Species Under Investigation

[The Knighty NI]

Having recently joined RNA World to donate some of my spare computer time, I am curious to find out what work plans there are for the future.

At present I am a hobbyist bee keeper with plans to expand over the next three years into full time beekeeping. One of the spurs that has prompted me to both take up the hobby and to consider full time bee keeping is the plight of bees. This interest covers the full range of pollinating bees including bees that cannot be kept on a commercial basis.

Have you any plans to do any research into the causative organisms and viruses that are taking such a heavy toll on the bee population globally? If so I would be honored to receive such work units.

Would I be right in thinking that you will follow the naming convention you have already adopted so that it will be possible to identify bee specific WU's

e.g.
Your Naming Convention
cms_GA[e30-50MB_Lin64s]_Danio-rerio-(zebrafish)_CU651621.lin.EMBL_RF00640_MIR167_1_1284912637_49431

How I visualize the various parts of your naming Convention
cms_GA[e30-50MB_Lin64s]_Beeresearch-(Nosema_ceranae/Varroa_destructor/Acarapis_woodi/DWV/Etc)-(bumbebee(Domus/Carinae/Leaf_Cutter/Carpenter/Etc))_CU651621.lin.EMBL_RF00640_MIR167_1_1284912637_49431

or would it be (excuse the pun) likely that you would create a sub project that interested parties could select this research specifically?

[Michael H.W. Weber]

Interesting questions.

Have you any plans to do any research into the causative organisms and viruses that are taking such a heavy toll on the bee population globally?

At present, RNA World uses complete genome sequences that are stored in the EMBL genome database, only. To my big surprise, it seems that in this otherwise quite elaborate collection, there is currently no bee genome included. As you most certainly will have a much better overview regarding the latin names of bee species (and as far as I understand, there is broad variety), you might like to take a look at this list and let us know of any bee species that may have escaped our attention. Regarding viruses you can take a look at this overview where all sequences are listed that are part of our systematic analyses. Systematic analyses means that these viruses will be examined for the presence of the complete currently known set of non-coding RNAs. And, for example, the "Israel acute paralysis virus of bees" is present in this data set and consequently is subject to our analyses already.
Now, EMBL is not complete as no database ever is. So, I have checked on scientific literature on bee genomes (using key words "bee" and "genome"), you may also want to take a look at that using PubMed. And I also took a look at NCBI/GenBank, the American counterpart of the european EMBL database, and here I found a set of several complete bee genomes.
Fortunately, we are currently extending our input data sets from the European EMBL to other databases, including NCBI. So, I have good news for you: these bee genomes will soon become part of our systematic analyses.

Would I be right in thinking that you will follow the naming convention you have already adopted so that it will be possible to identify bee specific WU's

e.g.
Your Naming Convention
cms_GA[e30-50MB_Lin64s]_Danio-rerio-(zebrafish)_CU651621.lin.EMBL_RF00640_MIR167_1_1284912637_49431

How I visualize the various parts of your naming Convention
cms_GA[e30-50MB_Lin64s]_Beeresearch-(Nosema_ceranae/Varroa_destructor/Acarapis_woodi/DWV/Etc)-(bumbebee(Domus/Carinae/Leaf_Cutter/Carpenter/Etc))_CU651621.lin.EMBL_RF00640_MIR167_1_1284912637_49431

Yes. The naming convention was chosen to allow for a maximum of WU content transparency. It also allows for the convenient programming of RNA World external monitor programs which can easily extract all the relevant information of a WU just by inspecting the filename.

or would it be (excuse the pun) likely that you would create a sub project that interested parties could select this research specifically?

Unfortunately, we cannot assign specific work units to specific people. This in fact is a restriction imposed by the BOINC architecture.
What we could certainly do is setup a special bee project to accelerate these WUs with respect to the bulk of systematic analyses and then deliver the related WUs in the usual random manner to everyone participating in RNA World. Here, we could also - as an exception from the rule - add non-complete but important sequence fragments, if desired. To justify this, however, we would need to work out a good rationale for what exactly the goal of such a sub-project would be. I agree that making sure that bees survive is of utmost importance. So, I appreciate any further input of ideas on such a project.

