Showing posts with label science. Show all posts
Showing posts with label science. Show all posts

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).


Note:
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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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.




Links:
- 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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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 (physicsworld.com) >>> They Might Be Giants (ParticleMen, YouTube).

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Jun 3, 2010

A Twitter view of the general meeting of the American Society for Microbiology - #asmgm

Word cloud for tweets containing the ASMGM hashtag
The above image is a word cloud generated from about 1200 tweets (that is, messages posted on the microblogging service Twitter). All these tweets are related to the general meeting of the American Society for Microbiology (ASM), which was recently held in San Diego, California (May 23-27).

Please wait for my next blog post, where I'm going to tell you about a few things that could be learnt about microbes by following the ASM meeting on the internet -- no matter your physical location on Earth (and beyond?). Also, I'm going to explain how I made the word cloud -- I'm pretty sure there must be a better and easier way to do this, so I would certainly appreciate your feedback on my next post.

Note: unfortunately, the tags in the cloud are not hyperlinked. The image was generated using Wordle.

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May 20, 2010

Media for Science Forum: poor organization, disappointing use of social media

A science journalism congress was held last week in Madrid, Spain, under the name Media for Science Forum (MFSF). This was a European congress dealing "with strategic issues about science communication and science journalism and its social dimension." One of its specific objectives was declared to be: "Explore new trends in Science Communication due to the web 2.0".

Well, this sounded really exciting to me (and registration was free!), so I planned to attend the congress. Unfortunately, the organization rejected my application due to the huge amount of requests received.

So, I couldn't attend the meeting in Madrid --but I followed the events from my home at London, using the internet.

This post describes my personal experience of MFSF, including a few thoughts about the use of social media. You are more than welcome to add your comments at the end of the post.


March 18th

I first learnt about the upcoming Media for Science Forum (MFSF) through an announcement made on the SINC webpage (in Spanish). SINC (www.plataformasinc.es) is a news agency focused on scientific research done at Spanish institutions and research done by Spaniards at foreign institutions.

After visiting the MSFS official webpage, I filled and sent the online registration form the very same day. Registration was free but seats were limited: the organization would contact me in due time to accept or reject my application.

After registration, I was expecting to receive an email, automatically generated by the system, acknowledging my registration and providing some additional information --this seems a common procedure for online forms--, but this message did not arrive.

Anyway, I sent a tweet to inform my Twitter followers about the event, suggesting a possible hashtag. I also announced the conference on the Science Writers Facebook page.


April 4th

Over two weeks passed, but I didn't receive any email from the organization, and no new information was posted on the MFSF website. So I sent them an email including all my personal information and a link to my CV. I also explained them that I needed to know about the success or failure of my application in a short time, as I eventually had to make some arrangements for my trip London-Madrid.


April 6th

The MFSF organization forwarded me an email, which was supposed to be sent to me on March 18th (but I had not received). The message thanked me for the registration and informed that I'd be contacted again by the organization about the possible success of my application. When? "Soon." No more details were included.


April 7th

I received an email with the following request: "We have had problems in our system, and I have to ask you to reconfirm the dates that you are planning to attend the Forum".

The problem is that the email did not come from the congress organization but from a known Spanish travel agency. I checked the MFSF website (again) looking for some explanation or connection to this travel agency: I couldn't find anything. Anyway, I replied with the requested information: I planned to attend both days (12th and 13th May).


April 12th

MFSF started to use Twitter and Facebook!

I thought: "Great, they'll keep us informed about what's going on."

Oh, how wrong I was...


April 14th

New email from the travel agency, including a message from the MFSF organizers: they started a blog!

"Excellent, another channel to keep in touch with us! Now we'll get some news!" -- or so I thought.

I wasn't sure if that message meant that my application had been successful, so I requested some information about it. They replied immediately: "Nobody is receiving any confirmation. The organizers are still receiving applications, and they haven't made any decisions yet. We will inform you in due time" (my Spanish-to-English translation).


April 28th

During the previous days I had exchanged a few messages with other members of a LinkedIn group (Periodismo científico y divulgativo, which is Spanish for "Science journalism"), and learnt that nobody seemed to have received any confirmation regarding their MFSF application.

