Posts about PLoS

Another Bee Study Finds CCD is Likely Due to Combination of Factors Including Pesticides

Abstract of open access science paper funded by the United States Department of Agriculture (USDA) Crop Pollination Exposes Honey Bees to Pesticides Which Alters Their Susceptibility to the Gut Pathogen Nosema ceranae:

Recent declines in honey bee populations and increasing demand for insect-pollinated crops raise concerns about pollinator shortages. Pesticide exposure and pathogens may interact to have strong negative effects on managed honey bee colonies. Such findings are of great concern given the large numbers and high levels of pesticides found in honey bee colonies. Thus it is crucial to determine how field-relevant combinations and loads of pesticides affect bee health.

We collected pollen from bee hives in seven major crops to determine 1) what types of pesticides bees are exposed to when rented for pollination of various crops and 2) how field-relevant pesticide blends affect bees”™ susceptibility to the gut parasite Nosema ceranae. Our samples represent pollen collected by foragers for use by the colony, and do not necessarily indicate foragers”™ roles as pollinators. In blueberry, cranberry, cucumber, pumpkin and watermelon bees collected pollen almost exclusively from weeds and wildflowers during our sampling.

Thus more attention must be paid to how honey bees are exposed to pesticides outside of the field in which they are placed. We detected 35 different pesticides in the sampled pollen, and found high fungicide loads. The insecticides esfenvalerate and phosmet were at a concentration higher than their median lethal dose in at least one pollen sample. While fungicides are typically seen as fairly safe for honey bees, we found an increased probability of Nosema infection in bees that consumed pollen with a higher fungicide load.

Our results highlight a need for research on sub-lethal effects of fungicides and other chemicals that bees placed in an agricultural setting are exposed to.

The attempts to discover the main causes of bee colony deaths and find solutions continues to prove difficult years after the problems became major. The complex interaction of many variables makes it difficult. And special interest groups pushing pesticides and the like, which have seemed to be major contributors to the problem for years, make it even more difficult (by preventing restrictions on potentially damaging pesticide use).

The challenges in determining what is killing bees are similar to the challenges of discovering what practices are damaging human health. The success of studying complex biological interactions (to discover threats to human health) is extremely limited. I am concerned we are far too caviler about using large numbers of interventions (drugs, pesticides, massive antibiotics use in factory farms, pollution…).

Related: Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep DyingGermany Bans Chemicals Linked to Bee Deaths (2008)Virus Found to be One Likely Factor in Bee Colony Colapse Disorder (2007)Study of the Colony Collapse Disorder Continues as Bee Colonies Continue to Disappear

Bacteria In Cave Isolated for 4 Million Years Highly Resistant to Many Antibiotics

PLoS published an interesting open access research paper on bacteria and their resistance to antibiotics. I am surprised how widespread and strong the antibiotic resistance was is the isolated bacteria that were studied. It raises more interesting questions about the important area of antibiotics.

The lead researcher on this study, Gerry Wright, previously published on antibiotic properties of bacteria found in soil.

Abstract of Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

Antibiotic resistance is a global challenge that impacts all pharmaceutically used antibiotics. The origin of the genes associated with this resistance is of significant importance to our understanding of the evolution and dissemination of antibiotic resistance in pathogens. A growing body of evidence implicates environmental organisms as reservoirs of these resistance genes; however, the role of anthropogenic use of antibiotics in the emergence of these genes is controversial.

We report a screen of a sample of the culturable microbiome of Lechuguilla Cave, New Mexico, in a region of the cave that has been isolated for over 4 million years. We report that, like surface microbes, these bacteria were highly resistant to antibiotics; some strains were resistant to 14 different commercially available antibiotics. Resistance was detected to a wide range of structurally different antibiotics including daptomycin, an antibiotic of last resort in the treatment of drug resistant Gram-positive pathogens.

Enzyme-mediated mechanisms of resistance were also discovered for natural and semi-synthetic macrolide antibiotics via glycosylation and through a kinase-mediated phosphorylation mechanism. Sequencing of the genome of one of the resistant bacteria identified a macrolide kinase encoding gene and characterization of its product revealed it to be related to a known family of kinases circulating in modern drug resistant pathogens. The implications of this study are significant to our understanding of the prevalence of resistance, even in microbiomes isolated from human use of antibiotics. This supports a growing understanding that antibiotic resistance is natural, ancient, and hard wired in the microbial pangenome.

