Master in Biological Sciences (MBS) at the University of Vigo, SPAIN

We are pleased to announce the launch of the Master in Biological Sciences (MBS) of the University of Vigo (Spain) for the academic year 2013-2014. The MBS aims to provide future professionals in biology with the knowledge, skills and insights they will need to take on top science-based positions around the world (academic, research, environmental and biomedical applications, bioinformatics).

The official language of the MBS is English. Non-English speaking students must demonstrate that they have acquired the minimum language skills to study the Master. No additional proof is required, although holding a B1 or equivalent title would be desirable. In addition, personal interviews with members of the Academic Commission might be required before admission.

The staff teaching in this master cover a wide range of areas giving students contact with renowned researchers, specialists in developing professional skills and practitioners from industry. They all have long-term teaching experience.

For those students interested in doing a PhD, there are two Doctorate Programmes linked to the MBS, and rated as excellent from the Spanish Education Ministry

Master outline

The MSc programme comprises 120 ECTS in total distributed between 2 academic years (60 ECTS each one). During the 1^st year, students will follow 4 general courses (Basic Module, 12 ECTS) on basic tools for designing and performing experimental tasks, analysing results and elaborating conclusions. This will be followed by the Elective Component (42 ECTS) where students will have the chance to follow specific tracks:

1. Molecular Biology for Health and Life Sciences
2. Environmental Sciences
3. Bioinformatics and Computational Biology
4. Green-Industries Management

The main part of the second year consists of a major project (Mandatory Major Project 48 ECTS), in which students will acquire advanced knowledge on different methodologies and techniques under the guidance of experienced experts to fulfil your professional requirements and possibly to gain a better position on the job market.

Finally, all students need to carry out a Master’s thesis (12 credits).

APPLICATION for academic year 2013-14

•       First pre-registration period: 28 June to 4 July 2013

•       Second pre-registration period: 27 August to 3 September 2013

DOCUMENTS that must accompany the application form:

•       DNI, NIE or Passport

•       Bachelor’s degree diploma

•       Brief CV

CONTACT

María Jesús Iglesias Briones (coordinator)

mbriones@uvigo.es

Master in Biological Sciences

Facultad de Biología

Campus Lagoas-Marcosende

Universidad de Vigo

36310 Vigo, Spain.

FURTHER INFORMATION

http://biology.uvigo.es

You can also download an informative poster  about the program.

ADVANCES IN ECOLOGICAL SPECIATION (AES) Conference, Portugal, 29-30 April 2013

I just received the following info about the AES Conference:

ADVANCES IN ECOLOGICAL SPECIATION (AES) Conference, CIBIO/UP, Portugal, 29-30 April 2013

LIVE BROADCAST of the AES Conference!

We are happy to announce that the AES Conference can be followed Live on streaming from http://tv.campusdomar.es/directo.html

If you want to join us please check out the program of the AES Conference from our website (http://www.aes-cibio.org/). The Live broadcast will be on Portugal local time (UTC/GMT+1hour).

Invited Speakers:

Dolph Schluter (Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, Canada)
Felicity Jones (Friedich Miescher Laboratory of the Max Planck Society, Tubingen, Germany)
Walter Salzburger (Zoological Institute, University of Basel, Switzerland)
Sebastien Renaut (Botany Department, University of British Columbia, Vancouver, Canada)
Roger Butlin (Department of Animal and Plant Sciences, University of Sheffield, UK)

You can also follow the AES Conference on:

https://www.facebook.com/AdvancesInEcologicalSpeciation

https://twitter.com/aes_cibio

The conference videos will be available afterwards at the Campus do Mar website, and you can dowload the book of abstracts right now.

Do as I say, not as I've been doing

Raising standards : Nature Immunology 14, 415 (2013) doi:10.1038/ni.2603 -- Nature journals' updated editorial policies aim to improve transparency and reproducibility:

. For example, authors will need to describe methodological parameters that may introduce bias or influence robustness and to provide precise characterization of key reagents, such as cell lines and antibodies, that may be subject to biological variability.
(...)
To help improve the statistical robustness of papers, the Nature journals will now employ statisticians as consultants on certain papers, at the editor's discretion and on the referees' suggestions. (...) Exploratory investigations often are not amenable to the same degree of statistical rigor as hypothesis-testing studies.
(...)
Those who would put effort into documenting the validity or irreproducibility of a published piece of work have little prospect of seeing their efforts valued by journals and funders; meanwhile, funding and efforts are wasted on false assumptions.

These are certainly much needed changes in NPG's policy, provided they are not just lip service while in practice neglecting valid statistical criticisms to their flagship papers. I remain skeptical. Would they put their money where their mouths are and demand openness for already published data or allow for retroactive post-review? (The infamous "your criticism won't add to the discussion" boilerplate reply?) Anyway, a few more links:

What We Have Here is a Failure to Replicate | Evolutionary Psychology:

Discussions of why replications aren’t more common – including Pashler’s remarks – focus extensively (but not exclusively) on incentives. If a researcher attempts to do an exact replication of published work, there are two possible results. If the result replicates successfully, it is likely to be difficult to publish because journals tend not to publish replications, though this is changing.(...) Other journals are proving more receptive to publishing replications – and failures to replicate – which will probably have some beneficial effect. In any case, my guess, though I don’t know, is that replications of results are cited relatively infrequently, especially compared to the original results. Publishing failures to replicate is likely no easier than publishing successes.

Authors, Don’t Call Us, We’ll Call You | Psychology Today:

Privileged access is only one of the many means by which political forces distort debates about evidence and select which conclusions are legitimized and which perspectives are marginalized. Because privileged access articles often escape rigorous peer review, the science is often flabby and grossly simplistic, and claims in privileged access articles can be extravagant.

