Aug 13, 2012

Keeping harmful protein fibres at bay

Misfolded proteins are not just useless — they can be toxic. Some of them form linear aggregates known as amyloid fibres that can lead to disorders such as Alzheimer’s and Parkinson’s diseases. Writing in PLoS Biology, James Shorter and colleagues describe a protein machinery that inhibits the formation and helps to dissolve such fibres.

Heat shock proteins (HSPs) assist other proteins in folding. The authors set out to study whether two small HSPs from baker’s yeast (Hsp26 and Hsp42) could affect the generation of amyloid fibres by a misfolded protein of the same organism (Sup35). Using purified proteins, the researchers showed that Hsp26 and Hsp42 inhibited amyloid formation. Moreover, they determined exactly which steps of the process were affected: Hsp42 slowed down an early structural reorganization of small aggregates before the fibres were formed, whereas Hsp26 inhibited fibre growth.

Yeast cells have a protein called Hsp104 that rapidly dissolves amyloid. However, humans and other animals lack such an enzyme, and so it was unclear how our cells can get rid of amyloid fibres. The authors report that Sup35 fibres can be dissolved by a combination of several yeast HSPs (Hsp40, Hsp70 and Hsp110) in the absence of Hsp104, especially if the fibres are pretreated with Hsp26 and Hsp42. What’s more, they obtained similar results when using the equivalent human HSPs to disaggregate α-synuclein amyloid fibres, which are involved in Parkinson's disease. Although amyloid disassembly took many days, the researchers propose that such system could be functional in long-lasting cells such as neurons.

Shorter and colleagues’ findings suggest that enhancing the activity of certain HSPs in affected cells — and/or introducing yeast Hsp104 — could help to dissolve the amyloid in disorders such as Parkinson’s disease. However, additional research would be needed to assess the efficacy and safety of such potential treatments before these could be tested in people.

Reference (and source of the image):

Duennwald ML, Echeverria A, Shorter J (2012). Small Heat Shock Proteins Potentiate Amyloid Dissolution by Protein Disaggregases from Yeast and Humans. PLoS Biol, 10(6): e1001346. DOI: 10.1371/journal.pbio.1001346

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Jun 9, 2012

Social media tools and academic publishing, a presentation by Alan Cann

The following video is a presentation by Alan J. Cann for Editing in the Digital World, 11th EASE General Assembly and Conference Tallinn, Estonia, 8-10 June 2012.

Abstract of the presentation as published in the conference programme:

Social media tools and academic publishing

Alan J. Cann, Internet Consulting Editor, Annals of Botany; Department of Biology, University of Leicester, Leicester, UK

As publishing moves from print-focused (slow, inflexible, expensive) to content-focused (digital delivery, article-level metrics/discussion), there is an increasing need for publishers to communicate with their audiences in ‘adjacent spaces’ beyond the traditional medium of the journal or book. Social technologies will continue to evolve rapidly for the foreseeable future, so publishers need to acquire sufficient expertise to remain agile in this area in the face of future developments. I will describe the Annals of Botany low-cost online social media strategy, which is extending the reach of the journal to new audiences and new demographic groups. This includees blogs as distribution hubs for content via RSS, Twitter and Facebook, and emerging tools such as Flipboard which allow content discovery on new platforms such as tablet computers.

And here you have a link to the AoB Blog.

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Sep 1, 2011

Microbiology blogs: a list of 20 great blogs for microbe lovers

Bertalan Meskó (@Berci) has compiled a list of microbiology blogs that you may find useful: Microbiology in the Blogosphere.

Envious, I decided to make my own list of microbiology blogs. After checking my Google Reader, I came up with a collection of 20 great blogs. I know there are many more out there, so please feel free to add a comment and suggest any microbiology blogs that may be missing from my list.

So, here they come, in strict alphabetical order:

1 - Aetiology by Tara C. Smith (@aetiology): "Discussing causes, origins, evolution, and implications of disease and other phenomena."

2 - Bactérioblog [in French] by Benjamin (@bacterioblog):"Le blog des bactéries et de l'évolution".