So I posted a message on the MFSF Facebook page, requesting information (to see my message there, you need to click on "Media for Science and others", as the default page only shows messages written by the organizers).

They never replied to my message on Facebook.


April 29th

Six weeks after my registration, and 13 days before the event, the MFSF organizers sent me an email: "Unfortunately your request to participate on the congress has been denied due to the huge amount of requests received."

You can imagine this didn't make me very happy.

Anyway, I still expected to know more about the MFSF talks and discussions through the internet, by making use of social media.


May 12th: first day of the congress

Early in the morning, I learnt from Twitter (actually, I think it was through this Topsy search) that the MFSF talks were going to be broadcasted through live web streaming.

Oh, wait, it appeared that only the opening talk was to be transmitted.

Note that I didn't get that information thanks to MFSF "Web 2.0" tools: their blog, Twitter and Facebook pages were all mute about this issue at the time (and even later).

The opening talk --the only one that was to be live streamed-- was untitled and in charge of the General Director of FECYT (Spanish Foundation for Science and Technology). This didn't sound very exciting to me. So, I forgot about MFSF for the rest of the day. My plan was to check the internet for related discussions on the following days.


May 13th: second and last day of the congress

At midday, I was surprised to know (through Twitter, but not MFSF Twitter) that the forum broadcast was still live!

Although with some interruptions in the service, they had been transmitting the whole thing!? Apparently, this was just an unplanned, happy idea. Well, I guess nobody had thought about this possibility before...???

Anyway, so I was able to watch the afternoon talks. These included brief descriptions of European scientific news services (such as AlphaGalileo), and the final conclusions (which were not such a thing but a list of general recommendations). Nice, but not incredibly useful.


Today, May 20th
Today I've been searching the internet, including Twitter, for reactions to MFSF (see links below). It seems that the congress was quite popular on Twitter: the hashtag #mfsf (not the one I suggested) became the second trending topic on Twitter in Spain. That's pretty good for a science journalism congress!

...Although it must be said that many tweets were messages of the lifecasting type ("On my way to Madrid...", "Having a beer in...", and the like), which in my opinion only contribute to the noise -- when they are tagged with a congress hashtag.

From what I can read on the internet, it seems that most people found the forum interesting -- too bad my application was rejected. On the negative side, MFSF was poorly planned, and failed to provide essential information to potential attendees and the general public.

In particular, their use of social media (blog, Facebook, Twitter) for updates and conversation was really disappointing -- and remember that one of their specific objectives was to "explore new trends in science communication due to the web 2.0". After the first hello message, MFSF published only 10 messages on Twitter and 13 updates on Facebook (numbers correct at the time of writing this) -- and all these messages were just announcements of new blog posts. No updates about registration issues, no announcements concerning the live web broadcasting, no comments on specific talks, no conversation at all. That is useless to me.


Reactions to MFSF:
- No hay que ser innovador... tan sólo parecerlo [in Spanish] by Javi Peláez. La aldea irreductible, May 12th, 2010.
- Media for Science Forum (1), (2) and (3) [in Catalan] by Miquel Duran. Edunomia, May 12-13-14, 2010.
- Media for Science Forum and (II) [in Catalan] by Pep Anton Vieta. Pepquímic, May 12-15, 2010.
- Media for Science Forum 2010 – ein Rückblick [in German] by Hans-Dieter Zimmermann. FHS eSociety Blog, May 18th, 2010.
- El estado del periodismo científico, en el Media For Science Forum de Madrid [in Spanish but with English introduction] by Pere Estupinyà. Knight Science Journalism Tracker, May 19th, 2010.

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Apr 12, 2010

Social media for microbiology education and research

Jump on the social media bandwagon, by Matt HammVincent Racaniello is a well-known Professor of Microbiology at Columbia University Medical Center, New York. As a complement to his research and his classes on virology, he successfully uses different social media tools (blogging, podcasting, microblogging) to spread the love for viruses -- I mean, to teach the public about viruses (the kind that make you sick... or not).

The following video is a recording of a great talk he gave at the Spring 2010 meeting of the Society for General Microbiology in Edinburgh, UK. In this presentation he explains -- in simple terms -- how he uses blogging, podcasting, and other social media tools for the popularization of virology.

