomy.

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