3 - BacterioFiles by Jesse Noar (@BacterioFiles): "The podcast for microbe lovers: reporting on exciting news about bacteria, archaea, and sometimes even eukaryotic microbes and viruses".

4 - Cornell Mushroom Blog by a collective of faculty, staff and students from Cornell University: "Even in the fullness of their horrific evilness, fungi are cool. That’s what we’re all about here."

5 - Curiosidades de la Microbiología [in Spanish] by Manuel Sánchez (@Manuel_SanchezA) (no relation!): "Este blog está dedicado a la Microbiología pero en general cualquier tema científico de interés tambien puede aparecer".

6 - Life of a Lab Rat ("occasional insights into the life of a lab rat") and Lab Rat ("Exploring the life and times of bacteria") by S. E. Gould (@labratting).

7 - Memoirs of a Defective Brain by The Defective Brain: "Science as told by malfunctioning neurones. A blog of Life, labs and bacteria."

8 - Microbichitos [in Spanish] by Miguel Vicente: "Los microbios no los vemos, pero sus efectos, para bien o para mal nos afectan a diario." Previously, Miguel used to blog at Esos pequeños bichitos.

9 - MicrobiologyBytes by Alan Cann (@MicroBytes): "The latest news about microbiology".

10 - MIKROB(io)LOG [in Slovenian] by Franc Nekrep (@fvnek): "srečevali se bomo mikrobiologi: študenti, učitelji, kolegi iz stroke pa seveda VSI LJUDJE DOBRE VOLJE..."

11 - MycoRant by Philip McIntosh (@MycoRant): "Philip has been writing, researching, publishing and doing other things in the realm of fungi since 1993".

12 - Mystery Rays from Outer Space by Ian York (@iayork): "This blog is intended to be a place for commentary on immunology, virology, and random other stuff that catches my eye."

13 - Skeptic Wonder ("protists, memes and random musings") and The Ocelloid ("Through the eye of a microbe") by Psi Wavefunction (@PsiWavefunction).

14 - Small Things Considered by Elio Schaechter, Merry Youle and collaborators: "The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet".

15 - The Artful Amoeba by Jennifer Frazer (@JenniferFrazer): "a blog about the weird wonderfulness of life on Earth". Older posts can be found here.

16 - The Febrile Muse by CMDoran (@TheFebrileMuse): "Portrayal of Infectious Diseases in Literature and the Arts".

17 - The Gene Gym by Jim Caryl (@mentalindigest): "Bad bugs, drugs and antibiotic resistance, all in a day's work at The Gene Gym, brought to you from the gym floor by a researcher (fitness instructor) in bacterial evolution".

18 - The Tree of Life by Jonathan Eisen (@phylogenomics), "evolutionary biologist, microbiologist and genomics researcher, Open Access and Open Science advocate".

19 - ViroBlogy by Ed Rybicki (@edrybicki): "Up-to-date Virology-related posts, mainly for students at the University of Cape Town".

20 - Virology blog by Vincent Racaniello (@profvrr): "about viruses and viral disease".

Note: I don't speak French or Slovenian, but that's what Google Translate is for, isn't it?

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Aug 25, 2011

Cornering multiple sclerosis -- still a long way to go

Multiple sclerosis is an autoimmune disease of the central nervous system that causes neurological disability in young adults. Several environmental and genetic factors have been linked to the disease, but the precise mechanisms involved, and whether neurological damage precedes inflammation or vice versa, remain unclear.

In a recent article published in Nature, an international consortium of researchers report the identification of 29 new susceptibility loci, most of which are related to immune system function and, in particular, to T-helper-cell differentiation.

Previous genome-wide association studies (GWAS) that analysed relatively modest numbers of multiple sclerosis patients identified more than 20 risk loci, especially some that encode components of the major histocompatibility complex (MHC). To identify a more complete set of susceptibility loci and obtain new insights into disease mechanisms, an international team of researchers carried out a large GWAS in which they analyzed over 465,000 autosomal single nucleotide polymorphisms (SNPs) from about 9,800 patients and 17,400 controls (that is, people not affected by multiple sclerosis) from 15 countries.

This analysis confirmed 23 loci that had previously been linked to the disease, and revealed another 29 new loci. Most of the risk attributable to the MHC could be accounted by four mutations, one in class-I locus HLA-A and three in class-II locus HLA-DRB1.

