Hiring a Lab Technician

7 Feb

I’m a Fatboy Slim fan, and when I decided to write today’s post, “Praise You” started playing in my head.  Besides the fact that I need to update my music taste, it reminded me that I want to thank all my faithful followers out there for waiting around for me to post again.

It’s been ages (2 years to the day) since I’ve posted and I salute you both.

Many things have changed since I was blogging last… I’m now the proud SciMom to two little rugrats, and a tenure-track faculty member at Wazzu.  [I feel somehow obligated to assert the obvious fact here that all opinions given in this blog are my own and have absolutely nothing to do with my university.]

That’s right folks, 2 virtual petri dishes that crawl and drool and snot all over the place, AND all the responsibilities of a brand-new, wet-behind-the-ears ass prof (assistant professor, for those of you confused about the abbreviation); I’m just a glutton for punishment.

This has given me a new-found sense of juxtaposition: freedom, weighed down by grant-writing; imagination, mired in the realities of funding priorities; and an awesome new job, potentially debunked at tenure-review time.

I, therefore, chose to attempt to squeeze into my painstakingly time-managed work-day schedule some time for fun-writing (aka, blogging).  The shape and form and overall thrust of this blog will largely remain the same – Microbes do, in fact, still rule the world, and I will continue to extoll their virtues.  However, I hope to also cover science and science events more broadly and may even share the odd job posting. (a clear transition into…)

With my very first blog as a new tenure-track faculty, I will shamelessly let you all know that I need to hire a lab technician.  I need someone with experience in soil microbiology and molecular biology, cultivation-dependent and independent techniques.  The pay is not particularly great to start and I can’t cover relocation costs, but the boss is usually pretty cool and she’s super enthusiastic about what she does.   And you should know that Eastern Washington/northern Idaho is not the big city, but rather the outdoor-enthusiast’s playland.  So, for the full job description and details, contact her directly.

Dogs, Dust, and the Hygiene Hypothesis

7 Feb

ResearchBlogging.org Since I’m still only getting about 3 or 4 hours of sleep at night, extracurricular reading for this blog has to be uber-interesting to maintain my attention long enough to keep me from falling asleep halfway through the abstract.  Not to say that anything microbial isn’t particularly interesting, but the bar has been set a little higher now that I’m a SciMom, and baby girl likes to eat… a lot.

So, in looking for something exceptionally interesting to blog about this week, I stumbled on the perfect storm for today’s paper, which piqued my interest for several reasons that may or may not be obvious you folks out in readerland.   First, I just had a baby a few months ago and find myself continuously thinking I need to do more research on this or that which will affect the baby’s health and wellbeing.  Second, I have “indoor pets”, namely several German Shepherds (see the shamelessly cute photo below) and two cats.  Third, I was diagnosed with allergy-induced asthma when I was about 9 years old and have struggled with it ever since (you may be wondering at this point, why on earth I would have so many indoor pets if I have allergic asthma… just call me a glutton for punishment, but I love my dogs).

The unifying theme of the paper, however, and overarching interest for me is, of course, due to the very cool and omnipresent impacts of microbial ecology.

Exactly how microbial ecology plays a role in a study on prenatal and early childhood exposure to indoor pets and how that affects immunoglobulin E may not be overtly obvious, so let me explain.

What does hygiene have to do with it?

First, you need a cursory understanding of something called the “hygiene hypothesis”.  It’s pretty huge in the health news these days so I wouldn’t be surprised if you’re at least vaguely familiar with the concept.  Essentially, it’s the idea expressed beautifully by Rob Dunn in Eating off the floor: How clean living is bad for you.  The basic idea is that the more of our little microscopic friends that we are exposed to early in life, the healthier we are overall due to stimulation of our immune systems in a way that allows natural development and response to true pathogens.  Early exposure to a range of microbes is thought to essentially “teach” our immune systems what is good, safe, or at least not a threat, versus those organisms that can really make us sick and should be eliminated.

The slightly longer than 5-second rule...

If we live in an environment where everything is sterile (at least as much as possible), our air is filtered, antimicrobials are everywhere, antibiotics are over-prescribed, and we aren’t exposed to microbes and parasites, then our immune systems may begin to overreact to anything and everything regardless of the potential harm it might cause us. This would explain the rise in autoimmune disorders and asthma, some even include eczema and hay fever.