I'm wondering if the talk could convince a few of the microbiologists in the audience to jump on the social media bandwagon...? Anyone?


The video is licensed under a Creative Commons Attribution license, and can be watched also at BioCrowd or at Virology Blog.


Image credits: "Jump on the social media bandwagon" by Matt Hamm. Source: Flickr. Image used under an Attribution-Noncommercial Creative Commons license.

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Mar 17, 2010

Year of Biodiversity: only for cute animals and plants?

International Year of Biodiversity LogoThe United Nations declared 2010 to be the International Year of Biodiversity. This sounds great, let's celebrate and protect the variety of life on Earth! We must learn more about current (and past) biodiversity and the impact that human activities have on the distribution and abundance of organisms. Also, we should explore any effective ways to protect biodiversity, if only because it benefits us.

However, it strikes me as short-sighted that most biodiversity advocates seem to care only about "the cute organisms" (cute by most human standards, I guess); that is, a few particular animals and plants. But... for Pete's sake, life on Earth goes well beyond a few vertebrates, trees and corals! Surprisingly, the true diversity of life is not obvious at all in the writings of most biologists, conservationists or environmental scientists when discussing biodiversity and its protection.

I know, I know -- when a clear message is to be delivered to the general public, you cannot be comprehensive. If you can mention only a couple of examples for endangered species, you better go for the much-like-us mammal, or the colourful bird, or the pretty tree or flower. Most of us can easily sympathize with a chimpanzee (that is, really, almost one of us) or with many animals: they have faces, with two eyes and a mouth, and it's hard not to see part of our own reflection there. We often show emotional responses also to trees, flowers or grasses (even mushrooms). So, when explaining the importance of biodiversity to a general audience, sticking to the cute guys might be the wise choice.

But how is this topic treated inside the scientific community? Well, in general, I don't see much difference. When biodiversity is discussed -- in general terms -- in scientific articles, editorials or websites, the focus is again on certain plants and animals that can be seen by the unaided human eye (that is, macro-organisms). By contrast, microbes are hardly ever referenced, if at all.

Why are microbes not even mentioned most of the times? Why are some particular organisms (let's call them "the cuties" for short) the focus of research and protectionist efforts? I can think of a few possible answers:

1 - The cuties, among all the living beings, might suffer the highest risk of extinction.
2 - Although there are other organisms at higher risk, the cuties are perhaps more important (in some way) either for the preservation of particular ecosystems or for human well-being.
3 - Our current knowledge of life diversity might be very limited, and is focused on particular organisms because of historical and technical reasons.

I guess that most scientists and many learned people would agree with me that answer number 3 seems about right (but if you think otherwise, please leave a comment). Actually, it seems that we know very little on the matter. Scientists are starting to agree -- I think -- on a broad definition of biodiversity. But the field faces (at least) two huge challenges. First, there are many organisms living on (and inside) this planet that we haven't met yet, and our estimates of how many species are awaiting discovery are little more than educated guesses. Second, although biodiversity can be measured at various levels, it's often understood as referring to the number and relative abundance of different species. And deciding if two organisms belong to a single species, or to two different ones, can be really hard. Moreover, the difficulty in agreeing on species definition depends greatly on the type of organism it applies to: whereas this issue causes some serious troubles when studying cuties, it appears almost insurmountable when trying to define microbial species. Why is this so? Well, I'm not getting into this here, but let's say that the species concept was originally created and crafted for the cuties, and microorganisms just don't fit into such clothes.

However, even lacking a suitable species definition (to the embarrassment of microbiologists), we can confidently say that the microbes are much more diverse than the cuties. This diversity is shown at different levels: genetics, biochemistry, ecology... You can find microbes almost everywhere, and often in amazingly high numbers. No matter if you count individuals or you measure biomass: microbes are the (silent?) majority. Some microorganisms are essential not just for the preservation of particular ecosystems but for the continuity of life on Earth as we know it (and when I write "life" I mean "life", not just "cuties"). Under any non-human-centred point of view, life is microbial -- with a few exceptions, yes.