A statistical analysis of the functions of the 52 loci (as annotated in the Gene Ontology database) showed that they are enriched for lymphocyte functions. In particular, many genes encoding cell surface receptors (such as CXCR5 and IL7R) with roles in T-helper-cell differentiation showed strong association with multiple sclerosis. In addition, the researchers identified two susceptibility loci with a role in vitamin D synthesis (CYP27B1 and CYP24A1) and others that encode known targets of therapies for multiple sclerosis such as natalizumab (VCAM1) and daclizumab (IL2RA). By contrast, very few genes with known roles in inflammation-independent neurodegeneration were identified.

The overrepresentation of susceptibility genes with roles in T-cell maturation suggests that multiple sclerosis is primarily caused by immune dysfunction, which is followed by neurological damage. However, the 52 variants can explain only ~20% of the heritability of the disease, and therefore a myriad of other susceptibility loci, each adding a tiny percentage to the overall risk of developing multiple sclerosis, remain to be identified.

Original article:
The International Multiple Sclerosis Genetics Consortium & The Wellcome Trust Case Control Consortium 2 (2011). Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis Nature, 476 (7359), 214-219 DOI: 10.1038/nature10251

The same story in the news:
- Study identifies 57 genes linked with MS, Multiple Sclerosis Society, UK (10 Aug 2011).
- Multiple sclerosis genes identified in largest-ever study of the disease by Alok Jha, The Guardian (10 Aug 2011).
- Scientists unravel genetic clues to multiple sclerosis by Kate Kelland, Reuters (10 Aug 2011).

During the last 10 months, I have written 18 Research Highlights (short pieces of 300-400 words that summarize recent scientific articles) for Nature Reviews Microbiology. This blog post is based on my first attempt to write a similar piece about a non-microbiological article. However, to make the post more 'blog-friendly', I have embedded some links to definitions of key terms. You can read the definitions by rolling your mouse over the highlighted terms, or you can click on the term to visit a website with more information. Also, I have added a couple of links to news articles that covered the same story.

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Jan 24, 2011

Time-lapse photography of growing mould - Amazing video!

Please watch the following video made by Nick Lariontsev, and then let me know if you don't think that microbes are fascinating things.

The video was made using time-lapse photography, with several fungi as 'actors': apparently, Aspergillus fumigatus, Botrytis, Mucor, Trichoderma and Cladosporium. You can see several pictures of the device used to take the photos at Nick's LiveJournal. See, for instance, this one (photo courtesy of Nick Lariontsev):

Nick - LiveJournal

I found the video via The Microbiology Daily (a Twitter newspaper) <<< @KristaMarquis (Twitter) <<< MicroCulture (Tumblr) <<< Fungi (Tumblr) <<< Interact With (Tumblr) <<< YouTube <<< Nick (LiveJournal).

Microbes rule!!

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Dec 11, 2010

Want to have some fun? Do some peer reviewing for a scientific journal!

Photo by Patrick Bell
Every December, the journal Environmental Microbiology publishes a collection of humorous quotes made by peer reviewers while assessing manuscripts submitted to the journal. Some of them are hilarious! I am extracting a few of them from the last two years, but I recommend reading them all!

Here you go:

Desperate referees:

This paper is desperate. Please reject it completely and then block the author’s email ID so they can’t use the online system in future.

The biggest problem with this manuscript, which has nearly sucked the will to live out of me, is the terrible writing style.

The writing and data presentation are so bad that I had to leave work and go home early and then spend time to wonder what life is about.

The finding is not novel and the solution induces despair.

Desperate authors:
WOW! You did ‘read it with interest’ in SEVEN MINUTES??!! [Ed.: this is an author contribution in response to an editorial decision (rejection) made within 7 min of submission]

freddemasi on Twitter

Holiday season:
Done! Difficult task, I don’t wish to think about constipation and faecal flora during my holidays!

The peaceful atmosphere between Christmas and New Year was transiently disrupted by reading this manuscript.

Merry X-mas! First, my recommendation was reject with new submission, because it is necessary to investigate further, but reading a well written manuscript before X-mas makes me feel like Santa Claus.