Strategies for challenging inaccuracies and outright misrepresentations in privileged access articles are limited. Journals that grant privileged access also often restrict publishing of letters to the editor to only what authors indicate a willingness to respond. A refusal to respond is effective censorship, causing criticism to be barred from publishing. Even when letters are accepted, they often have severe restrictions on their length (often 400 - 600 words), are often published much later than the privileged access articles, fail to be indexed in ISI Web of science or other electronic bibliographic sources, or are limited to e-letters, not the paper editions of the Journal. It is notable that the webpages of the journals making the most use of privileged access articles do not link subsequent critiques with the original article, so that anyone in defining the critiques has to search for them separately.

Non-consensual replication | john hawks weblog:

You are building one assumption upon another. The disturbing part is that the discipline accepts that some researchers just have a "knack" for making a particular experimental design work, and other researchers may have trouble recreating the exact conditions. That very attitude enables fraud, as we have seen repeatedly during the last few years. In science, if no one else can make the experiment work, it didn't happen.

Opinion: Missing Methods | The Scientist Magazine®:

How has the requirement to share every iota of technical detail with the research community given way to “as described elsewhere,” elsewhere being Never Never Land?  First, I blame the journal editorial boards.  The push in recent years to shorten papers and limit the number of figures has never been clearly rationalized to the research public.
(...)
Next, I blame the authors. Failure to transmit clear and detailed technical details is not just a sin against the scientific community, it’s also indicative of poor internal mentoring skills. (...) This brings up the worst consequence to our increasingly lax eye for technical detail: faster publication of findings in higher impact journals will mean squat if the data will not stand the test of time, and in our field, this means experimental reproducibility.
(...)
The recent proliferation of smaller journals devoted solely to publishing novel methods and technologies is a great advance in this regard.

Actually this last conclusion is wrong -- the existence of journals devoted to these details is an incentive for the authors to hide the details from other manuscripts, in the (sometimes unfulfilled) hope that this slice of research will be a publication on its own. That is, you persuade authors to think about the method, software and data/conclusions as independent entities, and consequently it will become not more, but less likely for them to provide you with the other elements.

Random Image (from here)

The Genetics of sexuality

This is just a short and random list of links (articles and comments) about the biological basis for homosexuality, that I decided to collect after some heated discussion in Brazil about it.First a few articles that I found particularly interesting.

David Bierbach, Christian T. Jung, Simon Hornung, Bruno Streit and Martin Plath. 2013. "Homosexual behaviour increases male attractiveness to females". Biol Letters:

Male homosexual behaviour—although found in most extant clades across the Animal Kingdom—remains a conundrum, as same-sex mating should decrease male reproductive fitness. In most species, however, males that engage in same-sex sexual behaviour also mate with females, and in theory, same-sex mating could even increase male reproductive fitness if males improve their chances of future heterosexual mating. Females regularly use social information to choose a mate; e.g. male attractiveness increases after a male has interacted sexually with a female (mate choice copying). Here, we demonstrate that males of the tropical freshwater fish Poecilia mexicana increase their attractiveness to females not only by opposite-sex, but likewise, through same-sex interactions. Hence, direct benefits for males of exhibiting homosexual behaviour may help explain its occurrence and persistence in species in which females rely on mate choice copying as one component of mate quality assessment.

Andrew B. Barron, Malin Ah-King, Marie E. Herberstein. 2011. "Plenty of sex, but no sexuality in biology undergraduate curricula". BioEssays, 33: 889--902:

Research over the last decades has stimulated a paradigm shift in biology from assuming fixed and dichotomous male and female sexual strategies to an appreciation of significant variation in sex and sexual behaviour both within and between species. This has resulted in the development of a broader biological understanding of sexual strategies, sexuality and variation in sexual behaviour. However, current introductory biological textbooks have not yet incorporated these new research findings. Our analysis of the content of current biology texts suggests that in undergraduate biology curricula variation in sexual behaviour, sexual strategies and sexuality barely feature, even though sex is discussed in a range of contexts. In this aspect, biological teaching is lagging behind current research. Here, we draw attention to new findings in the biology of sex, and suggest how these might be incorporated in undergraduate teaching to provide a more contemporary and inclusive education for biology students.

Julie E. Elie, Nicolas Mathevon,Clémentine Vignal. 2011. "Same-sex pair-bonds are equivalent to male–female bonds in a life-long socially monogamous songbird". Behavioral Ecology and Sociobiology, 65: 2197--2208:

Same-sex sexual behaviors are well documented in both captive and wild animals. In monogamous species, these behaviors are often exclusive, each individual having only one same-sex partner. A bias in sex ratio has been proposed as a social context yielding same-sex pair-bonding, but this hypothesis has rarely been tested. Focusing on a life-long pair-bonding songbird, the zebra finch Taeniopygia guttata, we tested whether same-sex pairing results from a shortage of individuals of the opposite sex. By experimentally skewing the sex ratio towards members of one sex, we observed a greater proportion of same-sex pair-bonds of that sex. Moreover, we assessed whether the quality and stability of social interactions were equivalent in same-sex and male–female pairs. Male–male and female–female same-sex bonds display the same behavioral characteristics as male–female ones: they are intense, highly selective, and stable affinitive relationships involving the same behavioral displays already described in wild birds. Moreover, same-sex male bonds were sufficiently strong not to split up when individuals were given the opportunity to reproduce with females. Because the pair-bond in socially monogamous species represents a partnership that may give advantages for survival (e.g., resources defense, fighting against predators, etc.), we propose that same-sex pairing in the zebra finch may result from the pressure to find a social partner.

