The Genome Generation, Elizabeth Finkel Melbourne University Press 2012 ISBN 978-0-522-85647-7

From the back cover:
The year 2001 marked more than just the beginning of Stanley Kubrick’s space odyssey, it marked the beginning of the genome era. That was the year scientists first read the 3 billion letters of DNA that make up the human genome. This was followed by a veritable Noah’s Ark of genomes—sponges and worms, dogs and cows, rice and wheat, chimps and elephants-180 creatures aboard so far.

So what have we learned from all this? How has it changed the way we practise
medicine, grow crops and breed livestock? What have we learned about evolution?

These are the questions science writer and molecular biologist Elizabeth Finkel asked herself four years ago. To find the answers she travelled the science frontier from Botswana to Boston, from Warracknabeal to Mexico and tracked down scientists working in the field. Their stories, told here, paint the picture of what it means to be part of the genome generation.
Elizabeth Finkel holds a PhD in biochemistry and spent ten years as a professional research scientist before becoming an award-winning journalist. She is a contributing editor to Cosmos magazine and also writes for the US magazine Science. Her numerous awards include a Queensland Premier’s Literary Award for her book, Stem Cells: Controversy at the Frontiers of Science. In 2011 she was named the National Press Club’s Higher Education Journalist of the Year.

Elizabeth Finkel tells the evolving story of DNA

in an intriguing and accessible way.

The Genome Generation is absolutely riveting. These tales from the frontier

are a ‘must read’ for everyone who wishes to understand our past—the logic of

evolution—or take a peep into our exciting future at the creation of ‘super plants’

through ‘digital agriculture’.

Is the genomic revolution an overhyped flop or are we on the edge of a life-changing revolution? This book stares down the myths and lays out the answers in engaging, compelling stories. This is an accomplished work of scientific literacy.

The Pundit’s considered comments about the Genome Generation will appear at this site as soon as he gets a chance to read the story. But the book is certainly handsomely produced, and Elizabeth Finkel is a wonderful science writer with a fabulous track record.

What’s the News: It’s no secret that having lunch messes with your biochemistry. Once that sandwich hits your stomach, genes related to digestion have been activated and are causing the production of the many molecules that help break food down. But a new study suggests that the connection between your food’s biochemistry and your own may be more intimate than we thought. Tiny RNAs usually found in plants have been discovered circulating in blood, and animal studies indicate that they are directly manipulating the expression of genes.

What’s the Context:

MicroRNAs, or miRNAs, are molecules involved in regulation of  gene expression, the transcription of genes into proteins. miRNAs bind to the  messenger RNAs that ferry genetic information from DNA to the  ribosomes, which translate messenger RNAs into proteins.

When a miRNA binds a messenger RNA, it keeps it from being translated, thus preventing that gene from being expressed.

How the Heck:

This team of researchers at Nanjing University had been studying the miRNAs that circulate in human blood and were surprised to find that some of the miRNAs weren’t homegrown but instead came from plants. One of the most common plant miRNAs was from rice, a staple of their Chinese subjects’ diets. Intrigued, they confirmed with a variety of tests in mice that the miRNA, which, in its native environs, usually regulates plant development, was definitely coming from food….more at link to Discover Magazine

Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are effector molecules of RNA interference (RNAi), a highly conserved RNA-based gene suppression mechanism in plants, mammals and other eukaryotes. Endogenous RNAi-based gene suppression has been harnessed naturally and through conventional breeding to achieve desired plant phenotypes. The present study demonstrates that endogenous small RNAs, such as siRNAs and miRNAs, are abundant in soybean seeds, corn kernels, and rice grain, plant tissues that are traditionally used for food and feed. Numerous endogenous plant small RNAs were found to have perfect complementarity to human genes as well as those of other mammals. The abundance of endogenous small RNA molecules in grain from safely consumed food and feed crops such as soybean, corn, and rice and the homology of a number of these dietary small RNAs to human and animal genomes and transcriptomes establishes a history of safe consumption for dietary small RNAs.

PMID: 19068223 [PubMed - indexed for MEDLINE] Ivashuta SI, Petrick JS, Heisel SE, Zhang Y, Guo L, Reynolds TL, Rice JF, Allen E, Roberts JK.