Season’s Greetings! I apologise for my slow response but a roast goose prevented me from answering emails for a few days.

Technical issues:
[...] maybe some beetle took a pee on one or the other of the samples [...]

You call the sample fresh water, this is confusing as it is saline water.

The trees are crap but, besides this, excellent work.

Writing style:
You know there is something important there but the language is so inaccessible that you cannot make up your mind if they are trying to hide something or they actually think that is a good style of writing.

This manuscript gets the title ‘worst written manuscript of the year reviewed by DJ’

The writing style is flowery and has an air of Oscar Wilde about it.

Great manuscripts:
This is a long, but excellent report. [...] It hurts me a little to have so little criticism of a manuscript.

I perused this manuscript while in the hotel prior to a friend’s wedding. I was suspicious that a state of relaxation had influenced my enjoyment of a paper on soil formation; so I read it again, this time squashed between two large people on the delayed flight home, and still enjoyed reading it.

Very much enjoyed reading this one, and do not have any significant comments. Wish I had thought of this one.

It is always a joy to review manuscripts such as this. Well-conceived, well executed, well edited. Clean. Pristine. From start to finish.

- Referees' quotes – 2010. Environmental Microbiology (2010) 12, 3303–3304.
- Referees' quotes – 2009. Environmental Microbiology (2009) 11, 3309–3310.

Image credits:
Image (desperate schoolboy) modified from a photo by Patrick Bell. Source: Flickr. This image is licensed under a Creative Commons Attribution 3.0 Unported License.

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Oct 6, 2010

Microbial pigments: an untapped resource for teachers, artists and researchers

Elvis Lives! - painted on agar media using the bacterium Streptomyces coelicolor
The journal PLoS Biology has launched a new series of articles on education "to present innovative approaches to teaching critical concepts, developments, and methods in biology." The title of the first article in the series is In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond.

From the article:

"Soil bacteria from the Streptomyces genus represent a source of interesting natural products that have been largely overlooked by artists, researchers, and teachers. This article is intended to encourage amateurs and professionals alike to explore this overflowing source of biopigments. Not only does this endeavor have the potential to lead us toward a fertile nexus between art and science, it may also lead to a more sustainable and environmentally friendly way to color the world around us in the future. The relevance of biopigments to many facets of science, technology, and society, makes this material an outstanding tool to engage students of varying academic interests across multiple age groups. Therefore, we encourage teachers of all levels to consider using biopigments as a vehicle to introduce the scientific method to their students. To facilitate the implementation of biopigments into science and art curricula, we have provided a list of useful online resources and information about procuring materials [...] as well as recommend ways to evaluate the effectiveness of the lesson [...]."

Original article (and image source):
Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10): e1000510. doi:10.1371/journal.pbio.1000510
Image: “Elvis Lives!” painted on agar media plates using the bacterium Streptomyces coelicolor.

Related links:
- Microbial Art, a collection of unique artworks created using living bacteria, fungi, and protists.
- Painting With Penicillin: Alexander Fleming's Germ Art. The scientist created works of art using microbes, but did his artwork help lead him to his greatest discovery? By Rob Dunn., July 12, 2010.
- Streptomyces: they're twisted! Twisted Bacteria, Aug 10, 2007.

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Aug 19, 2010

A voyage from molecular genetics to microbial ecology -- includes a fish tank and some cartoons

The March issue of International Microbiology included a very nice article by Roberto Kolter, professor of Microbiology and Molecular Genetics at Harvard Medical School. The title is Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology (freely available as PDF).

In the article, the author gives an entertaining account of the path that lead him to the study of biofilms -- that is, aggregations of microbes growing on solid substrates. He also highlights some of his recent research on the ecology of microbial islands.

There is also a fish tank anecdote. And I added a couple of microbial cartoons, just for fun!

Do microorganisms have microorgasms? (cartoon)
Microbes are excellent model organisms... at least for studies on basic cellular processes. As Jacques Monod put it: Ce qui est vrai pour le colibacille est vrai pour l’éléphant ("what is true for the colibacillus is true for the elephant"). That is why Roberto Kolter (and many other researchers) soon fell under the spell of bacteria and, in particular, the colibacillus Escherichia coli.

