Background: This series contains brief reports on each of the "600 studies" held on the GENERA database, published at Bifortified.org, in the order in which they were listed on 18 Sept 2013. The general purpose is to counter the extraordinary claims that the entries on this list demonstrate the human food safety of GM crops. See the Introduction to this series [link].
Great Big List of Studies: Entry 20 – Atkinson et al 2004 [fulltext pdf link]
This is a study on a GM protein being used as a surrogate for the in-plant GM protein in experimental lines of nematode resistant GM potatoes. The study was part of the University of Leeds' line of research in nematodes that has been going since at least 1995 – 18 years [link to publication history]. As yet, there are no commercial nematode resistant GM potatoes unless they are somehow released but unlisted.
The study does not support any claims about the human food safety of commercial GM crops.
The GM protein "OcIΔD86" was expressed in e-coli and fed in solution at three different concentrations to groups of ?10 young Sprague Dawley rats over 28 days. The authors reported some significant differences in the liver and cecum weights of the rats. There was also some initial work assessing the characteristics of the protein from an allergenic viewpoint.
The first two words of the study title, "Prima Facie" means "First look", and this description of their work was reinforced in the text of the study with the phrasings
- "Our goal was to provide an initial study of toxicity…"
"We chose to use isolated cystatin and not the protein expressed in plants in this first work…" [emphases added]
However when the University of Leeds made a field trial application to the UK's DEFRA (Department for environment, food and rural affairs) in 2007, reference 07/R31/01  all such preliminary wordings were removed and suddenly this 'first work' became conclusive evidence…. 
- "The lack of toxicity of the cystatin to mammals has already been established (Atkinson et al., 2004)." P10
"These plants are not intended for animal feed. The cystatin has been shown not to be toxic to mammals (Atkinson et al., 2004)." P17 [emphasis added]
The GM freeze organisation put out a substantial objection to the crop's environmental release [link] noting (amongst other things) that the GM inserts only offered a partial resistance, to which the nematodes would quickly develop a full resistance.
In 2009 the University of Leeds made another application for field trial approval, reference 09/R31/01 
These trials were to test GM potatoes engineered for nematode resistance through dsRNA techniques. Under a section on human health they wrote… 
- "dsRNA: A potential advantage of using RNAi is that transgenic plants do not produce a protein." P7
which made me wonder what problem they saw with having a transgenic protein such as "OcIΔD86" in their GM potatoes, or more generally in all approved commercial GM crops.
To assuage any risks associated with dsRNA they boldly pointed to a paper by Monsanto [Ivashuta et al 2009] which claimed safety. Using a logic that FSANZ would've been proud of they argued that since endogeneous dsRNAs are already present in food plants it should be safe, given a long human history of consumption, without giving recognition to the fact that since their novel dsRNA invention had never been in the food supply before conclusions of safety based on previous consumption over a long period couldn't apply. After all, proteins have always been in the food supply, but the novel GM proteins do require regulatory assessment in an effort to reduce the risks to human safety. The need for the development of regulatory assessment procedures to meet the new commercial developments in dsRNA are being more actively discussed in the science [Heinemann et al 2013 – fulltext pdf – references Ivashuta] although some years after the first dsRNA crops have already been approved without testing of dsRNA safety.
The group at Leeds are also testing other forms of nematode resistance.
All this said, there are actually potato varieties with complete or partial resistance to various strains of nematodes. See The British Potato Variety Database [link]. The solution to nematodes, according to GM freeze, is a five year crop rotation.
Unusual archive link structures at DEFRA that weren't recognised by newsvine: