Museum of Science in Boston Brings Together Microbiome Luminaries

This video below, entitled Friends with Benefits: The Human Microbiome, is one worth watching. It was recorded Feburary 6, 2013 and hosted by the Museum of Science in Boston with funding from the Lowell Institute (original ad). It features four brilliant microbiome researchers - each of them arguably have transformed the life sciences in just the past few years. They each speak for 15 minutes and then have a Q&A with the audience. I've noted the times at which each speaker appears in case you want to skip ahead. They appear in the following order:

• Introductions - 0 to 2:00 
• Prof. Rob Knight (U. Colorado) - 2:00 to 26:10, Development of the Human Microbiome
• Prof. Eric Alm (MIT) - 26:10 to 41:00, A Year in My Microbiome
• Prof. Marty Blaser (NYU School of Medicine) - 41:00 to 1:01, Long Term Pertubations of the Microbiome 
• Prof. John Cryan (University College Cork, Ireland) - 1:01 to 1:23, Microbiota-Gut-Brain Axis
• Roundtable Q&A - 1:23 to 1:30 - Between speakers
• Roundtable Q&A - 1:30 to end - Between speakers and audience (perhaps the best part!)

NIH issues press release on Wolbachia and our bacteriophage work

I do not often mention our bacteriophage work on this blog, but a large arm of the lab studies the evolution, mechanisms, and relevance of bacteriophage. Bacteriophages are the "smart bombs" of the microbial world - viruses that specifically target and often kill bacteria. The NIH Evolution of Infectious Disease Program, which funds this work, kindly put out a press release today on it. (This work is perhaps most well known for the discovery of rampant horizontal gene transfer of bacteriophage between obligate intracellular bacteria that were once presumed impervious to bacteriophages and large-scale gene transfers). For all those young scientists struggling to get their first grant, its humbling to reflect that this work almost never saw the light of day some years ago. Two reviews on this research are:

• Phage WO of Wolbachia: lambda of the endosymbiont world (Trends in Microbiology, 2010)
• The complexity of virus systems: the case of endosymbionts (Current Opinion in Micro, 2012)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Inside Life Science

View All Articles | Inside Life Science Home Page

Taking the 'Bite' Out of Vector-Borne Diseases

Emily Carlson
Posted March 27, 2013

Mosquitos, ticks, worms—these all are "middle men" when it comes to disease spread. They can carry and transmit bacteria, viruses and other pathogens to us that cause dengue fever, Lyme disease and other vector-borne infections. As one approach to help reduce and even eliminate these diseases in people, researchers funded by the National Institutes of Health are studying the basic mechanisms that let the infection-causing organisms flourish inside their hosts.

The mosquito is just one of the many organisms that Wolbachia infects. Credit: James Gathany, CDC.

A "Mind-Blowing" Bacterium

One such bacterium that scientists are interested in is called Wolbachia.

"It's probably the coolest bacterium in the world," says NIH's Irene Eckstrand.

Wolbachia infects more than a million species, including insects, shrimp, spiders, mite and tiny worms. It lives and reproduces in its host's cells, primarily reproductive ones. The bacterium can manipulate these cells in ways that boost its own survival and reproductive success.

Seth Bordenstein, a Vanderbilt University scientist who studies Wolbachia, says the bacterium alters the reproductive life of its insect and other hosts in four "mind-blowing ways":

1. It kills infected males.
2. It turns genetic males into females by shutting down certain hormones.
3. It allows infected females to reproduce asexually.
4. It promotes the survival of embryos from infected females only.

Ecology and Evolution

"Aside from stimulating the imagination, Wolbachia serves as a tool for studying the evolution and ecology of infectious diseases," notes Eckstrand, who co-manages an NIH-National Science Foundation program that's dedicated to this topic.

A Wolbachia cell infected with bacteriophages. Credit: Seth Bordenstein, Vanderbilt University.

When Bordenstein, whose research is supported through the program, started studying Wolbachia about a decade ago, scientists thought that the bacterium and ones like it didn't frequently acquire new genetic machinery. The theory was that living inside other cells isolated the bacterial genomes, inhibiting the exchange of genetic elements with other bacteria that enables evolution.

Since that time, the theory—and Wolbachia itself—have evolved. Bordenstein discovered that Wolbachia can move to different cells and to new hosts, some of which are infected with other types of bacteria as well as different Wolbachia strains. This co-infection allows the bacterium to acquire new genetic elements.

Scientists also have learned that Wolbachia harbors a bacteria-infecting virus, called a bacteriophage, that can introduce other genetic elements. Bordenstein found that Wolbachia's interaction with the bacteriophage and its exchange of genetic elements through co-infections creates a cycle of evolution with implications for how diseases spread.

Disease Control

Elephantiasis caused by parasitic worms (top) affects more than 120 million people, primarily in Africa and Southeast Asia. Credit: CDC.

While Wolbachia doesn't directly infect mammals, it is the root cause of several serious mammalian diseases. It infects parasitic worms that, by way of mosquitos, can cause heartworm in our pets. Other types of Wolbachia-infected worms hitch rides to ultimately reach human hosts, where they can trigger severe inflammatory responses that lead to river blindness and elephantiasis. In an ironic twist, researchers are actually using Wolbachia to help fight these infections.

One strategy that Bordenstein is beginning to explore focuses on bacteriophage enzymes that can wipe out Wolbachia. Some organisms, including the parasitic worms, actually need the bacterium to reproduce. By eliminating the Wolbachia infection, the enzymes could render the worms sterile and unable to further spread disease.

Scientists also are harnessing Wolbachia's wanton ways to control the spread of dengue virus, which is transmitted to humans by mosquitoes. Researchers have discovered that Wolbachia-infected mosquitoes can't replicate the dengue virus. Releasing more Wolbachia into the mosquito population or finding and introducing the Wolbachia genes that interfere with replication are promising new avenues for reducing the spread of dengue. The approach could potentially apply to other vector-borne diseases like sleeping sickness, which is transmitted by the tsetse fly.

According to Bordenstein, studying Wolbachia has yielded some surprising new insights on microbial evolution that could help us understand, treat and prevent certain infectious diseases. "It's what gets me up every day and keeps me excited about doing this work," he says.

Learn more:

• Bordenstein Lab , Blog  and Twitter  Pages
• Collection of Articles About Wolbachia 
• Ecology and Evolution of Infectious Diseases Program 
• NSF Special Report on the Ecology of Infectious Diseases 

Also in this series:

• The Quake that Brought Back Cholera
• Living Laboratories: How Model Organisms Advance Science
• Solving the Sleeping Sickness 'Mystery'

This Inside Life Science article also appears on LiveScience .

New TED talk on the teeming microbes in buildings

Is science getting cooler by the day or what? Check out this TED talk (with a very high tech/3D animation by Autodesk) on why we need to think about what microbes are in our buildings, from the air we breath when the windows are closed to what's in the bathroom. This is an idea whose time has come. I am thrilled to be meeting her and other faculty/students at the University of Oregon in the very near future when I visit the NIH Center for Systems Biology called The Microbial Ecology and Theory of Animals (META) Center. Graduate student Ashley Bateman, @MicrobesRock, invited me to speak on our work on the hologenome theory.

"Our bodies and homes are covered in microbes -- some good for us, some bad for us. As we learn more about the germs and microbes who share our living spaces, TED Fellow Jessica Green asks: Can we design buildings that encourage happy, healthy microbial environments?

Jessica Green wants people to understand the important role microbes play in every facet of our lives: climate change, building ecosystems, human health, even roller derby -- using nontraditional tools like art, animation and film to help people visualize the invisible world."  Source

Have you used a MOOC? Crowdsourcing feedback.

In December, I wrote an introductory blog on MOOCs entitled The Digitization of Education: What is all the fuss about MOOC? It is very basic and almost outdated, but it does have a great Ted talk video by Cousera's founder Daphne Koller that I recommend. Vanderbilt is on board with Cousera.

Still in their infancy, MOOCs are popping up around the country's universities and I imagine some readers of this blog have first hand experience or at least more insight on what its like to start or use a MOOC. Any answers to these questions wouldl be of help to myself and readers.

    1. How has the experience been with setting up or using a MOOC?
    2. What is fundamentally different or unexpected in using a MOOC?
    3. What has worked well? What would you do differently in MOOCs?
    4. Do you receive a break or compensation from your normal teaching load?

Are there bacteria in the brain?

BREAKING: I am posting this without much commentary because I have not had time yet to read the paper in full. A new report in PLOS ONE collates evidence that bacteria regularly inhabit the brain of immunocompromised brains. On the surface, the evidence seems pretty strong. mRNA detection and sequencing, in situ hybridizations, and brain tissue transplants from humans to mice....For those that would rather skip the science jargon, there is one press release from Boston.com. Is the brain microbiome a new frontier? As a related point, we published a paper in 2011 in Genetics on immunocompromised wasps that have remarkable bacterial infections in their brains (Figure 2D), resulting in altered mate preference behavior (Figure 8).

Citation: Branton WG, Ellestad KK, Maingat F, Wheatley BM, Rud E, et al. (2013) Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status. PLoS ONE 8(1): e54673. doi:10.1371/journal.pone.0054673

Abstract

The brain is assumed to be a sterile organ in the absence of disease although the impact of immune disruption is uncertain in terms of brain microbial diversity or quantity. To investigate microbial diversity and quantity in the brain, the profile of infectious agents was examined in pathologically normal and abnormal brains from persons with HIV/AIDS [HIV] (n = 12), other disease controls [ODC] (n = 14) and in cerebral surgical resections for epilepsy [SURG] (n = 6). Deep sequencing of cerebral white matter-derived RNA from the HIV (n = 4) and ODC (n = 4) patients and SURG (n = 2) groups revealed bacterially-encoded 16 s RNA sequences in all brain specimens with α-proteobacteria representing over 70% of bacterial sequences while the other 30% of bacterial classes varied widely. Bacterial rRNA was detected in white matter glial cells by in situ hybridization and peptidoglycan immunoreactivity was also localized principally in glia in human brains. Analyses of amplified bacterial 16 s rRNA sequences disclosed that Proteobacteria was the principal bacterial phylum in all human brain samples with similar bacterial rRNA quantities in HIV and ODC groups despite increased host neuroimmune responses in the HIV group. Exogenous viruses including bacteriophage and human herpes viruses-4, -5 and -6 were detected variably in autopsied brains from both clinical groups. Brains from SIV- and SHIV-infected macaques displayed a profile of bacterial phyla also dominated by Proteobacteria but bacterial sequences were not detected in experimentally FIV-infected cat or RAG1^−/− mouse brains. Intracerebral implantation of human brain homogenates into RAG1^−/− mice revealed a preponderance of α-proteobacteria 16 s RNA sequences in the brains of recipient mice at 7 weeks post-implantation, which was abrogated by prior heat-treatment of the brain homogenate. Thus, α-proteobacteria represented the major bacterial component of the primate brain’s microbiome regardless of underlying immune status, which could be transferred into naïve hosts leading to microbial persistence in the brain.

Figure 1. Deep sequencing detection of bacterial and bacteriophage RNA sequences in human brain.

(A) Total sequence tags that were unambiguously identified as belonging to a bacterial phylum were grouped for each patient from which the percentages for each phylum were displayed. All patients showed a predominance of Proteobacteria-associated sequences. (B) Despite inter-individual variability the mean percentage of Proteobacteria sequences among the HIV, ODC and SURG groups was similar. (C) The majority of bacterial sequences identified in all patient samples belonged to the Proteobacteria phylum, which showed the greatest similarity to the α-proteobacteria class. (D) The majority of bacteriophage sequences identified matched Proteobacteria-tropic phage sequences although bacteriophage sequences were not detected in the SURG samples. doi:10.1371/journal.pone.0054673.g001

My talk at the University of Illinois at Urbana-Champaign

Earlier this week I had the pleasure of visiting The House that microbiologist Carl Woese Built - The University of Illinois at Urbana-Champaign. With nearly a 100 evolutionary biologists and ecologists along with National Academy Members sprinkled across the integrative departments, its a wonder world of life sciences research. Indeed, famed virus hunter Nathan Wolfe happened to be visiting the campus the same day.

Here's my seminar on The Hologenome / Speciation by Symbiosis (Part I: 0 to 31:20) and Microbial Genome Evolution (Part II: 31:20 to Q&A). I usually am hypercritical of my own talks and find all sorts of things wrong with them. This seminar is perhaps the one time that the talk went off without a hitch. I even landed a few laughs with a joke on hybrid lethality (phew).

Related blog posts:
1. The story behind Speciation by Symbiosis? (April 26, 2012)
2. Is the microbiome part of the organism or the environment? (May 11, 2012)
3. Is the microbiota species specific? (June 23, 2012)

4. ASM's "Small Things Considered" spotlights the Speciation by Symbiosis article (August 16, 2012)

Darwin Day

Yesterday was a mild victory for promoting science, reason, and the future in the United States. Congressman Rush Holt (D-NJ) introduced a resolution to declare February 12th, DARWIN DAY, in honor of the 1809 birthday of one of the greatest scientists.  Sadly, this resolution will not make it far, I fear, but change in government happens by small steps. This motion, coupled with the enacted Golden Goose Award introduced by Nashville's own Jim Cooper to honor federally funded research (my blog post on its origin), are steps that should give us hope.

Here's a very short video of Rep. Holt's introduction of the Darwin Day resolution. It may just energize you a little bit more today. It did for me.

Part IV: Thoughts on Survival/Success in the New Era of Academia

Here is the last installment of tweets on this theme folks. Hope they've been of some help. Id like to pivot you to Josh Drew's blog post this week on the same theme. He has some things that just need be said more often. Here's an excerpt.

However, it occurs to me that the majority of the tasks I do ever day I have had very little to no formal training in. In a given week I 1) teach, 2) advise students, 3) apply for funding, 4) do research, 5) manage a graduate program and 6) write.  Now here’s the crux getting a Ph.D. is actually fairly poor preparation for the majority of these activities. 

In my case, I recall explicitly asking for a course on grantsmanship in graduate school. The idea was generally scoffed at, for reasons that I can only speculate as a cultural one. What is noteworthy is that in this new era of academia with limited federal funding, we are all getting more serious about what we do, who we train, and how we train them. This shift is part of the good in what can seem to be a troubling pattern in science funding.

1/27/13: If Life is the greatest show on earth, then biologists get to be at the circus for their entire career #tosrb #hallelujah

1/29/13: Scientists almost never get career breaks; They work hard & persevere in the face of doubt. Recognition comes retroactively #tosrb #Woese

1/29/13: Excellent training of students requires honesty to them, even when its hard. Excellent learning requires being honest w yourself #tosrb

1/30/13: When giving a seminar/lecture of excellence, remember to inspire regularly. Engagement is the button that turns on self-illumination #tosrb

2//13: EXPLORE not where your field is now, but where it is going to be in 3 years. It will transform and transcend you in your endeavors. #tosrb

Part III - Thoughts on Success/Survival in the New Era of Academia

Third installment...for background see previous two blog posts.

Thoughts on Success/Survival in the New Era of Academia Part I
Thoughts on Success/Survival in the New Era of Academia Part II

1/25/13: Biology PIs run small businesses too. Our labs must be well managed and produce a product that is sold to the granting agencies #tosrb

1/25/13: So much of attaining excellence is the confidence and courage to simply try. Anything less is a prescription for status quo #tosrb

1/25/13: Imagine a future in which you better engage your students or solve bigger questions - now pull that future forward to right now #tosrb

1/26/13: 6 NIH grants or 10 NSF grants is a career's worth of research. You dont got many chances to spur a paradigm. Choose wisely #torsb

1/26/13: PIs must give equal time to broadcasting and receiving info with students. I do this because my students are smarter than me #tosrb

Part II - Thoughts on Survival/Success in the New Era of Academia

Yesterday, I started Part I of a blog post series on survival/success tips for the new era in Academia.  My hope is that I can pass on some insight to those that are just beginning their careers - from students to new PIs. By doing so, by coaching through accrued wisdom, together we can speed up the pace of excellence in science for future trail blazers, rather than wait for people to learn these things themselves over a long career. 

As noted, I will post several of these tweets on a daily basis. Red highlights indicate ones that I think rise about the rest. As always, comments and questions are encouraged!

1/24/13: Students must recognize that they will be pushed to the brink, because their PIs know better than them how far they can go #tosrb

1/24/13: Letting go of limitations is part of the journey to excellence, for students and colleagues alike. Academics should heed this. #tosrb

1/24/13: I can't or I don't or I'm not are words that we should never ever use. We hide the gift of new knowledge for humanity if we do #tosrb

1/24/13: Science is the noblest of occupations for it discovers new truths. And that discovery is driven by 20-something's. Remarkable #tosrb

1/24/13: Education is the sibling of science for without it we can not build a family of humanity that sustains itself #torsb


Thoughts on Success/Survival in the New Era of Academia Part I

Thoughts on Survival/Success in The New Era of Academia - Part 1

Considering what has transpired in my career thus far and its still a career in its early phases, I have accrued just a few nuggets of wisdom that are useless if they are not shared. Let's start with the obvious. A career in the life sciences has its bountiful share of stress, which can frequently limit passion. Im not optimistic for the future of science if passion continues to dwindle for young scientists given the current funding climate. Take this observation for instance. Students in bio (red line) lose their interest in academic research jobs as they spend more time in grad school. Wow. Are PIs that bad at training their students to enjoy the job? Are we not taking in qualified enough students who can find strength through the struggles?

Citation: Sauermann H, Roach M (2012) Science PhD Career Preferences: Levels, Changes, and Advisor Encouragement. PLoS ONE 7(5): e36307. doi:10.1371/journal.pone.0036307

As a graduate student, I wished that I had a better idea of what it took to be successful in academia; I was told not to worry - that there would be plenty of jobs because the baby boomers would be retiring. That led to some false hopes. Fortunately, few students are being told this today. Not so fortunately, the latest stats indicate that 14% of life science phd land an academic job. As a postdoc, I wondered what it took to secure an academic job in a highly competitive environment. What was I supposed to do different than grad school? As a beginning investigator, I wondered how to get funded? This happened to be right around the time federal funding percentages were plummeting to historical lows (whoops). I wrote six grants before I got my first NSF grant. The answer to all these questions is the same. DO NOT TAKE NO FOR AN ANSWER. Perseverance is what make the difference. We can persevere if we imagine what excellence is and pull our future forward to meet that excellence. Excellence is always ahead of us and can always be attained by any of us. Just dont give up.

Success, which is what we are talking about here, is a state of mind more than a thing. In this light, I started tweeting nuggets of wisdom under the Twitter hashtag #tosrb for thoughts of my initials. I have heard from some colleagues and students that these shots of insight are useful. That is my hope, that I can pass on some insight to those that are just beginning. By doing so, by coaching through accrued wisdom, we may speed up the pace of excellence in science for future trail blazers, rather than waiting for people to learn these things themselves over a long career. 

Over this coming week, I will post several of these tweets on a daily basis. Red highlights indicate ones that I think rise about the rest. As always, comments and questions are encouraged!

1. 1/23/13: If u dont train your students to be better than u, then u are failing them and the society who benefits from future scientists #tosrb
2. 1/23/13: Most grad students transform in grad school. Fewer transcend. 14% ultimately get academic jobs. We need to talk about why. #tosrb
3. 1/23/13: Grad school is not a right of passage once students enter it, but rather the beginning of a 5 year boot camp. No guarantees at end. #torso
4. 1/23/13: Only 14% of life science PhDs in US get tenure track jobs in comparison to 55% of law students becoming lawyers. Change is needed #tosrb
5. 1/24/13: PI's must recognize that any recognition imparted to them is because of their students. Anything else is a failure in leadership #tosrb

3 Facts You May Not Know About Bees and Colony Collapse Disorder

We need bees for our future. They are essential for 130 crops and command 16 billion dollars of industry value. Yet bees are disappearing from the bizarre phenomenon of Colony Collapse Disorder without signs of an obvious disease. Several of my colleagues in the insect and microbiome fields are working hard to better understand and solve this major problem, including Jay Evans, Nancy Moran and Irene Newton. It seems as if not just one infectious agent causes colony collapse disorder but rather it arises as a tragedy of diverse reasons.

