scholarly journals From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses

Antibiotics ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 663 ◽  
Author(s):  
Johannes Wittmann ◽  
Dann Turner ◽  
Andrew D. Millard ◽  
Padmanabhan Mahadevan ◽  
Andrew M. Kropinski ◽  
...  
Keyword(s):  
New Technologies ◽  
Phage Genome ◽  
International Committee ◽  
Genome Sequences ◽  
New Members ◽  
Phage Group ◽  
New Family ◽  
Archaeal Viruses ◽  
Long Time ◽  
Bacterial Viruses

Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family “Schitoviridae”, including eight subfamilies and numerous new genera.

scholarly journals Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

2021 ◽  
Author(s):  
Mart Krupovic ◽  
Dann Turner ◽  
Vera Morozova ◽  
Mike Dyall-Smith ◽  
Hanna M. Oksanen ◽  
...  
Keyword(s):  
New Taxa ◽  
Executive Committee ◽  
International Committee ◽  
New Members ◽  
Vice Chair ◽  
Archaeal Viruses ◽  
Bacterial Viruses

AbstractIn this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).

scholarly journals VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1268
Author(s):  
Cristina Moraru ◽  
Arvind Varsani ◽  
Andrew M. Kropinski
Keyword(s):  
Web Service ◽  
Phage Genome ◽  
International Committee ◽  
Length Ratio ◽  
Fast Analysis ◽  
Percent Identity ◽  
Archaeal Viruses ◽  
Traditional Algorithm ◽  
Genomic Regions ◽  
Similarity Thresholds

Nucleotide-based intergenomic similarities are useful to understand how viruses are related with each other and to classify them. Here we have developed VIRIDIC, which implements the traditional algorithm used by the International Committee on Taxonomy of Viruses (ICTV), Bacterial and Archaeal Viruses Subcommittee, to calculate virus intergenomic similarities. When compared with other software, VIRIDIC gave the best agreement with the traditional algorithm, which is based on the percent identity between two genomes determined by BLASTN. Furthermore, VIRIDIC proved best at estimating the relatedness between more distantly-related phages, relatedness that other tools can significantly overestimate. In addition to the intergenomic similarities, VIRIDIC also calculates three indicators of the alignment ability to capture the relatedness between viruses: the aligned fractions for each genome in a pair and the length ratio between the two genomes. The main output of VIRIDIC is a heatmap integrating the intergenomic similarity values with information regarding the genome lengths and the aligned genome fraction. Additionally, VIRIDIC can group viruses into clusters, based on user-defined intergenomic similarity thresholds. The sensitivity of VIRIDIC is given by the BLASTN. Thus, it is able to capture relationships between viruses having in common even short genomic regions, with as low as 65% similarity. Below this similarity level, protein-based analyses should be used, as they are the best suited to capture distant relationships. VIRIDIC is available at viridic.icbm.de, both as a web-service and a stand-alone tool. It allows fast analysis of large phage genome datasets, especially in the stand-alone version, which can be run on the user’s own servers and can be integrated in bioinformatics pipelines. VIRIDIC was developed having viruses of Bacteria and Archaea in mind; however, it could potentially be used for eukaryotic viruses as well, as long as they are monopartite.

scholarly journals VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses

2020 ◽  
Author(s):  
Cristina Moraru ◽  
Arvind Varsani ◽  
Andrew M. Kropinski
Keyword(s):  
Web Service ◽  
Phage Genome ◽  
International Committee ◽  
Length Ratio ◽  
Fast Analysis ◽  
Archaeal Viruses ◽  
Traditional Algorithm

