redux-framework domain was triggered too early. This is usually an indicator for some code in the plugin or theme running too early. Translations should be loaded at the init action or later. Please see Debugging in WordPress for more information. (This message was added in version 6.7.0.) in /home/metasu5/public_html/wp-includes/functions.php on line 6114updraftplus domain was triggered too early. This is usually an indicator for some code in the plugin or theme running too early. Translations should be loaded at the init action or later. Please see Debugging in WordPress for more information. (This message was added in version 6.7.0.) in /home/metasu5/public_html/wp-includes/functions.php on line 6114wordpress-seo domain was triggered too early. This is usually an indicator for some code in the plugin or theme running too early. Translations should be loaded at the init action or later. Please see Debugging in WordPress for more information. (This message was added in version 6.7.0.) in /home/metasu5/public_html/wp-includes/functions.php on line 6114wp_haswell domain was triggered too early. This is usually an indicator for some code in the plugin or theme running too early. Translations should be loaded at the init action or later. Please see Debugging in WordPress for more information. (This message was added in version 6.7.0.) in /home/metasu5/public_html/wp-includes/functions.php on line 6114We will give an introduction to the Shanghai subway system and how we may contribute to the MetaSUB consortium. Then lessons learned from the three phases of the MicroArray and Sequencing Quality Control (MAQC\/SEQC, www.nature.com\/nbt\/focus\/maqc\/, www.nature.com\/focus\/maqc2\/, and\u00a0www.nature.com\/nbt\/collections\/seqc\/) project will be shared, hoping to help the planning and execution of MetaSUB.<\/span><\/p>\n —<\/p>\n I will highlight and describe the Sao Paulo subway system, describe some of our aims and goals with this project, and introduce our team of student volunteers and how we plan to collect samples.<\/p>\n —<\/p>\n We did swabs of subways in Tokyo and Sendai. Based on questionnaire data (\u201cWhat are you touching in subway?\u201d) from respondents, i.e. crowdsourced workers (lancers.jp), stairwell railings were selected as sampling sites for this preliminary study. We prepared tools for crowdsourced sample collection: i.e. data submission website, swab-kit, letterpack, Japanese instruction, and GeoLocation-tagging using Global Positioning System (GPS) from mobile —<\/p>\n The Center for Research in Infectious Diseases of the National Institute of Public Health is now 30 years old. Since its creation, the research activities of the Center have attempted to blend basic and applied research in infectious diseases. Until the last 5 years, the core of CISEI research dealt with HPV, vector borne diseases (mainly malaria and dengue) and antibiotic resistance. In the past 10 years, we incorporated novel approaches such as NGS and bioinformatics to modernize and leverage research. Currently, a more diversified agenda is planned for the coming decade, which includes the incorporation of epidemiologists and mathematicians to develop a fully integrative and multidisciplinary agenda in infectious disease research to support the National epidemiological surveillance infrastructure and operation.<\/p>\n —<\/p>\n Shotgun metagenomics has been an incredibly useful tool, but current sequencing protocols are unable to capture some of the most valuable information about microbial communities: genetic linkage information. Short sequence reads provide very little information on which genes, polymorphisms, or plasmids reside in the same cells. We introduce an adaptation of the 3C and Hi-C protocols to metagenomics that enables some of this linkage information to be recovered. We also introduce a protocol that enables high throughput sequencing of full – length 16S rDNA genes on the Illumina MiSeq, and discuss\u00a0application of this and the standard V4 amplicon protocol to the human skin microbiome in healthy and diabetic patients.<\/p>\n —<\/p>\n While analysis of metagenomic samples are primarily concerned by taxonomic annotation, using protein domain annotation can provide valuable additional information on the metabolic processes at play. I will present new computational paradigms that have been recently developed in the lab to identify and classify very divergent protein sequences in genomes and metagenomes. This opens the way to much finer annotations implying an unprecedented zooming into the metabolic processes of different environments. We shall briefly present the ideas of the computational method and its impact in the understanding of ecological and evolutionary information about marine ecosystem function, on which we are currently applying our method.<\/p>\n —<\/p>\n\u201cSao Paulo Subway Genomics\u2013Plan of Action\u201d<\/a> –\u00a0Houtan Noushmehr, University of S\u00e3o Paulo, Brazil<\/h3>\n
\u201cPathoMap Japan Node\u201d<\/a> –\u00a0Haruo Suzuki, Yamaguchi University, Japan<\/h3>\n
\nsensing. We discuss possible problems, including too much cleaning (every 2-3 days) in Tokyo subway, and effects of sample storage temperature on microbial community.<\/p>\n\u201cMultidisciplinary Research in Infectious Diseases: The CISEI Research Agenda\u201d<\/a> –\u00a0Jesus Martinez Barnetche, Center for Research in Infectious Diseases, National Institute of Public Health, Mexico<\/h3>\n
\u201cMetagenomics 3C, Full Length 16S Sequencing on Illumina, and the Human Diabetic Skin Microbiome\u201d<\/a> –\u00a0Catherine Burke & Aaron Darling, University of Technology Sydney, Australia<\/h3>\n
\u201cAccurate Functional Annotation of Metagenomic Samples\u201d<\/a> –\u00a0Hugues Richard, University Pierre et Marie Curie, France<\/span><\/h3>\n
\u201cThe Microbiome of the Eye\u201d<\/a> –\u00a0Zhi Xie, Sun-Yat-Sen University, China<\/h3>\n