CAN RESTRICTION SITE AVOIDANCE IN A VIRAL GENOME BE USED FOR PREDICTION OF PHAGE HOSTS?

2018 ◽  
Author(s):  
I. RUSINOV ◽  
◽  
A. ERSHOVA ◽  
M. KHACHATURYAN ◽  
A. KARYAGINA ◽  
...  
Keyword(s):  
Viral Genome ◽  
Restriction Site ◽  
Site Avoidance

scholarly journals Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis

2001 ◽  
Vol 11 (6) ◽  
pp. 946-958
Author(s):  
Eduardo P.C. Rocha ◽  
Antoine Danchin ◽  
Alain Viari
Keyword(s):  
Restriction Site ◽  
Bacterial Species ◽  
Genetic Material ◽  
Type Ii ◽  
Parasite Relationship ◽  
Host Parasite ◽  
Restriction Modification ◽  
Evolutionary Role ◽  
Restriction Modification Systems ◽  
Site Avoidance

Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host–parasite relationship between bacteria and phages.

scholarly journals Effects of mutations in phage restriction sites during escape from restriction–modification

2017 ◽  
Vol 13 (12) ◽  
pp. 20170646 ◽  
Author(s):  
Maroš Pleška ◽  
Călin C. Guet
Keyword(s):  
Restriction Site ◽  
Response To Selection ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Sites ◽  
Restriction Modification ◽  
Insight Into ◽  
Restriction Modification Systems ◽  
Site Avoidance

Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage λ and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.

An Electron Microscopic Study of an Avian Reovirus that Causes Arthritis

1971 ◽  
Vol 29 ◽  
pp. 254-255
Author(s):  
E, R. Walker ◽  
N. O. Olson ◽  
M. H. Friedman
Keyword(s):  
Electron Microscopy ◽  
Viral Genome ◽  
Inner Core ◽  
Avian Reovirus ◽  
Electron Microscopic ◽  
Outer Coat ◽  
Acid Type ◽  
Chicken Eggs ◽  
Icosahedral Particle ◽  
Mature Virus

An unidentified virus, responsible for an arthritic-like condition in chickens was studied by electron microscopy and other methods of viral investigation. It was characterized in chorio-allantoic membrane (CAM) lesions of embryonating chicken eggs and in tissue culture as to: 1) particle size; 2) structure; 3) mode of replication in the cell; and 4) nucleic acid type.The inoculated virus, coated and uncoated, is first seen in lysosomal-like inclusions near the nucleus; the virions appear to be uncoated in these electron dense inclusions (Figure 1), Although transfer of the viral genome from these inclusions is not observable, replicating virus and mature virus crystals are seen in the cytoplasm subsequent to the uncoating of the virions.The crystals are formed in association with a mass of fibrils 50 to 80 angstroms in diameter and a ribosome-studded structure that appears to be granular endoplasmic reticulum adapted to virus replication (Figure 2). The mature virion (Figure 3) is an icosahedral particle approximately 75 millimicrons in diameter. The inner core is 45 millimicrons, the outer coat 15 millimicrons, and the virion has no envelope.

IDENTIFYING THE C677T POLYMORPHISM OF MTHFR GENE BY PCR-RFLP TECHNIQUE

2011 ◽  
pp. 28-35
Author(s):  
Keyword(s):  
Internal Control ◽  
Restriction Site ◽  
Mthfr Gene ◽  
C677t Polymorphism ◽  
Mthfr Genotype ◽  
Restriction Digest ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Sequencing Technique ◽  
Volunteer Group

Background: The C677T polymorphism of MTHFR gene is a risk factor of many diseases. This study is aimed at: (1) Improving a PCR-RFLP process with the own designed primers to identify the C677T polymorphism of MTHFR gene. (2) Evaluating the prevalence of the C677T polymorphism of MTHFR gene in volunteer group. Materials and method: DNA samples was extracted from peripheral blood of 60 volunteers. Designing primers by using FastPCR software, then improving PCR technique. Standardizing the optimal conditions of restriction digest by HinfI. Confirming the results of polymorphism by DNA sequencing technique. Results: We designed successfully primers to amplify fragment of MTHFR gene including C677T polymorphism and an obligatory restriction site of HinfI (as internal control). 0.5 µl of HinfI enzyme (10 U/µl) is enough for restriction digest. The MTHFR genotype frequencies were: 71.67 % (677CC); 25% (677CT); and 3.33 % (677TT). Conclusion: We standardized successfully PCR-RFLP technique to identifying C677T polymorphism of MTHFR gene. Keywords: C677T polymorphism, MTHFR gene, PCR-RFLP

DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

2020 ◽  
Author(s):  
E.V. Korneenko ◽  
◽  
А.E. Samoilov ◽  
I.V. Artyushin ◽  
M.V. Safonova ◽  
...  
Keyword(s):  
High Throughput ◽  
Viral Genome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Moscow Region ◽  
Fecal Samples ◽  
Genus Level ◽  
Zoonotic Viruses ◽  
Reservoir Hosts ◽  
Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon

2020 ◽  
Vol 20 ◽  
Author(s):  
Rami Obeid ◽  
Elias Wehbe ◽  
Mohamad Rima ◽  
Mohammad Kabara ◽  
Romeo Al Bersaoui ◽  
...  
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Viral Genome ◽  
Virus Genome ◽  
Enzyme Linked Immunosorbent Assay ◽  
Virus Family ◽  
Crop Fields ◽  
Wide Range ◽  
Almost All ◽  
Das Elisa

Background: Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particularly tobacco, causing a production loss. Objectives: Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon. Methods: Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crops samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome. Results and Discussion: PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain. Conclusion: Our study is the first in Lebanon revealing TMV infection in crop fields, and highlighting the danger that may affect the future of agriculture.

Localization of Three Major Capped 5′ Ends of Polyoma Virus Late mRNA's Within a Single Tetranucleotide Sequence in the Viral Genome †

1980 ◽  
Vol 33 (2) ◽  
pp. 902-908 ◽  
Author(s):  
Andrew J. Flavell ◽  
Alison Cowie ◽  
John R. Arrand ◽  
Robert Kamen
Keyword(s):  
Viral Genome ◽  
Polyoma Virus
Sign in / Sign up

Export Citation Format

Share Document