For some time, Kolter studied the regulation of cell growth in E. coli. Under the right conditions, cells divide to yield daughter cells, which grow and divide quickly again, and so on -- and the bacterial population undergoes exponential growth. This exponential phase of growth (a.k.a. log phase) is typically followed by a stationary phase, when the growth rate slows down due to a scarcity of nutrients and accumulation of toxic products. Eventually, the bacterial population shrinks, in what is known as death phase (you can visit Cells alive! or Wikipedia for basic information on bacterial growth).

These processes are typically studied in the laboratory using shaken cultures. The shaking of flasks and test tubes keeps the broth composition uniform throughout the flask, and provides a continuous supply of fresh air that helps microbes grow fast. As a result, the cells are in a planktonic state; that is, they grow in suspension in the broth.

Shaker sick microbes (cartoon)From these shaker-sick cultures, Kolter and coworkers learnt a few interesting things about what happens during the stationary and death phases. In the International Microbiology article, he summarizes their findings as follows:

"And what we found through genetic analyses was rather extraordinary. Death allowed new life; we were witnessing evolution in real time [...]. Underlying the usually observed death phase was a dynamic world of dying and growing bacteria. There were constant population takeovers such that pre-existing fitter bacterial mutants grew as the original population met its demise. Evolutionary cheating we would call it later on [...]"
In other words, the adverse conditions occurring in the E. coli cultures during the death phase (toxic products, little food) appeared to have two contrasting effects. It was obvious that many cells were dying -- but, at the same time, successive waves of different spontaneous mutants were able to thrive and outgrow their dying siblings in this less-than-optimal environment. These findings were reviewed in two papers with memorable titles: Life after log and GASPing for life in stationary phase.

Isn't that a fascinating microcosms? The little creatures in the test tube were not just dying; they were evolving!

Pathogenic microbes (cartoon)

And now, the fish tank anecdote. Or, in Kolter's own words, the epiphany of the fish tank:
"The years that followed represented for me a dramatic turn of direction in my research. One might ascribe the change to some sort of “post-tenure depression”; I refer to it as the “epiphany of the fish tank” now. [...]
Microbial life on surfaces, for decades studied by Bill Costerton and other intrepid pioneers of the biofilm field, had been long ignored by most microbial physiologists and molecular geneticists, myself included. However, things changed for me in 1994 when, noticing my depressed state, members of my laboratory gave me a fish tank in a effort to draw me out of the blues. As I sat locked-up in the office staring at the tank, I realized that by studying shaken cultures of E. coli I had been barking up the wrong tree. The water in the fish tank remained crystal clear, it was on the surfaces where most microbial activity was occurring."

Biofilm of Desulfovibrio desulfuricans.That observation applies well beyond fish tanks. It is possible that the majority of microbes on Earth spend most of their lives in aggregates attached to surfaces, and therefore not in a free-floating or swimming, planktonic state. Obviously, they are not solitary guys: we could view biofilms in nature as quite complex 'societies' or 'cities' where different types of microorganisms inhabit buildings made out of sticky macromolecules (polysaccharides, proteins, DNA). Importantly, microbes in biofilms are sometimes resistant to the action of antibiotics, to which the same organisms are sensitive when in planktonic state.

So, have microbiologists been "barking up the wrong tree" all this time? Well, not exactly. Experiments using shaken cultures have been, and will continue to be, extremely useful. They are, without doubt, highly valuable to learn about the biochemistry, genetics and many other aspects of the biology of microbes. And they have been instrumental in providing us with antibiotics and vaccines to fight infectious disease.

But it is true that shaken cultures are sometimes not the best research models, especially if we try to understand 'the real life' of a microbe in its natural environment.

Biofilms formed by Bacillus subtilis.The 'fish tank epiphany' lead Kolter into biofilm research. A first approach he and his collaborators took was to study the biofilms formed by certain Bacillus subtilis strain. The accompanying image shows --on the left-- a beaker with a floating film that the microbe forms when grown in a standing (not shaken!) liquid culture, and --on the right-- a magnified view of a colony grown on an agar plate. Although these biofilms consist only of a single organism, they are actually highly structured, with several layers composed of different cell types engaged in various activities: some cells are actively producing the matrix (not the Wachowskis' movie but the glue that keeps the biofilm together), others are swimming around, and there are also some cells in the process of becoming spores. How close is that to a multicellular organism?