Related: Alligator Blood Provides Strong Resistance to Bacteria and VirusesBacteria Survive On All Antibiotic DietClay Versus MRSA Superbug

Genes Counter a Bacterial Attack

Gene against bacterial attack unravelled

Humans have an innate defence system against deadly bacteria. However, how the step from gene to anti-bacterial effect occurs in the body is not yet known. To date, B. Pseudomallei, a bacterium suitable for bioweapons, had managed to elude medics. It can remain hidden in the human body for many years without being detected by the immune system. The bacteria can suddenly become activated and spread throughout the body, resulting in the patient dying from blood poisoning. AMC physician Joost Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless.

Wiersinga focussed on the so-called Toll-like receptors. These are the proteins that initiate the fight against pathogens. There are currently ten known Toll-like receptors which are located on the outside of immune cells, our body’s defence system. The toll-like receptors jointly function as a 10-figure alarm code. Upon coming into contact with the immune cell each bacterium enters its own Toll code. For known pathogens this sets off an alarm in the immune system and the defence mechanism is activated. Yet B. pseudomallei fools the system by entering the code of a harmless bacterium. As a result the body’s defence system remains on standby.

Yet some people are resistant: they become infected but not ill. Wiersinga found a genetic cause for this resistance. He discovered which toll receptor can fend off B. pseudomallei. He did this by rearing mice DNA in which the gene for Toll2 production was switched on and off. ‘The group where the gene for Toll2 was switched off, survived the bacterial infection’, says Wiersinga. ‘The other receptor that we investigated, Toll4, had no effect – even though for the past ten years medics had regarded this as the most important receptor.’ The ultimate aim of this study is to develop a vaccine.

PLoS paper: MyD88 Dependent Signaling Contributes to Protective Host Defense against Burkholderia pseudomallei

Related: Bacteria Can Transfer Genes to Other BacteriaDisrupting the Replication of BacteriaAmazing Designs of Lifeposts on medical research

Algorithmic Self-Assembly

Paul Rothemund, scientist at Cal Tech, provides a interesting look at DNA folding and DNA based algorithmic self-assembly. In the talk he shows the promise ahead for using biological building blocks using DNA origami — to create tiny machines that assemble themselves from a set of instructions.

Algorithmic Self-Assembly of DNA Sierpinski Triangles, PLoS paper.

I posted a few months ago about how you can participate in the protein folding, with the Protein Folding Game.

Related: Viruses and What is LifeDNA Seen Through the Eyes of a CoderSynthesizing a Genome from ScratchEvidence of Short DNA Segment Self AssemblyScientists discover new class of RNA

Bird Brain Language Research

Molecular Mapping of Movement-Associated Areas in the Avian Brain: A Motor Theory for Vocal Learning Origin

Vocal learning is a critical behavioral substrate for spoken human language. It is a rare trait found in three distantly related groups of birds-songbirds, hummingbirds, and parrots. These avian groups have remarkably similar systems of cerebral vocal nuclei for the control of learned vocalizations that are not found in their more closely related vocal non-learning relatives. These findings led to the hypothesis that brain pathways for vocal learning in different groups evolved independently from a common ancestor but under pre-existing constraints. Here, we suggest one constraint, a pre-existing system for movement control.

Using behavioral molecular mapping, we discovered that in songbirds, parrots, and hummingbirds, all cerebral vocal learning nuclei are adjacent to discrete brain areas active during limb and body movements. Similar to the relationships between vocal nuclei activation and singing, activation in the adjacent areas correlated with the amount of movement performed and was independent of auditory and visual input.

Based upon these findings, we propose a motor theory for the origin of vocal learning, this being that the brain areas specialized for vocal learning in vocal learners evolved as a specialization of a pre-existing motor pathway that controls movement.

Related: bird tagged postsWhy do We Sleep?

More Dinosaurs Fighting Against Open Science

Controversy at the American Chemical Society by John Dupuis

So, what’s my take on this? First of all, I’m not surprised. Unfortunately there are some scholarly societies that operate more like for-profits when it comes to their publishing arms and ACS is certainly one of the most notable for that sort of thing. While it should be shocking that ACS is acting more like Elsevier than Elsevier at times, sadly it isn’t.

Secondly, what should we, as librarians do about it? Mostly we need to advocate. We need to push our vendors towards business models that favour open access, we need to reassure them that we’re interested in a sustainable model for scholarly publishing

I agree. It is sad that so many organizations distort behavior though poor management structures but that is the world we live in. My management improvement blog focused on how to manage better. And I have posted several times about the need to shift our support to open access science and away from those who want continue outdated strategies that restrict the advancement of scientific ideas.