Food Chem Toxicol. 2009 Feb;47(2):353-60. Epub 2008 Nov 27.

REPOSTED FROM GMO PUNDIT Blog.

(see original blog post here)

European legislation in the field of genetic engineering is so narrow that it blocks the ability of researchers to take progress from publicly funded basic research on plants through to practical applications. We, 41 scientists who have received funding for basic research on plants from the Swedish Research Council, urge politicians and environmental groups to take the necessary steps to change the relevant legislation so that all available knowledge can be used to develop sustainable agricultural and forest industries.
One of the “Grand Challenges” facing mankind is to find ways to provide food, fuel and clean water to a burgeoning population using agricultural and forestry practices that are environmentally and economically sustainable. Research on plants has made tremendous progress and we now understand well how plants grow, how they protect themselves against disease and environmental stress and what factors limit production in agriculture and forestry. The prerequisite for progress has been basic research, especially studies of plant genes.

The application of this basic knowledge with the goal of making agriculture and forestry sustainable and environmentally friendly has been hindered by European gene technology legislation. These regulations impose very strict controls on the use of plant varieties developed by genetic engineering, while varieties developed via traditional breeding are released with no checks whatsoever. Some environmental groups leading opinion against GM plants criticise the use of genetic engineering by arguing that developments are linked to large multinational companies, that there is uncertainty about the risks, that they cannot be used in an agri-environment without increasing the use of chemicals and that only multinational companies benefit from GM plants. Let us examine these arguments.

Second: There is no scientific uncertainty on the issue of whether GM crops pose more risk to consumers or the environment than conventionally produced crops varieties. The legislation was formulated when there was not yet sufficient data on this but now we know better. 500 independent research groups have received 300 million € from the EU to study the risks. The conclusion in a summary of the results (“A decade of EU-funded GM research”) is that “GMOs are not per se more risky than conventional plant breeding technologies”. We are basic research scientists and we know that the changes produced by genetic engineering are easier to control than those produced in other ways. The legislation argues the opposite, and imposes controls only on GM plants. To put this in other terms; the logic of the current legislation would suggest that only drugs produced by genetic engineering should be evaluated for side effects.
One of the main arguments against GM crops has been that varieties providing for a more sustainable agricultural sector have not yet been launched. The problem is that this is unlikely to happen with the current legislation. While plants resistant to disease – developed in the traditional way – can be grown at once, it takes many years to get a GM variety with the same properties approved for cultivation. The process from basic research – through applied research – to the finished seed marketed by a company is not only time consuming but also very expensive for GM crops: it costs an estimated minimum of 100 million SEK. Publicly funded researchers or small businesses will never have such resources and thus cannot translate advances made in basic research into a product for consumers. Only a few multinational companies are able to take these costs and therefore give the impression of a monopoly.

The regulatory framework is contributing to the lack of competition and the appearance of monopolies; it is not simply patent rights or unsound business practices, as is often claimed.

The environmental movement’s opposition to genetically modified plants runs counter not only to a transition to sustainable agriculture but also, paradoxically, to their “fight against the major chemical companies.” The costs associated with the introduction of GM varieties give these companies a monopoly on a huge market; 10% of the world’s agricultural land is planted with GM crops today. In addition, companies that have as one part of their business the production of agrochemicals get “revenue insurance” from GM varieties because the use of GM crops often leads to a reduced demand for their agricultural chemicals.

Ultra-right religious groups in the U.S. are trying to raise a quasi-scientific version of creationism as an alternative to evolution. In Europe we look at this public debate with amazement, as if it went against the notion that the Earth is round. However, in Europe we have instead much quasi-scientific scaremongering about the risks of GMOs, and this is fuelled by some groups within the environmental movement. The Swedish environmental movement has a proud tradition of working from a sound scientific basis. For many of us, an early involvement in the non-profit environmental movement was an essential element in choosing our current careers; we wanted to contribute to a better world. The environmental movement should view it as a warning that many of us, with sadness, abandoned it when we felt we could no longer belong to organizations that sided with anti-science and populist forces – without subverting our scientific principles. We urge the Swedish environmental movement to unite with science and act as a rational, informed voice to influence their more vocal foreign counterparts.

