Tag: microbenet

Undergraduate Research: Built Environment Genomes #microBEnet #Sloan

Just a quick post here.  We are continuing working on our Undergraduate Research projects in the “microbiology of the built environment” in my lab as part of our microBEnet project.  For more on the project we did last year on genome sequencing see this web site:Undergraduate Research: Built Environment Genomes | microBEnet: The microbiology of the Built Environment network.

And here is a video with some details on the project:

Also check out our new undergraduate project on sampling microbes in aquariums.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting

Meeting went well.  Here is a storification of it:

http://storify.com/phylogenomics/lake-arrowhead-microbial-genomes-2012-lamg12.js?template=slideshow[View the story “Lake Arrowhead Microbial Genomes 2012 #LAMG12” on Storify]

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Posts from #microBEnet that may be of interest

Quick post here – posting links to recent blog posts on the microBEnet blog that may be of interest here.  The microBEnet blog is part of the microBEnet project that I run on microbiology of the built environment.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Quick summary of session at #ASM2012 on “The Great Indoors” #microBEnet

 The session at the ASM 2012 meeting on “The Great Indoors” seems to have gone well. I will be writing up a more detailed report but here is a quick summary done via “Storify”.

http://storify.com/phylogenomics/asm2012-microbenet.js[<a href=”http://storify.com/phylogenomics/asm2012-microbenet” target=”_blank”>View the story “Session at #ASM2012 on The Great Indoors: Recent Advances in the Ecology of Built Environments ” on Storify</a>]

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some notes from GSC13 session on microbiology of the built environment #microBEnet

At the GSC13 meeting a few months ago there was a session on microbiology of the built environment which was sponsored by my microBEnet project.

Posting some details from the meeting here.

Meeting notes and reports

Talk videos:

Paula Olsiewski

  http://www.scivee.tv/flash/embedCast.swf

The Indoor Standards – What Parameters Do We Need to Record? Jeffrey Siegel (University of Texas at Austin, USA)

http://www.scivee.tv/flash/embedCast.swf

Minimal Metadata for the Built Environment: A MIxS Extension Lynn Schriml (University of Maryland, USA)

http://www.scivee.tv/flash/embedCast.swf

The Home Microbiome Project: Unraveling the Relationship Between Human-associated and Home-associated Microbial Signatures. Jack Gilbert (University of Chicago/Argonne National Laboratory, USA)

http://www.scivee.tv/flash/embedCast.swf

The Indoor Virome! Scott Kelley (San Diego State University, USA)

http://www.scivee.tv/flash/embedCast.swf

The Role of VAMPs in the MoBEDAC Initiative Mitchell Sogin (Marine Biological Laboratory, Woods Hole, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBEDAC – Handling Fungal Data From MicroBE Jason Stajich (University of California, Riverside, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBeDAC – Integrated data and analysis for the indoor and built environment Folker Meyer (Argonne National Laboratory, USA)

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Coming up at the #ASM2012 mtg. "The Great Indoors: Recent Advances in the Ecology of Built Environments"

The American Society for Microbiology meeting is starting tomorrow and there are multiple things related to microbiology of the built environment there.  These include a session that was organized by Brendan Bohannan which I am chairing.

The details of the session are below:

Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments

Session Date/Time: Sunday Jun 17, 2012 3:00 PM – 5:30 PM

Session Room: Esplanade Ballroom 300

Description: Although humans in industrialized countries spend nearly 90% of their time in enclosed buildings, we know very little about the biology of the indoor environment. However, this is starting to change. Over the past few years, the field of indoor ecology has grown dramatically. Ecologists are beginning to apply ecological theory and concepts to understanding buildings as ecosystems. A new understanding of the biodiversity of built environments is emerging, as well as a new appreciation of the importance of interactions between humans and non-human life indoors. The proposed symposium will showcase this emerging understanding. We will feature presentations that demonstrate the utility of ecological theory for understanding built environments, that describe the dynamics of biodiversity indoors and that illustrate the interactions of humans with indoor ecology. Our focus will be on the ecology of the dominant forms of non-human life indoors – microorganisms – and their interactions with humans.