Nathan W. Bailey, Marlene Zuk. 2009." Same-sex sexual behavior and evolution." Trends in Ecology and Evolution, 24: 439--446:

Same-sex sexual behavior has been extensively documented in non-human animals. Here we review the contexts in which it has been studied, focusing on case studies that have tested both adaptive and non-adaptive explanations for the persistence of same-sex sexual behavior. Researchers have begun to make headway unraveling possible evolutionary origins of these behaviors and reasons for their maintenance in populations, and we advocate expanding these approaches to examine their role as agents of evolutionary change. Future research employing theoretical, comparative and experimental approaches could provide a greater understanding not only of how selection might have driven the evolution of same-sex sexual behaviors but also ways in which such behaviors act as selective forces that shape social, morphological and behavioral evolution.

And then some links to commentaries that were on my feeds

• The Real Story on Gay Genes | Michael Abrams at Discover Magazine
• Suppressed records of “depraved sex acts” by penguins finally released after a century « Why Evolution Is True
• Female bonobos 'advertise' homosexual bonds | Ella Davies at BBC Nature
• La neuroendocrinologia de la homosexualidad | Sapere Audere
• The Genetic Fatality of What You Are « Into Oblivion
• Krauss does it again, so soon! | Rationally Speaking
• The Intelligent Homosexual’s Guide to Natural Selection and Evolution, with a Key to Many Complicating Factors | Jeremy Yoder at the Scientific American Blog Network
• 23andMe Studies the Genetics of Sexual Orientation | The 23andMe Blog
• What we know—and don’t know—about the biology of homosexuality | Kate Shaw at Ars Technica

update (a few minutes later...): In fact I was searching my feeds for an article criticizing the anthropomorphization of animal sexual behavior, but couldn't find it. Here it is.

Reports on 'gay' animal research criticised › News in Science (ABC Science):

"Consistently any scientific report of same-sex sexual contact in any animals is reported as gay or lesbian behaviour," says Barron. (...) "Gay and lesbianism is more than same-sex copulation in humans. Let's not turn this animal behaviour into something that it isn't," he says. "Scientists would never call it gay."

And Barron says in many cases the animals in the scientific study didn't even copulate but simply showed some form of atypical male or female behaviour.

(...)

And Leach says in some fields of research - for example evolutionary psychology - scientists are actively linking human behaviour to animal behaviour. "You read this stuff not just about gay behaviour but about female versus male behaviour and it's irritating," she says.

"I get really tired of evolutionary psychology explanations that my behaviour has to do with hunters and gatherers."

The original critique is this one: Andrew B. Barron and Mark J. F. Brown. 2012. "Science journalism: Let's talk about sex." Nature 488: 151-152.

Seminar at UVigo: Aquatic microbial ecology through the lens of high-throughput DNA/RNA sequencing

Aquatic microbial ecology through the lens of high-throughput DNA/RNA sequencing

Who: Ramiro Logares (Institute of Marine Sciences (ICM), CSIC, Barcelona)
When: 23 Feb 2012 - 12:00
Where: Salón de Actos de la Facultad de Ciências (Universidad de Vigo)
Microbes play key roles in global ecosystem functioning and nutrient cycling. In the oceans and other aquatic environments, they may represent the most diverse organisms in terms of taxonomy and metabolism. Understanding diversity, spatiotemporal distributions, interactions and evolution of microbes are among the most important current challenges in ecology and evolutionary research. During the last 30 years, molecular tools have been used to investigate these topics. The last five years have been particularly exciting, as the arrival and increasing availability of high-throughput DNA/RNA sequencing revolutionized the field, bringing new opportunities and challenges. High-Throughput sequencers can generate massive amounts of information at relatively low costs, and today one single run can produce about 500 Gigabases of data.This power allows us to tackle questions that have been difficult to address with previous technologies. For example: What is the magnitude of total microbial diversity? What organisms inhabit the rare biosphere? To what extent environmental and/or neutral processes determine microbial metacommunity assembly? These new technologies also challenge our capability to analyze huge datasets, as well as our current computer power. In this presentation, I will introduce some high-throughput sequencing techniques that are popular in aquatic microbial ecology (focusing in oceans and lakes), discuss a number of questions that they allow to investigate and show a few case studies.

You can also follow it live on http://tv.campusdomar.es

Update: The lecture was recorded and can be seen here.

Conference on Astrobiology at the University of Vigo

Next Wednesday (November 16th) from 10:00 to 13:30 the University of Vigo will host a series of talks and a round table on "Astrobiology: the challenge of searching for life on the Universe today". It will take place at the Auditorium (Salón de actos) of the Experimental Sciences building. Judging by the poster, the talks might be in galician.

PS: I'm not involved in the organization of the event, just spreading the word.

Sao Paulo Advanced School of Astrobiology - SPASA 2011

I received this announcement from an alumnus friend, who is one of the organizers.

Sao Paulo Advanced School of Astrobiology -SPASA 2011 -- Making Connections

The applications are open for the "Sao Paulo Advanced School of Astrobiology – Making Connections (SPASA 2011)", promoted by the Department of Astronomy of the Universidade de Sao Paulo and by the Sao Paulo Research Foundation (Fapesp), Brazil.

Location: University of São Paulo, São Paulo, Brazil
Date: December 11 -- 20, 2011
Home Page: www.astro.iag.usp.br/~spasa2011
Target audience: Undergraduate, graduate students and early career post-docs in biology, physics, astronomy, chemistry, earth sciences and related areas.
Application Deadline: September 20, 2011, through the event website.
Language: English

Objective: Astrobiology is a multidisciplinary field that aims to study origin, evolution, distribution and future of life on the Universe, with a broad and multidisciplinary scope, requiring a constant dialogue between different areas. This is a new and very promising scientific research field, with the ambitious goal of seeking for answers to some of the most complex scientific questions. The SPASA aims to bring together renowned experts from different countries with students of different fields in a multidisciplinary event that will address some of the general themes of research in astrobiology, as well as more specific topics in the frontier of science that are being developed worldwide. Stimulating the connection between topics and the exchange of knowledge among the participants is the main goal of the event.

