Tag Archives: microbiology

Everything (or, at least a lot) about Microbiology at UC Davis

So – getting lots of calls and emails and having local meetings with people interested in microbiology at UC Davis.  Rather than continuing to answer each person separately I am just going to put everything together on this page. Departments and groups with a major focus on microbiology.

Departments with a lot of people working on microbiology

Continue reading Everything (or, at least a lot) about Microbiology at UC Davis

Bad microbiology reporting of the month award: C-Net on IBM "Sequencing the City" meeting

Well, I am still really annoyed by this unbearable article on C-Net yesterday: IBM sees big opportunity in sequencing microbes by Daniel Terdiman.  The article is about this “Sequencing the City” meeting organized by IBM that was on Tuesday and Wednesday.  I talked at the meeting on Tuesday (I could not go on Wednesday).  For more about my talk see: What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)?.  But I am not criticizing the meeting here.  I am criticizing the article in C-Net which has many many flaws. For example consider:

According to James Kaufman, a research manager at the Almaden Research Center, the move to study metagenomics — the study of systems of micro-organisms — came from what he called a tipping point in big data. As more and more government-funded institutions study organisms and bacteria, they’ve collected more information about them, and submitted much of their work to centralized databases. “So there’s a growing library of genomes across the field of life,” Kaufman said. “That made possible metagenomics.”

What?  Metagenomics has been around for a long time.  Sure, many people in the field are taking advantage of so called big data, but there was no “tipping point” needed to launch the field.  This is just completely misguided.
And then even worse

The result: We can now look at and understand whole ecosystems at the bacterial level. One example of how that manifests is what IBM refers to as the Human Microbiome Project. According to an IBM document, that’s about characterizing “microbial communities found at multiple human body sites to discover correlations between changes in the microbiome with changes in human health.”

So – there have been dozens of high profile papers from the Human Microbiome Project.  There are hundreds of web pages with information about the project.  It was started years and years ago.  And the reporter quotes an “IBM document” to tell us what the Human Microbiome Project is?   And even worse the reporter says “what IBM refers to as the Human Microbiome Project” like they ran it / designed it.  Good that they refer to it as the Human Microbiome Project.  You know why?  Because that is what it is known as to all the other $(&@)(* people in the whole (%&# world.

The reporter goes on to write

This kind of work is not entirely new, but the scientists who will be gathering at IBM Research this week are grappling with one conundrum: they don’t know what they don’t know. So a big topic of conversation, and a big part of what IBM would like to see advanced, is “the ability to do metagenomics on the scale of a city or the world….That will depend on software services available in the cloud,” Kaufman said. “It has to be cheap, easy, and accessible from anywhere. That’s what we’re really good at.”

Once again making it seem like IBM is somehow leading this field.  Not to pick on IBM here.  I am glad they organized the meeting.  But either the reporter just got handed a press release from IBM and wrote it up, or did not do any type of background research, or both.  Sure IBM would like to see this.  But so would lots of other people.  Why make this all about IBM?  There are so many people who have done interesting work in the area of “microbiology of the built environment” – why are none of them even discussed?  What exactly is the point of this article if not to simply be a PR piece for IBM?  Aaaaaarg.

UPDATE 5/9 Storify of some of the Tweets about the meeting

A special special issue of RNA Biology – dedicated to Carl Woese and Open Access too

A must read for, well, everyone out there: RNA Biology: Table of Contents for a special issue dedicated to / about Carl Woese.  The issue includes an amazing collection of papers:

A special issue in memoriam of Carl Woese
Renée Schroeder
Page 169
http://dx.doi.org/10.4161/rna.28566

Introduction to special Carl Woese issue in RNA Biology
Robin R Gutell
Pages 170 – 171
http://dx.doi.org/10.4161/rna.28393

Carl Woese: A structural biologist’s perspective
Peter B Moore
Pages 172 – 174
http://dx.doi.org/10.4161/rna.27428

Early days with Carl
Ralph Wolfe
Page 175
http://dx.doi.org/10.4161/rna.27429

Molecular phylogenetics before sequences: Oligonucleotide catalogs as k-mer spectra
Mark A Ragan, Guillaume Bernard and Cheong Xin Chan
Pages 176 – 185
http://dx.doi.org/10.4161/rna.27505

Constraint and opportunity in genome innovation
James A Shapiro
Pages 186 – 196
http://dx.doi.org/10.4161/rna.27506