So, just to recapitulate... Some animals and plants appear to be on the brink of extinction because of human actions, and it doesn't seem a good idea to let them go. However, we don't know how many types of organisms are out there, or how many of them are endangered by our activities, and we don't understand the long-term effects of the extinction of any particular life form. Yes, more research is definitely needed.

But we do know that life is incredibly diverse and mostly invisible to the human eye, and that the cuties are not even the tip of the iceberg. So, any serious research or scientific communication on the diversity of life should include (in my opinion) some mention to microbes, the main actors on this movie -- at least we should acknowledge our ignorance! Microbes play key roles in nature: shouldn't we worry about the preservation of microbial diversity?

Don't get me wrong: I don't want any cuties to become extinct. But I think that scientists can do a much better job when discussing biodiversity.



Further reading:

If you find the topic of this post interesting, you must read the following excellent articles written by Sean Nee, University of Edinburgh, UK (articles can be downloaded from the author's website):

- The great chain of being. Nature (2005) 435: 429.

"Our persistence in placing ourselves at the top of the Great Chain of Being suggests we have some deep psychological need to see ourselves as the culmination of creation."

- Extinction, slime and bottoms. PLoS Biology (2005) 2(8): e272.
"There is an old Chinese curse: ‘May you live in interesting times.’ According to those who know about such things, we live in a momentous time, the time of the Sixth Mass Extinction! But most of us do not feel at all cursed. Because, in fact, the Sixth is quite different to the previous Big Five—no-one would notice this one if we were not repeatedly reminded of it by ecologists."

- More than meets the eye: Earth's real biodiversity is invisible. Nature (2004) 429: 804-805.
"We are still at the very beginning of a golden age of biodiversity discovery, driven largely by the advances in molecular biology and a new open-mindedness about where life might be found. But for this golden age to be as widely appreciated as it should, our view of the natural world must change — as radically as did our view of the cosmos when we began looking at it with technologies that allowed us to see more than can be seen with the naked eye."

- Beyond the tangled bank (pdf). This manuscript seems a slightly longer version of More than meets the eye: Earth's real biodiversity is invisible. Interestingly, it includes many references that were not incorporated into the published article.


I also recommend a thought-provoking article by Maureen A. O’Malley & John Dupré, University of Exeter, UK:

- Size doesn’t matter: towards a more inclusive philosophy of biology. Biology and Philosophy (2007) 22, 155-191.


NOTE added on April 17, 2010:
A Letter has just been published by Andrew Beattie and Paul Ehrlich in Science, highlighting what The Missing Link in Biodiversity Conservation is:
"the many millions of species within the numerous phyla of microbes and invertebrates, which represent perhaps 95% of total species and genetic biodiversity."
The authors propose to deliver a new message to the public:
"a new message, one we would like to label "production biodiversity": By protecting microbes and invertebrates, we also protect the primary industries upon which we all depend."

I agree!


Related links:
- (Added April 20, 2010) A commentary on the same subject has been published by Mercè Piqueras in her blog, La lectora corrent (in Catalan): La biodiversitat invisible.

- (Added June 23, 2010) See Dear New Scientist by Ed Rybicki, who reminds us that "the greatest part of the biodiversity on this (and probably any other) planet is viruses."

- (Added August 19, 2010) Preserving endangered species – of gut microbes, by Grant Jacobs. Or the need to preserve the human gut microbes found in ancient rural populations.

- (Added September 11, 2011) Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet, by Jonathan Eisen.

- (Added September 11, 2011) Don’t forget to count microbes, by David Hooper & Bonnie Bassler.


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Dec 13, 2009

Science cookies, courtesy of Not So Humble Pie

Gel electrophoresis cookies
I would never advise you to eat an agarose gel after electrophoresis, or a Petri dish with live microbes growing on it. Well, actually, don't eat any of them even before electrophoresis or before seeding any microorganisms! Unless...

Petri dish cookies
Well, unless the agarose gels and the Petri dishes are beautiful, edible cookies made by Ms. Humble from Not So Humble Pie!

Yummy!

Periodic Table cookiesGinger bread scientists
Can science be... delicious??