Changing the genetic engineering legislation is not only a very important issue for Europe. Poorly funded plant breeding researchers and organisations in many third world countries are also being deprived of one of their best tools to provide better local crops because of the obvious risk of being excluded from the GM-hostile European market.

We therefore urge our politicians to change this outdated law. It should be the characteristics of a plant that determines whether it should be checked, not the technology used to produce it. We do not believe that all checks on the cultivation of GM plants should be removed. Varieties that are toxic or could cause allergies or environmental problems must be subjected to governmental control and independent evaluation – but these same controls should apply to ALL varieties, whether they are produced by genetic engineering or not.

Our desire is that the world’s farmers will be offered seeds that have been developed to provide the most energy-and water-efficient and chemical-free agriculture and forestry as possible, but current genetic engineering legislation prevents this.

Professor Nina Fedoroff of the Pennsylvania State University is the lead protest letter signatory.

The biotech crop regulation changes mooted by the EPA were announced March 2011 in the Federal Register here (pdf).

Scientist co-signatories on the Fedoroff Letter say that the EPA is going down a troublesome path that is not based on science, and which will frustrate and delay innovations needed to provide farmers with better cropping methods.  Because of the delays and unneeded extra cost burdens such a  policy shift would create, it would surely undermine global food security.

The text of Fedoroff Letter is provided below (see here for the full original letter).

Nina Fedoroff has (together with Robert Haselkorn,and Bruce M. Chassy) written a very readable  editorial about this issue in the FASEB biology journal:
“EPA’s Proposed Biotech Policy Turns a Deaf Ear to Science” (pdf). This great FASEB editorial fully explains the nature of the problem that is brewing with the current EPA policy direction.

Such expanded regulation would serve only to increase costs, hinder research, undermine the long-term viability of public university research programs, and limit product development from the private sector. The proposed actions would threaten our ability to produce high quality food at an affordable price and to feed a growing population.

They would also weaken the competitive advantage of U.S. public research programs in the global research arena, all with no increase in safety for consumers, farmers, or the environment — indeed, the contrary would be the case in many instances.

The academic community is committed to ensuring that the environmental and food safety benefits of biotechnology-derived plants continue to accrue, and it is essential that all agencies respect the scientific basis for regulation and division of regulatory responsibilities established by the Coordinated Framework. It is critical that regulations focus on scientifically demonstrated hazards, rather than being driven by issues of perception or political expediency. Therefore, we urge that the pending EPA regulatory actions be reconsidered and the rule-making proposal be limited to requirements for substances that have traditionally been regulated by the EPA, such as PIPs, and then only to those requirements that are fully justified on the basis of sound science.

Readers of Biofortified should start bending the ears of congressional representatives — and get the  EPA’s attention by every available communication channel — to make sure this potentially serious misadventure does not happen.

We, the undersigned members of the National Academy of Sciences, write today to voice our concern over the latest proposal from the U.S. Environmental Protection Agency (EPA) to further expand its regulatory coverage over transgenic crops in a way that cannot be justified on the basis of either scientific evidence or experience gained over the past several decades, both of which support the conclusion that molecular modification techniques are no more dangerous than any modification technique now in use. The increased regulatory burdens that would result from this expansion would impose steep barriers to scientific innovation and product development across all sectors of our economy and would not only fail to enhance safety, but would likely prolong reliance on less safe and obsolete practices.

Since then, extensive research, coupled with years of experience, led to the conclusion that there is no scientific basis to single out plants produced by transgene insertion for a special regulati•ry review, nor to distinguish these products from others on the basis of the process used to create them. There is now abundant evidence that the most appropriate regulatory approach would be to require review only of truly novel traits introduced into plants without regard to the methods used for their introduction. Yet the regulatory apparatus in the U.S. has increasingly moved in the opposite direction towards ever greater regulation and increased data requirements for transgenic plants, despite the abundant accumulation of data attesting to their safety.

The scientific community has a strong interest in keeping regulations science-based and Commensurate with the risk of the products at issue. This past March, EPA announced in the Federal Register a draft proposed rule to codify data requirements for plant incorporated protectants (PIPS). This draft was forwarded by EPA to the U.S. Department of Agriculture (USDA), Department of Health and Human Services and Congress for review in accordance with the Federal Insecticide, Fungicide, and Rodenticide Act.

