Potency and breadth of human primary zikv immune sera. Antigenic mismatch between circulating strains and vaccine strains results in. Mapping and gis applications range from free to costing tens of thousan. Antigenic cartography, a new computational method of quantifying antigenic distances between strains has been applied to human and equine in. Antigenic peptide prediction is based on a table that underlines the occurrence of amino acid residues in experimentally known segmental epitopes. List of online bioinformatics tools and software used for capacity. The installation instructions shown here are only for macs.
In some cases twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. Many electronic charts have advanced features such as 3d contours, satellite imagery, and advanced turnbyturn routing. It reports segments if they have a minimum size of 8 residues. This course will provide an introduction to antigenic cartography and the use of new tools and packages available for performing serological analysis using the r programming language, with no assumed previous programming or computer knowledge. At the oreilly etech conference in march i gave a talk describing antigenic cartography, a new method being used to visualize virus evolution and to aid in the design of vaccines, in the context of influenza. The mapping, says kawaoka, identifies clusters of viruses featuring novel mutations which, according to the new study, can effectively predict the molecular characteristics of the next seasonal influenza virus. In some cases, as in the image above, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen this is the first antigenic map of the influenza ah3n2 virus from 1968 to 2003. Receiving world wide antigenic data for human flu, generating vaccine strain selection reports, providing technical assistance to collaborators in who national laboratories. Is there any website to download free dnastar lasergene software for mac. Predictions are based on a table that reflects the occurrence of amino acid residues in experimentally known segmental epitopes.
Cai z, zhang t, wan xf 2010 a computational framework for influenza antigenic cartography. The viruses labeled with the cluster names hk68, en72, vi75, tx77, bk79, si87, be89, be92, wu95, sy97 and fu02 were adapted from smith et al. Antigenic cartography and antibody landscapes centre for. Geological survey the usgs covers many topics in geology, mapping, and water resources. Antigenic cartography is the product of collaboration between researchers in virology, immunology, computational biology, mathematics, and computer science. Longer peptides may have a greater conformational similarity to the native protein and be more likely to induce antibodies that recognise the natural protein. This guest post was written by terry jones, former antigenic cartographer and founder of fluidinfo at the oreilly etech conference in march i gave a talk describing antigenic cartography, a new method being used to visualize virus evolution and to aid in the design of vaccines, in the context of influenza. May 23, 2016 because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. Antigenic cartography is a useful technique to visualize and minimize errors in immunological data by projecting antigens to 2d or 3d cartography.
Although its utility was first established in both research and public health in the context of the influenza virus, the techniques of antigenic cartography have subsequently been applied to many other. An examination of cartographic design is a cartographic classic by arthur h. The influenza antigenic 2d a and 3d b cartography for h3n2 viruses from 1968 to 2003. Please click here and then click on the sign up link on that page, if you would like to use alpha release of our webbased. Antigenic cartography construction was implemented in java based on. Eugene skepner software developer and consultant the. Antigenic characterization of recent h5n1 highly pathogenic. Antigenic cartography of h1n1 influenza viruses using sequence. Antigenic cartography is a computational and mathematical tool for the analysis of binding assay data, providing a quantification and visualisationcalled antigenic mapsof antigenic data.
One grid in 2d map or one unit in 3d map corresponds to a twofold change in hi assay. Because 2d cartography may not be sufficient to capture the antigenic relationship from the highdimensional immunological data, we developed an antigenic cartography tool, antigenmap 3d, to construct 3d antigenic cartography. A task for theoretical cartography is to develop a typology of dynamic spatial phenomena and formulate principles and rules of. As of current with a slightly tweaked menu and using xyz input files we are able to show a 3d model of antigen relations with jmol however, jmol does not like the atoms in the xyz input file having their antigen names. Likewise but using a 3d instead of a 2d antigenic map, barnett et al. My slides from the talk are online having the flu is something of a generic. As discussed previously, the behaviour of ah3n2 viruses in ha and hi assays has changed in recent years and their antigenic analyses have become more complex.
Several methods based on various physiochemical properties of experimental determined epitopes flexibility, hydrophibility, accessibility have published for the prediction of antigenic determinants, of which the antigenic index and preditop are good examples. The influenza a h1n1 virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. Who recommendations for the viruses used in the 202014. Sep 28, 2015 the influenza a h1n1 virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. Mapublisher cartography software seamlessly integrates more than fifty gis mapping tools into adobe illustrator to help you create beautiful maps. I need recommendation about antigenic software or epitope. Cartography predates the invention of geographic information system gis by thousands of years. Apr 23, 2008 maps point the way to fighting the flu virus. Each strain is coloured to represent the antigenic. Although zikv is thought to compose a single antigenic serotype, indepth evaluation of the antigenic relatedness of zikv across genetic variants has been limited to a relatively small series of early convalescent human immune sera 412 weeks against a. The one rpg mapping tool ive used to good effect that is available on mac is hexographer.