The B. subtilis biofilm is a very useful model -- but you may well think that a beaker containing a single microbial species is a very artificial setting.

Then, how can scientists study biofilms in natural environments? For Kolter, the inspiration came -- no fish tank involved -- from the writings of biologist E. O. Wilson. In collaboration with Robert MacArthur, Wilson developed in the 1960s the theory of island biogeography, which has become fundamental in ecology and evolutionary biology. The theory tries to explain the factors that control the number of species in a natural community (it was originally developed for islands but now it is applied to any ecosystem that is surrounded by other ecosystems). Kolter was fascinated by the ways Wilson studied newly formed islands to put the theory to the test (what Wilson actually did was to fumigate some small islands to kill all arthropods, and then observe how the islands were recolonized). However, Kolter was wise enough and did not try to make free from microbes any islands (that would be tough!). His approach, much less destructive, consisted of studying two natural microbial islands: the pitchers of a carnivorous plant, and the human lungs.

Sarracenia purpureaThe first island is Sarracenia purpurea, a carnivorous plant feeding on the insects and spiders that fall into its water-filled pitchers. Kolter and collaborators found that the inside of unopened, newly formed pitchers was sterile -- there you go, a microbial island is born! This allowed them to analyse the composition of the nascent bacterial population in the pitchers during the season, as microbes colonized the island. Among other results, the researchers found that pitchers containing certain mosquito larvae (keystone predators) had a greater bacterial diversity.

The second microbial island studied by Kolter and coworkers is the respiratory tract of humans suffering from cystic fibrosis (CF). As long as you are healthy, your lungs are supposed to be mostly sterile. However, respiratory diseases such as CF or asthma open the gates to outside microbial colonizers, which can make a lot of harm. In CF, the major microbial pathogen is the bacterium Pseudomonas aeruginosa, which forms biofilms inside the lungs and can easily become resistant to antibiotics. Using culture-independent methods, Kolter's laboratory compared the microbial communities in the lungs of different CF patients. The researchers showed that the presence of P. aeruginosa was correlated with lower microbial diversity, worse lung function, and patient age. In other words, it appears that the arrival of P. aeruginosa (an 'invasive species') greatly affects the microbial community in CF lungs, resulting in a decrease in diversity. The researchers suggest that the composition of the microbial community could be a better predictor of disease progression than the presence of P. aeruginosa alone.

Well, that was a long post. Please read Roberto Kolter's article (it is free), which includes a few more interesting thoughts and quotes. The concept of microbial islands is fascinating. And the growing interaction between the long-time isolated fields of ecology and microbiology is, I think, changing the way microbiologists view their study subjects. Hopefully, ecologists will also become more aware of the organisms that rule the planet -- which are not humans, you know.

Reference for Roberto Kolter's article:
Roberto Kolter (2010). Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology. Int. Microbiol., 13, 1-7. DOI: 10.2436/20.1501.01.105 (pdf)

Related links:

- Biology of microbial communities - Interview to Roberto Kolter (video). JoVE, May 2007.

- Roberto Kolter - Bacillus subtilis and bacteria as multicellular organisms (podcast). Meet the Scientist, episode 20, March 2009. MicrobeWorld.

- The evolution of the biofilm concept: a long and winding road (free PDF), by J.W. Costerton. Sartoniana (2008) 21:59-67.

- About the existence of microbes (viruses) in healthy and diseased human lungs: Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals (2009). PLoS ONE 4(10): e7370. doi:10.1371/journal.pone.0007370 (free article).

Image credits:

- Cartoons by Sanja Saftic. Many thanks to her for allowing me to use the cartoons for this blog post. Source: - Microbiological Edutainment.

- Color-enhanced scanning electron microscope (SEM) image of a biofilm formed by Desulfovibrio desulfuricans bacteria. Image by PNNL - Pacific Northwest National Laboratory. Source: Flickr.

