Previous Online Discussions of the AHTEG

Dear All,

Please use this thread to recommend additional background materials on "Roadmap for Risk Assessment" to the SWG Chair as soon as possible but no later than 15 June 2010.

The SWG Chairs in consultation with the whole AHTEG will update the existing list of background materials linked to the document "Guidance on Risk Assessment of LMOs" no later than the 31 August 2010.

Thank you and best regards,
Manoela

Dear All,

As chair of the SWG on the Roadmap, I would like to remind you in general of the possibility that you have to submit background materials for the Roadmap for Risk Assessment. When you submit materials, could you please indicate for which part of the document you think that it is particularly relevant.

In particular, I would like to invite people that have already mentioned their wish to submit background materials during the AHTEG, to do so now:
Dave Heron has asked to replace one ofthe documents by an updated and more relevant version, and to delete the former, outdated version of the document.
Piet van der Meer has asked to include the PRRI Guidance.
Just for the sake of tranparancy I would like to invite Dave and Piet to post these submissions formally on this discussion site.
I hope I have not forgotten any other specific request, but if I did, please consider this as an invitation to post your request.

Hans

Dear Hans:
Here I am sending you additional background references for the Roadmap. I indicated for all of them where I think they are more relevant, since some are clearly relevant in different parts of the roadmap, there is some repetition, but I tried to be more inclusive in Step one, considering that these references could be use for the following steps.
Have a nice day.
Sol

Dear all,

I want to thank all of you who contributed background material for the Roadmap for your efforts. I would like to close this part of our efforts for the time being.
Our next step is to devise a 'protocol' how these background materials can be incorporated into the list of references to the Roadmap (http://bch.cbd.int/onlineconferences/roadmapref_ahteg_ra.shtml).

I already made some remarks about this issue in my previous submission. I have indicated (by striking them) some documents that I think are not of direct relevance to the Roadmap. Meanwhile, I have been giving this some more thoughts, and I think that a number of these documents could still be refered to, as background material for the other issues section in the Roadmap.
This is something that we have to spend more discussion on.
I will try to have a discussion paper ready for this, a.s.a.p. but at the latest by July 24.
Remember we have to have this work finalized by August 31.

If you still have background materials to be added, I would propose that you can still submit them, but I may not be able to take them into account for the writing of my discussion paper.

Finally, I want to add two more references to the list, two 'trait' documents, on EPSPS and on Cry1Ac:
http://cera-gmc.org/docs/cera_publications/pub_01_2010.pdf
http://cera-gmc.org/docs/cera_publications/pub_02_2010.pdf

pdfs for these papers are attached.

Best wishes,

Hans

Manoela,

Thanks. I hope to find time the next two weeks to collect the materials that I would recommend as back ground materials. let me start by recommending the PRRI Guide on risk assessment, of which i attach the current version.

Piet

I would suggest this reference for Step 1 of the Roadmap:

https://bat.genok.org/bat/

Dear all,

I have gone through the list of background material in the BIRC, and made some recommendation about there use as background material for the Roadmap; see the attached document.

The original document was tabled in the first session of the AHTEG.

Best regards,

Hans

Dear all,

As an addition to the previous document, I attach here a document that provides links to background material that has been entered into the BIRC over the last year.
References have been treated in the same way as described in the previous document; see in the previous documents for what strikethrough means; also comments have been highlighted similarly.

Best regards,

Hans

Dear all,

I would like to provide the following documents as background references for the Road Map and to the BCH.  Since there are a considerable number, I have uploaded pdf documents to an ftp server that can be accessed by the following means:

1) Open Internet Explorer
2) In the address bar, enter ftp://ftp.agr.gc.ca/pub/outgoing/bio-jsc/
3) Go to File and select Login As.
4) In the window that opens, select Log on anonymously in the bottom left corner
5) The User name should automatically be selected as Anonymous
6) Enter your email address where it indicates E-mail Address
7) Click Log On
8) Copy the files to your desktop

Firefox should also work or any other web browser that has built-in ftp capabilities. The documents will remain on the server for 7 days, after which they are automatically removed

The following files are available:

Research Articles

GENOMICS, PROFILING and MOLECULAR ANALYSIS

File: Catchpole2005.pdf
Citation: Catchpole et al. 2005. Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. PNAS 102:14458-14462
**Available free online**

File: Kristensen2005.pdf
Citation: Kristensen et al. 2005. Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. PNAS 102:1779-1784
**Available free online**

File: Lehesranta2005.pdf
Citation: Lehesranta et al. 2005. Comparison of tuber proteomes of potato varieties, landraces, and genetically modified lines. Plant Phys 138:1690-1699
**Available free online**

File: Albo2007.pdf
Citation: Albo et al. 2007. Proteomic analysis of a genetically modified maize flour carrying CRY1AB gene and comparison to the corresponding wild-type. Maydica 52:443-455

File: Baker2006.pdf
Citation: Baker et al. 2006. A metabolomic study of substantial equivalence of field-grown genetically modified wheat. Plant Biotechnol J 4:381-392

File: Baudo2006.pdf
Citation: Baudo et al. 2006. Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J 4:369-380

File: Corpillo2004.pdf
Citation: Corpillo et al. 2004. Proteomics as a tool to improve investigation of substantial equivalence in genetically modified organisms: The case of a virus-resistant tomato. Proteomics 4:193-200

File: Defernez2004.pdf
Citation: Defernez et al. 2004. NMR and HPLC-UV profiling of potatoes with genetic modifications to metabolic pathways. J Agric Food Chem 52:6075-6085

File: Gregersen2005.pdf
Citation: Gregersen et al. 2005. A microarray-based comparative analysis of gene expression profiles during grain development in transgenic and wild type wheat. Transgenic Res 14:887-905

File: Ruebelt2006a.pdf
Citation: Ruebelt et al. 2006a. Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of genetically modified crops. 3. Assessing unintended effects. J Agric Food Chem 54:2169-2177

File: Ruebelt2006b.pdf
Citation: Ruebelt et al. 2006b. Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of genetically modified crops. 2. Assessing natural variability. J Agric Food Chem 54:2162-2168

Review Article

File: Bradford2005.pdf
Citation: Bradford et al. 2005. Regulating transgenic crops sensibly: lessons from plant breeding, biotechnology and genomics. Nature Biotechnology 23:439-444

File: Abdeen2010.pdf
Citation: Abdeen et al. 2010. Transcriptome analysis reveals absence of unintended effects in drought-tolerant transgenic plants overexpressing the transcription factor ABF3. BMC Genomics 11:69

File: ElOuakfaoui2005.pdf
Citation: El Ouakfaoui and Miki 2005. The stability of the Arabidopsis transcriptome in transgenic plants expressing the marker genes nptII and uidA. Plant J 41:791-800

File: Manabe2007.pdf
Citation: Manabe et al. 2007. CSR1, the sole target of imidazolinone herbicide in Arabidopsis thaliana. Plant Cell Physiol 48:1340-1358.

Reviews

File: Miki2009.pdf
Citation: Miki et al. 2009. Selectable marker genes and unintended changes to the plant transcriptome. Plant Biotechnol J 7:1-8
Schnell2009.pdf

File: Batista2008.pdf

COMPARISONS TO CONVENTIONAL PLANT BREEDING

Citation: Batista et al. 2008. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. PNAS 105:3640-3645
**Available free online**

File: Ching2002.pdf
Citation: Ching et al. 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 319
**Available free online**

File: Fu2002.pdf
Citation: Fu and Dooner 2002. Intraspecific violation of genetic colinearity and its implications in maize. PNAS 99:9573-9578
**Available free online**

File: Cheng2008.pdf
Citation: Cheng et al. 2008. Effect of transgenes on global gene expression in soybean is within the natural range of variation of conventional cultivars. J Agric Food Chem 56:3057-3067

File: Gorbunova1999.pdf
Citation: Gorbunova and Levy 1999. How plants make ends meet: DNA double-strand break repair. Trends Plant Sci Rev 4:263-269.

File: Gaut2007.pdf
Citation: Gaut et al. 2007. Recombination: an underappreciated factor in the evolution of plant genomes. Nature Rev Genet 8:77-84

File: Bennetzen2000.pdf
Citation: Bennetzen 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251-269

File: Adams2005.pdf
Citation: Adams and Wendel 2005. Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8:135-141

File: Grandbastien1998.pdf
Citation: Grandbastien 1998. Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3:181-187


Best regards,
Phil

Attached are suggested additional references from Norway (well actually California, summer holiday!).