As cool as all that is, it is only a hypothesis at the moment, which means we need (lots) more evidence (a.k.a. data) to be able to assert these ideas as a theory, much less a fact (of course we all know that in Science, reaching the status of “theory” is as good as it gets… only the media and snopes assert “facts”).  And it’s even a fairly vague hypothesis at that.  We’re not sure which types of microbes we need to be exposed to, how many, at what times, and precisely which aspects of our immune system will or won’t be affected.

The word for the day: Pets

There is currently a lot of work ongoing around the globe to get at some of these different aspects of the hygiene hypothesis and hopefully begin to provide us with the data we need to assert that, in fact, microbial exposure is a good thing for the development of the human immune system.  One such study came out in 2010  in the Journal of Allergy and Clinical Immunology which compared the microbial communities in dust of homes with and without pets.  They proved what all us pet-owners already know, that the dust of homes with pets supported a much more diverse microbial population than the homes without pets.

Dust mite

In this most recent paper, Suzanne Havstad and her colleagues took this idea one step further.  They set out set out to provide more details of the dynamic interplay between these pet-based dust microbial populations and the human immune system.  This particular puzzle piece involved testing immunoglobulin E (IgE) levels in the blood of young children in response to their exposure, or lack thereof, to indoor pets.

What is IgE, anyway?

Admittedly, the various components of human immune system (and vertebrate biology, for that matter) are well outside the scope of my own training and expertise.  I will therefore refer you to the following article on Immunoglobulin E and this medical article on pediatric asthma (you’ll find the bits on the hygiene hypothesis in under “Pathophysiology”).

In a  nutshell, IgE is part of our immune system which is triggered by allergens and parasites in your environment, including worms.  It causes inflammation that helps your body defend against intruders and keep you healthy.  However, it’s also thought to play a very significant role in pediatric asthma since blood IgE levels in asthma sufferers are typically much higher than non-asthmatics.  Essentially, some people’s immune systems overreact to things like dust, pollen, dander, etc, which leads to excessive production of IgE which in turn causes inflammation of tissues in lungs and bronchial tubes and asthma (not being able to breathe) is the result.

What Suzanne Havstad and her colleagues were able to conclusively prove was that children who were exposed to indoor pets in utero or in their early years had significantly lower IgE levels than those who weren’t exposed to pets.  The more diverse microbial community of the homes with pets must be interacting with the children’s immune systems and fostering the lower IgE levels, right?  It’s certainly possible and makes all the sense in the world to somebody like me.

However, just because [A (pets) = B (more diverse dust  microbial communities)] and [A (pets) = C (lower IgE levels)], doesn’t necessarily in this case mean that B =C as well.  There could be any number of other factors for children in the homes with indoor pets that may or may not have been measured, such as lifestyle, diet, exercise, and exposure to other allergens or toxins in their environment.  These other factors could also be influencing IgE levels.

However, what makes this study more compelling is that they also found an effect of the child’s mode of delivery:  vaginally versus Cesarean section.   The reason I say that this makes the study more compelling is because it’s been found that infants delivered vaginally have an entirely different microbiome (indigenous microbial community) than those delivered by C-section.  This lends some weight to the idea that microbial populations influence IgE levels.

What does it all mean?

This study seems to doubly lend support to the idea than early microbial exposure impacts human immune

A shamelessly cute German Shepherd puppy.

response, particularly via IgE levels.   Indoor pets can clearly increase the diversity and abundance of the microbial populations of your household dust (not a fact, that in and of itself, I really want to spend a lot of time thinking about) and exposure to that dust may actually be a good thing, in moderation (i.e. we probably shouldn’t spoon-feed the dust to anybody), for children’s developing immune systems.  Take home message: every kid needs a dog, or a cat, or both, or to at least get a little dirty every now and then… which means my little girl has got this covered!
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Havstad, S., Wegienka, G., Zoratti, E., Lynch, S., Boushey, H., Nicholas, C., Ownby, D., & Johnson, C. (2011). Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood Journal of Allergy and Clinical Immunology, 128 (4), 880-8850000 DOI: 10.1016/j.jaci.2011.06.039

Back at Blog

17 Jan

Ok, it’s been 8 months, 34 weeks, 241 days, loads of morning sickness, and one brand new baby since my last post, but I’m back to work and back at blog.

I can’t make any promises about the frequency of my posts in the new year, but I will do my best to keep up on comments and make some meaningful contributions to the science bloggosphere in the months to come.