Carl Woese’s vision of cellular evolution and the domains of life
Eugene V Koonin
Pages 197 – 204
http://dx.doi.org/10.4161/rna.27673

From Woese to Wired: The unexpected payoffs of basic research
Ann Reid
Pages 205 – 206
http://dx.doi.org/10.4161/rna.27701

Carl Woese, Dick Young, and the roots of astrobiology
John D Rummel
Pages 207 – 209
http://dx.doi.org/10.4161/rna.27702

Life is translation
Bojan Zagrovic
Pages 210 – 212
http://dx.doi.org/10.4161/rna.27718

Organelle evolution, fragmented rRNAs, and Carl
Michael W Gray
Pages 213 – 216
http://dx.doi.org/10.4161/rna.27799

Remembering Carl Woese
Kenneth R Luehrsen
Pages 217 – 219
http://dx.doi.org/10.4161/rna.27800

Woese on the received view of evolution
Sahotra Sarkar
Pages 220 – 224
http://dx.doi.org/10.4161/rna.27883

This article is open accessSecondary structure adventures with Carl Woese
Harry F Noller
Pages 225 – 231
http://dx.doi.org/10.4161/rna.27970

A backward view from 16S rRNA to archaea to the universal tree of life to progenotes: Reminiscences of Carl Woese
Roger A Garrett
Pages 232 – 235
http://dx.doi.org/10.4161/rna.28228

Carl Woese in Schenectady: The forgotten years
Larry Gold
Pages 236 – 238
http://dx.doi.org/10.4161/rna.28305

History and impact of RDP: A legacy from Carl Woese to microbiology
James R Cole and James M Tiedje
Pages 239 – 243
http://dx.doi.org/10.4161/rna.28306

Casting a long shadow in the classroom: An educator’s perspective of the contributions of Carl Woese
Mark Martin
Pages 244 – 247
http://dx.doi.org/10.4161/rna.28002

Looking in the right direction: Carl Woese and evolutionary biology
Nigel Goldenfeld
Pages 248 – 253
http://dx.doi.org/10.4161/rna.28640

Ten lessons with Carl Woese about RNA and comparative analysis
Robin R Gutell
Pages 254 – 272
http://dx.doi.org/10.4161/rna.28718

Memories of Carl from an improbable friend
Harris A Lewin
Pages 273 – 278
http://dx.doi.org/10.4161/rna.28866

mBio – home of some really cool, #openaccess microbiology papers

Am really enjoying the suite of papers coming out in mBio – the Open Access PLOSOne like journal from the American Society for Microbiology.  Here are some examples of recent papers that caught my eye:

And many many more.  Kudos to ASM and mBio.

Metadata to collect while collecting plant associated microbial samples in the field

Another question for Twitter with some answers by Storify. Not I am putting in below the fold here so that the Storify emded only launches for those who want it to …
//storify.com/phylogenomics/metadata-to-collect-while-collecting-plant-associa.js[View the story “Metadata to collect while collecting plant associated microbial samples in the field” on Storify] In addition Russell Neches in my lab would like to add the following comments, which were too long for the comment option here.

The most important thing for interpreting -omic data is context. For
genomic data, this mostly means compare and contrast analysis against
other genomes, although there are other tools (GWAS-type studies,
ChIP-seq/chip, footprinting…). For metagenomes, comparisons against
other similar metagenomes can be of limited utility if the taxa
represented do not overlap very much.

The easiest thing would be to bring a smart phone and log GPS

coordinates and take wide and closeup photos, and make absolutely sure

that each one is explained in the field notes. This doesn’t necessarily
provide quantitative information, but it’s *REALLY* helpful to anyone

trying to analyze the data who wasn’t on the field mission. And it’s
cheap and easy.

For quantitative metadata, there are usually a number of abiotic
parameters that drive community structure, and many of these are
relatively easy to instrument. For example, pH, temperature and moisture
are very strongly correlated with community structure in terrestrial
soils. These parameters are very easy to measure. There are of course
other parameters that might be interesting; CO2, CO, CH4, C2H5OH, O2,
N2, nitrate, nitrite, phosphorous… but these are somewhat more
difficult to instrument at the moment, and (as far as I know) are
usually not as correlated with the very broad impact of pH, temperature
and moisture unless the system is near an extreme (e.g., the whole
system goes anaerobic, or metal-starvation in the open ocean).