Selected participants from all countries will have travel and accommodation expenses covered by the Sao Paulo Research Foundation.

Effects and choices of food

Below there are a few links about recent research on food, as reported by Science Daily. Which means that the reported news are based on press releases -- and as such may be overly optimistic and certainly not the last word on the subject.

"New evidence that caffeine is a healthful antioxidant in coffee":

Scientists are reporting an in-depth analysis of how the caffeine in coffee, tea, and other foods seems to protect against conditions such as Alzheimer's disease and heart disease on the most fundamental levels.

"Coffee reduces breast cancer risk, study suggests":

Recently published research shows that coffee drinkers enjoy not only the taste of their coffee but also a reduced risk of cancer with their cuppa. More detailed research published May 10 in BioMed Central's open access journal Breast Cancer Research shows that drinking coffee specifically reduces the risk of antiestrogen-resistant estrogen-receptor (ER)-negative breast cancer

"Goat milk can be considered as functional food, Spanish researchers find":

Researchers at the University of Granada have found that goat milk has nutritional characteristics beneficial to health. They have determined that goat milk has many nutrients that make it similar to human milk.

"Anticancer effect of mushrooms demonstrated":

City of Hope researchers have investigated compounds in natural foods for their potential anticancer benefits, with a focus on food items that are easily found in grocery stores to ensure greater access and availability. Shiuan Chen, Ph.D., associate chair and professor of City of Hope's Department of Cancer Biology, identified phytochemicals in mushrooms that block the ezyme aromatase from producing estrogen. Controlling aromatase activity can help decrease estrogen levels, which controls and kills hormone-dependent breast cancers. In addition, mushrooms also demonstrate the ability to inhibit cancer call activity and slow tumor growth.

"Resveratrol studies confirms potential health boost":

A University of Florida review of research finds the polyphenol compound known as resveratrol found in red wine, grapes and other fruits may not prevent old age, but it might make it more tolerable. News stories have long touted resveratrol as a cure for various diseases and a preventative against aging.

"Changes in specific dietary factors may have big impact on long-term weight gain":

In a series of three separate studies looking at how changes in multiple dietary and other lifestyle factors relate to long-term weight gain, Harvard School of Public Health (HSPH) researchers found that modest changes in specific foods and beverages, physical activity, TV-watching, and sleep duration were strongly linked with long-term weight gain. Changes in diet, in particular, had the strongest associations with differences in weight gain.

"Are the French becoming bored with wine?":

One of the most familiar aspects of French culture -- its love of wine -- might be lost as successive generations abandon the imaginative representations of wine linked to national identity, according to a study in the International Journal of Entrepreneurship and Small Business. The findings suggest that the transmission of French wine heritage to future generations is in terminal decline.

"It's not an apple a day after all -- it's strawberries: Flavonoids could represent two-fisted assault on diabetes and nervous system disorders":

A recent study from scientists at the Salk Institute for Biological Studies suggests that a strawberry a day (or more accurately, 37 of them) could keep not just one doctor away, but an entire fleet of them, including the neurologist, the endocrinologist, and maybe even the oncologist.

"Red wine: Exercise in a bottle?":

As strange as it sounds, a new research study published in the FASEB Journal, suggests that the "healthy" ingredient in red wine, resveratrol, may prevent the negative effects that spaceflight and sedentary lifestyles have on people. The report describes experiments in rats that simulated the weightlessness of spaceflight, during which the group fed resveratrol did not develop insulin resistance or a loss of bone mineral density, as did those who were not fed resveratrol.

"Research reveals new secret weapon for Tour de France: Beetroot juice":

Winning margins in the Tour de France can be tight -- last year just 39 seconds separated the top two riders after more than 90 hours in the saddle. When every second counts, riders do everything possible to gain a competitive advantage -- from using aerodynamic carbon fibre bikes to the very latest in sports nutrition.

"Molecular gastronomy: Science behind the art of cooking":

Dr Juan Valverde believe that Molecular Gastronomy (a scientific discipline that studies what happens when we cook) has a lot of untapped potential in Ireland.

"Dry onion skin has a use":

More than 500,000 tonnes of onion waste are thrown away in the European Union each year. However, scientists say this could have a use as food ingredients. The brown skin and external layers are rich in fibre and flavonoids, while the discarded bulbs contain sulphurous compounds and fructans. All of these substances are beneficial to health.

"Why diets don't work: Starved brain cells eat themselves, study finds":

A report in the August issue of the Cell Press journal Cell Metabolism might help to explain why it's so frustratingly difficult to stick to a diet. When we don't eat, hunger-inducing neurons in the brain start eating bits of themselves. That act of self-cannibalism turns up a hunger signal to prompt eating.

"Can eggs be a healthy breakfast choice?":

Eggs, one of the most commonly consumed breakfast foods in the United States, have long been a subject of controversy. Are they healthy or are they a high-cholesterol trap? The answer depends on what the hen eats, says a Tel Aviv University researcher.

"Gazpacho ingredients lose vitamin C during preparation":

In summer, more dishes like gazpacho -a cold soup containing raw vegetables, bread, olive oil and vinegar- are consumed. A new study has revealed that ingredients' vitamin C content as well as other organic acids is lower in the resulting mixture, meaning that it should be eaten immediately after preparation.

 "Antioxidant spices, like turmeric and cinnamon, reduce negative effects of high-fat meal":

Eating a diet rich in spices, like turmeric and cinnamon, reduces the body's negative responses to eating high-fat meals, according to Penn State researchers.

Talk at UVigo: Fine-grain parallelism of MrBayes on multi- and many-core architectures, by Frederico Pratas

Announcement I received about an invited talk at my building, since my group is part of the Galician Network of High Performance Computing (R-GHPC2). I guess the talk will be given in english -- at our meetings we usually find a common ground between english, spanish, galician and portuguese.