Today, I ease into things with a re-post from one of my favorite microbial blogs, Small Things Considered over at the American Society for Microbiology blog site.

Have a look and consider (again – hopefully) this important question: The vast quantities of information and sequence data we gain from molecular techniques, without appropriate application and mindful interpretation, what does it really mean and where does it really get us in the end?

That Scary Restroom Microbiota

by Elio Schaechter and Joshua Fierer

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ASM Opening Sessions

21 May

Tonight the 2011 General Meeting of the American Society for Microbiology opened with “Microbes Among Us: Marvel or Menace.”

The opening session began with introductions by the current president of the organization, Dr. Bonnie Bassler from Princeton University(one of my personal heroines – so great to see her in person for the first time!).  She gave very brief introductions to each of the various award winners this year, many of whom will actually give lectures throughout the meeting at special sessions dedicated to their particular award.  It seems quite a few of the awards are sponsored by some of the big vendors at the meeting, and I realize this is not a new concept since awards have almost always been named after those who gave the money to support the award.  But for some reason, it bugs me just a little; I start to feel like science is becoming akin to pro-sports where we can’t even watch the game anymore without bombarded with advertising.   Pet peeve, I guess.

Dr. Bassler then introduced those members of the Geneal Meeting Program Committee responsible for the new format of the metting and primarily responsible for putting it all together: Dr. Margaret McFalll-Ngai and Dr. Arturo Casadevall.  At that point Dr. McFall-Ngai took over the introductions of the night’s speakers.

Sidenote: At this point I was struck by the number/proportion of those names mentioned, whether serving in some major function in the organization or listed among the award winners, who were either currently at or were in the very recent past from ivy league and top tier institutions.  I had to wonder whether this was a sort of ‘chicken or the egg’ phenomenon: were these people naturally driven and exceptionally intelligent so that they all over-acheived anyway, or did their being at these types of institutions give them greater visibility and a ‘foot-in-the-door’ with this type of organization?  Or maybe a little of both… food for thought.

Dark Energy

Dr. Nicole Dubilier from the Max Planck Institute kicked things off with a fascinating talk entitled “The Art of Harnessing Dark Energy: Symbioses Between Chemosynthetic Bacteria and Marine Invertebrates.”  Of course deep-sea hydrothermal vents are one of my favorite ecosystems to learn and teach about so I was riveted through her talk.  Even so, she really did a nice job with the presentation, neat, clear and stayed on time!

Mussels

Dr. Dubilier began with her work on deep sea mussels, in which she discovered 2 different bacterial symbionts.  The first uses methane and the second uses sulfur for chemical energy to fix carbon (the same way that plants use sunlight to fix carbon).  She has some beautiful FISH (Fluorescent In-situ Hybridization) images where you could literally see the bacteria, each tagged with a different color, living within the cells of the tissues of the mussels.  Each bacteria was in a different type of tissue!

From these types of images she was also able to see another type of bacteria which she later determined to be a parasite that actually lived within the nucleus of the mussel’s cells.  Those cells that were host to either the symbiotic methane oxidizers or sulfur oxidizers, were not also host to the third parasitic bacteria.  More work is now underway to determine how the symbiotic bacteria may aid in defending against the parasitic invasions of the third bacteria.  (Here’s a link to a 2005 paper on the dual symbiosis in Applied and Environmental Microbiology)

After the initial work with the deep-sea hydrothermal mussels, her work then lead to the discovery of these very same symbionts and the parasitic bacteria in every other species of marine muscle that they’ve been able to study to date.

Worms

Dr. Dubilier has also worked extensively with gutless marine oligochaetes – the ocean’s equivalent of earthworms.  She discovered that all of these types of marine worms have 5 to 6 co-occurring bacterial symbionts which provide most of their digestive processes, and each worm species has a very specific set of the 5 to 6 bacterial symbionts.  These bacteria are located just inside the worm cuticle (a.k.a. skin), but exterior to the worm’s cells (extracellular).

This research was an interesting story in which her work involved extensive study of the proteins and genes expressed by these bacterial symbionts to determine how they were serving the worms, (i.e. what substrates they were utilizing in the environment to create biomass for the worms) then these pathways were verified by environmental measurements.  Not so long ago, environmental microbiologists would have taken extensive measurements of the environment to form hypotheses on how the microbial symbionts were serving their host, then probe for genes to verify it.  Now, with all the new tools we have available, all the new technology, we arrive at much the same answers, but we do it the other way around.