I came across the talk below and received a major upgrade in my knowledge on Colony Collapse Disorder. Noah Wilson-Rich's Tedx Boston talk raises several counter-intuitive facts about urban beekeeping and its impact on the colony collapse mystery. The 3 most salient facts he describes are below, followed by his full Ted talk.

• Colony Collapse Disorder is not a new problem. Say what... that's not what Ive been aware of.   Yet Noah shows at 6:03 in his talk that bee die offs have occurred periodically over the last 1000 years.

• Survival of bees is greater in urban beekeeping (62.5%) than the more traditional rural beekeeping (40%). Can we get some microbiome folks working on this please? Do bees reared on city roof tops have a better microbial community than those reared rurally? Noah's Best Bees Company uses a probiotic nutritious blend (Apivax) to inhibit fungal infections and upregulate the bee immune system.

• Honey yield is greater in urban beekeeping (26.25%) versus rural beekeeping (16.75%). Here honey yield is measured as average pounds for first year.

I like Noah's approach. He is trying to figure out ways to increase bee health as a complement to others focussed on figuring out how Colony Collapse Disorders arise. The merger of these two paths will undoubtedly be fruitful when it occurs in the future.

Diet Cures Multiple Sclerosis

Source

I am fascinated by how changes in the gut microbiome can alter the course and even reverse human disease. Take the recent surge of fecal transplants for instance to treat chronic diseases such as IBD, Clostridium difficile, Crohn's, and multiple sclerosis (blog post). I am also intrigued by how plant strong and paleo diets seem to be increasingly beneficial for health.

Here is an inspirational TEDx talk by Dr. Terry Wahls (@TerryWahls) on how she used pubmed.gov to research and develop a hunter gatherer diet rich in phytonutrients that cured her multiple sclerosis - an autoimmune disease of the central nervous system. Note that her approach focussed on the beneficial vitamins and phytonutrients from these foods. She did not mention the changes in the gut bacteria that are also occurring on this diet and that can have positive repercussions on the body's metabolites. I hope her message helps others.

Diet changes the gut microbiome, which in turn changes the metabolic, neuronal, and inflammatory networks that may cause or cure many chronic 'Western' diseases. Nothing short of awesome. The regenerative power of the gut microbiome is akin to stem cells and here to stay.

The Robogut: Bring Your Insides Out [video]

This state-of-the-art Robogut at the University of Guelph is used to simulate the inner workings of the human gut with bottles, gas chambers, and tubes. Amazing research. The goal is to mine the liquid gold products of the human microbiome and use them for applications to human health. Who would have thought to turn the complexity of the intestine into an in vitro culturing system. Im inspired by the creativity and applications here. I imagine some of you out there might have some fresh ideas for what you'd like to do with such an apparatus. Leave your comments below.

Apparently, this same lab just used the apparatus to grow a cocktail of good bacteria to treat patients with Clostridium difficile. Link to cbcnews story from today.

                         

Source: thestar.com

Related Blog Post:

Can a fecal transplant cure IBD, Colitis, Crohn's, C. difficle, Multiple Sclerosis..?

The Superorganism - Vlog 3

In this video blog, I use the analogy of Superman to describe the Superorganism - a collection of organisms that together gives powers (i.e., fitness) to a single animal or plant. Other similar terms such as Bosch & McFall-Ngai's metaorganism and Rosenbergs' hologenome are pulled together to discuss what it will take to know if these terms are real evolutionary units of Life, real entities that the frontier of Biology must confront. As mentioned previously, I view these vlogs so far as experiments that will only survive or not with your feedback. I look forward to your criticisms or support on the video blogging vs. text blogging and the concepts in the videos. Thanks a bunch, Seth

Related vlog or blog posts:

1. Phylosymbiotic Vlog 1
2. The Large Immune Effect Vlog 2
3. Science of the Superorganism
4. The Story Behind Speciation By Symbiosis

Microbiology / Science Trends in Web Search (2004-2012)

Just caught wind of this Google Trends tool that shows you the worldwide web search interest in any term you give it from the period 2004-2012. It then scales the data over time as a percentage from 0 to 100%, with 100% being the peak of the search intensity.

So I dipped into some science words. Interesting trends below...