 Talks

  • Jonathan Eisen microBEnet: the microbiology of the built environment network
  • Nicholas Be: Examination of the environmental air microbiome using deep sequencing
  • Katie Kirsch: A microbial analysis of environmental surfaces in hotel rooms
  • Mark Hernandez: Stability of airborne microbes to master environmental variables
  • John Senko: Microbial communities associated with flue gas desulfurization systems
  • Kimberly Ross: Drinking water delivery networks as microbial ecosystems
  • Jordan Peccia: The effect of environmental conditions on the allergenic potency of Aspergillus fumigatus spores
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

ABC radio news story on Indoor Ecology

Quick post here and it is not about OccupyUCDavis
Check out the story from ABC news (Australia, that is): Indoor ecology – RN Future Tense – 24 November 2011. Their summary:
We’re used to hearing about threats to our outdoor environment. But we rarely think about some of the challenges that we face in our indoor environment.
A growing number of researchers are interested in the idea of ‘indoor ecology’ – treating the indoors like the outdoors and studying the spaces that surround many of us every day.
It has a lot of good stuff about the Sloan Foundation program.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

An ecosystem in my house? Yes indeed. And with microbes too. #BostonGlobe #microBEnet

Well I am very excited about this article in the Boston Globe today: Ecosystem, sweet ecosystem – The Boston Globe. By Courtney Humphries the article discusses the Sloan Foundation program in the “Indoor Environment” that is focusing on microbial ecology of the built environment. I am, well, really into this area of work and have a grant from the Sloan Foundation in their program to crete something called “microBEnet” which stands for “microbiology of the Built Environment network.” And in case you were wondering, yes, the BE is supposed to be capitalized and the m in microbe is not. My work in microBEnet is focused on Science 2.0 activities to help boost interaction and communication and outreach relating to studies of microbiology of the built environment. Check out the microBEnet site for more detail on that project (more on this in a bit).
Anyway, a little while ago I was interviewed by Courtney Humphries about studies of microbes in the built environment and the conversation seemed to go pretty well. And I kind of forgot about it due to some family things going on in my life. And then yesterday I saw the article. It is quite nice. It starts off with a nice drawing of a house making it look like an ecosystem

and the headline/lead in is really quite perfect “Ecosystem, sweet ecosystem.” is the headline with the subtitle “What if we studies the indoors as an environment all it’s own”.  She goes on to quite Hal Levin (my collaborator on microBEnet), Jessica Green (the head of the BioBE center in Oregon focusing on biology of the built environment), me, Paula Olsiewski (the Program Officer at Sloan in charge of the Indoor Environment program) and Bill Nazaroff from Berkeley, who is also funded by the Sloan Foundation to work in this area.

The article is definitely worth a read.  Only issue really is that I have a feeling people may be distracted by some sort of storm hitting the East Coast right now.  Well, after the storm hits, microbiology of the indoor environment will likely be even more important to pay attention to.

If you want to brush up on studies of microbiology of the built environment check out some of the resources we have made and/or collated at microBEnet including:

Stay tuned for more, from microBEnet, from Sloan funded researchers, and from others studying microbiology of the built environment.  We spend on the order of 90% of our lives in built environments like buildings, cars, trains, etc.  It’s about time we started studying such environments as ecosystems …
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some recent posts (of mine) from http:microbe.net on microbes of the built environment that may be of interest

Just thought I would post a little list here of some recent blog posts I have made at a relatively new blog for my microBEnet project.  I may cross post occasionally but for now just going to post a list:

Would love it if people checked out the blog: http://www.microbe.net/microbenet-blog/ and the web site http://www.microbe.net/ and let me know what you think.   
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Travel and meeting notes from #IndoorAir2011 in Austin Texas #microBEnet

Here are some quick notes from my trip to Austin Texas for the Indoor Air 2011 meeting.

