Opening up to Diversity talk by @phylogenomics at #UCDPHSA

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Talk by Jonathan Eisen at the UC Davis PreHealth Student Alliance (#UCDPHSA) meeting 10/12/14

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Opening up to Diversity talk by @phylogenomics at #UCDPHSA

  1. 1. Opening Up to Diversity ! Jonathan A. Eisen @phylogenomics ! October 12, 2014 ! UC Davis Pre-Health Student Alliance
  2. 2. Diabetic at Conference
  3. 3. Diabetic at Conference
  4. 4. Diabetic at Conference
  5. 5. Diabetic at Conference
  6. 6. Pubmed Searching
  7. 7. Interesting Relevant Paper
  8. 8. Paywall
  9. 9. Symptom of A New Disease
  10. 10. Symptom of A New Disease Closed Accessitis
  11. 11. Symptom of A New Disease Elsevieritis Closed Accessitis
  12. 12. Disease Known for Many Years Elsevieritis Closed Accessitis
  13. 13. Public Library of Science (PLoS) • Started in 2000 by • Harold Varmus • Pat Brown • Michael Eisen • First action was to circulate an open letter on publishing
  14. 14. The Letter We support the establishment of an online public library that would provide the full contents of the published record of research and scholarly discourse in medicine and the life sciences in a freely accessible, fully searchable, interlinked form. Establishment of this public library would vastly increase the accessibility and utility of the scientific literature, enhance scientific productivity, and catalyze integration of the disparate communities of knowledge and ideas in biomedical sciences.We recognize that the publishers of our scientific journals have a legitimate right to a fair financial return for their role in scientific communication. We believe, however, that the permanent, archival record of scientific research and ideas should neither be owned nor controlled by publishers, but should belong to the public and should be freely available through an international online public library.To encourage the publishers of our journals to support this endeavor, we pledge that, beginning in September 2001, we will publish in, edit or review for, and personally subscribe to only those scholarly and scientific journals that have agreed to grant unrestricted free distribution rights to any and all original research reports that they have published, through PubMed Central and similar online public resources, within 6 months of their initial publication date.
  15. 15. The Letter We support the establishment of an online public library that would provide the full contents of the published record of research and scholarly discourse in medicine and the life sciences in a freely accessible, fully searchable, interlinked form. Establishment of this public library would vastly increase the accessibility and utility of the scientific literature, enhance scientific productivity, and catalyze integration of the disparate communities of knowledge and ideas in biomedical sciences.We recognize that the publishers of our scientific journals have a legitimate right to a fair financial return for their role in scientific communication. We believe, however, that the permanent, archival record of scientific research and ideas should neither be owned nor controlled by publishers, but should belong to the public and should be freely available through an international online public library.To encourage the publishers of our journals to support this endeavor, we pledge that, beginning in September 2001, we will publish in, edit or review for, and personally subscribe to only those scholarly and scientific journals that have agreed to grant unrestricted free distribution rights to any and all original research reports that they have published, through PubMed Central and similar online public resources, within 6 months of their initial publication date.
  16. 16. J-Can you get people to sign this and FAX it to me. 1-786-549-0137. Craig and Claires sigs would be greatly appreciated. I assume I can put your name on it, no? I set up a site http://www.publiclibraryofscience.org to keep lists of people who have signed. -M
  17. 17. PLoS After the Letter (2003) • > 25,000 people signed the letter •Small increase in open access support • But not enough • So PLoS announced the launch of their own journals •PLoS Biology •PLoS Medicine
  18. 18. Open Data Experiments
  19. 19. Open Data Experiments Useful but not convinced
  20. 20. Real Life Intervened
  21. 21. RhoGam • Supplier • RhoGAM should be administered within 72 hours of known or suspected exposure to Rh-positive red blood cells. • Wikipedia • It is given by intramuscular injection as part of modern routine antenatal care at about 28 weeks of pregnancy, and within 72 hours after childbirth.[5] It is also given after antenatal pathological events that are likely to cause a feto-maternal hemorrhage.[6] • Question • What happens if you do it even later?
  22. 22. Pubmed Search
  23. 23. Relevant Paper
  24. 24. Paywall You can purchase online access to this article (and all its versions) for a 24- hour period. Articles are US $ 29.95, with some exceptions where prices may vary. Click "Buy Now" to display the price
  25. 25. Relevant Paper 2
  26. 26. Paywall
  27. 27. Access Blocked - What Next? • Bought lots of articles ! • Tried to contact experts ! • Got friends to get some articles from libraries ! • Got more and more pissed off
  28. 28. Baby Lost • Benjamin Augustin Eisen stillborn August 29, 2003
  29. 29. Lack of Access • Scientist without access ! • Would access have helped? ! • Is limiting access useful or needed? ! • Goal of much of scientific and medical research is to spread knowledge
  30. 30. Closed Accessitis Still Prevalent Elsevieritis Closed Accessitis
  31. 31. Cure for Diabetes?