(Found via FriendFeed)

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Jun 7, 2009

Social media for scientists

The following slidecast (that is, a slideshow including audio) is an excellent presentation by Mary Canady and William Gunn on social media for scientists. Topics covered: LinkedIn, Twitter, social bookmarking (delicious, citeulike, Mendeley), FriendFeed, science blogs.

If you are a scientist and you think social media is completely useless for you as a researcher... well, you are wrong and must watch this!



(Found via Twitter)

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Apr 25, 2009

Microbiology on Twitter?

Just for fun, I searched Twitter using some microbial-related terms (not many, as the query cannot be more than 140 characters long!). I have added an RSS feed for this query to the side bar on this blog.

[Note (added on 15th Nov): I removed the RSS feed from the side bar -- the automated search was not very useful]

Is Twitter useful for scientists or for science educators? For some, it seems to be.

Will Twitter (or a similar tool) be of general use among scientists in a near future? Perhaps.

As a new user, I know very little about Twitter. But interesting things are happening there.

I just find difficult to make sense out of most of them...

But I´ll keep trying.

And you should, too.

On Twitter, I am TwistedBacteria (obvious). But, definitely, you should be following at least MicroBytes and MicrobeWorld.

I also created a Twibe (a group of Twitter users interested in a common topic) called Microbiology.

(Thanks so much to Alan Cann for introducing me to the Twitter universe!)

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May 14, 2008

Neglected diseases in the news

Trypanosoma forms in blood smear from patient with African trypanosomiasisThe so-called neglected diseases comprise a number of parasitic and bacterial infections which are the most common afflictions of humankind. So, how can these diseases be "neglected"? When you get sick, you don't ignore your illness, do you? But we all can ignore a disease... as long as we ourselves don't suffer it.

Neglected diseases are especially endemic in low-income populations in developing regions of Africa, Asia, and the Americas. They mostly affect the poorest people, living in remote rural areas, urban slums or conflict zones. In the meantime, the rest of humankind just "neglect" those pains, as exemplified by the poor coverage on news media.

(If you already know about these diseases, just jump to the paragraph starting with "An interesting study...")

According to the Global Network For Neglected Tropical Disease Control, the most prevalent neglected tropical diseases are:



























DiseaseCausative agents
Affected people
Soil-transmitted helminthiasesSeveral nematodes: roundworm (Ascaris lumbricoides), whipworm (Trichuris trichiura), hookworms (Ancylostoma duodenale, Necator americanus)Over 2 billion infected; over 70,000 deaths/year
Lymphatic filariasis (elephantiasis)Several nematodes: Wuchereria bancrofti, Brugia malayi, B. timoriOver 120 million infected; 40 million with clinical symptoms
River blindness (onchocerciasis)A nematode (Onchocerca volvulus)37 million infected; 500,000 visually impaired; 270,000 blind
Schistosomiasis (bilharzia)Several flukes (trematodes) of the Schistosoma genus200 million infected; over 200,000 deaths/year
TrachomaA bacterium (Chlamydia trachomatis)84 million infected; 8 million visually impaired or irreversibly blind



But, unfortunately, the list of neglected diseases is much longer, including:
[disease name, causative agent]

Wow, if you are still reading this, you must be really interested. Or you've just jumped over all those boring, unpronounceable words. That's OK. But the title of the post said "in the news", so let's go.


ResearchBlogging.orgAn interesting study has just been published on the open-access journal PLoS Neglected Tropical Diseases, showing that these diseases rarely make the headlines... Oh, wait, we already knew that. True —but this report seems to be the first one trying to analyze, in a quantitative manner, the international media coverage of neglected diseases, as a support for future advocacy work.

The authors searched the archives of 11 English-language media, from January 2003 to June 2007, including 6 newspapers (The New York Times, Los Angeles Times, Washington Post, The Guardian, The Daily Telegraph, The Financial Times), BBC Online, CNN.com, Agence France Presse (AFP), and two news magazines (Time and The Economist). They analyzed coverage of "neglected diseases" in general, with a focus on African trypanosomiasis, leishmaniasis and Chagas' disease (probably not the most neglected). The researchers also interviewed leading health journalists, highlighting factors influencing reporting.