Thursday, June 30th of 2011, 12:00 PM
Room 3, Wing B, ground floor of the Experimental Sciences building, University of Vigo

Fine-grain parallelism of MrBayes on multi- and many-core architectures
Frederico Pratas, from the Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento (INESC-ID), Lisboa, Portugal

Currently, we are facing a situation where applications exhibit increasing computational demands. In particular, we observe a considerable increase of complexity in algorithms due to both the increasing amounts of data available for analysis (e.g., genomic databases) and the need for more accurate and precise results (e.g., more complex particle interaction models). In this talk we address how MrBayes, a bioinformatics application that performs Bayesian inference of phylogenetic trees, can benefit from modern multi- and many-core computing architectures. We focus on exploiting fine-grain parallelism by distributing the evaluation of the conditional likelihoods (cl). Namely, we use different types of architectures: General-purpose Processors, Graphics Processing Units (GPU) and Cell Broadband Engine (Cell/BE). Besides, reconfigurable hardware can also be used as a very efficient co-processing solution to accelerate this type of applications. Therefore, we also consider the design steps and implementation of MrBayes on Field Programable Gate Arrays (FPGAs). Overall the results show that, although we can efficiently accelerate the computation of cl on GPUs and FPGAs due to their characteristics, there are still important constraints related with the access to the data in the main memory, which incurs in huge overheads. The general-purpose processors show the best results in terms of speedup.

This talk is supported by the Galician Network of high Performance Computing.
PS: In a previous communication, the address was "Room S4, Wing C, 2º floor" but there should be no problem since they are very near.

Cleanliness is next to godliness

At the Red Queen blog of the Brazilian scienceblogs there's an ongoing discussion on a post about the use of the white coat - by clinicians, but not only - outside of the clinical premises. There's even a picture where we can see almost everybody gowned up at the cafeteria of the medical school...

I remember working in such a setting, and I always felt uneasy seating beside someone with a lab coat saying "hematology" or "parasitology" and sharing the jar of orange juice. Besides the garment, we already had our badges and other displays of hierarchy. But I had some friends who told me that it's common to have two coats, one for "inside" (=working) and another one for "outside" (=showing), specially in high profile hospitals. BTW I didn't use one at this time, and in my lab activities from high school and undergrad days I had a blue collar coat used by lathe operators.

Anyway, I was curious about the real, established risks of parading with a lab coat inside and around a hospital, and so as usual I started digging for references. Here are some articles that analyzed hospital uniforms for the presence of pathogens - the list is very incomplete, so additions are welcome!

Bacterial flora on the white coats of medical students (Journal of Hospital Infection (2000) 45(1): 65-68):

This study has demonstrated that the white coats of medical students are more likely to be bacteriologically contaminated at points of frequent contact, such as the sleeve and pocket. The organisms identified were principally skin commensals including Staphylococcus aureus. The cleanliness of the coat as perceived by the student was correlated with bacteriological contamination, yet despite this, a significant proportion of students only laundered their coats occassionally. This study supports the view that the students' white coat is a potential source of cross infection on the ward and its design should be modified in order to facilitate hand washing. Hospitals training medical students should consider taking on the burden of providing freshly laundered white coats for the students.

The Endangered White Coat (Clin Infect Dis. (2010) 50 (7): 1073-1074):

Although little clinical evidence exists regarding the impact of these potential fomites on NI, some data seem to give credence to the thought that clothing may play a role in transferring pathogens. Several studies have shown that physicians' white coat sleeves and pockets are frequently colonized with bacteria associated with NI[12–15]. Mackintosh et al [16] also showed that several pathogens transferred well from fabrics to hands. Scott et al [17] showed that several types of pathogens can be transferred from contaminated soiled cloth and surfaces to fingertips in detectable numbers. In a costbenefit analysis, Puzniak et al [18] showed that gown and glove use together lowered the incidence of vancomycin-resistant enterococci infection in a medical intensive care unit, which would seem to support the claim that clothes are a potential fomite for NI.

Bacterial contamination of health care workers' white coats (AJIC: American Journal of Infection Control (2009) 37 (2): 101-105):

Among the 149 grand rounds attendees' white coats, 34 (23%) were contaminated with S aureus, of which 6 (18%) were MRSA. None of the coats was contaminated with VRE. S aureus contamination was more prevalent in residents, those working in inpatient settings, and those who saw an inpatient that day. This study suggests that a large proportion of health care workers' white coats may be contaminated with S aureus, including MRSA. White coats may be an important vector for patient-to-patient transmission of S aureus.

The health professional's role in preventing nosocomial infections (Postgraduate Medical Journal (2000) 77 (903): 16-19):

Gloves, gowns, and masks have a role in preventing infections, but are often used inappropriately, increasing service costs unnecessarily. While virulent microorganisms can be cultured from stethoscopes and white coats, their role in disease transmission remains undefined. There is greater consensus about sterile insertion techniques for intravascular catheters—a common source of infections—and their care. By following a few simple rules identified in this review, health professionals may prevent much unnecessary medical and financial distress to their patients.

Survival of Enterococci and Staphylococci on Hospital Fabrics and Plastic (Journal of Clinical Microbiology (2000) 38 (2): 724-726):

The transfer of gram-positive bacteria, particularly multiresistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE), among patients is a growing concern. One critical aspect of bacterial transfer is the ability of the microorganism to survive on various common hospital surfaces. (...) Antibiotic sensitivity had no consistent effect on survival. The long survival of these bacteria, including MRSA and VRE, on commonly used hospital fabrics, such as scrub suits, lab coats, and hospital privacy drapes, underscores the need for meticulous contact control procedures and careful disinfection to limit the spread of these bacteria.