Michael.

[The Knighty NI]

Wow Michael nice reply Thank you. I was not expecting an answer that is so encompassing.

Let me set this at the right level right away so that your team don't look for answers were I would have probably far less knowledge than you. I am not an expert on bees and their Latin classifications, nor an expert on all the bee (I use this generically to cover Apis and Bombus) diseases and viruses. Rather consider me to be a very interested party who is studying bees and looking for ways that I can assist at a practical level with the use of my time and or the resources I have available.

From my studies over the last 5-6 months I am pretty sure in the UK there only two main classifications of bee, Apis and Bombus. There will almost certainly be some other related classification's which cover false or mimic species. W heather these species are pollinators or not I don's know. Commercially Apis are the main stream honeybee and Bombus are more commonly known as Bumble Bees. There are other pollinators although no links between the decline of butterfly's, wasps and other pollinators has come under discussion to my knowledge at present.

Should common links between other pollinating insects and bees be established in terms of disease and virus, then these would need to be included in any study to see what common factors may be involved in the transfer of disease and viruses.

What we could certainly do is setup a special bee project to accelerate these WUs with respect to the bulk of systematic analyses and then deliver the related WUs in the usual random manner to everyone participating in RNA World. Here, we could also - as an exception from the rule - add non-complete but important sequence fragments, if desired. To justify this, however, we would need to work out a good rationale for what exactly the goal of such a sub-project would be. I agree that making sure that bees survive is of utmost importance. So, I appreciate any further input of ideas on such a project.

In terms of the links provided I will spend some time looking to see what exists in the list's that is common to my current knowledge. However, I am contacting the Bumblebee Conservation Trust (BCT) to ask for their assistance in this. http://www.bumblebeeconservation.org.uk ... ees_id.htm
The potential to get a lot of computing power resources behind any sub-projects you decide to run exist with this organization because both Kate Humble and Chris Packham (TV presenters on both Spring Watch and Autumn Watch) are very concerned with bee population decline. I am sure that should any bee related sub-processing project that you run will get national TV coverage on both Spring Watch and Autumn Watch here in the UK. Primarily because it will give some feeling of personal involvement by the general public and we do like to get involved. The BCT may be a good source for assistance with choosing the right rational and goals for any sub-project you decide to run.

When the next meeting of the BBKA (Bournemouth Bee Keeping Association) occurs in three weeks time, I will seek to find out what other resources are available that I can tap into to assist you to identify species, diseases and viruses.

Once again thank you for your reply Michael. Now that I have the bit between my teeth to as to speak, I am going to peruse what ever avenues of investigation are available, gain as much knowledge as possible and get as many resources opened up as possible.

[Michael H.W. Weber]

As I said, I am not a bee specialist nor do I currently know much about what actions have already been undertaken to investigate the bee population decline in more detail. All I know is that viruses are under suspicion and I have spent some thoughts on this: RNA World looks at RNAs. Modern sequencing technologies allow for detailed inspection of changes in RNA levels/composition in isolated cell types as well as in whole organisms. I think that a complete transcriptome sequencing of an RNA extract prepared from healthy bees compared to infected bees (if possible at different stages of the progressing disease) of the same hive should allow to identify differences (if present) in the cellular program (in terms of RNA profile alterations) that might be caused by e.g. a virus/parasite.
In fact, application of such techniques would be what the RNA World project needs in general to validate its computational results in the laboratory. Unfortunately, although we could technically carry out such lab experiments, at present, we do not have the funding to either afford the required sequencer plus related consumables or purchase the relevant services from a company. As a consequence, we have to rely on experimental data acquired and published by other researchers. If we could find a sponsor donating such an instrument (e.g. Roche's GS Junior system; ranging at around 150 k ?), analyses such as that briefly outlined above might however become a reality.

For now I think we should continue collect some more information on the bee problem in this thread.

Michael.

[The Knighty NI]

That's Great

Dr Robert Paxton from Queen's University Belfast, is among those funded through the initiative. His project will look at the impact of emergent diseases on major UK insect pollinators and how we might mitigate against them.