MICROBIOME

-reassuring but no surprise here. Looks like we're now in an exponential growth phase

MICROBIOTA

- odd oscillations that I cant quite put a finger on, but note increasing trend over time

MICROBIAL DIVERSITY

-Note how popular this term was 8 years ago, prior to rush of studies on microbial diversity in hosts, now referred to as microbiome and microbiota

MICROBIAL ECOLOGY

-same problem as microbial diversity, above

DARWIN, EVOLUTION

-Yowza, trend seems to show pretty big decline with a flatline now. Is this correlated to rise of anti-evolution bills, I wonder.

SCIENCE

-again, I take this as a concerning sign. Sigh

SCIENCE EDUCATION

-uggghh, more sighs

FACEBOOK

-positive control in this experiment works!

Grant Writing Inspiration [picture]

Bringing out the big guns for a dose of grant writing inspiration today

Coffee, check

Spicy hot cocoa to add kick, check

Candle (and cello music) ambiance, check

Darwin bobble, check

Matryoshka doll for symbiosis, check

Foam earth ball to toss against wall, check

Brain upgrade initiating....

"The Large Immune Effect" - Vlog 2

In this 2nd video blog (vlog), I introduce the concept of the Large Immune Effect - a colloquial term first introduced in our Speciation by Symbiosis Review in Trends in Ecology and Evolution 27(8):443. The Large Immune Effect refers to the collection of evolution studies that provide evidence that immune genes are the most rapidly evolving in human and other animal's genomes and undergo the most adaptive evolution. As a result, immune genes are agents of change that can drive population shifts in the microbiome which may parallel the evolutionary history of the host. Its interconnections with Phylosymbiosis are presented, which is a term that was previous discussed in video blog (vlog) 1. As mentioned previously, I view these vlogs so far as experiments that will only survive or not with your feedback. I look forward to your criticisms or support on the video blogging vs. text blogging and the concepts in the videos. Thanks, Seth

"Phylosymbiotic" - Vlog 1

I've decided to incorporate video blogs in order to make some of the information exchange here more immersive and interactive. While I can't see the others watching or reading these blogs, I do know that I appreciate video over reading myself. Scientists are often out of the comfort zone on video, and stick to what they know best - writing. But in my opinion we need not worry so much as the point of social media, blogging, and microblogging is to connect. Video blogging can be easier and more immersive, thus establishing better connections. Through video and the general media, science has a better opportunity to increase scientific literacy. So here goes jumping into the video blogosphere head first. Hope others consider doing this too -Seth

The Digitization of Education: What is all the fuss about MOOC?

Have you heard the buzz around Massive Open Online Education (MOOC) over the last year? How much do you really know? From the Khan Academy videos to the water cooler talk among department colleagues who are rightfully concerned about the future of their profession, there is a tidal wave of change potentially coming to Universities. 


Information technology has changed every industry it has touched and it is currently in the nascent stages of changing academia. Ten years from now if information technology has its way, education will be far different, more immersive, and hopefully more beneficial to the masses than it is today. The division of student and professor will possibly be blurred as the conventional rules of linear lecturing will be decommissioned to an academic world that the student hasn't created, but nonetheless gets to affect through their own online learning.

I have been looking for a good article or video on MOOCs to brush up on my basic understanding of them. This one is it. Coursera co-founder Daphne Koller gives a perfect 20 minute breakdown via her TED talk. It touches on the need, promise, opportunities, and fears of MOOCs.

For a critique of the MOOC movement, see this recently published article.  The MOOC movement is not an indicator of educational evolution.

The Science of The Superorganism: Host-Microbiota Specificity, Again

What determines the constituents and abundance of microbes in a host? 

A critical question emerging in the science of the Superorganism (our genes + microbial symbionts) is how exactly does the microbial symbiont community inside us assemble? Is it random? Do we just acquire the bacteria that are around us when we're born? Does our diet affect which bacteria thrive in our guts? Do our genes interact with the admixture of microbes in the environment to select for specific ones that confer beneficial traits?

Numerous studies show the influence of diet on the assemblage of the microbial community. But emerging studies in the past year, which have received less attention, indicate the host selects for specific species of bacteria as well. Here are three highlight stories:

1. Hawlena et al (2012) show that in fleas and ticks, the composition of the microbial symbiont community is not determined by their vertebrate host (rodents) or environment, but by their arthropod host. Specifically, ticks have different communities of microbes than fleas, and species of ticks share more similar microbial communities than species of fleas. Other factors such as rodent host did not matter as much.

