{"id":7653,"date":"2016-02-12T17:35:06","date_gmt":"2016-02-12T22:35:06","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/?p=7653"},"modified":"2019-03-08T03:27:35","modified_gmt":"2019-03-08T03:27:35","slug":"microbial-dark-matter-agbt-2016","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/microbial-dark-matter-agbt-2016\/","title":{"rendered":"Microbial Dark Matter | AGBT 2016 Dispatch #2"},"content":{"rendered":"<p>What do Pigeons, Single cell sequencing and Dark Matter have in common? Find out on today\u2019s episode of Serving of Science!<\/p>\n<p><iframe loading=\"lazy\" width=\"760\" height=\"428\" src=\"https:\/\/www.youtube.com\/embed\/hW5UvuoeOi4?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p>It\u2019s Day 2 of AGBT and I can\u2019t even begin to tell you about all the amazing talks I\u2019ve heard so far which included topics about pigeons, single cell sequencing, and Microbial Dark Matter, so without further delay \u2013 let\u2019s get right into it.<\/p>\n<p>The first plenary session had some amazing talks and the ones that spoke to me were talks from Sam Aparicio of the British Colombia Cancer Research Center and Luis Diaz of Johns Hopkins Hospital.<\/p>\n<p>We understand today that cancers are heterogenous. Over time, certain clones may evolve to resist drugs or evade immune cells and there is spatial variation in how these genetically different clonal populations are distributed. <a href=\"http:\/\/molonc.bccrc.ca\/aparicio-lab\/\" target=\"_blank\" rel=\"noopener noreferrer\">Sam Aparicio<\/a> discussed the use of single cell sequencing to understand tumor evolution and cancer biology. He also discussed experiments where fragments of biopsied tumors were implanted in mice \u2013 to 1) see if the site of engraftment matters &#8211; which it does and 2) how stable these xenografts are over time \u2013 stability depended on the initial selection of mutations in the clones. Single cell sequencing has given insights into the complexity of these tumors and what\u2019s amazing is that in less than a decade we\u2019ve gone from sequencing bulk cells and large chunks of tumors to sequencing single cells to understand the role and biology of these single cells that make up the tumor mass.<\/p>\n<p>Today, we have the most comprehensive view of the coding regions of most human cancers via exome sequencing, but the problem is \u2013 how do we make sense of all this information \u2013 how do we put this knowledge to something usable. <a href=\"http:\/\/www.hopkinsmedicine.org\/profiles\/results\/directory\/profile\/0013086\/Luis-Alberto-Diaz%20Jr-MD\" target=\"_blank\" rel=\"noopener noreferrer\">Luis Diaz<\/a>&#8216;s talk emphasized the use of knowledge and technology to understand and study recurrence. He summed up his talk by saying we are more limited by biology than technology. Which, if you think about\u2026 is a pretty interesting place to be at.<\/p>\n<p>The primary focus of the morning session was to better understand cancer and tumor biology and how we can leverage knowledge and advances in current technology to better assess the state of the tumor after resection or chemotherapy.<\/p>\n<p>The afternoon sessions focused on evolutionary genomics, ancient DNA, and population genetics &#8211; again with some amazing talks, but the talks I really liked were those given by Beth Shapiro from the University of CA Santa Cruz and Eddy Rubin of DOE Joint Genome Institute.<\/p>\n<p>I just love <a href=\"https:\/\/pgl.soe.ucsc.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Beth Shapiro<\/a> \u2013 she cracks me up every time I listen to her. Her talk focused on sequencing the genome of the once abundant, yet now extinct Passenger Pigeon. Because there was no reference genome of this species, they decided to use the reference genome of a close relative \u2013 the band tailed pigeon. What was really interesting was that the mtDNA of the passenger pigeons showed no diversity, which was strange, although their genomic DNA showed tons of diversity \u2013 especially at the ends of the chromosomes, while the middle was not as diverse, which suggests possible recombination at the ends of chromosomes. It\u2019s just amazing that technology today is helping us understand and put together these puzzle pieces and make sense of an event like never before.<\/p>\n<p><a href=\"http:\/\/jgi.doe.gov\/about-us\/organization\/strategic-management\/eddy-rubin\/\" target=\"_blank\" rel=\"noopener noreferrer\">Eddy Rubin<\/a>\u2019s talk I think was my favorite. His talk focused on looking at the microbes that we cannot culture in the lab \u2013 which is about 98% and that\u2019s a lot. He first talked about generating complete draft genomes of uncultured bacteria using whole genome microbial sequencing. What followed is just amazing. He observed that while UGA codon is a stop codon in most bacteria, in some bacteria this stop codon now coded for an amino acid \u2013 Glycine \u2013 this is just mindboggling. This just added complexity to the already complex genome. Eddy then talked about Kryptonia, which are microbes found in hot springs \u2013 until today traditional 16S metagenomic sequencing didn\u2019t pick up them up in environmental surveys, because Kyrptonia had mismatches in the universal 16S primer site \u2013 WOW\u2026 I mean I really wonder how many such microbes we\u2019ve yet to uncover. Finally Eddy ends by saying that the holy grail of biology is not finding Yeti or the Lockness Monster, but to identify a new domain of life \u2013 which will help us understand how we evolved.