During the study period, they found only 113 articles on neglected diseases. In comparison, there were over 1000 articles on HIV/AIDS in the AFP database alone during the same period. There was wide disparity in coverage between the various media: the BBC had the highest coverage (20 articles), while CNN had the least coverage (only 1 article). Coverage of global health issues was particularly poor in the American media.

As the authors recognize, it would be useful to expand the analysis, including more international media and languages other than English. However, the selected media may be considered a useful sample, and some patterns emerged:
" For example, the penchant for a local angle was even parochial at times. Stories get written about leishmaniasis in pets before humans, as was seen in The Daily Telegraph. "
In the interviews, journalists explained that the main obstacles for reporting on these issues were: a lack of real news development, the drive to cater to domestic audiences, and competing health interests.
" “Poor people dying from an illness is not news,” unless there is some change or development, one producer from an international broadcaster said. But HIV/AIDS was widely reported on “because it sells stories” and has the funding and attention of policymakers. "
That's perfectly understandable: news media need to make a living, and only "newsworthy" stories get the attention. Here, the role of health agencies (either public or private) is essential: all journalists said health agencies were not communicating adequately about the burden of neglected tropical diseases. Some organizations (World Health Organization, Bill & Melinda Gates Foundation) were criticized for the difficulty in reaching officials for comment, while non-governmental organizations such as Médecins Sans Frontières (MSF) were cited as good sources for stories.

News coverage was also difficult due to the lack of powerful "human" stories from the field (including interviews with patients).
" The “human element” was powerful, but few journalists were able to get such stories first-hand from the field. This represented a real constraint for coverage. One communications advisor (consulting for DNDi) said health agencies needed to present stories featuring “real people” rather than “experts in their ivory towers” and the “yuck” factor about these diseases needed to be played up to “grab the public imagination” rather than facts about the lifecycle of the parasite. "
Remarkably, journalists who did cover these diseases were often personally motivated. Andrew Jack (Financial Times), who authored the largest number of articles detected in the study, said his reporting was “100%” driven by his interest.

In other words, a single individual can make a difference.


Original article (open access):
Balasegaram, M., Balasegaram, S., Malvy, D., Millet, P., Hotez, P.J. (2008). Neglected Diseases in the News: A Content Analysis of Recent International Media Coverage Focussing on Leishmaniasis and Trypanosomiasis. PLoS Neglected Tropical Diseases, 2(5), e234. DOI: 10.1371/journal.pntd.0000234



Related links:


Image credits:
Trypanosoma forms in blood smear from patient with African trypanosomiasis. Source: Public Health Image Library (PHIL). Content provider: CDC/Dr. Myron G. Schultz.

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Mar 11, 2008

Too many techniques, too little time

Evaluating Techniques in Biomedical Research, Cell PressAre you overwhelmed by the progress in biological techniques?

Have you recently read about some interesting research but could not follow the basic details of a technical procedure?

Are you breathing?

In case you do want to understand a little bit more about those ... techniques, you can try this collection of articles:

Evaluating Techniques in Biomedical Research (Dec. 2007)

(All articles are freely available)

Topics: 3D structure determination by electron microscopy, X-ray crystal structures, proteomics, two-hybrid experiments, DNA microarrays, chromatin immunoprecipitation, RNA interference, fluorescence microscopy, FRET, and biostatistics.

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Mar 8, 2008

Women scientists, sixty years ago

Microscopic image (200-fold magnification) of Candida albicansNew York City, 1949. During the last three years, Elizabeth Hazen had been isolating hundreds of microbes from dirt samples taken at different locations. Many microbiologists at the time were following a path open by Alexander Fleming, Selman Waksman and others, who discovered that some soil microbes produced certain substances—antibiotics—with powerful activities against bacteria. However, rather than looking for a new agent against prokaryotic microbes, Elizabeth searched for a medicine to fight fungal infections. For this purpose, she grew the soil microbes and tested the cultures against disease-causing fungi (Cryptococcus neoformans, Candida albicans [see image]). Whenever a culture showed an interesting activity, she put it in a glass Mason jar and mailed it to Albany, 250-km away. Here, Rachel Brown—a chemist—used the culture for purification and characterization of the active compound. Then, Rachel mailed the fruit of her efforts back to New York, where the microbiologist tested the sample again for fungicidal potency. Through this collaboration, the two scientists isolated several antifungal compounds that, unfortunately, were too toxic when tested in laboratory animals.