Based on initial reviews of that draft proposal and recent EPA actions associated with biotechnology-derived crops, it is clear that the Agency is departing from a science-based regulatory process, walking down a path towards one based on the controversial European “precautionary principle” that goes beyond codifying data requirements for substances regulated as PIPs for the past 15 years.

We are particularly troubled by proposals to expand EPA’s current oversight into areas such as virus resistance and weediness that have been adequately addressed by USDA since 1986. Already, EPA has expanded its oversight into virus resistance, which previously had been the purview of USDA’s Animal and Plant Health Inspection Service (APHIS) and which EPA prudently proposed in 1994 to exempt from its regulations. With the draft proposed rules, EPA would further expand its regulations and data demands to other areas historically covered by USDA-APHIS without the slightest justification based on either data or experience.

It is most troubling that EPA is also proposing to increase its regulation to cover matters which are still not deemed to be threats even after years of study, such as potential gene transfer from plants to soil microorganisms. In other actions, EPA has expressed its right to regulate plants engineered for altered growth (e.g., by suppression of ethylene production), the same way it regulates synthetic plant growth regulators. The Agency does so based on a generous interpretation of the enabling legislation, despite the absence of any scientifically credible hazard.

Such an expansion in regulatory purview would reverse long established and highly successful policy under the Coordinated Framework. Such a shift would (1) create a duplicative regulatory system for very low risk products delivering substantial, demonstrated environmental benefits; (2) increase costs, reduce efficiency and prolong the review timelines thereby discouraging innovation; (3) dramatically increase the hurdles already facing academic institutions and companies attempting to improve so-called minor use or specialty crops through modern biotechnology; and (4) adversely impact trade in safe and wholesome commodities produced by U.S. growers because of the stigma attached to anything characterized as a “pesticide” — a regulatory label for DNA that is unique to the U.S. — and with no concomitant increase in product safety. In addition, any expansion in regulatory oversight not resulting from documented risk could have global ramifications, as policymakers in other countries routinely consider U.S. policymakers as leaders in the regulation of crops derived from biotechnology.

Indeed, it is astonishing that EPA would attempt such an expansion of its regulatory activity in this sphere. We now have more than 25 years of experience with biotechnology-derived crop plants. None of the hypothetical risks articulated at the dawn of this era has been realized and caused new environmental problems. On the contrary, billions upon billions of meals derived from these crops have been eaten by humans and livestock around the world with no ill effects. Moreover, environmental impacts of production agriculture and the carbon footprint of agriculture have been significantly reduced through the use of transgenic crops. At the same time, farmers have benefited economically, socially, and through improved health. These indisputable results make a compelling case that existing regulatory burdens should be reduced and refocused. There is absolutely no justification in either scientific data or experience for the regulatory expansion proposed by EPA.

Over the last two decades, advances in sequencing and genomic analysis have revealed that biotechnology is more precise and less disruptive to the genome than traditional plant breeding. In point of fact, recent genomic, proteomic and metabolomic comparisons of varieties bred through conventional and transgenic methods demonstrate that transgenic plants with incorporated novel traits more closely resemble the parental variety than do new varieties of the same plant produced by more traditional breeding or mutagenesis techniques. These findings confirm that transgene insertion is not inherently risky nor does it present new and greater hazards than conventional plant breeding.

In conclusion, recent EPA actions signal an intent to expand the Agency’s regulatory oversight into products regulated by USDA for over two decades and to products for which there has never been a justification for regulation. These actions are not only inconsistent with regulatory directives mandated by the current Administration, they also erode the integrity of the Coordinated Framework. Such expanded regulation would serve only to increase costs, hinder research, undermine the long-term viability of public university research programs, and limit product development from the private sector. The proposed actions would threaten our ability to produce high quality food at an affordable price and feed a growing population. They would also weaken the competitive advantage of U.S. public research programs in the global research arena, all with no increase in safety for consumers, farmers, or the environment — indeed, the contrary would be the case in many instances.