Overall, some intriguing work on not only host-symbiont interactions, but chemosynthesis as well.

Wrapping Up

There were two speakers following Dr. Dubilier: Dr. Liping Zhao of Shanghai Jiao Tong University, and Dr. Susan Lindquist from the Whitehead Institute.  Dr. Zhao discussed the human gut microbiota and prevention of metabolic diseases, and Dr. Lindquist covered heat-shock proteins and their involvement in prion diseases and heritability.  Both were very interesting and I hope to be able to cover at some point in the future, but that’s it for tonight, folks.    Tomorrow things start bright an early with an entire session on the aftermath of the Deepwater Horizon.

ASM New Orleans: Here we come!

19 May

The American Society for Microbiology 

Some of you may already be aware of the rapidly approaching 111th General Meeting of the American Society of Microbiology (ASM) in New Orleans, May 21st through the 24th.  I’m pretty excited to say this will be my very first opportunity to attend the ASM meeting.  This may be a little surprising considering the fact that if you have any idea what this blog is all about, you know that Microbiology is what I do, it’s what I study, immerse myself in, and it’s what I love.

So why on earth haven’t I attended one of these meetings before?  It just so happens that my work (study, love, etc) also falls within the realm of soils, biogeochemistry, environment, and ecology, as well.  Accordingly, over the course of my professional life to date, I have only attended soils, environmental, and ecological professional meetings.  I have been advised by colleagues in the past that the ASM meetings are extremely large and primarily catered to medical/clinical and basic microbiology crowds and that I would actually glean the most useful knowledge (for my particular line of work) from the more applied meetings.

My Agenda at the ASM Meeting

This year I decided to find out for myself about the ASM General Meeting (and blog it thoroughly).  I’ve taken it as my personal mission to track down and report on as much environmental microbiology (and microbial ecology) at the meeting as I possibly can.  My cover will be as a lowly postdoc presenting a poster on my most recent work with fungi and Pb-contaminated soils.  Wish me luck!

In the meantime…

I’ve heard some talk about the new way of doing things at this year’s meeting and thought I’d look into it a little beforehand.

At the inaugural meeting of ASM  in 1899, at the time called the Society of American Bacteriologists, there were roughly 30 professionals in attendance (Miller, et al. 2010).  In recent years you can expect upwards of 10 to 15 thousand attendees in any given year with a very wide range of areas of expertise, a veritable smorgasbord of high-tech vendors, and people from all over the world, from students and undergraduates to postdocs and profs, even true, historical icons.  However, the clinical microbiology community still accounts for roughly 1/3 of the meeting’s attendance.  Obviously, there have been some big changes in the society and this year’s dynamic platform is an attempt to adjust the design and flow of the meeting to accommodate the new demographic, while still meeting the needs of the core.

This year a new mission statement for the meeting was adopted by the Society: “The ASM General Meeting showcases the central role of microbes in the biosphere by communicating today’s cutting edge science in the diverse areas influenced by microbes.” (Miller, et al. 2010) Which actually sounds quite promising, if you ask me.

Apparently, one of the most dramatic changes to the general meeting involves the number and nature of session and includes a parallel meeting, specifically tailored to the needs of the clinical microbiology community entitled “Medical Microbiology Track.”  Not exactly my cup of tea, but to each his own.

Each morning there will be only 4 concurrent sessions focused on topics of broad interest, which is a reduction in the number of session since years past.  The goal is to “showcase” inspirational interdisciplinary science with minimal overlap and maximum appeal.

That all sounds well and good, (actually it sounds pretty fantastic and exciting to the incorrigible science dork), but we’ll have to see how it all plays out in the real world.

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ResearchBlogging.orgMiller JF, McFall-Ngai M, & Casadevall A (2010). A New Design for the ASM General Meeting. mBio, 1 (5) PMID: 21151775

Updates

6 May

I’m writing a few quick lines today on a personal note because I just realized how long it’s been since I made a post here.  First, I apologize to my faithful readers (all 3 of you!) and promise to be back in the swing of things sometime in the next few weeks.

By way of explanation, let me just say that there have been some life-changing events recently that threw my schedule asunder and are largely to blame for the lapse in scientific blogging on my part.