About the meeting:
I got involved in helping organize a session at this conference as part of my microBEnet project.  More on the planning and the meeting later but here are some quick notes just to get them out there.  I wrote a bit about the run up to the meeting in the following posts:

The meeting.
Below are some notes about the trip with twitter posts, pictures, and a few comments.  I will post later with some more “scientific lessons learned” and such.  But wanted to get this out there before I forgot details.

Headed out June 6.
Was going to head out June 7 but decided to head out late on June 6 so I could get to the meeting a bit earlier.  I am posting my tweets below as a guide to the trip.  Tweets are highlighted in yellow.

Had a two plus hour layover in Las Vegas airport.  What a horrible place with all the noise, the slot machines, and such.  So I finally found a place that was reasonably quiet for dinner.  Plus it had the hockey game on so I was happy.

  • How to have fun at Vegas airport – sit near security & watch ; apparently what happens in Vegas stays at security
  • @PsiWavefunction sorry – you missed the hidden joke – I can’t tell story because what happens at security …. twitpic.com/582r4r

When I got on the plane to Austin, I got the window seat in the emergency exit row that has the most room.  And eventually someone came to sit in the middle seat.  And he seemed, well, a bit off.  I did not realize why until a Southwest attendant came to ask people if they could ha\ndle the duties of the exit row and the attendant started asking this person when he had his last drink.  And then they decided he was drunk and nicked him out of the exit row. 
  • Wow, on plane about to leave for Austin; southwest attendant moved person out of exit row next to me b/c he was drunk twitpic.com/582uko
  • Good call Southwest – keeping planes safe (see last post)
Arrived in Austin.  Had to wait a bit for a shuttle to the “Airport Hilton” which was weird to me because they told me it was in the terminal.  Liars.  So I snooped around at the pet bathroom area:

Finally got to the hotel – was very very tired.  And I took some pics and went to sleep.

Day 2: 
Got up pretty late and had some coffee in the cafe in the lobby and took some pictures

Then I headed out to downtown to my new hotel.  Nice view from my room.

And I met Jason Stajich at the hotel and then David Hillis from UT Austin picked us up to go to lunch (well, David came to pick me up but I had met up with Jason and invited him, assuming it would be OK with Hillis).  Hillis is truly one of my favorite people in all of science.  He took us to a good Mexican place nearby.  And we talked about all sorts of things over lunch.  Hillis wrote a funny post about this on Facebook but since it is not “public” I cannot link to it here.  Mostly he was commenting on the strange looks we got when talking about microbes living in and on people. 
And then Hillis dropped us off and Jason came by my room while I grabbed some stuff to take over to the convention center. 

We then walked on over to the Convention Center and as always I took some pics of the interesting stuff along the way:

I registered and dropped in on some talks:
  • Learning about affect of copper vs Aluminum surfaces in HVACs on microbial growth: copper seems to control growth better #IndoorAir2011
Did not post much since I did not yet know the rules about twitter usage at the meeting.  I ran back to my hotel to get something I forgot and then headed back to the Convention Center again.  This is one reason I like staying in hotels right next to meetings.

On my way out I bumped into Norm Pace who was on his way in.
After a few minutes at my hotel I returned to the Convention Center for more talks and meeting people:
I went to a talk or two but did not last long.  Not enough on microbes this day. And so I headed to the product show with Russell Neches a PhD student in my lab.  