  32. 32. New Diabetes Stem Cell Paper in Cell
  33. 33. Full Text of Paper
  34. 34. Paywall
  35. 35. HHMI Supports Open Access
  36. 36. Social Media Critiques
  37. 37. HHMI Responds
  38. 38. HHMI Responds
  39. 39. Cure for Cell Accessitis? Elsevieritis Closed Accessitis
  40. 40. Cure for the Disease?
  41. 41. The Microbe Era MICROBES RUN THE PLANET
  42. 42. The Built Environment The ISME Journal (2012), 1–11 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE Architectural design influences the diversity and structure of the built environment microbiome Bacteria of Public time, the Steven W Kembel1, Evan Jones1, Jeff Kline1,2, Dale Northcutt1,2, Jason Stenson1,2, Ann M Womack1, Brendan JM Bohannan1, G Z Brown1,2 and Jessica L Green1,3 1Biology and the Built Environment Center, Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR, USA; 2Energy Studies in Buildings Laboratory, Department of Architecture, University of Oregon, Eugene, OR, USA and 3Santa Fe Institute, Santa Fe, NM, USA 0 Average contribution (%) Door in Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome—the community of microorganisms that live indoors—is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in in patient out ventilation and in outdoor air. The phylogenetic Stall Stall diversity handles rooms exposed to mechanical or window of airborne bacterial communities was lower indoors than outdoors, and mechanically Faucet ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors. The ISME Journal advance online publication, 26 January 2012; doi:10.1038/ismej.2011.211 Subject Category: microbial population and community ecology Keywords: aeromicrobiology; bacteria; built environment microbiome; community ecology; dispersal; environmental filtering Introduction Humans spend up to 90% of their lives indoors Toilet seat Toilet flush handle Sink floor microbiome—includes human pathogens and com-mensals interacting with each other and with their Microbial Biogeography of Public Restroom Surfaces Gilberto E. Flores1, Scott T. Bates1, Dan Knights2, Christian L. Lauber1, Jesse Stombaugh3, Rob Knight3,4, Noah Fierer1,5* Bacteria of Public Restrooms 1 Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America, 2 Department of Computer Science, University of Colorado, Boulder, Colorado, United States of America, 3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America, 4 Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, United States of America, 5 Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America Abstract We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear linkages between communities on or in different body sites and those communities found on restroom surfaces. More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the efficacy of hygiene practices. Figure 3. Cartoon illustrations of the relative abundance of discriminating taxa on public restroom surfaces. Light blue indicates low abundance while dark blue indicates high abundance of taxa. (A) Although skin-associated taxa (Propionibacteriaceae, Corynebacteriaceae, Staphylococcaceae and Streptococcaceae) were abundant on all surfaces, they were relatively more abundant on surfaces routinely touched with hands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, Ruminococcaceae, Lachnospiraceae, Prevotellaceae and Bacteroidaceae) were most abundant on toilet surfaces. (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were in low abundance on all restroom surfaces, they were relatively more abundant on the floor of the restrooms we surveyed. Figure not drawn to scale. doi:10.1371/journal.pone.0028132.g003 Citation: Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, et al. (2011) Microbial Biogeography of Public Restroom Surfaces. PLoS ONE 6(11): e28132. doi:10.1371/journal.pone.0028132 Editor: Mark R. Liles, Auburn University, United States of America Received September 12, 2011; Accepted November 1, 2011; Published November 23, 2011 Copyright: ! 2011 Flores et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported with funding from the Alfred P. Sloan Foundation and their Indoor Environment program, and in part by the National Institutes of Health and the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: noah.fierer@colorado.edu Introduction More than ever, individuals across the globe spend a large portion of their lives indoors, yet relatively little is known about the microbial diversity of indoor environments. Of the studies that have examined microorganisms associated with indoor environ-ments, differences in the relative abundances of specific some surfaces (Figure 1B, Table S2). Most notably, were clearly more abundant on certain surfaces restrooms than male restrooms (Figure 1B). Some family are the most common, and often most abundant, found in the vagina of healthy reproductive age women Figure 2. Relationship between bacterial communities associated with ten public restroom surfaces. Communities were PCoA of the unweighted UniFrac distance matrix. Each point represents a single sample. Note that the floor (triangles) and toilet (asterisks) form clusters distinct from surfaces touched with hands. doi:10.1371/journal.pone.0028132.g002 most have relied upon cultivation-based