How Important Is the Environment in the Emergence of Nosocomial Antimicrobial-Resistant Bacteria? (Clin Infect Dis. (2008) 46 (5): 686-688):

Numerous studies have demonstrated that the environment of a patient's room can become colonized with bacteria, such as Acinetobacter species, VRE, Clostridium difficile, and methicillin-resistant S. aureus, as well as with viruses, such as influenza virus and norovirus [8]. But the importance of this colonization in leading to patient-to-patient transmission has not been shown with a high level of scientific evidence.

Survival of Nosocomial Bacteria and Spores on Surfaces and Inactivation by Hydrogen Peroxide Vapor (Journal of Clinical Microbiology (2009) 47 (1): 205-207):

In summary, we found that dried inocula of a range of nosocomial pathogens survived on surfaces for several weeks but were rapidly inactivated by HPV in a 100-m3 room. HPV has a potential role in decontaminating surfaces and equipment contaminated with such organisms.

Antibacterial and Laundering Properties of AMS and PHMB as Finishing Agents on Fabric for Health Care Workers' Uniforms (Clothing and Textiles Research Journal (2007) 25 (3): 258-272):

This study examined whether antibacterial finishes can effectively reduce the presence of bacteria on fabric used for health care workers' uniforms (HCWUs). (...) PHMB-treated specimens had a significantly larger reduction against both Staphylococcus aureus and Klebsiella pneumoniae bacteria before laundering and after 5, 10, and 25 laundering cycles than did AMS-treated specimens and no-treatment specimens.

Survival of Some Medically Important Fungi on Hospital Fabrics and Plastics (Journal of Clinical Microbiology (2001) 39 (9): 3360-3361):

These data indicate that many of the fungi (Candida, Aspergillus, Mucor, and Fusarium) which are associated with nosocomial infections in patients survived for at least a day and often longer on fabrics and plastics routinely used in hospitals. (...) While similar data do not exist for other fungi,the findings that other fungi can exist for extended periods on common hospital fabrics and plastics suggest that similar transfers from contaminated materials to hands, and vice versa, are likely. These survival data indicate that in this age of increasing antifungal resistance, when treatments for patients are becoming more limited, appropriate disinfection of the environment and conscientious contact control procedures are essential for optimal control of infections in hospitals.

Laboratory instrument contamination with dermatophytes – a risk for dermatophytosis (Letters in Applied Microbiology (2007) 44 (1): 112-113):

Nocardia asteroides and S. schenckii were also isolated from a shelf and a lab coat. Dermatophytes are a group of pathogenic fungi that invade keratinized tissues. Thus, the presence of dermatophytes on laboratory equipment is a risk for dermatophytosis. Dermatophytoses are common fungal infection of humans, and are considered to be one of the major public health problems in the world. User interfaces of laboratory instruments in medical mycology laboratories, such as microscopes, centrifuges, balances, flame and so on, may serve as potential reservoirs for the transmission of fungi.

Study Finds Lab Coat to Skin MRSA Transmission - Skin & Allergy News:

Researchers at Virginia Commonwealth University in Richmond used pigskin as an in vitro model to demonstrate that large inoculums of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and pan-resistant Acinetobacter (PRA) bacteria could be transferred from a white cotton lab coat to pigskin 1 minute, 5 minutes, and 30 minutes after inoculation.

Bacterial contamination of uniforms (Journal of Hospital Infection (2001) 48 (3): 238-241):

Microbiological sampling of nurses' uniforms was undertaken using a Casella slit sampler. Staphylococcus aureus, Clostridium difficile and vancomycin-resistant enterococci were detected on uniforms both before and after a span of duty. Recommendations for provision and changing of nurses' uniforms are made.

Survival of nosocomial bacteria on hospital fabrics (Indian J Med Microbiol (2003) 21 (4): 291):

The results indicate that nosocomial bacteria can survive for many days on fabrics. The survival time observed by us is longer than that reported in a previous study.[4] This could be due to higher inoculum used by us. The effect of inoculum concentration on cell viability is dependent on the concept of cryptic growth in which bacteria in a nutrient limiting condition can live on nutrients from dying cells.[5] Further, gram negative bacilli were not included in the previous study.

When elephants teach us about trolleyology

Train Crushes Elephants Trying to Protect Young (NYT, 23/09/2010):

The baby elephants became trapped as the herd was crossing the rail line in a densely forested area in northern West Bengal State late on Wednesday night. The adults had crowded around the calves to protect them when they were hit, said Atanu Raha, the chief state forest conservator. The two calves were among the dead.

If you want to know more about the trolley problem, this blog post is a good place to start (and there's always wikipedia).

some more links from iEvoBio

Continuing with my twitter voyeurism of iEvoBio, here are some web pages (softwares and servers) mentioned today at the meeting:

• http://geophylo.appspot.com/
• http://datadryad.org/
• http://www.treebase.org/treebase-web/home.html
• http://ispecies.org/
• http://iphylo.org/linkout/Main_Page
• http://code.google.com/p/biodiverse/
• http://www.cs.auckland.ac.nz/~remco/DensiTree/DensiTree.html
• http://packages.python.org/DendroPy/
• http://code.google.com/p/beagle-lib/
• http://phylo.bio.ku.edu/software/sate/sate.html
• http://code.google.com/p/dadi/
• http://bioinfo-srv1.awh.unomaha.edu/phylomarker/
• http://www.iplantcollaborative.org/grand-challenges/about-grand-challenges/current-challenges/iptol/tree-visualization
• http://cortana.biochem.dal.ca/software/
• http://www.tolkin.org/
• http://gramene.org/
• http://www.pypop.org/
• http://www.stat.wisc.edu/~ane/bucky/index.html
• http://picante.r-forge.r-project.org/
• http://mol.colorado.edu/
• http://code.google.com/p/gensent/
• http://code.google.com/p/treezip/

There is also a Nature Preceedings collection  about the event that is certainly worthwhile to take a look.