The academic community is committed to ensuring that the environmental and food safety benefits of biotechnology-derived plants continue to accrue, and it is essential that all agencies respect the scientific basis for regulation and division of regulatory responsibilities established by the Coordinated Framework. It is critical that regulations focus on scientifically demonstrated hazards, rather than being driven by issues of perception or political expediency. Therefore, Administrator Jackson, we urge you to reconsider the pending EPA regulatory actions and limit the rulemaking proposal to requirements for substances that have traditionally been regulated by EPA as PIPs, and then to only those requirements that are fully justified on the basis of safety and sound science.

I sign this letter on behalf of the more than 60 members of the U.S. National Academy of Sciences listed below. The list includes many of America’ most eminent biological scientists, including Nobel Laureates Dr. James Watson and Dr. Gunter Blobel.

Sincerely,
Dr. Nina V. Fedoroff
Member, National Academy of Sciences
2006 National Medal of Science Laureate
Science and Technology Adviser to the. Secretary of State and to the Administrator of USAID, 2007-10
Evan Pugh Professor, Pennsylvania State University
Huck institutes of the Life Sciences
211 Wartik
State College, PA 16801
nvflPpsu.edu

Book available as pdf for free download (see link below)

Previous posts at GMO Pundit have covered GM insect protected eggplant being developed as a new crop variety in India. This insect-protected crop, making use of Bt protein trait, could avoid a large amount of current synthetic pesticide spraying in India and prevent many poisoning risks to farmers and their familes. The Hindu newspaper story quoted below highlights how concerns about GM eggplant (brinjal) potentially  interferring with ayuvedic medicines in India have delayed governmental approval of insect-protected brinjal.

The Hindu : Sci-Tech / Agriculture : Lab test report to pave way for Bt brinjal release NEW DELHI, August 8, 2011

The government has ordered a laboratory test of to find out if genetically modified brinjal is fit for preparation of ayurvedic medicines, with a senior official saying its report in next two months could pave the way for commercial release of Bt brinjal.“Genetic Engineering Approval Committee (GEAC) under Ministry of Environment and Forest has ordered for lab test to assess compositional analysis to find out if ayurvedic principles are disturbed in Bt brinjal,”, the official said.P. Anand Kumar, Principal Scientist, National Research Centre on Plant Biotechnology (NRCPB) under Ministry of Agriculture told reporters here that the test is being conducted in National Institute of Nutrition (NIN), Hyderabad.
NIN is India’s premier nutrition research institute working under the aegis of Indian Council of Medical Research (ICMR), Ministry of Health and Family Welfare.The lab test report which is expected in next two months would pave the way for commercial release of Bt brinjal, he said.The NRCPB scientist said the test was ordered to clear apprehensions in a section on whether Bt variety of brinjal would have the same efficacy for preparing ayurvedic medicines as the non-GM.India had put on hold commercial cultivation of genetically modified brinjal in February 2010 in the backdrop of intense opposition from NGOs and several States.Mr. Kumar said there was no differences about scientific efficacy of GM crops among the Ministry of Agriculture, Ministry of Science and Technology, ICAR and other governmental institutions…

Fortunately these issues are thoroughly examined in a recent book by Dr Kam Rao about the mooted medicinal qualities of brinjal that are allegedly threatened by biotech version of the crop. The executive summary of this book is provided below, as is a free-access link to the full book in pdf format. 


The bottom line message of this book: brunjal is not a medicinal plant. Solanum medicines come from other Solanum species. 

USE OF BRINJAL (SOLANUM MELONGENA L.) IN ALTERNATIVE SYSTEMS OF MEDICINE IN INDIA (click link to download full book as a pdf file)

C Kameswara Rao
August 1, 2011

EXECUTIVE SUMMARY
The activists opposing the commercialization of Bt brinjal have asserted that Bt brinjal would seriously affect the use of brinjal in the Alternative and Complementary Systems of Medicine (ACSM) in India, through ‘loss of synergy’. The then Minister for Environment and Forests (MoEF), Government of India (GoI), repeatedly echoed this view. While there was no appropriate and substantial documentation to justify this highly sensationalized claim in the MoEF’s Bt brinjal moratorium document (MD) of February 9, 2010 or elsewhere, the much repeated high decibel noise has clouded public mind and it became necessary to clarify on the issue in detail.