Finally there was a session that appealed to me:
  • Yuguo Li, Bill Nazaroff, Hal Levin, Charlie Weschler &; Jan Sundell now discussing continuity between indoor & outdoor air #IndoorAir2011
  • Charlie Weschler “Outdoor measurements are useless in exposure analysis? No! Ozone” When outdoor ozone up so is indoor #IndoorAir2011
  • Weschler: Why care about ozone? Morbidity and mortality go up when ozone does #IndoorAir2011
  • Bill Nazaroff discussing indoor vs outdoor exposures and a tutorial on particles which come in a whole zoo of forms #IndoorAir2011
  • Nazaroff working on models to predict indoor exposure from measures of outdoor air #IndoorAir2011
  • Having serious jargon/context #fail issues at talks at #IndoorAir2011 tho Nazaroff from Berkeley nearly flawless in being jargon free #wow
  • RT @IAQnerd: “43 chemicals found in virtually every pregnant woman” #indoorair2011 #TSCA #NAGP #holisticmoms #healthychild
  • My collaborator on microbe.net #microBEnet Hal Levin now discussing microbes indoor/outdoor #IndoorAir2011
  • It is funny that at the #IndoorAir2011 sessions there have been troubles with WindowsOS – do indoor air researchers dislike windows?
  • Funny notion from speaker at #IndoorAir2011 – windows define buildings as much as doors so why not say we are “Inwindows”
  • Speaker at #IndoorAir2011 “Indoor air is much more important than outdoor air” but $$ is in outdoor air – though I & others don’t agree
  • @phylogenomics VIA @ryneches Richard Corsi has given us permission to tweet, advises against emulating congressmen. #indoorair2011
  • @B_EMC Yuguon Li
  • @B_EMC actually I think it was Jan Sundell who said that

And then eventually I headed to dinner with Jason Stajich and took some more pics.  We wandered around town a bit before ending up at the Shoreline Grill and David Coil,  a post doc from my lab, showed up a bit later to meet us there.

Day 3

Got up reasonably early and took some pics from my room in the AM

Then headed over to the conference center as soon as I could because Craig Venter was on the agenda for the AM session.