- Beaker and colony: highly structured biofilms formed by Bacillus subtilis strain NCIB 3610. Source: International Microbiology.

- Sketch of carnivorous plant: Sarracenia purpurea. Source: Wikimedia Commons.

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Jun 25, 2010

They Might Be Giants: Science is Real - a music video

Via my Daily on Twitter >>> Michael Banks (Twitter) >>> Rocking the physics message ( >>> They Might Be Giants (ParticleMen, YouTube).

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Jun 22, 2010

TED videos: excellent talks about life, the universe and everything -- including microbes

Modified TED logoTED is a nonprofit organization devoted to "ideas worth spreading." They are mostly known because of their growing collection of fascinating talks about a wide array of topics, including science, art and anything in-between (or around). The talks are recorded and the videos are freely available at their website, where you can also find information about the speakers and interactive transcripts (including translations to various languages).

In this post I'm collecting links to all the TED videos I could find related to the microbial world.

Topics include: life in the deep oceans, medical mysteries, bacterial Esperanto, predicting pandemics, robots turned into microbiologists, new approaches to handle infectious diseases, looking for life on Mars and beyond, fungi that could save the world, bacteria that may have caused mass extinctions...

Awesome, huh?

I'm also embedding a video for one of the latest TED talks: Seth Berkley: HIV and flu -- the vaccine strategy. The speaker, epidemiologist Seth Berkley, is the founder of the International AIDS Vaccine Initiative. In this talk, filmed last February, he spoke about new methods for making vaccines for AIDS and flu.

I also recommend reading this interview on the TED blog, where Seth Berkley commented on the same subject. I am copying here a few remarkable quotes:

I was very disappointed by public concerns that we ordered too much flu vaccine and that some might get wasted. (...) I think that both declaring this a global pandemic and accelerating vaccine production as quickly as possible were the right decisions. If you want to prepare a population for an emergency it means that you might ultimately spend some money that isn’t used.
That's a good point. Many criticisms have been raised in the last months against WHO decisions in relation to the recent flu pandemic. And some of those criticisms were undeserved, in my opinion.

In the interview, Berkley explained why so much effort was put on developing treatments --rather than preventive vaccines-- for AIDS. And he described the extraordinary work they're doing with the International AIDS Vaccine Initiative.

To the question "Are the members of the younger generation of scientists as invested in creating a vaccine as was the case 10 years ago or so?" he responded:
Sadly not. (...) The problem is not that young scientists don’t think vaccines are incredibly important, the problem is that it is seen as such a difficult problem, such a long-term problem that what they’re worried about is: Can they build a career on it? Can they get the types of breakthroughs they need in a rapid time frame that would make it a productive place to work?
It is disturbing that the "productivity" concept not only is doing harm to many researchers' careers but may also be slowing down the development of much-needed medical treatments...

Why not focus just on the treatment of infected people, and forget about an AIDS vaccine? Berkley explained:
(...) from a public policy point of view, there’s great expense involved in dealing with the epidemic through treatment and reaching people when they’re already infected. (...) But this is a long-term entitlement program, because once you put somebody on treatment, they have to get treatment for the rest of their lives and they develop conditions, they develop toxicity and they need other treatments. So, there’s almost a sense now that all of the bright lights of that unbelievable effort -- the unprecedented emergency program for AIDS relief, Bush’s triumph that people look on as being a great thing that he did, will create a demand that gets higher and higher and higher just to keep up with where we are.
So, making an effective vaccine against AIDS may be very difficult. But it is worth the effort.

And finally, as promised, this is the list of other TED videos related to the small living beings (in chronological order, newest first):

[Added October 15th, 2010 -- Eben Bayer: Are mushrooms the new plastic? "Product designer Eben Bayer reveals his recipe for a new, fungus-based packaging material that protects fragile stuff like furniture, plasma screens -- and the environment." July 2010. Found via MicrobiologyBytes.]

TED video: Magnus LarssonMagnus Larsson: Turning dunes into architecture. "Architecture student Magnus Larsson details his bold plan to transform the harsh Sahara desert using bacteria and a surprising construction material: the sand itself." July 2009.