This article analyzes the issues raised and provides a detailed survey of authentic literature on the use of brinjal (Solanum melongena) and other species of Solanum in the ACSM in India, in particular Ayurveda, Siddha, Unani and Homoeopathy.


The issues addressed are 
a) Alternative and Complementary Systems of Medicine, 
b) Problems in establishing the identity of Indian medicinal plants,
c) Patterns of distribution of therapeutically active chemical compounds in plants,
d) Establishing identity of medicinal plant species cited in classical literature,
e) Reliability of sources of information on medicinal plants,
f ) Botanical and vernacular nomenclature of brinjal and relevant species of Solanum,
g) Dr G Sivaraman’s letter to the MoEF, and his reference to the CSIR publication Wealth of India, and Nair and Vasudevan’s book,
h) Use of species of Solanum in Ayurveda, Siddha, Unani and Homoeopathy,
i) Other issues raised by Dr Sivaraman (synergy, use of raw brinjal in medicine and safety of cooked Bt brinjal),
j) a concluding statement, 
k) 36 references, and
j) an Appendix containing the list of species of Solanum occurring in India. 


Amonga host of literature sources consulted, the more important ones are 
a) the Ayurvedic formulary of India, 
b) the Ayurvedic Pharmacopoeia of India, 
c) Siddha Materia Medica, 
d) Formulary of Siddha Medicines and 
e) an extensive compilation, the Database of Medicinal plants.


There is a lot of confusion in the botanical identity and nomenclature of several species of Solanum occurring in India. Several names of brinjal in Samskrith, Tamil, Arabic, Persian and Urdu are also applied to other species of Solanum in the classical literature on Ayurveda, Siddha, and Unani, which is the main reason for erroneously considering some other species of Solanum as equivalent to brinjal (Solanum melongena) and attributing the medicinal uses of the former to the latter. While there can be honest errors of judgement, this state of confusion is being used deliberately, to oppose commercialization of Bt brinjal.


The bottom line is that while such wild species as Solanum indicum, Solanum nigrum, Solanum surattense and Solanum xanthocarpum are used in different ACSM both as single drugs and in formulations, Solanum melongena is not a significant drug and is not an ingredient in any formulation, in any of the ACSM. While every system indicated certain negative effects of brinjal including its allergenic potential, the Siddha system actually prohibits its consumption in certain disease conditions. The claim that brinjal is an important medicine in treating respiratory diseases has no basis in literature. The other claim that brinjal reduces cholesterol was clinically disproved in Brazil. The assertion that the transgenic Bt gene affects synergy in medicine using brinjal is inaccurate and irrelevant when brinjal is not used in medicine. The stray mention of some insignificant uses vii of brinjal as medicine was probably based on the properties of brinjal available centuries ago when the texts of classical medicine were compiled. These minor uses are no longer relevant as the present day cultivated brinjal (there is no wild brinjal) has undergone extensive genetic modification in conventional breeding during domestication through selection of more palatable and safer varieties, which means minimal active principles. In effect, Bt brinjal does not pose any threat to the use of non-Bt brinjal in medicine, as the scope for gene flow from Bt brinjal to non-Bt brinjal is almost non-existent.


USE OF BRINJAL IN ALTERNATIVE SYSTEMS OF MEDICINE IN INDIA
C KAMESWARA RAO
FOUNDATION FOR BIOTECHNOLOGY AWARENESS AND EDUCATION
BANGALORE 560004
August 2011
Issued in Public Interest
(Solanum melongena L.)
All Rights Reserved
© Foundation for Biotechnology Awareness and
Education, No. 1, Gupta’s Layout, Southend Road,
Bangalore 560005, India


Citation: Kameswara Rao, C. 2011. Use of brinjal (Solanum melongena L.) in alternative systems of
medicine in India. FBAE, Bangalore.
Phone: 919845145777; E-mail: pbtkrao@gmail.com

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

Genome and plasmid comparisons of Enteroaggregative E. coli strains, Rasko  and others NEJM 2011, illustrated by comparisons of the main chromosome, and two plasmids, one encoding antibiotic resistance, including extended spectrum beta-lactamase, the other (pAA) encoding enteroaggregative virulence traits.