techniques to detect organisms residing on a variety of household surfaces [1–5]. Not surprisingly, these studies have identified surfaces in kitchens and restrooms as being hot spots of bacterial contamination. Because several pathogenic bacteria are known to survive on surfaces for extended periods of time [6–8], these studies are of obvious importance in preventing the spread of human disease. However, it is now widely recognized that the majority of microorganisms cannot be readily cultivated [9] and thus, the communities and revealed a greater diversity of bacteria on indoor surfaces than captured using cultivation-based techniques [10–13]. Most of the organisms identified in these studies are related to human commensals suggesting that the organisms are not actively growing on the surfaces but rather were deposited directly (i.e. touching) or indirectly (e.g. shedding of skin cells) by humans. Despite these efforts, we still have an incomplete understanding of bacterial communities associated with indoor environments because limitations of traditional 16 S rRNA gene cloning and sequencing techniques have made replicate sampling and in-depth characterizations of the communities prohibitive. With the advent of high-throughput sequencing techniques, we can now investigate indoor microbial communities at an unprecedented depth and begin to understand the relationship between humans, microbes and the built environment. the stall in), they were likely dispersed manually after women used the toilet. Coupling these observations with those of the distribution of gut-associated bacteria indicate that routine use of toilets results in the dispersal of urine- and fecal-associated bacteria throughout the restroom. While these results are not unexpected, they do highlight the importance of hand-hygiene when using public restrooms since these surfaces could also be potential vehicles for the transmission of human pathogens. Unfortunately, previous studies have documented that college students (who are likely the most frequent users of the studied restrooms) are not always the most diligent of hand-washers [42,43]. Results of SourceTracker analysis support the taxonomic patterns highlighted above, indicating that human skin was the primary source of bacteria on all public restroom surfaces examined, while the human gut was an important source on or around the toilet, and urine was an important source in women’s restrooms (Figure 4, Table S4). Contrary to expectations (see above), soil was not identified by the SourceTracker algorithm as being a major source of bacteria on any of the surfaces, including floors (Figure 4). Although the floor samples contained family-level taxa that are common in soil, the SourceTracker algorithm probably underestimates the relative importance of sources, like high diversity of floor communities is likely due to the frequency of contact with the bottom of shoes, which would track in a diversity of microorganisms from a variety of sources including soil, which is known to be a highly-diverse microbial habitat [27,39]. Indeed, bacteria commonly associated with soil (e.g. Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were, on average, begun to take of outside from plants hours after were shut proportion of the human back to pre-vious which 26 Janu-ary Journal, mechanically had lower diversity than ones with open win-dows. availability of fresh air translated proportions of microbes associ-ated human body, and consequently, pathogens. Although this that having natural airfl ow Green says answering that clinical data; she’s hoping hospital to participate in a study they move around. But to quantify those con-tributions, Peccia’s team has had to develop new methods to collect airborne bacteria and extract their DNA, as the microbes are much less abundant in air than on surfaces. In one recent study, they used air fi lters to sample airborne particles and microbes in a classroom during 4 days during which students were present and 4 days during in indoor microbial ecology research, Peccia thinks that the field has yet to gel. And the Sloan Foundation’s Olsiewski shares some of his con-cern. “Everybody’s gen-erating vast amounts of data,” she says, but looking across data sets can be diffi cult because groups choose dif-ferent analytical tools. With Sloan support, though, a data archive and integrated analyt-ical tools are in the works. To foster collaborations between micro-biologists, architects, and building scientists, the foundation also sponsored a symposium on the microbiome of the built environment 100 80 60 40 20 Door out Soap dispenser Toi l et f lo o r SOURCES Soil Water Mouth Urine Gut Skin Bathroom biogeography. By swabbing different surfaces in public restrooms, researchers determined that microbes vary in where they come from depend-ing on the surface (chart). on February 9, 2012
  43. 43. The Human Microbiome
  44. 44. Antimicrobials are in Everything
  45. 45. Become a Guardian of Microbial Diversity
  46. 46. Diversity in STEM
  47. 47. Diabetic at Conference
  48. 48. Diversity in STEM
  49. 49. Diversity in STEM
  50. 50. Diversity in STEM #DoSomething

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