Session on Microbiomes of the Built Environment.  First speaker – Beverly Wright.
Next speaker – J. Craig Venter.
  • Next up at #IndoorAir2011, Craig Venter – as an aside his most recent pub is one w/ me on stalking the 4th domain http://tinyurl.com/64rtyvc
  • Jesse Ausubel – says there must be meaning in the universe b/c speaker at Indoor Air meeting is named “Venter” #IndoorAir2011
  • Ausubel says he is “an advertisement” for Craig Venter and gives a bit of an biography of Craig in 2 minutes #IndoorAir2011
  • Ausubel gave a very glowing, flowing, comprehensive, yet remarkably short intro to Craig Venter #IndoorAir2011
  • Venter: discussing converting the analog code of DNA into a digital code of data “digitizing DNA” #IndoorAir2011
  • Venter used three slides to cover the history of genome sequencing #IndoorAir2011
  • Venter predicts in the future companies will pay people to sequence their genomes to get the data #IndoorAir2011
  • Venter discussing microbes in mouth says “think about that while the person next to you is coughing, or you are kissing them” #IndoorAir2011
  • Venter suggesting that esophageal cancer samples have unique microbial composition – says cause vs effect not known #IndoorAir2011
  • Venter: w/ metabolomics can track which chemicals in blood come from human metabolism vs. food vs. bacteria/microbes #IndoorAir2011
  • Venter: you are not just who you are and what you eat but also what you feed your bacteria #IndoorAir2011
  • Venter: some think his most brilliant discovery was figuring out how to sail around sea and do science at same time #IndoorAir2011
  • Venter: emphasizes the #PLoSBiology collection on ocean metagenomics including his/my GOS papers ploscollections.org/article/browse… #IndoorAir2011
  • Venter showing reference genome plots of Doug Rusch such as ploscollections.org/article/slides… #IndoorAir2011
  • Venter showing Jeff Hoffman sampling frozen lakes in Antarctica – massive amounts of biomass and biodiversity #IndoorAir2011
  • Venter saying very low diversity in microbes 1mile deep in ocean/crust — suggests that UV light may be driver of diversity #IndoorAir2011
  • Venter: working on air microbes – it was much harder than anticipated and thanks Sloan foundation for their patience #IndoorAir2011
  • Venter: very little biomass recovered from indoor air; have to run samplers for long time; but they get contaminated; #IndoorAir2011
  • Venter: v. hard to get water clean enough (i.e., without DNA contamination) to use in studying samples w/ very little biomass #IndoorAir2011
  • Note – I don’t buy the “UV light” connected to diversity explanation Venter just gave at #IndoorAir2011 – just reporting what he is saying
  • @subsurface_life he was not talking about richness but variation among close relatives; says there is less genetic diversity w/in species
  • Venter: now looking at samples from the Space Station #IndoorAir2011
  • Venter: in New York Indoor Air – the major source of DNA is human; #2 is rodent; microbes are a small % #IndoorAir2011
  • Venter: outdoor air in NYC most DNA is rodent, human a bit less than in indoor air #IndoorAir2011
  • @subsurface_life millions of reasons other than UV – just posted a separate tweet saying I don’t believe it
  • Venter: in NYC there is lots of iron in the outdoor air; “if you are anemic that might be good but otherwise probably not” #IndoorAir2011
  • @pzmyers apparently, though unclear how they sampled — did say that at Scripps Pier the #1 signal was insect
  • @Toxicpath @pzmyers unclear how the air sampling worked so not sure why they were getting so much rodent/human DNA vs. insect, bacterial
  • Venter has now shifted to discussion synthetic biology #IndoorAir2011
  • Venter shows a very very simple animation and says “We have this very sophisticated movie to show this” #ScienceHumor #IndoorAir2011