2. Salem et al (2012) show in firebugs that the "fitness of symbiont deprived bugs could be completely restored by re-infection with the original microbiota, while reciprocal cross-infections of microbial communities across both pyrrhocorid species only partically rescued fitness, demonstrating a high degree of host-symbiont specificity" In particular, survivorship decreases and nymphal development time to adulthood increases in aposymbiotic and cross-infected species, but not control or re-inoculated species. Even mating frequency is reduced. This study has a really beautiful set of functional data.

3. Engel and Moran (2013) describe a specific and stable microbial community of honey bees, suggesting long-term coevolution between bee-specific bacteria and bees.

If anyone has any important studies to highlight on this topic, please let me know so I can post them.

Note: we also found species-specific microbiotas that changed in constituents and abundance in parallel with the speciation events of their Nasonia wasp hosts. Related blog posts on this work:

• The story behind Speciation by Symbiosis (April 26, 2012)
• Is the microbiome part of the organism or the environment? (May 11, 2012)
• Is the microbiota species specific? (June 23, 2012)
• ASM's Small Things Considered Spotlights Our Article (August 16, 2012)

Neil Degrasse Tyson | Video from Vanderbilt Lecture

Scientists and educators do not frequently achieve celebrity status. But shouldn't they? Shouldn't we live in a society where we have more science rock stars like Neil Tyson or the late Carl Sagan. Part of the decline of scientific literacy in America is due to the fact that scientists are not made more visible to the public, that politics trumps facts and smart policy, and that scientists are not valued equally to sports stars or media celebrities.

The media needs to buy into this concept so that science advances as fast as fashion and special effects in our culture. 

Last night, Neil Degrasse Tyson visited Vanderbilt. His visit inspired these brief remarks shared above. I recorded a few snippets of his opening remarks and views on science education. 

Dr. Neil Degrasse Tyson, an American astrophysicist and science communicator, discusses his arrival to Nashville, his talk, twitter, and his books in a very humorous way.

Tyson discusses the difficulties in advancing science education in America, the consequences it has on society, one way in which the fall of American science education can be reversed, and his responsibilities to educating the public, not congress.

Tyson discusses the decreasing trend line of American scientific literacy, the forces that want to change the science curriculum, and the national imperative in science literacy that his new show, COSMOS, will bring to Fox watchers.

Animated 3D Video of Human Microbiome

A quick post on a really good video from the Knight Lab on how the Human Microbiome (wiki) varies across body space (skin, mouth, vagina, gut) and across time (from infant to adult). Its a really nice way to sum up years of data in three minutes! I can also imagine that we all can immediately use this video in teaching the microbiome. Hence, this is why I am posting to the blog rather than twitter, where it may get lost in the twittersphere feed.

What is Open Access Publishing & Why Is It Important?

Answer: Open Access Publishing is the future.

This video should be mandatory watching for all scientists, students, and anyone remotely interested in using research to make decisions about your health and future.

Open Access Publishing allows you to read the articles you want for free. Afterall, you probably paid for some portion of the research through your tax dollars going to fund the federal science budgets.

The bearded guy with the plad shirt is Jonathan Eisen, who I credit for getting me interested in social media and open access publishing. He and others have done the same for countless other scientists. His Ted Talk on the ubiquity of microbes is worth a watch.

Animated Doodle Video of Wolbachia | Eliminate Dengue Project

As many readers of this blog know, the Wolbachia | Eliminate Dengue Project is a Bill and Melinda Gates Foundation project spearheaded by Scott O'Neill at Monash University in Melbourne.  Ive posted on it recently here. Yesterday, they posted this great animated doodle video for everyone to understand how Wolbachia, a bacterial infection of arthropods, is being used to stop mosquito transmission of dengue virus, the causative agent of Dengue (a.k.a bone break) fever.

Is this serious? You betcha. The World Health Organization estimates that over 40% of the world's population is at risk and a whopping 100 million dengue virus infections occur worldwide each year. Numbers of infection are also on the rise.