AbstractNucleotide based intergenomic similarities are useful to understand how viruses are related with each other and to classify them. Here we have developed VIRIDIC, which implements the traditional algorithm used by the International Committee on Taxonomy of Viruses (ICTV), Bacterial and Archaeal Viruses Subcommittee, to calculate virus intergenomic similarities. When compared with other software, VIRIDIC gave the best agreement with the traditional algorithm. Furthermore, it proved best at estimating the relatedness between more distantly related phages, relatedness that other tools can significantly overestimate. In addition to the intergenomic similarities, VIRIDIC also calculates three indicators of the alignment ability to capture the relatedness between viruses: the aligned fractions for each genome in a pair and the length ratio between the two genomes. The main output of VIRIDIC is a heatmap integrating the intergenomic similarity values with information regarding the genome lengths and the aligned genome fraction. VIRIDIC is available at viridic.icbm.de, both as a web-service and a stand-alone tool. It allows fast analysis of large phage genome datasets, especially in the stand-alone version, which can be run on the user’s own servers and can be integrated in bioinformatics pipelines. VIRIDIC was developed having viruses of Bacteria and Archaea in mind, however, it could potentially be used for eukaryotic viruses as well, as long as they are monopartite.

scholarly journals Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

2019 ◽  
Vol 69 (1) ◽  
pp. 110-123 ◽  
Author(s):  
Jakub Barylski ◽  
François Enault ◽  
Bas E Dutilh ◽  
Margo BP Schuller ◽  
Robert A Edwards ◽  
...  
Keyword(s):  
Marker Gene ◽  
International Committee ◽  
New Taxon ◽  
New Family ◽  
Archaeal Viruses ◽  
Wide Range ◽  
The Family ◽  
Comprehensive Picture ◽  
Bacillus Phage

Abstract Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods—including comparative genomics, core genome analysis, and marker gene phylogenetics—to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae—a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.

IDLE WELLS REHABILITATION IN THE FIELDS OF EXTREME NORTH

2015 ◽  
pp. 66-71
Author(s):  
A. V. Kustyshev
Keyword(s):  
New Technologies ◽  
Long Time ◽  
Extreme North

The paper reviews the new technologies developed for rehabilitation of wells being out of operating for a long time. It presents a complex of works needed for such wells brining back into operation

scholarly journals Recent Progress in Torovirus Molecular Biology

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 435
Author(s):  
Makoto Ujike ◽  
Fumihiro Taguchi
Keyword(s):  
Molecular Biology ◽  
Recent Progress ◽  
Reverse Genetics ◽  
Cultured Cells ◽  
Host Adaptation ◽  
Economic Losses ◽  
New Family ◽  
Enteric Diseases ◽  
Long Time ◽  
Medical Importance

Torovirus (ToV) has recently been classified into the new family Tobaniviridae, although it belonged to the Coronavirus (CoV) family historically. ToVs are associated with enteric diseases in animals and humans. In contrast to CoVs, which are recognised as pathogens of veterinary and medical importance, little attention has been paid to ToVs because their infections are usually asymptomatic or not severe; for a long time, only one equine ToV could be propagated in cultured cells. However, bovine ToVs, which predominantly cause diarrhoea in calves, have been detected worldwide, leading to economic losses. Porcine ToVs have also spread globally; although they have not caused serious economic losses, coinfections with other pathogens can exacerbate their symptoms. In addition, frequent inter- or intra-recombination among ToVs can increase pathogenesis or unpredicted host adaptation. These findings have highlighted the importance of ToVs as pathogens and the need for basic ToV research. Here, we review recent progress in the study of ToV molecular biology including reverse genetics, focusing on the similarities and differences between ToVs and CoVs.

Hacking humanitarians: Defining the cyber perimeter and developing a cyber security strategy for international humanitarian organizations in digital transformation

2020 ◽  
Vol 102 (913) ◽  
pp. 367-387
Author(s):  
Massimo Marelli
Keyword(s):  
Cyber Security ◽  
Armed Conflict ◽  
New Technologies ◽  
International Committee ◽  
Digital Transformation ◽  
Red Cross ◽  
Digital Environment ◽  
Security Strategy ◽  
Humanitarian Action ◽  
Humanitarian Organizations

