scholarly journals How to name and classify your phage: an informal guide

2017 ◽  
Author(s):  
Evelien M. Adriaenssens ◽  
J. Rodney Brister

AbstractWith this informal guide, we try to assist both new and experienced phage researchers through two important stages that follow phage discovery, i.e. naming and classification. Providing an appropriate name for a bacteriophage is not as trivial as it sounds and the effects might be long-lasting in databases and in official taxon names. Phage classification is the responsibility of the Bacterial and Archaeal Viruses Subcommittee (BAVS) of the International Committee on the Taxonomy of Viruses (ICTV). While the BAVS aims at providing a holistic approach to phage taxonomy, for individual researchers who have isolated and sequenced a new phage, this can be a little overwhelming. We are now providing these researchers with an informal guide to phage naming and classification, taking a “bottom-up” approach from the phage isolate level.

2010 ◽  
Vol 7 (5) ◽  
pp. 8265-8308
Author(s):  
I. Nalbantis ◽  
A. Efstratiadis ◽  
E. Rozos ◽  
M. Kopsiafti ◽  
D. Koutsoyiannis

Abstract. The modelling of modified basins that are inadequately measured constitutes a challenge for hydrological science. Often, models for such systems are detailed and hydraulics-based for only one part of the system while for other parts oversimplified models or rough assumptions are used. This is typically a bottom-up approach, which seeks to exploit knowledge of hydrological processes at the micro-scale at some components of the system. Also, it is a monomeric approach in two ways: first, essential interactions among system components may be poorly represented or even omitted; second, differences in the level of detail of process representation can lead to uncontrolled errors. Additionally, the calibration procedure merely accounts for the reproduction of the observed responses using typical fitting criteria. The paper aims to raise some critical issues, regarding the entire modelling approach for such hydrosystems. For this, two alternative modelling strategies are examined that reflect two modelling approaches or philosophies: a dominant bottom-up approach, which is also monomeric and very often, based on output information and a top-down and holistic approach based on generalized information. Critical options are examined, which codify the differences between the two strategies: the representation of surface, groundwater and water management processes, the schematization and parameterization concepts and the parameter estimation methodology. The first strategy is based on stand-alone models for surface and groundwater processes and for water management, which are employed sequentially. For each model, a different (detailed or coarse) parameterization is used, which is dictated by the hydrosystem schematization. The second strategy involves model integration for all processes, parsimonious parameterization and hybrid manual-automatic parameter optimization based on multiple objectives. A test case is examined in a hydrosystem in Greece with high complexities, such as extended surface-groundwater interactions, ill-defined boundaries, sinks to the sea and anthropogenic intervention with unmeasured abstractions both from surface and groundwater. Criteria for comparison are the physical consistency of parameters, the reproduction of runoff hydrographs at multiple sites within the basin, the likelihood of uncontrolled model outputs, the required amount of computational effort and the performance within a stochastic simulation setting.


Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1268
Author(s):  
Cristina Moraru ◽  
Arvind Varsani ◽  
Andrew M. Kropinski

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.


2016 ◽  
Vol 9 (2) ◽  
pp. 166-190 ◽  
Author(s):  
Miguel Saraiva ◽  
Irina Matijosaitiene ◽  
Mónica Diniz ◽  
Vilius Velicka

Purpose The purpose of this paper is to respond to the need for comparative studies on methodologies for implementing Crime Prevention through Urban Design and Planning (CP-UDP) at the local level, particularly in peripheral Europe where CP-UDP’s top-down standards have poor dissemination and acceptance. This paper debates how local partnerships can help reduce crime and how a CP-UDP-based model can be introduced into municipal planning. Design/methodology/approach The paper discusses the challenge of CP-UDP in the framework of a post-crisis Europe and Europe 2020. Because there is a large gap between theory and practice, lack of a shared holistic approach, and scepticism, or lack of knowledge, of public authorities, at local-level planning professionals and the police have devised bottom-up initiatives based on interdisciplinary partnerships with the community. The paper describes, discusses and compares the implementation of such approaches in Lisbon (Portugal) and Vilnius (Lithuania). Findings The paper addresses the processes and challenges of establishing synergies and working relationships between police officers, public officials and the community, and it discusses six main causes for its (un)success. When these conditions were met, crime and social constraints reduced. Practical implications Lessons learned are deemed crucial to disseminate knowledge and best practices, paving the way for proper top-down policies and planning legislations in these and other countries. Originality/value This paper analyses the potentialities and shortcomings of local-level implementation of CP-UDP strategies as an alternative to failed top-down strategies in two realities mostly unknown of the international scientific community. The case study material is previously unpublished internationally.