However, while these parameters are easy to measure, they can also
fluctuate on time-scales that are relevant to microbial growth. As a
result, the temporal (and perhaps spacial) variation of these parameters
may be more important to the community structure than their “typical”
values. In way that is tends to frustrate field mission planning, it is
the temporal fluctuations *PRIOR* to sampling that are relevant.

There are two approaches : telemetry and local assistance. Telemetry
(“measurement from afar”) means placing instrumentation at the site that
has the ability to log or transmit data. Local assistance would vary
depending on the context of the site, but basically amounts to
partnering with someone who actually lives near the study site and
somehow convincing them to take measurements for you. Of course, the two
approaches are not mutually exclusive.

The simplest and probably best approach would be to partner with someone
near the study site who teaches fourth grade. Send them enough simple
gardener’s soil chemistry meters for their class (plus some extra for
the ones that inevitably get lost, disassembled or turned into
implements of mayhem and destruction).

For example, a quick search on Amazon turns up dozens of fairly
inexpensive gardening tools for measuring pH, moisture, temperature and
light intensity. Here’s one that looks like it might be useful :

http://www.amazon.com/Digital-Soil-Light-Tester-Plants/dp/B000RN23DM/

Here’s an even cheaper one that does pH, moisture and light, doesn’t
need a battery, and costs less than seven bucks :

http://www.amazon.com/Moisture-Meter-Light-Test-Function/dp/B007FMVOVK/

If you were asking a class of fourth graders to help gather metadata for
you, using instruments like these would cost perhaps $300, including
instruments, stationary, surveying flags, etc. Make that $500, and send
lots of extra stationary. Fourth grade classrooms never have enough
stationary.

Of course, if you’re going to ask people to do work for you, you must
treat them accordingly. Taking careful, regular measurements and writing
them down in a notebook is the bread-and-butter of science, and people
who do this work are called “scientists,” not “helpers.” There are
myriad implications to this, but one that I hope more people will
consider is sharing authorship. It is fair, it is honest, and it is
inexpensive.

The other option is telemetry. Thanks in no small part to the Arudino
project, this has gotten vastly easier and cheaper. At the cost of
learning a little bit about soldering and digital logic, you can wire up
virtually any sensor you like to a microcontroller, and then push that
data over a variety of communications platforms. There are Arduino
shields that interface with Ethernet, Wifi, Bluetooth, GSM, and even
satellite networks. Even a satellite uplink interface can be hacked
together for less than $200.

Of course, there are a lot of people interested in telemetry of various
sorts, and so you can find Arduino derivatives that have a lot of the
work done for you. For example, if you happen to want to want pH
telemetry, and your site happens to be within a few dozen meters of
someplace you can safely leave an old laptop, this product might
interest you :

http://www.sparkyswidgets.com/Products/Store/Details/tabid/81/ProductID/4/Default.aspx

Here’s another Arduino variant with an onboard FLASH logging interface,
solar/LiPo power management, a real time clock, a temperature sensor,
and interfaces for standard Arduino shields (e.g., a GSM shield), and an
interface for Xbee-style boards (e.g., bluetooth, Xbee, GPS, FM radio,
Wifi).

http://www.seeedstudio.com/wiki/Seeeduino_Stalker_v2.3

Attach sensors. Write software. Add battery and solar panel. Put into
watertight box. Deposit at field site.

Correcting for rRNA copy # in qPCR experiments

Asked this question on Twitter and thought I would share answers here via Storify.  I am putting it below the fold to allow people to avoid the Storify embed if they want to.
//storify.com/phylogenomics/correcting-for-rrna-copy-in-qpcr-data.js[View the story “Correcting for rRNA copy # in qPCR data” on Storify]

IBM will save the planet with this magical hydrogel – NOT

Well, press releases can drive me crazy.  And this one is one of the worst I have seen in a while: IBM News room – 2013-01-24 IBM and The Institute of Bioengineering and Nanotechnology Develop New Antimicrobial Hydrogel to Fight Superbugs and Drug-Resistant Biofilms – United States

This new fangled gel they have made they are very proud of.  That is good.  Pride in ones work is a good thing.  But getting the science wrong and making misleading statements is not.  Some statements I have issues with include