You can enhance your gps chartplotter by adding an electronic cartography chart to your unit. Segments are only reported if the have a minimum size of 8 residues. Maps point the way to fighting the flu virus scientific. The tree can also be colored by cumulative antigenic change similar to dimension 1 in antigenic cartography.
Anchor express has the right electronic cartography card or gps software for your unit. The dengue antigenic cartography consortium is an international collaboration of leading dengue researchers to systematically characterise antigenic variation among a large sample of dengue viruses. They have pointers to a lot of cartographic software. A computational framework for influenza antigenic cartography. The global antigenic diversity of swine influenza a viruses europe. Create maps from templates choose from a variety of beautifully designed world, regional, and country templates ready to edit and make your own. Free download map symbol collections for use with ortelius map design software for mac os x. This map demonstrates that there is lack of antigenic drifts during the first wave of this pandemic influenza as all of these viruses are mixed altogether.
However, a 2d cartography may not be sufficient to capture the antigenic relationship from highdimensional immunological data. Use the date slider to select viruses sampled within the time interval indicated. Hello, my apologies on the first mail that was sent. A robust antigenic cartography can facilitate influenza vaccine strain selection since the antigenic map can simplify data interpretation through intuitive antigenic map. The general approach of software cartography, as illustrated in figure 1, is as. Because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. Nowadays, progression in gis and cartography software technology have converged in a suite of truly open and flexible tools which reduce time for map and chart production from days to hours, including for noncartographic specialists. Antigenic cartography was used to visualise the hi data. Using antigenic cartography, a technique developed to probe the forces underlying the antigenic evolution of influenza viruses, we are testing for. We will see in this lesson, why the map outputs from gis are not always optimal, and learn the main advantages. We formed the dengue antigenic cartography consortium, an open collaboration of.
This project aims at providing a desktop application for working with antigenic maps. This is the first antigenic map of the influenza ah3n2 virus from 1968 to 2003. Nearly all mapmaking software aimed at rpgs is exclusively for windows, which makes it hard for gms who are mac owners to find anything to create maps, if they dont have the technical and artistic skills that mapmaking with a photoediting suite requires. The jpl cartographic applications group is involved with many projects involving digital cartography, geographic information systems, digital elevation models, terrain analysis and remote sensing. Antigenic cartography therefore offers an improved understanding of genetic and antigenic evolution. This method is highly applicable to other important pathogens displaying antigenic diversity, such as fmd. Cartographica is designed for people who need to work with geospatial data to create maps, analyze data, convert between formats, and discover new information about your data and the world in which it exists. Finally, we subjected our data to analysis using antigenic cartography, finding that zikv are highly antigenically similar, with only a 4fold range across all antigenic distances between viruses, consistent with a single serotype.
However, antigenic cartography construction is not trivial due to the challenging features embedded in the immunological data, such as data incompleteness, high noises, and. Figure 2c is an antigenic cartography generated using a hi dataset with 2009 h1n1 influenza viruses spanning from april of 2009 to june of 2009. A deep understanding of the antigenic patterns and evolution of human influenza. A molecule that is capable of binding to an antibody or to an antigen receptor on a t cell, especially one that induces an immune response. Antigenic patterns and evolution of the human influenza a. Dengue viruses cluster antigenically but not as discrete serotypes. The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strains make sequencebased antigenic distance estimates an attractive approach to researchers. Antigenic mismatch between circulating strains and vaccine strains results in significantly. This guest post was written by terry jones, former antigenic cartographer and founder of fluidinfo. Author summary influenza antigenic cartography is an analogy of geographic cartography, and it projects influenza antigens into a two or. Antigenic cartography is the process of creating maps of antigenically variable pathogens more details. There are several factors that should be considered when looking for custom map design tools. Predictions are based on a table that reflects the occurrence of amino acid residues in.
Antigenic variation may be classified into two types, antigenic drift that results from a change in few amino acids and antigenic shift which is the outcome of acquiring new structural proteins. The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of. Source data and gif files for rotational views of 3d antigenic maps in figure 1 have. Antigenic map showing the evolution of the influenza a h3n2 virus evolution from 1968 to 2002. A new vaccine is required every year because influenza virus has the ability to undergo antigenic drift.