The first was a Microbiology faculty-position interview out of state which took much of my time in preparation as it was the first interview of this type I have ever undergone.   The next (these are not necessarily in order of importance) was that I found out I’m expecting my first child.  I will spare you the gruesome details of my first trimester, and all the physical, emotional, and psychological changes underway, to simply state that it’s taken me a bit to get back on track with anything outside my basic work responsibilities, of which, my blog is not a part.

At any rate, I’m feeling better.  They did offer me the faculty job, but when it came out that I was preggo, it was determined (how to say this politely?) that it just wouldn’t work out.  So, I’m very happily staying put for a while and very excited to get back to blogging about all things microbial on a more regular basis… at least until the baby arrives in November, after which time, all bets are off until I’m back at work!

In the spirit of the day…

14 Feb

Despite the fact that I really don’t celebrate VD (Valentine’s Day, in case you were thinking something else), I thought I would show a little love, share a warm-fuzzy, and re-post this from Suzanne Kennedy (clearly, a woman after my own heart) at the MoBio Blog,  The Culture Dish.

Oh how do I love thee? Let me count the ways…

Show some LOVE for Environmental Microbiology

Do you love your work? Does nothing make you happier than a day out in the field collecting soil from the rainforest floor, in a boat collecting Vibrio contaminated water from Puget Sound, traipsing the forest looking for animal droppings from wild birds in Venezuela, or aboard the Alvin collecting biofilms from deep sea floor hydrothermal vents?

It’s important to love your work and fortunately for us, there is so much to love about microbiology and the environment. But to find out what is best about working in this field, I asked the question to several of my scientist friends:  What do you love about your work? Why do you study environmental microbiology and what is it that makes it the best field of work?

And below are some of the best responses. Some are my own, but most are responses I received from people who study some of the most unusual samples from the most extreme environments in the world.  I think you will agree that environmental microbiology provides experiences unlike any other field. Let us know your reasons for loving your work!

14 Reasons to Love Environmental Microbiology:

1. You get to play outside in the mud, snow, water or clouds (see picture at end of article).

2. There is virtually an unlimited number of research projects to choose from. “Microbiologist William B. Whitman, estimates the number of bacteria in the world to be five million trillion trillion. That’s a five with 30 zeroes after it. Look at it this way. If each bacterium were a penny, the stack would reach a trillion light years.”

3. Your research will have an impact on everything living on the planet, humans, animals, and plants. Basically all the Kingdoms benefit from what you do.

4. You have the opportunity to visit exotic and remote locations.  

Graduate student Rick Davis explains, 

“I think I’ve been really lucky with the places I get to study– I got to go to Samoa, Hawaii, and Yellowstone this year!”

He also added reason number 5: 

5.  Environmental microbiologists are more laid back and generally more collaborative than competitive, which allows for greater progress and more fun at conferences!

John Mackay, a molecular biologist and director of business development at the plant diagnostic company, Linnaeus, tells me:

6. You can cruise around the seas for months, sequence a bit of sea water and write the whole lot off on your research grant!

7. You can work on things you can eat or drink – I recommend wine and truffles!

8. When you find new species (almost a given!), you can name them after yourself.

 New discoveries are also what motivates Charlie Lee from the University of Waikato, a Postdoctoral researcher in microbial ecology studying the Dry Valleys of Antarctica. He echoes the sentiment that discovery is almost a guarantee:

9. Most systems we look at are relatively poorly understood, and it’s always exciting to discover something for the first time.

 Tom Niederberger, a Postdoctoral researcher in marine biosciences at the University of Delaware, has more to add:

10. The international travel is a great reward. The world is your playground as microbes have colonized basically all habitats on earth, and it’s great to travel around sampling not only the microbes, but new cultures/food/travel etc. and not being chained to the lab and pipette. Also the international collaborations and conferences also are great.

11. But I think what is most important is that microbes in the environment are essential not only for the health of the planet (e.g. global nutrient cycling / global climate change) but they are also intimately linked to the healthy functioning of our bodies. i.e. the are really important!

12. Also,there is the excitement of the unknown. Most of the organisms cannot be cultured and we know nothing about them…I think this is great motivation and it will keep you busy, and there are always new problems to solve and new questions to ask.

All excellent points!

And from a molecular biologist from Colorado State University (who wished to remain anonymous) come two excellent points I hadn’t considered:

13. Extremists don’t kidnap environmental microbiologists. Actually, they give them back.
 
14.
If you get tenure, who’s going to boot you out?  Exxon?

Did I mention that environmental microbiologists are funny?

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