Author(s):  
Cristina Moraru ◽  
Arvind Varsani ◽  
Andrew M. Kropinski

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.


2021 ◽  
Author(s):  
◽  
Tamatamaarangi Whiting

<p>At the heart of the thesis is the establishment of a new type of landscape practice based upon leveraging the power and potential of computational tools to serve cultural attitudes to land and land management. The research acknowledges that a new approach to landscape understanding is required, one that extends the current discipline’s mode of notation and representation/visualisation and ‘experience’ within the design process. It questions current forms of mapping and representational media and highlights limitations when communicating ‘non-traditional’ cartographic data, such as cultural and spiritual sites arguing that there are opportunities for a more holistic experiential interaction.  By utilising a holistic approach influenced by key Māori kaupapa including kaitiakitanga, manaakitanga, and mauri, the research offers up a novel digital methodology that draws from a range of existing data (demographics, climate etc.) and initiates the creation or capturing of new data.  This extended method of ‘bottom up’ data collection combined with virtual 3D modelling and visualisation, enables traditional understandings of landscape to extend to the experiential in the creation of an immersive, interactive and open collaborative 3D environment. This is further investigated through a process consisting of data conversion to mesh production for game engine use, incorporating diverse data sets to create new knowledge landscapes - an information-rich land model which in turn generates interactive 3D landscapes for end users.  The process itself uses commonplace photogrammetry techniques as a means to capture selected areas of the cultural landscape recording both mesh and texture/image map. We then employ the software ‘Unreal Engine 4’ (Game development platform). The development of the gamification model allows location specific data to be ‘plugged in’ for landscape ecosystem monitoring also providing the potential for real time resource management.  Future speculation of the cultural landscape enables climate events to be simulated and tested, giving an understanding of implications and risks with a view to local response and mitigation. From a design perspective the method/model allows designers to respond effectively with Māori end users and their real needs, potentially collapsing traditional modes of engagement and consultation between designer-client relationships providing a more bottom up collaborative approach.</p>


2019 ◽  
Vol 69 (1) ◽  
pp. 110-123 ◽  
Author(s):  
Jakub Barylski ◽  
François Enault ◽  
Bas E Dutilh ◽  
Margo BP Schuller ◽  
Robert A Edwards ◽  
...  

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.


2011 ◽  
Vol 15 (3) ◽  
pp. 743-758 ◽  
Author(s):  
I. Nalbantis ◽  
A. Efstratiadis ◽  
E. Rozos ◽  
M. Kopsiafti ◽  
D. Koutsoyiannis

Abstract. The modelling of human-modified basins that are inadequately measured constitutes a challenge for hydrological science. Often, models for such systems are detailed and hydraulics-based for only one part of the system while for other parts oversimplified models or rough assumptions are used. This is typically a bottom-up approach, which seeks to exploit knowledge of hydrological processes at the micro-scale at some components of the system. Also, it is a monomeric approach in two ways: first, essential interactions among system components may be poorly represented or even omitted; second, differences in the level of detail of process representation can lead to uncontrolled errors. Additionally, the calibration procedure merely accounts for the reproduction of the observed responses using typical fitting criteria. The paper aims to raise some critical issues, regarding the entire modelling approach for such hydrosystems. For this, two alternative modelling strategies are examined that reflect two modelling approaches or philosophies: a dominant bottom-up approach, which is also monomeric and, very often, based on output information, and a top-down and holistic approach based on generalized information. Critical options are examined, which codify the differences between the two strategies: the representation of surface, groundwater and water management processes, the schematization and parameterization concepts and the parameter estimation methodology. The first strategy is based on stand-alone models for surface and groundwater processes and for water management, which are employed sequentially. For each model, a different (detailed or coarse) parameterization is used, which is dictated by the hydrosystem schematization. The second strategy involves model integration for all processes, parsimonious parameterization and hybrid manual-automatic parameter optimization based on multiple objectives. A test case is examined in a hydrosystem in Greece with high complexities, such as extended surface-groundwater interactions, ill-defined boundaries, sinks to the sea and anthropogenic intervention with unmeasured abstractions both from surface water and aquifers. Criteria for comparison are the physical consistency of parameters, the reproduction of runoff hydrographs at multiple sites within the studied basin, the likelihood of uncontrolled model outputs, the required amount of computational effort and the performance within a stochastic simulation setting. Our work allows for investigating the deterioration of model performance in cases where no balanced attention is paid to all components of human-modified hydrosystems and the related information. Also, sources of errors are identified and their combined effect are evaluated.