  • Venter: creating prokaryotic chromosomes in yeast; waiting for Norm Pace to learn him about “just say no to prokaryote term” #IndoorAir2011
  • Venter: says massive growth in population means that new biotech. dvlpmts (e.g., synthetic biology, fuels, etc) are needed #IndoorAir2011
  • Venter ends with discussion of ethics and synthetic biology #IndoorAir2011
  • They just asked Venter @ryneches twitter question “Can I have your boat?”#indoorair2011
Then Bill Nazaroff
  • Now starting session on “Microbiomes of the Built Environment” supported by @SloanFoundation -1st speaker is Bill Nazaroff #IndoorAir2011
  • Nazaroff “Newton meets Darwin and the Indoor Microbiome” discussing sociology of science #IndoorAir2011
  • Nazaroff quoting John Harte from “Towards a synthesis of the Newtonian and Darwinian worldviews” #IndoorAir2011
  • Here is a link to John Harte’s excellent paper on Newtonian vs Darwinian synthesis http://bit.ly/lBrK4C #IndoorAir2011
  • Note I worked at RMBL for two summers when John Harte was there – I really like him – and lived w/ his son there #IndoorAir2011
  • Nazaroff: successful collaborations come from small groups working on close contact rather than large teams #IndoorAir2011
  • Nazaroff: finding ways to keep egos under control is a key issue in scientific collaborations #IndoorAir2011
  • Nazaroff: DNA based methods are game changing in Indoor Microbiome studies but we still need to ask the right questions #IndoorAir2011
  • Nazaroff discussing work w/ Jordan Peccia looking at microbial surveys in classrooms as well as BIMERC project at Berkeley #IndoorAir2011
Then Norm Pace
  • Now up, the one and only Norm Pace – discussing rRNA surveys of human occupied indoor environments #IndoorAir2011 #Oneofmyscienceheroes
  • Pace: his job here is to help people transition from whatever microbiology they learned in a past life to modern microbiology #IndoorAir2011
  • psgcom #indoorair2011 check out www.microbe.net for more on Sloan Foundation funded work on Microbes of the Indoor Environment #microbenet
  • Pace: lots of microbes in tap water (good source of protein) but to understand those microbes you need to use sequences #IndoorAir2011
  • Here is a list we made of Sloan Foundation projects on microbes in the built environment microbe.net/grantees/ #microBEnet #IndoorAir2011
  • Pace: using fluid impingers to sample air – need ones with massive throughput #IndoorAir2011
  • Pace: key point – for studying microbes via DNA cleanliness (i.e., no contaminating DNA) is more important than sterility #IndoorAir2011
  • Pace: Indoor air microbiology is mostly about microbes shed by humans #IndoorAir2011
  • Pace: key for future of IndoorMicro is bring together people from different fields; that’s why we created http://microbe.net #IndoorAir2011
M. Taubel.
  • Next: M. Taubel on diversity and dynamics of bacteria in house dust #IndoorAir2011
  • Taubel: Interested in “hygeine hypothesis” and how exposure to microbes affects asthma, allergy, automimmune dvlpmt #IndoorAir2011 #fb
  • @Chris_Evelo Well, don’t forget each human cell has a lot more DNA than each microbial cell (well, for most microbes) #IndoorAir2011
  • Taubel referencing bacteria-dust studies in BMC Microbiology 8:56 and J. Allergy Clin Immunol 124: 834 #IndoorAir2011
  • Taubel: not going into details of methods b/c 90% of people understand methods and 10% only care about results #IndoorAir2011
  • Taubel used a term I have not seen: SLOTUs – species level operational taxonomic units; though I note I 1st read it as SLUTS #IndoorAir2011
  • Taubel: mattress dust has lower richness of bacteria (# of species) than floor dust #IndoorAir2011
  • Taubel: most of what they find in house dust is similar to microbes found on people #IndoorAir2011
Denina Hospodsky