Hans, I have sent the .pdfs directly to your email.


Best,

David Q

23 June 2010

Hi Hans,

Thanks for allowing some extra days for sending background documents for the roadmap. Those extra days were very welcome because the incident with the rainwater tank in our yard left us without water and electricity for a couple of days, and I spent most of my time digging and repairing cables. Most is back to normal now.

Returning to the back ground documents: the advantage of submitting a bit later is that I saw that many of the documents I had in mind have already been submitted by others.

I propose to include in addition the following documents that provide some further context to the risk assessment addressed in the roadmap:
• A PRRI briefing paper on the background, objectives and progress of public research in modern biotechnology.
• Some papers that compare conventional breeding and genetic modification with regard to unintended changes on DNA level. See the list below.
• A UNIDO manual with practical guidance for national authorities that are in the process of developing biosafety regulations. This manual is currently being used in the UNIDO distant learning biosafety courses. The current version of that manual contains an overview of the international context relevant to biosafety, and offers guidance on some of the practical aspects of applying the procedures of the CPB, such as assigning tracking numbers to notifications, registering notifications in a database, writing a draft letter of acknowledgement etc. Under the heading risk assessment, the manual makes reference to the work of the AHTEG. The next version of this manual will include a new part with practical guidance on what is needed to establish adequate regulatory oversight capacities. This next version will be available in the Summer, and I will send the updated version.

Regards
Piet


Papers that compare conventional breeding and genetic modification with regard to unintended changes on DNA level


Batista, R., Saibo, N., Lourenco, T., & Oliveira, M.M. (2008). Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proceedings of the National Academy of Sciences of the United States of America, 105, 9, pp  3640-3645. <Go to ISI>://WOS:000253846500082

Baudo, M.M., Lyons, R., Powers, S., Pastori, G.M., Edwards, K.J., Holdsworth, M.J., & Shewry, P.R. (2006). Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnology Journal, 4, 4, pp  369-380 <Go to ISI>://000238256500001

Baudo, M.M., Powers, S.J., Mitchell, R.A.C., & Shewry, P.R. (2009). Establishing Substantial Equivalence: Transcriptomics. In Methods in Molecular Biology, Transgenic Wheat, Barley and Oats, (eds H.D. Jones & P.R. Shewry), Vol. 478, pp. 247-272. Humana Press, a part of Springer Science + Business Media, LLC 2009. <Go to ISI>://BIOSIS:PREV200900189501

Coll, A., Nadal, A., Collado, R., Capellades, G., Messeguer, J., Mel E., Palaudelm M., & Pla, M. (2009). Gene expression profiles of MON810 and comparable non-GM maize varieties cultured in the field are more similar than are those of conventional lines. Transgenic Research, 18, 5, pp  801-808. http://dx.doi.org/10.1007/s11248-009-9266-z.

Kogela, K.H. Lars M. Voll, Patrick Schäfera, Carin Jansena, Yongchun W, Gregor Langena, Jafargholi Imani, Jörg Hofmann, Alfred Schmiedl, Sophia Sonnewald, Diter von Wettstein, R. James Cook, and Uwe Sonnewald (2010). Transcriptome and metabolome profiling of fieldgrown transgenic barley lack induced differences but show cultivar-specific variances. http://www.pnas.org/cgi/doi/10.1073/pnas.1001945107.

Schouten, H.J and Evert Jacobsen (2007). Are Mutations in Genetically Modified Plants Dangerous? Letter to the Editor. Journal of Biomedicine and Biotechnology. Volume 2007, Article ID 82612, 2 pages. doi:10.1155/2007/82612. (attached).

Shewry, P.R., Baudo, M., Lovegrove, A., & Powers, S. (2007). Are GM and conventionally bred cereals really different? Trends in Food Science & Technology, 18, 4, pp  201-209. <Go to ISI>://WOS:000245784600003

Coming to think of it, I do not recall having seen the UNEP Technical Guidelines being suggested as background document

Piet