The project will combine the expertise of five leading laboratories across the UK and the EU in a three-year project, focusing on diseases caused by Deformed Wing Virus and a fungus-like microorganism called Nosema ceranae. These are among the most serious diseases that affect honeybees and have recently been found to infect some bumblebees as well. Using laboratory and field experiments, including radar tracking of individual flying bees, researchers will investigate the direct impact of both diseases on honeybees and bumblebees.

The team will also test two new methods to control the microorganisms that cause such diseases based on probiotic bacteria and RNA interference technology. New ways of controlling bee diseases will be of immediate benefit to the pollinator industry and hobby beekeepers in ensuring sustainable pollination in the UK.

Thinking about writing to the project being run by Dr Paxton to find out what availability there will be for the RNA. However, I am not sure from a courtesy point of view if this should be done via Wellcome Trust as they are the funding organization?

List of the nine bee research projects they are funding on this page:
http://www.wellcome.ac.uk/News/2010/News/wtx059955.htm

Would you like me to place copies of emails I write to various sources as this thread progresses?

What are your thoughts?

Greg.

[Michael H.W. Weber]

Would you like me to place copies of emails I write to various sources as this thread progresses?

Yes, that would be nice. You can send these to me by email if you like.

Of all the projects listed on the website of the link you provided, there is only one (Dr Eugene Ryabov, University of Warwick, member of a workgroup that appears to have specialized on Picorna viruses; their funded project on this topic started just yesterday) that attempts to address the molecular basis of the problem. I did a little research on that and it seems that there is a mite which attaches to the bees and sucks out the bee's hemolymph (similar to our blood). Specifically, it is the mite Varroa destructor. It seems to deliver RNA viruses like deformed wing virus (DWV) when feeding on the bees. So, that's when RNA comes into play...
And, by the way, this DWV virus is already part of our analyses.

Some general information on the problem is found here.

Michael.

[Salmonella]

Interesting research non-coding RNA. Long!
Long non-coding RNA prevents the death of maturing red blood cells

As of June 2011, ~100 lncRNAs have been functionally annotated in lncRNAdb (a database of literature described lncRNAs)
http://en.wikipedia.org/wiki/Long_non-coding_RNA

And only? This is not enough!

[Michael H.W. Weber]

These long non-coding RNAs appear to be responsible for a multitude of processes in cells. An extremely interesting research field... Just remember that only a few percent of the human genome are coding for proteins but almost everything is transcribed (i.e. put into RNA). Explain that!

Michael.

[robertmiles]

I've found some information on the problems of bees.

http://www.sciencedaily.com/releases/20 ... 192320.htm

http://www.msnbc.msn.com/id/20612274/

http://www.physorg.com/news174746800.html


I've also lost several more about overheated high fructose corn syrup having pairs of the fructose molecules combine into hydroxymethylfurfural, which is toxic to honeybees.

[Ananas]

These long non-coding RNAs ...

I hope that's not a too stupid question ... is that what we see as "Intron" results?

[Michael H.W. Weber]

These long non-coding RNAs ...

I hope that's not a too stupid question ... is that what we see as "Intron" results?

Not in the context of this thread although with respect to size the Intron_gpI belongs to the upper third of ncRNAs we are searching for (they represent large cataltic RNAs, i.e. ribozymes). Here is more information.

Michael.

[Michael H.W. Weber]

I've found some information on the problems of bees.

http://www.sciencedaily.com/releases/20 ... 192320.htm

http://www.msnbc.msn.com/id/20612274/

http://www.physorg.com/news174746800.html


I've also lost several more about overheated high fructose corn syrup having pairs of the fructose molecules combine into hydroxymethylfurfural, which is toxic to honeybees.

Some further information:
Link to the original article regarding HFM: http://pubs.acs.org/stoken/presspac/pre ... /jf9014526

Honey bee genome overview: http://www.ncbi.nlm.nih.gov/genome/48
Current assembly status: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AADG06

Bumblebee genome overview: http://www.ncbi.nlm.nih.gov/genome/2739

Some additional bee-related genome information: http://www.ncbi.nlm.nih.gov/genome?term=bee

Michael.