(I might update this entry later if other links appear. Stay tuned!)

some links from iEvoBio - the poor guy's bookmarking

OK, let me just note down these interesting links discussed at iEvoBio - I'm not there but the tubes are - while I prepare for SMBE next week.

• http://leptree.net/
• http://www.evoio.org/
• http://www.nexml.org/
• https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS
• http://www.evolutionaryontology.org/
• http://www.eol.org/
• http://lifewatch.eu/
• http://www.cate-project.org/
• http://scratchpads.eu/
• http://kiwi.cs.dal.ca/GenGIS/Main_Page
• http://prefuse.org/doc/api/prefuse/data/Tree.html
• http://www.cs.nmsu.edu/~cdaostore/
• http://markov.uoregon.edu/software/phyesta/
• http://gmod.org/wiki/Main_Page
• http://www.obofoundry.org/cgi-bin/detail.cgi
• http://www.ibarcode.org/nextgen
• http://www.dnabank-network.org/
• http://www.dataconservancy.org/
• http://phylotouch.jsphylosvg.com/
• http://code.google.com/p/phylobox/ and http://phylobox.appspot.com/
• http://exon.niaid.nih.gov/nexplorer/
• http://synthesis.eol.org/news/eol-treemap-viewer and http://kurie.github.com/EOL-tree-viewer/#COL
• https://www.phenoscape.org/wiki/Phenex
  

via @rdmpage and @phylogenomics (this blogpost will be updated a few times...)

Geno-luddites on the rise

There is a very nice, though short discussion on the cut-and-paste of a bacterial genome onto its cousin at Edge's Reality Club. This comment by Nassim N. Taleb called my attention:

If I understand this well, to the creationists, this should be an insult to God; but, further, to the evolutionist, this is certainly an insult to evolution. And to the risk manager/probabilist, like myself & my peers, this is an insult to human Prudence, the beginning of the mother-of-all exposure to Black Swans.

And if I understood correctly his position, we shouldn't do anything that exposes us so much to Black Swans. I agree that some aspects of this research (and all the news coverage that followed)  downplays the role of evolution. But as reminded by PZ Myers in the same discussion, there is a much larger number and variety of naturally-occurring threats to us. (HT @aerocleber).

PS: The title comes from this post, brought to my attention by @phylogenomics.

Oh, Dientamoeba is not happy...

... she is so fragile.

I'm sorry, but I couldn't resist this one. The original picture is from here.

BTW, I know it's a "she" because that's its gender in portuguese (nothing more profound than that :)

El cocalero

Evo Morales and the Populist Paradox - Project Syndicate:

According to his opponents, Morales is reproducing the tradition of caudillismo, concentrating power in his hands and turning government institutions into mere formalities. But his immense popularity over the past five years suggests that most Bolivians do not seem very worried in putting their country's democracy at risk. (...)

Thus, despite official speeches intended to support state intervention, Morales's government benefits mainly from the workings of the market. The failure of state plans and projects is overlooked because of the small but expanding internal market, which is invigorated by de facto economic liberalism involving the growth of smuggling and drug traffic. These illicit activities are not intended, but they increase the income of peasants, transporters, builders, and businessmen.

This is the paradox of twenty-first-century socialism: economic liberalism is the foundation for a policy that aspires to replace it. This might also be its greatest limitation as a political project.

And then I read the news (here in portuguese and here in spanish) that Evo Morales affirmed that human baldness - specially among europeans - and homosexuality are caused by the excess of feminine hormones given to farm chicken (calling them "transgenic"), and that dutch potatoes have fish hormones, which must be peeled to remove the excess of "poison"; he furthermore criticized Coca-Cola, western medicines and defended the use of traditional pottery. At least for the Coca-Cola quarrel, we know the reason. He wants the real thing:

A certain US soft drinks giant may disagree, but Bolivia has come up with a fizzy beverage it says is the real thing: Coca Colla. The drink, made from the coca leaf and named after the indigenous Colla people from Bolivia's highlands, went on sale this week across the South American country.

It is black, sweet and comes in a bottle with a red label - but similarities to Coca-Cola end there. One is a symbol of US-led globalisation and corporate might; the other could be considered a socialist-tinged affront to western imperialism.

Or he is already having too much of it.

[links] flaxseed, unpublished results, gene patenting and some comments

CBC News - Film - Japanese vets admit on film to Nanjing atrocities:

On Dec. 13, 1937, Japanese troops marched into Nanking and murdered 300,000 Chinese people, including many civilians, in a six-week orgy of violence. Chinese authorities say as many as 20,000 women were raped. Japanese historians and journalists refer to the event as an "incident" and many deny the casualty rate was so high.

Lula Succession Race Starts as Rousseff, Serra Resign - BusinessWeek:

Rousseff, a former member of Brazil’s Marxist underground who has never run for office, may increase public spending, Bank of America said. Serra, who as recently as July 2009 newspaper column criticized Brazil’s “stratospheric” interest rates and strong exchange rate, raises questions about how independent the central bank would be under his government, the bank said.

Short Sharp Science: Is this the end of gene patenting? - New Scientist:

A court in New York yesterday ruled that patents on two genes linked to breast cancer are invalid. By declaring that the genes can't be patented because they are essentially products of nature rather than inventions, the US District Court for the Southern District of New York state has effectively cast doubt on whether patents on 2000 other human genes - around 20 per cent of the total - are valid, The Times of London reports.