TED video: Nathan WolfeNathan Wolfe: hunting the next killer virus. "Virus hunter Nathan Wolfe is outwitting the next pandemic by staying two steps ahead: discovering deadly new viruses where they first emerge -- passing from animals to humans among poor subsistence hunters in Africa -- before they claim millions of lives." February 2009.

TED video: Bonnie BasslerBonnie Bassler: discovering bacteria's amazing communication system. "Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves." February 2009.

TED video: Hans RoslingHans Rosling on HIV: New facts and stunning data visuals. "Hans Rosling unveils new data visuals that untangle the complex risk factors of one of the world's deadliest (and most misunderstood) diseases: HIV. He argues that preventing transmissions -- not drug treatments -- is the key to ending the epidemic." February 2009.

TED video: Kary MullisKary Mullis' next-gen cure for killer infections. "Drug-resistant bacteria kills, even in top hospitals. But now tough infections like staph and anthrax may be in for a surprise. Nobel-winning chemist Kary Mullis, who watched a friend die when powerful antibiotics failed, unveils a radical new cure that shows extraordinary promise." February 2009.

TED video: James NachtweyJames Nachtwey fights XDR-TB. "Photojournalist James Nachtwey sees his TED Prize wish come true, as we share his powerful photographs of XDR-TB, a drug-resistant strain of tuberculosis that's touching off a global medical crisis. Learn how to help at" October 2008.

TED video: Paul StametsPaul Stamets: six ways mushrooms can save the world. "Mycologist Paul Stamets lists 6 ways the mycelium fungus can help save the universe: cleaning polluted soil, making insecticides, treating smallpox and even flu." March 2008.

TED video: Peter WardPeter Ward: Earth's mass extinctions. "Asteroid strikes get all the coverage, but "Medea Hypothesis" author Peter Ward argues that most of Earth's mass extinctions were caused by lowly bacteria. The culprit, a poison called hydrogen sulfide, may have an interesting application in medicine." February 2008.

TED video: Paul EwaldPaul Ewald: can we domesticate germs? "Evolutionary biologist Paul Ewald drags us into the sewer to discuss germs. Why are some more harmful than others? How could we make the harmful ones benign? Searching for answers, he examines a disgusting, fascinating case: diarrhea.". March 2007. (I embedded this video in a previous post.)

TED video: Bill StoneBill Stone explores the world's deepest caves. "Bill Stone, a maverick cave explorer who has plumbed Earth’s deepest abysses, discusses his efforts to mine lunar ice for space fuel and to build an autonomous robot for studying Jupiter’s moon Europa." "How do you take a robot and turn it into a field microbiologist?" March 2007.

TED video: Laurie GarrettLaurie Garrett on lessons from the 1918 flu. "In 2007, as the world worried about a possible avian flu epidemic, Laurie Garrett, author of "The Coming Plague," gave this powerful talk to a small TED University audience. Her insights from past pandemics are suddenly more relevant than ever." February 2007.

TED video: Penelope BostonPenelope Boston says there might be life on Mars. "So the Mars Rovers didn't scoop up any alien lifeforms. Scientist Penelope Boston thinks there's a good chance -- a 25 to 50 percent chance, in fact -- that life might exist on Mars, deep inside the planet's caves. She details how we should look and why." February 2006.

TED video: Larry BrilliantLarry Brilliant wants to stop pandemics. "Accepting the 2006 TED Prize, Dr. Larry Brilliant talks about how smallpox was eradicated from the planet, and calls for a new global system that can identify and contain pandemics before they spread". February 2006.

TED video: Joe DeRisiJoe DeRisi solves medical mysteries. "Biochemist Joe DeRisi talks about amazing new ways to diagnose viruses (and treat the illnesses they cause) using DNA. His work may help us understand malaria, SARS, avian flu -- and the 60 percent of everyday viral infections that go undiagnosed." February 2006.

TED video: David GalloDavid Gallo on life in the deep oceans. "With vibrant video clips captured by submarines, David Gallo takes us to some of Earth's darkest, most violent, toxic and beautiful habitats, the valleys and volcanic ridges of the oceans' depths, where life is bizarre, resilient and shockingly abundant." February 1998.

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