Author(s):  
Mart Krupovic ◽  
Dann Turner ◽  
Vera Morozova ◽  
Mike Dyall-Smith ◽  
Hanna M. Oksanen ◽  
...  

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).


2021 ◽  
Author(s):  
◽  
Tamatamaarangi Whiting

<p>At the heart of the thesis is the establishment of a new type of landscape practice based upon leveraging the power and potential of computational tools to serve cultural attitudes to land and land management. The research acknowledges that a new approach to landscape understanding is required, one that extends the current discipline’s mode of notation and representation/visualisation and ‘experience’ within the design process. It questions current forms of mapping and representational media and highlights limitations when communicating ‘non-traditional’ cartographic data, such as cultural and spiritual sites arguing that there are opportunities for a more holistic experiential interaction.  By utilising a holistic approach influenced by key Māori kaupapa including kaitiakitanga, manaakitanga, and mauri, the research offers up a novel digital methodology that draws from a range of existing data (demographics, climate etc.) and initiates the creation or capturing of new data.  This extended method of ‘bottom up’ data collection combined with virtual 3D modelling and visualisation, enables traditional understandings of landscape to extend to the experiential in the creation of an immersive, interactive and open collaborative 3D environment. This is further investigated through a process consisting of data conversion to mesh production for game engine use, incorporating diverse data sets to create new knowledge landscapes - an information-rich land model which in turn generates interactive 3D landscapes for end users.  The process itself uses commonplace photogrammetry techniques as a means to capture selected areas of the cultural landscape recording both mesh and texture/image map. We then employ the software ‘Unreal Engine 4’ (Game development platform). The development of the gamification model allows location specific data to be ‘plugged in’ for landscape ecosystem monitoring also providing the potential for real time resource management.  Future speculation of the cultural landscape enables climate events to be simulated and tested, giving an understanding of implications and risks with a view to local response and mitigation. From a design perspective the method/model allows designers to respond effectively with Māori end users and their real needs, potentially collapsing traditional modes of engagement and consultation between designer-client relationships providing a more bottom up collaborative approach.</p>


Author(s):  
Asha Embrandiri ◽  
Shlrene Quaik ◽  
Madu Ijanu Emmanuel ◽  
Mariyam Rahma ◽  
Parveen Fatemeh Rupani ◽  
...  

Microplastics are plastics with smaller than 5mm particle size and they originate from sequential degradation of larger plastic molecules or are manufactured, and they have found use in many realms of life. Their gradual degradability and ingestion by aquatic organisms have become an environmental concern. Microplastics are regarded as a “tiny problem” requiring massive attention. Occurrences of microplastics have been detected in almost all environment matrices. Although several committees have taken steps towards handling the menace, most of the regulations' guidelines refer to “all wastes” in general, leaving many loopholes. This chapter views microplastics, occurrences, detection, and existing policies. The roles of industry and individuals in preserving the ecosystems are deliberated. In summary, emphasis on the bottom-up strategy to curb the escalating amount of plastics waste in our environment is sought and adoption of the “avoid the avoidable” attitude for a more holistic approach in tackling the severity of the impending threat.


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