Chemical structure of Nystatin A1But, finally, Elizabeth and Rachel found a useful fungicidal agent with a lower toxicity. It was produced by a soil bacterium isolated from a sample that Elizabeth had collected, while on holiday, in Warranton, Virginia. She had taken a bit of soil at the edge of a cow pasture, near a dairy barn, at the farm of a certain Walter B. Nourse. Because the microbe appeared to be a new species of streptomycetes, it received the name Streptomyces noursei, in honor of Mr. Nourse. The fungicidal agent was initially named fungicidin, but it was soon renamed nystatin, as both Elizabeth and Rachel worked for the New York State Department of Health (although in different locations). Since then, nystatin has been widely used to treat candidiasis and other fungal infections.


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This post modestly celebrates March 8th, International Women's Day. The discovery of nystatin seems a good example of an important contribution of women scientists to microbiology, natural product chemistry, and medicine. A related story is that of Alma Whiffen, who discovered cycloheximide—also known as actidione—around the same time (1947). She isolated the compound from cultures of a soil microbe, Streptomyces griseus. Cycloheximide has antifungal activity, and was employed to treat fungal infections in plants; however, it is not useful for human treatment. The compound is better known as a general inhibitor of protein synthesis in eukaryotes, and it is widely used for research purposes. Read more here:

More related links:

Image credits: Wikipedia.

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Feb 11, 2008

Research Blogging

Research BloggingFrom now on, some of my posts (only those discussing peer-reviewed research) will be indexed by Research Blogging, a community-run non-profit organization. Their web site allows readers to find and share blog posts about peer-reviewed research. Additionally, I will edit the code of some of my previous posts, in order to adapt them to the indexing requirements. However, the content of the re-edited posts will remain the same (even with mistakes!).

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Oct 7, 2007

A new web 2.0 for scientists

From a post at Science Blog:

"Scientists from Harvard and some other universities from different countries started a project, in which they try to establish a web 2.0 application for scientists. This platform would facilitate the communication between researchers and would increase the efficacy of the research work."

Learn more at Facebook for researchers: www.researchgate.com

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Oct 2, 2007

An imaginary experiment


Imagine that you are a principal investigator, or the director of a research center (well, some of you may already be, or will be in the future?).

And you have infinite funding and contacts, so that getting the money and the right staff is not a problem (yes, this is definitely fiction).

***** What would you do with that superpower? *****

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Sep 20, 2007

Your favorite life science blogs?

The Scientist is making a survey to find the most popular life science blogs: Vote for your favorite life science blogs. Anyone can vote and add a comment. This is an opportunity to discover new interesting blogs, too!

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Aug 14, 2007

Make Love (and Proteins), Not War

"Protein Synthesis: An Epic on the Cellular Level" is an educational film directed in 1971 by Robert Alan Weiss. It seems that the movie has been viewed by generations of science students in the United States. Now, thanks to the internet, we all can enjoy. The film starts with a three-minute introduction by Professor Paul Berg (who later shared half of the 1980 Nobel Prize for Chemistry with the team of Walter Gilbert and Frederick Sanger). The screen then fills with a bunch of people dancing, singing and having fun... and making proteins. Ribosomal subunits, initiation or elongation factors, messenger or transfer RNAs, are impersonated by dancers in colored costumes.

Music sound track: "Protein Jive Sutra".

Yes, this is a true "molecular happening"!



The video is available for download from the web of Kenyon College (MP4 format, 38 MB, a lengthy download).

Or watch the video again at YouTube.

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Creative Commons License Except where otherwise noted, blog posts by Cesar Sanchez in Twisted Bacteria are licensed under a Creative Commons Attribution 3.0 Unported License. Please let me know if any quotes or images on this blog are improperly credited. E-mail: TwistedBacteria AT gmail DOT com . Social media icons by Oliver Twardowski and AddThis.