AbstractDigitalization and new technologies have an increasingly important role in today's humanitarian activities. As humanitarian organizations become more active in and reliant on new and digital technologies, they evolve from being simple bystanders to being fully fledged stakeholders in cyberspace, vulnerable to adverse cyber operations that could impact on their capacity to protect and assist people affected by armed conflict or other situations of violence.This shift makes it essential for humanitarian organizations to understand and properly map their resulting cyber perimeter. Humanitarian organizations can protect themselves and their activities by devising appropriate cyber strategies for the digital environment. Clearly defining the digital boundaries within which they carry out operations lays the groundwork for humanitarian organizations to develop a strategy to support and protect humanitarian action in the digital environment, channel available resources to where they are most needed, and understand the areas in which their operational dialogue and working modalities need to be adapted for cyberspace.The purpose of this article is to identify the unique problems facing international humanitarian organizations operating in cyberspace and to suggest ways to address them. More specifically, the article identifies the key elements that an international humanitarian organization should consider in developing a cyber security strategy. Throughout, the International Committee of the Red Cross and its specificities are used as an example to illustrate the problems identified and the possible ways to address them.

scholarly journals Genome Sequences of Mycobacteriophages Jane and Sneeze, New Members of Cluster G

2017 ◽  
Vol 5 (11) ◽  
Author(s):  
Catherine M. Mageeney ◽  
Cimrin Bhalla ◽  
Charles A. Bowman ◽  
Bhavishya Devireddy ◽  
Adrienne P. Dzurick ◽  
...  
Keyword(s):  
Costa Rica ◽  
Mycobacterium Smegmatis ◽  
Mobile Element ◽  
Genome Sequences ◽  
New Members ◽  
Content Type ◽  
The Right

ABSTRACT Jane and Sneeze are newly isolated phages of Mycobacterium smegmatis mc2155 from Hillsborough, NJ, and Palo Verde, Costa Rica, respectively. Both are cluster G, subcluster G1 mycobacteriophages. Notable nucleotide differences exist between genomes in the right half, including the presence of mycobacteriophage mobile element 1 (MPME1) in Jane.

scholarly journals The History, Present and Future of Allergen Standardization in the United States and Europe

2021 ◽  
Vol 12 ◽  
Author(s):  
Julia Zimmer ◽  
Jennifer Bridgewater ◽  
Fatima Ferreira ◽  
Ronald van Ree ◽  
Ronald L. Rabin ◽  
...  
Keyword(s):  
United States ◽  
New Technologies ◽  
The United States ◽  
Cross Product ◽  
Immunological Methods ◽  
The European Union ◽  
Product Standardization ◽  
Long Time ◽  
Allergen Standardization ◽  
Synthetic Medicinal

The topic of standardization in relation to allergen products has been discussed by allergists, regulators, and manufacturers for a long time. In contrast to synthetic medicinal products, the natural origin of allergen products makes the necessary comparability difficult to achieve. This holds true for both aspects of standardization: Batch-to-batch consistency (or product-specific standardization) and comparability among products from different manufacturers (or cross-product comparability). In this review, we focus on how the United States and the European Union have tackled the topic of allergen product standardization in the past, covering the early joint standardization efforts in the 1970s and 1980s as well as the different paths taken by the two players thereafter until today. So far, these two paths have been based on rather classical immunological methods, including the corresponding benefits like simple feasability. New technologies such as mass spectrometry present an opportunity to redefine the field of allergen standardization in the future.

scholarly journals Machine learning classification of new asteroid families members

2020 ◽  
Author(s):  
Valerio Carruba
Keyword(s):  
Machine Learning ◽  
Family Members ◽  
Classification Algorithms ◽  
New Members ◽  
Machine Learning Classification ◽  
New Family ◽  
Robotic Telescope ◽  
Traditional Approaches ◽  
Asteroid Families

<p>Asteroid families are groups of asteroids that are the product of collisions or of the rotational fission of a parent object.  These groups are mainly identified in proper elements or frequencies domains.   Because of robotic telescope surveys, the number of known asteroids has increased from about 10,000 in the early 90's to more than 750,000 nowadays. Traditional approaches for identifying new members of asteroid families, like the hierarchical clustering method (HCM), may   struggle to keep up with the growing rate of new discoveries. Here we used machine learning classification algorithms to identify new family members based on the orbital distribution in proper (a,e,sin(i)) of previously known family constituents. We compared the outcome of nine classification algorithms from stand alone and ensemble approaches.  The Extremely Randomized Trees (ExtraTree) method had the highest precision, enabling to  retrieve up to 97% of family members identified with standard HCM.</p>

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