Lew Harriman

  • Next speaker is Lew Harriman from a consulting company http://MasonGrant.Com: focused on water availability #indoorAir2011
  • Harriman: buildings are designed to be dry, not damp; though I note damp doesn’t always mean bad #IndoorAir2011
  • Harriman: measurements of relative humidity usually focus on air but probably should measure on surfaces #IndoorAir2011
  • Now up Miia Pitkaranta from Finland: seasonal variation in microbes in buildings & affect of H20 biocenter.helsinki.fi/bi/dnagen/indo… #IndoorAir2011
  • Miia Pitkaranta refs on Indoor Microbiology AEM 74:233 & BMC 8: 56 #IndoorAir2011
  • Pitkäranta: species richness in dust is very high; ~ 10-20% of species cultivable; phylogenetic diversity of fungi high #IndoorAir2011
  • Pitkäranta: spatial variation in microbes in dust from different parts of buildings very high #IndoorAir2011
Gunilla Bok
  • Next at #IndoorAir2011 Gunilla Bok: Identification of mould fungi by blast similarity searches and phylogenetic analysis
  • Kudos to meeting organizers of #IndoorAir2011 for diversity of speakers: young -> old; diverse country, genders, etc
  • Next & last this AM: Alina Handorean on phylogenetic analysis of microbes from bioaerosols from a flooded building #IndoorAir2011
Hal Levin
  • Hal Levin, my collaborator on #microBEnet http://microbe.net is now talking at #IndoorAir2011
  • Hal Levin trying to determine what is known about environmental factors that influence indoor microbial ecology #microBEnet #IndoorAir2011
  • Levin: some environmental factors affecting microbial ecology: humidity, temp, ventilation, surfaces, chem composition, pH #IndoorAir2011
  • Nazaroff points out that human occupants have profound influence on microbial ecology #IndoorAir2011
  • Another speaker suggested building age is important in microbial ecology indoors #IndoorAir2011
Mike Frankel
  • Now up Mika Frankel discussing influence of season and sampling methods on inferred microbial composition #IndoorAir2011
  • Frankel sampling in airborne and settled dust in four rooms in five homes #IndoorAir2011
  • Personal opinion – I am not a big fan of very short talks at meetings – I like 20-30 minutes not 10-15 #IndoorAir2011
Brendan Bohannan
  • Now up Brendan Bohannan – arguably one of the greatest speakers in the whole field of microbial ecology #IndoorAir2011
  • Bohannan is involved in the BioBE center (Biology and the Built Environment Center) at U. Oregon biology.uoregon.edu/biobe/?p=124 #IndoorAir2011
  • Bohannan discussing “How Communities Assemble”: two major categories – sampling & filtering #IndoorAir2011
  • Bohannan: filtering in microbial ecology is fact that some environments support growth of some taxa over others #IndoorAir2011
  • Bohannan: sampling in microbial ecology is the idea that in some cases microbes you see are just sampling from larger pool #IndoorAir2011
  • Bohannan: microbes in buildings are mostly from sampling/filtering from two pools – outdoor air & human occupants #IndoorAir2011
  • Bohannan: trying to understand how microbial communities assemble in a hospital #IndoorAir2011
  • Bohannan: indoor air is different from outdoor air (he knows this is not surprising); outdoor much more diverse #IndoorAir2011
  • Bohannan: are indoor samples subsets of the species found outdoors? No – appear to be very distinct types of microbes #IndoorAir2011
  • Bohannan: comparing indoor & outdoor air microbes to those in soil, humans, etc; indoor air more like skin; outdoor like soil #IndoorAir2011
  • Bohannan: microbes in some rooms like outdoor air/soil, in other rooms like people; #IndoorAir2011 differences may be due to ventilization
  • Bohannan: higher the airflow in room, the lower the frequency of organisms closely related to human pathogens #IndoorAir2011
  • Bohannan: suggests architects in future could design buildings with “microbial comfort” in mind and not just human comfort #IndoorAir2011
Jordan Peccia
  • Norm Pace points out that should be very careful w/ term pathogen esp. when we don’t know actual pathogenicity #IndoorAir2011
  • Jordan Peccia discussing growth of Aspergillis spores #IndoorAir2011
  • Note -before Pace said should say “organisms related to pathogens” I said “organisms closely related to human pathogens”#IndoorAir2011 #Ego
  • Peccia – are all Aspergillis spores the same (in terms of allergenicity and other things)? #IndoorAir2011
  • After talks the whole of #IndoorAir2011 is heading to the Salt Lick Bar-B-Que Restaurant saltlickbbq.com #NotVegetarianFriendly
  • Peccia: culturability & qPCR can significantly (5-50x) underestimate allergenicity of A. fumigatus spores produced at low T° #IndoorAir2011
  • If I had videos of Brendan Bohannan’s talks I have recently seen, I would make a mashup & use it for my talk tomorrow at #IndoorAir2011
Ming-Ching Liang