<\/p>\n<p>I also had a chance to attend the concurrent sessions later in the day where the focus was on\u00a0single cell transcriptomics and epigenetics. Here are some highlights:<\/p>\n<ul>\n<li><a href=\"http:\/\/linnarssonlab.org\/cortex\/\" target=\"_blank\" rel=\"noopener noreferrer\">Sten Linnarsson<\/a> from Karolinska Institute discussed how we can capture the brain\u2019s complexity, cell-cell interaction and communication by sequencing single cells. Using single cell sequencing he was able to identify that radial glia are able to differentiate into three different cell types. Neurons are vastly more complex and diverse than other organs. Single cell sequencing is capable of classifying new cell types, dynamics of cell evolution, and the putative interactome. Sequencing single cells is an emerging and powerful technique that not only gives information about the cell itself, but also spatial information and how that cell reacts to its extracellular matrix.<\/li>\n<li><a href=\"http:\/\/www.thetcr.org\/user\/view\/849\">Chia-Lin Wei<\/a> of Lawrence Berkeley National Laboratory talked about the complex chromatin structure within the nucleus and how it is compartmentalized. She used an approach called Chia-PET to capture interacting complexes and study the interacting chromatin complex. She further discussed the impact and interaction between epigenetic modifications, non-coding elements, and polycomb group proteins.<\/li>\n<li><a href=\"http:\/\/www.nationaljewish.org\/Providers\/Researchers\/Max-Seibold\" target=\"_blank\" rel=\"noopener noreferrer\">Max Seibold<\/a> of National Jewish Health performed large scale single cell transcriptomics of the human airway epithelium. He discussed how single cell sequencing gives information about the diversity of the cells that make up the human airway epithelium. With such information we can further study the impact of environmental factors and lifestyle (smoking, pollution, etc) on gene expression. Max was also able to identify that cells previously thought to be terminal are actually plastic in nature.<\/li>\n<li><a href=\"https:\/\/www.linkedin.com\/in\/mohanbolisetty\" target=\"_blank\" rel=\"noopener noreferrer\">Mohan Bolisetty<\/a> from the Jackson Laboratory talked about alternative splicing in RNA. ~7 annotated isoforms per gene and over 80-90% of the genome encodes for multiple isoforms. There is tissue specific and cell-specific alternative splicing. In Drosophila, Dscam1 encodes for 38,016 isoforms using mutually exclusive exon splicing (MXE). Mohan discussed how current technology has allowed him to study alternative splicing and quantify isoforms.<\/li>\n<li><a href=\"http:\/\/www.einstein.yu.edu\/faculty\/10178\/masako-suzuki\/\" target=\"_blank\" rel=\"noopener noreferrer\">Masako Suzuki<\/a> of the Albert Einstein college of Medicine discussed DNA methylation and her talk focused on how representing DNA methylation in percentages doesn\u2019t provide information of the variation in methylation at CpG sites \u2013 whether the methylation is uniform or stochastic is lost. Masako suggested an additional metric \u2013 Methylation Entrophy. Methylation entrophy is a metric that provides information about how uniform or stochastic DNA methylation is throughout the CpGs in the target region tested. Such a method will better help us represent DNA methylation.<\/li>\n<\/ul>\n<p>I can\u2019t tell you how exciting this experience has been so far and I can\u2019t wait to tell you about the next sessions. I&#8217;d be more than happy to answer your questions, so please ask away in the comments section below! Remember to follow me on the Behind the Bench blog and <a href=\"https:\/\/twitter.com\/iontorrent\">Twitter<\/a>.<\/p>\n<p>&nbsp;<\/p>\n<p><strong>Post a comment to let me know what you think and be sure to catch recaps of <a href=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/sharing-data-is-caring-agbt-2016\/?socid=social_btb\" target=\"_blank\" rel=\"noopener noreferrer\">Day 1<\/a>\u00a0,\u00a0<a href=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/small-step-sequencing-agbt-2016\/?socid=social_btb\" target=\"_blank\" rel=\"noopener noreferrer\">Day 3<\/a>,\u00a0and <a href=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/agbt-2016-dispatch-4\/?socid=social_btb\" target=\"_blank\" rel=\"noopener noreferrer\">Day 4<\/a> of AGBT and our complete <a href=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/what-you-missed-at-agbt-2016-a-complete-recap\/?socid=social_btb\" target=\"_blank\" rel=\"noopener noreferrer\">AGBT Recap<\/a>.<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p>*For Research Use Only. Not for use in diagnostic procedures<\/p>\n","protected":false},"excerpt":{"rendered":"<p>What do Pigeons, Single cell sequencing and Dark Matter have in common? Find out on today\u2019s episode of Serving of Science! It\u2019s Day 2 of AGBT and I can\u2019t even begin to tell you about all the amazing talks I\u2019ve heard so far which included topics about pigeons, single cell sequencing, and Microbial Dark Matter,<\/p>\n","protected":false},"author":120,"featured_media":7654,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[113],"tags":[103,116,166,6],"division":[],"class_list":{"0":"post-7653","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-events-and-tradeshows","8":"tag-16s-rrna-microbial","9":"tag-agbt-2016","10":"tag-methylation-analysis","11":"tag-next-generation-sequencing","12":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.8 (Yoast SEO v27.8) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Microbial Dark Matter | AGBT 2016 Dispatch #2 - Behind the Bench<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/microbial-dark-matter-agbt-2016\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Microbial Dark Matter | AGBT 2016 Dispatch #2\" \/>\n<meta property=\"og:description\" content=\"What do Pigeons, Single cell sequencing and Dark Matter have in common? Find out on today\u2019s episode of Serving of Science! 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