Related: Open Access and PLoSI Support the Public Library of ScienceProblems with Bonuses

Publishers Continue to Fight Open Access to Science

Publishers prepare for war over open access

On one side are the advocates of open-access journals – publications that make academic papers freely available and recoup costs by charging authors to publish. The model seems increasingly successful. New open-access journals are springing up weekly and could gain support if the US acts on plans make all its publicly funded health research freely available via a government archive.

Lined up against them are the academic publishers. The idea of open-access journals is frightening for an industry whose profits are based on subscription charges.

Dezenhall’s strategy includes linking open access with government censorship and junk science ”“ ideas that to me seem quite bizarre and misleading. Last month, however, the AAP launched a lobby group called the Partnership for Research Integrity in Science & Medicine (PRISM), which uses many of the arguments that Dezenhall suggested.

It is sad to see journals that were founded to promote science so flawed in their thinking today. As I said last month in Science Journal Publishers Stay Stupid: “It is time for the scientific community to give up on these journals and start looking to move to work with new organizations that will encourage scientific communication and advancement (PLoSarXiv.orgOpen Access Engineering Journals) and leave those that seek to keep outdated practices to go out of business.” Organizations can’t ignore principles when choosing tactics. Tactics that might be ok in other situations, should not be acceptable to scientists publishing scientific information. When journals move to harm science to preserve their outdated business practices they deserve to lose the respect of scientists.

Related: Finding Open Scientific PapersOpen Access Journal WarsAnger at Anti-Open Access PROpen Access Article Advantage

I Support the Public Library of Science

I support PLoS graphic

I am a fan of the Public Library of Science, as I have mentioned previous. Yesterday I donated some money to support their great efforts. From the PLoS site:

During this time of transition from traditional to open access publishing, we must develop creative ways to support the launch of new journals, the investment in new publishing technologies, and efforts to increase awareness of, and commitment to, open access.

Related posts:

YouTube+ for Science from PLoS

SciVee is a new site by the great people at PLoS, with support from NSF and San Diego Supercomputer Center. It is very early in the launch of this effort but it looks very promising.

SciVee allows scientists to communicate their work as a multimedia presentation incorporated with the content of their published article. Other scientists can freely view uploaded presentations and engage in virtual discussions with the author and other viewers. SciVee also facilitates the creation of communities around specific articles and keywords. Use this medium to meet peers and future collaborators that share your particular research interests.

Of course plenty of great videos are already online but this looks like another great effort at helping improve communication of scientific ideas by the Public Library of Science. And there are advantages to a community lead by scientists that not only posts videos but encourages scientific discussion on the related matters. I am hopeful (and confident) this will become a great resource.

Related: Science and Engineering Webcast DirectoryStanford Linear Accelerator Center Public LecturesGoogle Engineering and Technology Webcasts
Originally I posted this to my employers blog: Engineering and…. It turns out it was made public prematurely – SciVee update.

Science Journal Publishers Stay Stupid

Science publishers get even stupider by Andrew Leonard:

The American Association of Publishers and everyone associated with it should be ashamed of trying to protect their profit margins by slandering the open access movement as government intervention and censorship. Research paid for with government funds should be freely accessible to the general public.

I wish it was amazing that these people have so little grasp of what has been going on in the world the last 5 years (but I must say such failure to adapt seems to be a common trait in too many organizations). Previously I have posted on the importance of continuing the scientific tradition of open debate and open access. In the past there have been distribution complexities that made paid journals an acceptable compromise. That people working at journals don’t see that the internet changes that is going to lead to their rapid irrelevance. They had to figure this out a couple of years ago. Given they still haven’t, I must say that they really don’t seem to have much understanding of science or modern communication methods. Given their industry that is sad. It is time for the scientific community to give up on these journals and start looking to move to work with new organizations that will encourage scientific communication and advancement (PLoSarXiv.orgOpen Access Engineering Journals) and leave those that seek to keep outdated practices to go out of business.

“It is not necessary to change. Survival is not mandatory.” Dr. W. Edwards Deming

Related: Publishers launch an anti-OA lobbying organizationAnger at Anti-Open Access PROpen Access and PLoSHoward Hughes Medical Institute Takes Big Open Access StepThe Future of Scholarly Publication (our post from May 2005):

I do object to scientific knowledge being kept out of the scientific and public community. The ability to use the internet to more effectively communicate new knowledge should not be sacrificed to protect the old model journals had for sustaining themselves. They should find a way to fund themselves and make their material available for free on the internet (I think some delay for free public access would be fine – the shorter the delay the better). Or they should be replaced by others that do so.
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