The centre for pathogen evolution, department of zoology, university of cambridge, uk antigenic cartography. Topics in cartography degree programs include quantitative methods, webbased cartography, remote sensing and laboratory courses in imageprocessing software. The size of the interval can be changed by grabing the left end of the bar with the mouse, to move the interval, use the right end of. The first antigenic map of the influenza ah3n2 virus from 1968 to 2003. Software package for mapping lowdivergent sequences against a large reference genome using the. Why is it such a successful method of studying relationships between virus strains. Concepts and applications for influenza antigenic cartography. The goal of this study was to evaluate for the first time the antigenic characteristics of an extensive and representative collection of recent egyptian h5n1 hpai viruses by the antigenic cartography and principal component analysis pca and to assess the antigenic differences of clade 2.
A handson introduction to antigenic cartography and antibody landscapes. Software for the the detection of antigenic peptides several methods based on various physiochemical properties of experimental determined epitopes flexibility, hydrophibility, accessibility have published for the prediction of antigenic determinants, of which the antigenic index and preditop are good examples. Pdf a computational framework for influenza antigenic. Software for the the detection of antigenic peptides. In particular, guinea pig rbc are now preferred for antigenic.
Each strain is coloured to represent the antigenic cluster to which that strain belongs, while the antisera used in the hi assays are shown as uncoloured open shapes. Antigenic peptide prediction bioinformatics tools omicx. Antigenic peptides are determined using the method of kolaskar and tongaonkar 1990. A combination of antigenic and genetic data is routinely used to identify emergent antigenic variants. An antigen is usually a foreign substance, such as a toxin or a component of a virus. Antigenic cartography is a method that positions viruses and antisera as points in a map, such that. The technique provides, for the first time, quantitative measurements and a visualisation of phenotypic differences among the objects of binding assays, such as viral strains. Mapdiva is the proud recipient of the best mac application at the 2011 swipe design awards for our ortelius cartography software. Io cartography free to try time cycles software mac os x 10. Antigenic variation or antigenic alteration refers to the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters the proteins or carbohydrates on its surface and thus avoids a host immune response. Import industrystandard gis data formats and make crisp, clean maps with all attributes and georeferencing intact using the adobe illustrator design environment.
Ortelius introduces super smart cartography tools that speedup the process of manual map making, plus a full graphics suite to support your creativity. Responsible for the development of the toolset for antigenic cartography to support scientific research of biological viruses. A single antigenic determinant or epitope is between 5 and 8 amino acids and therefore a peptide of 1520 amino acids will contain one or more epitopes. Dengue antigenic cartography consortium who collaborating. This program predicts those segments from within a protein sequence that are likely to be antigenic by eliciting an antibody response. The book was based on robinsons doctoral research which investigated the relationship between science and art in cartography and the resultant refinement of graphic techniques in mapmaking to present dynamic geographic information. Antigenic variation not only enables the pathogen to avoid the immune response in its current host, but also allows reinfection of. Jun 12, 2019 a handson introduction to antigenic cartography and antibody landscapes. Antigenmap 3d presents an online, interactive, and robust 3d antigenic cartography construction and. Students may learn traditional surveying and drafting techniques along with advanced spatial tools, such as gis software, computer graphics and data from satellites, aerial photography. Antigenic definition of antigenic by the free dictionary. In some cases, as in the image on the left, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. Im a trying to adapt jmol for usage as a viewer for antigenic cartography data.
Up to 10 years ago, maps were made by professional cartographers, who had the time and the need to carefully plan where each map feature would be placed and consider the visual impact of the map. Antigenic cartography of h1n1 influenza viruses using. May 30, 2008 this guest post was written by terry jones, former antigenic cartographer and founder of fluidinfo. Mapping the evolution of pathogens who collaborating centre. The role of antigenic cartography in monitoring derek smith department of zoology, university of cambridge, uk department of virology, erasmus medical center, nl antigenic map influenza a h3n2 19682004 smith et alscience 305, 3776, 2004. We present two variations of software cartography, an of. This tool is able to produce results with an accuracy about 75 per cent. These include price, functionality, and whether you need high quality map data. Collaboration on h5 antigenic cartography preliminary antigenic map of h5 hemagglutinin in recognition of the rapid genetic and antigenic evolution of highly pathogenic avian influenza viruses of the h5 subtype, investigators from the university of cambridge, the university of wisconsin at madison, and erasmus medical center in rotterdam are. In some cases, as in the image above, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. I need recommendation about antigenic software or epitope mapping software.