  • Able to colonize on almost any tissue or surface, microbial biofilms – which are adhesive groupings of diseased cells present in 80% of all infections – persist at various sites in the human body, especially in association with medical equipment and devices.
    • Huh?  Diseased cells?  What does this even mean?
  • When applied to contaminated surfaces, the hydrogel’s positive charge attracts all negatively charged microbial membranes, like powerful gravitation into a blackhole.
    • Again – huh?  How is this like gravitation in a black hole?
  • However, unlike most antibiotics and hydrogels, which target the internal machinery of bacteria to prevent replication, this hydrogel kills bacteria by membrane disruption, precluding the emergence of any resistance.
    • This is the killer statement.  They have apparently invented a treatment that no organism can resist.  It is therefore perfect.  Sort of like, well, penicillin?  Oh no, wait.  Sort of like chloroquine.  Oh no, wait.  I mean, sort of like streptomycin right?  Sorry – I meant tetracycline.  No no – I meant …. aaaaaaaaaaarrg.
I could go on.  Sounds like a possibly interesting new development.  But when you make absurd claims about it, and get the science all messed up, it does not give me that warm fuzzy feeling.  Annoyingly some news sources are basically just quoting from the PR with no skepticism.  For example, see this Daily Mail article. And this blip in The Star.  At least this in “The Conversation” has some comments on this being possibly overblown.  Anyway, shame on IBM for being more about hype than science.

RIP Carl Woese: Collecting posts / notes / other information about my main science hero here

My tribute to Carl Woese 12/30/12

Sadly, Carl Woese has passed away.  I am collecting some links and posts about him here in his memory.  He was without a doubt the person who most influenced my career as a scientist.

News stories about Woese’s passing

Some of my posts about Woese

Woese Tree of Life pumpkin (by J. Eisen)

Storification of Tweets and other posts about his passing //storify.com/phylogenomics/rip-carl-woese.js?template=slideshow[View the story “RIP Carl Woese” on Storify]

Other posts worth reading about Woese’s passing

Some videos with Woese 





Miscellaneous

My graduate student Russell Neches used a laser to etch a picture of Carl Woese on a piece of toast.

http://www.mendeley.com/groups/2940711/papers-by-carl-woese/widget/21/3/

The evil germy pacifier story is getting out of hand – w/ Dr. Glass misleading the charge

From Wikipedia

Oh for crying out loud.  This is getting out of control.  Two weeks ago I wrote about an over the top story in US News and World Report about pacifiers and microbes: The Tree of Life: Germophobia 101: there are microbes on pacifiers ….  The culprit in this story was a Dr. – Dr. Tom Glass – who was the lead presenter of some study at a meeting.  His study involved counting the number of colony forming units on used vs. new pacifiers.  And low and behold used ones were covered in germs.  Amazingly, this led Glass to say ridiculous things like

In the long run, it may be that what you do now [using a pacifier] may have a lot to do with whether a child ends up developing atherosclerosis or type 2 diabetes.

Completely misleading and deceptive and dangerous I would say.  And alas, the story has been crawling it’s way around the web picking up speed.  Now it is at Time.Com with another story about Glass’ work: Bacteria on Binkies: A Recipe for Crankiness | TIME.com.  Glass apparently is now blaming biofilms of pacifiers for all the problems.  And again Dr. Glass is (mis)leading the charge against pacifiers.

A lot of times when a child is cranky, the first thing a parent does is reach for a pacifier,” says Dr. R. Tom Glass, the study’s principal investigator and a professor of forensic sciences, pathology and dental medicine at Oklahoma State University. “But what are you using to treat the crankiness? It’s a vicious cycle.

and

“biofilms can potentially increase the likelihood of colic or ear infections and could possibly heighten the risk of allergies or asthma, says Glass.”

The reporter does present some skepticism from parents and from the literature.  But come one – why even report this crap from Glass.  I mean – I am all for keeping babies from getting sick and pacifiers very well may be a source of some nasties.  But let’s think about the big picture here.  Parents buy pacifier.  Parents open package.  Parents give to baby.  Baby puts in mouth.  Baby drops pacifier and it gets dirt on it as well as some germs.  Baby puts back in mouth.  Pacifier gets left on counter.  Things from babies mouth grow on pacifier.  Baby puts pacifier back in mouth.  And so on.  Tell me again where the pacifier introduces bad germs to this system?

UPDATE: some reading material

Can food safety be fun? Not sure, but this video is OK. #microbes

Continuing with my running theme of microbe-related music videos here is another one. It has good and bad parts. But then again, don’t we all …