Then I headed back to my hotel for a bit and took a few more pics.

I decided not to go to the Salt Lick BBQ party mostly because I wanted to stay near the water.  And so eventually a few of us gathered together and I found a place near the hotel/convention center.  Jason Stajich and I got there early and went to Clive Bar which was very nice. 

And then Shannon Williamson showed up and we eventually made it across the street to a little “cart” restaurant that was rated very highly called Cazamance.

  • Of course I wants to eat here with a “Tree of Life” logo – Cazemance – food was great (@ Cazamance) [pic]: http://4sq.com/kUJDm6

I had a bit of insomnia as usual when travelling and was then woken up when I finally fell asleep by a helicopter nearby:

Day 4

Got up early again.  Headed out to breakfast and coffee and worked on my talk for a while.  There was a session this AM in which I was speaking.  The session was on microbiomes of the built environment and it was coorganized by Hal Levin as part of my microBEnet project.

Posted my slides (which I had worked on over breakfast)

Jesse Ausubel gave the opening talk:
  • Jesse Ausubel from Sloan Foundation up at #IndoorAir2011: the Known, Unknown & Unknowable (KUU) Framework to developing a research agenda
  • Ausubel: Sloan Foundation started by ex-GM head- though no connection now, he notes maybe we should study microbes in cars #IndoorAir2011
  • Ausubel: built environment of course critical to development – the more we understand it the better #IndoorAir2011
  • Ausubel refs Josh Lederberg & his interest in biodefense – if we want to detect anthrax in air need to know the background #IndoorAir2011
  • Sloan originally interested in general survey of microbes in the built environment & basic science in this area #IndoorAir2011
  • Key to Sloan $$$: they are seed money/science venture capital – they hope it leads to “powerful organized gang” i.e. a field #IndoorAir2011
  • Ausubel: what can Sloan do? funds specific projects as well as the “glue” to hold projects together e.g., http:microbe.net #IndoorAir2011
  • Ausubel: Sloan Foundation very supportive of open science including #openaccess to literature and sharing in various ways
  • Sloan has supported many #PLoS activities including the new PLoS Hubs in Biodiversity http://hubs.plos.org/
  • Ausubel says we should think about “macroprojects” that need collaboration- asks if there are BigScience needs #IndoorAir2011
  • Ausubel says it is the unknown that sets the research agenda for fields & allows for marketing to get more resources #IndoorAir2011

Aino Nevalainen

  • Aino Nevalainen : introducing microbiology and the indoor environment #IndoorAir2011
  • “I have feeling I have to do a 100 meter sprint on a distance that is a marathon” – i.e., too much to cover, too little time #IndoorAir2011
  • Nevalainen: quoting Leviticus regarding leprous plague and what to do Leviticus 14: 33-38, 39-42, 43-47 #IndoorAir2011
  • Nevalainen: priests were the first indoor air consultants, regarding quarantine and leprosy #IndoorAir2011
  • Nevalainen refs. MH Gordon 1904 Bacterial test for estimating pollution of air. Sppl. for 32. Ann Rep of the Local Gvmt Board #IndoorAir2011
  • Nevalainen refs Richards 1954 J. Allergy 25: 429 – Atmopspheric molds spores in and out of doors #IndoorAir2011
  • Nevalainen refs JACI 62: 22-26 Hirsch et al. 1978, Ann Occup Hyg 27: 341-358 Ager and Tickner 1983, Lidwell and WC Noble 1975 #IndoorAir2011
  • Nevalainen refs studies of humans as source of microbes in air: Sciple etal. ’67, Duguid & Wallace ’48, Noble & Davies ’65 #IndoorAir2011
  • Nevalainen refs nice reivew of microbial ecology of skin by Roth and James 1988: IDs factors modifying normal flora #IndoorAir2011
  • Nevalainen sources of indoor microbes: outdoor air, uses of buildings (people, pets, etc), microbial indoor habitats #IndoorAir2011
  • Nevalainen does not mention plants as a source of indoor microbes – something I am interested in studying … #IndoorAir2011
  • Nevalainen: aerosols in indoor air behave in same general way as those outdoors #IndoorAir2011
  • Nevalainen: microbial exposure associated w/ health, both positive (e.g., protection agst allergy) negative (e.g., pathogens) #IndoorAir2011
  • Nevalainen: microbes growing on building surfaces are “bad microbes” in the sense that they should be an area of concern #IndoorAir2011
  • Nevalainen: the way ahead – more info on exposure & health; more info on whether culturable are good models for all microbes #IndoorAir2011

Then I gave my talk and we had multiple break out sessions which seemed to go well discussing the future of indoor microbiology studies.

Then headed to a dinner I hosted for Sloan Funded researchers working on microbiology of the built environment.  Again to the Shoreline Grill (I did not realize this is where we were going to have the big dinner when I had gone there a few days before)

Then drinks and people started to show up

Then dinner with a mini break in the middle to see the bats which fly out from under this bridge nearby.

Then back to dinner and dessert:

  • Best question of the day “So what about the viruses” #microBEnet – don’t ignore the viruses

More dinner pics

Then to drinks at the Four Seasons and eventually to sleep:

  • Cool – the Four Seasons in Austin has a cowboy boot vending machine twitpic.com/59euel

At the airport I bumped into William Gunn from Mendeley:

I made a few last posts:

And headed home

To where I was greeted by my family and my cats:

Then I posted some final links:

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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