Animal studies paint misleading picture : Nature News:

Published animal trials overestimate by about 30% the likelihood that a treatment works because negative results often go unpublished, a study suggests. This is a surprisingly strong bias, says the study's lead author, Malcolm Macleod, a neurologist at the Centre for Clinical Brain Sciences at the University of Edinburgh, UK. The work, published today in PLoS Biology, analyses the effect of publication bias in animal models of disease.

Flaxseed lowers high cholesterol in men, study suggests - Science Daily:

Suzanne Hendrich, an ISU professor in food science and human nutrition, led a study that examined the effects of flaxseed lignan in 90 people diagnosed with high cholesterol. The results showed that consuming at least 150 milligrams of flaxseed lignans per day (about three tablespoons) decreased cholesterol in men, but not women, by just under 10 percent over the three months that they were given the flaxseed. While Hendrich admits that's considerably less than the expected outcome from cholesterol-lowering drugs -- approximately 10 to20 percent for three months, depending on the individual -- it's still enough to make flaxseed a more natural option for some men.

PS: I still haven't found a good formula for when to publish here and when to publish on my rant blog... as long as nobody complains I won't think too much about it. I'm liking this tumblr blog, it doesn't take up my time and I have more freedom than on twitter. For now I use it as a fancy bookmark. And I know that writing too many twitter updates is not an effective approach. On a related note, I had to stop following a lot of interesting tweeters and then I set up a twitter list so that I can read them on my spare time using hootsuite. Which means that I won't be following them on real time...

Soon it will take a Ph.D. to rap

Here is the latest addition to the list of academic contributions to rap. In a sense.

A few other ones after the break:

More on the microbial encyclopaedia

Yesterday (depending on your GMT) I commented about a very nice article on Nature, but forgot to include a few links discussing the work:

• Biologists rally to sequence 'neglected' microbes (Nature news from 17 November 2009, behind a paywall)
• Microbial encyclopaedia guided by evolution (Nature news from 23 December 2009)
• Choice genomes sequenced (Nature editor's summary from 24 December 2009)
• Filling in the evolutionary blanks, genome by genome (blog post by Iddo Friedberg)
• Presenting a genomic encyclopedia of bacteria (and archaea) (Ars Technica article)
• the homepage for the Integrated Microbial Genomes - Genome Encyclopedia of Bacteria and Archaea Genomes (IMG/GEBA) database
• torrent file for current GEBA data at biotorrents (keep it cool, IP maximalists, it's legit)

Jonathan Eisen has a more complete list of links, together with the story behind this paper - read it, it's long but certainly inspiring.

How many microbes live on Earth?

Jonathan Eisen posted on his twitter an  interesting news on BBC about his most recent publication on Nature ("A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea", Nature 462:1056-1060). First of all, congratulations for the nice work! Since the original BBC article is in Spanish, I have tried to translate it here. You will soon realize that neither English nor Spanish are my first languages; I'll fix the mistakes as they are spotted by someone, and I assume responsibility for the remaining errors.

Scientists from US and Germany presented the first issue of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) that collects all living microorganisms on Earth.

It is expected that the publication - whose details appear on Nature Magazine - help researchers to better understand the several roles played by the microorganisms on this planet. It is estimated that the Earth harbors around one nonillion (1 followed by 30 zeros) microbes and despite around 2000 microorganisms already have their genomes deciphered, a large number remains unexplored. The Encyclopedia is being compiled by the Joint Genome Institute under the US Department of Energy, and the German Collection of Microorganisms and Cell Cultures.

Only single-celled ones

"This is a rich sample of the diversity of microbe genomes" says professor Jonathan Eisen, main author of the investigation. "To rely on a better sampling of the whole tree of life give us a better reference point to predict gene functions" he adds. The encyclopedia includes all prokaryotic organisms of the planet, which means the unicellular organisms. Unlike eukaryote organisms like us, yeast and the fungi, the prokaryotic cells don't have a membrane covering their DNA. This organisms are divided in two large groups: the Bacteria, which include the small minority of pathogens that makes us sick, and the Archaea, which are organisms that can survive in extreme environments like thermal waters. Up until now there have been sequenced around one thousand prokaryotic genomes. Almost all of them are pathogenic organisms.
According to professor Eisen "it has been like tracing a world map and including only three cities". Now the new encyclopedia analyzes the main representatives of the big branches of the prokaryotic family tree and the present study shows 56 genomes of this group. As explained by the scientists, even though it is known that microbes can exchange genes with other species (a process called lateral transfer) their position in the family tree, called phylogeny, is more important when we want to pinpoint where new genes appear and how they spread.

The beginning

"Microbes are mediators in almost all known biological processes of the planet" says professor Eddy Rubin, project leader. "And the sequencing of their genomes have revolutionized our understanding of the diverse roles they play". The information obtained with this first group of 56 organisms, adds the scientist, may help researchers in improving processes like biofuel production, bioremediation (to "clean" contaminated surroundings), and the way by which carbon is sequestered in the environment. According to the investigators, this is just the beginning of the project and they expect to be able to sequence all the diversity of microorganisms on Earth, including the hundreds or maybe thousands of microbe genomes currently unknown.  "The known phylogenetic diversity of Bacteria and Archaea is huge, with hundreds of big lineages and probably millions or hundreds of millions of species" says professor Eisen. "This encyclopedical project is starting from the top - with the big phylogenetic groups - with 100 genomes from all tree. "But we are just scratching the surface in the characterization of Earth's diversity" adds the researcher.

My only dispute in this article is that they lead to the impression that all single-celled organisms are prokaryotes. Yes, they fix that in the next sentence when they mention yeasts - which are (mostly?) unicellular - as eukaryotes, but then (unless my semantic interpretation is wrong) they introduce another misunderstanding since yeasts are fungi. But now I understand how hard it must be to convey concepts like phylogeny or Archaea to a broad audience. And I am not sure if "leader" is the best translation for "director"...