An amazing amount of genetic analysis has been rapidly published about the huge recent outbreak of foodborne illness in Germany caused by a pathogenic E. coli. Much of this has been discussed in previous posts at this blog (accessible using the tag EHEC EAEC STEC).

Adding to this, yet another paper decoding the genomes of germs isolated from this outbreak has just been published in New England Journal of Medicine. The full content of this publication is freely available at the New England Journal of Medicine website. The main conclusions of this paper are as follows:

Our findings suggest that horizontal genetic exchange allowed for the emergence of the highly virulent Shiga-toxin–producing enteroaggregative E. coli O104:H4 strain that caused the German outbreak. More broadly, these findings highlight the way in which the plasticity of bacterial genomes facilitates the emergence of new pathogens.

But there is a swag of discoveries in this paper that are medically important and which give rich insights into the way in which gene movement between different types of bacteria is responsible for the emergence of new pathogens. They are really worthy of some further explanation (as given below), particularly since this kind of natural evolution of pathogens is so readily and wrongly interpreted by crank-science conspiracy theorists as the deliberate laboratory creation of some evil drug company.

This new paper in presenting findings with numerous different natural strains of  pathogenic E. coli provides no hint at all of laboratory interference with natural evolution of germs. The German outbreak strain is in fact incredibly similar to a whole family of other germs that have been isolated in widely different locations around the planet over the last several years.

EHEC or EAggEC?

The most distressing feature of the recent huge European outbreak of foodborne E. coli disease is the severe kidney damage occurring with many of the victims of infection. Features of severe kidney disease seen among the patients are given the medical term haemolytic uraemic syndrome (abbreviated to HUS). Another type of symptom seen in this foodborne disease epidemic is the occurrence of bloody diarrhoea. E. coli bacteria that cause these patterns of disease in the past have been called enterohaemorrhagic E. coli or EHEC.

Unusually for EHEC infections, the recent German HUS outbreak strain exhibited a distinctive pattern of bacterial cell attachment to the lining of the human gut that that had been previously noted in in another type of disease-causing E. coli  found with distressing frequency in developing countries in cases of diarrhoea among children. This type of E. coli are referred to as enteroaggregative E. coli (EAggEC also called EAEC)

 Most often in the past, such EAggEC have been distinct from EHEC in not being able to produce a potent toxin called Shiga toxin that is a major cause of the severe kidney damage in patients infected with EHEC. But a very unusual feature of the 2011 German outbreak strains is that they are also able to produce Shiga toxin, so the question comes up: are they modified forms of EHEC who have gained ability to produce the aggregate of pattern of attachment to human gut linings, or are they modified forms of aggregative E. coli that have gained ability to produce Shiga toxin?

German Shiga toxin producing enteroaggregative E. coli is not EHEC.

The investigation reported in this issue of the New England Journal of Medicine provides a clear cut answer to this question. It is able to provide answers because it examines the genetic make up of a wide collection of enteroaggregative E. coli and comprehensively compares their genetic content to the genetic code of the German outbreak strain.

This family comparison reveals that the major part of the genetic composition of the outbreak E. coli strain is very similar to a variety of other enteroaggregative E. coli and quite dissimilar the common pathogenic EHEC type E. coli .

This confirms yet again the strains are probably best called Shiga toxin producing EAggEC, and that it is misleading to call them EHEC.

Further analysis of the detailed argument presented in this report confirms that the German outbreak strain arose relatively recently from other enteroaggregative E. coli by addition of a block of genes that is part of a welland characterised an familarbacterial virus (repeatedly seen in nature) that has become inserted at a particular place in the main E. coli chromosome. This newly inherited bacterial virus — or prophage as it called — contains a gene that encodes ability to produce Shiga toxin. The authors say ” outbreak strain is not a prototypical enterohemorrhagic E. coli strain that has acquired the virulence features of enteroaggregative E. coli.”

The report also reveals that the Shiga toxin output from the German outbreak strain can be greatly increased by exposure of the germ to certain antibiotics, a finding that has also been seen with EHEC type bacteria. This underlines the common advice that antibiotic treatment can worsen the prognosis for patients suffering this particular type of infection.

The outbreak strain carries three SPATEs.


This report introduces one other possible explanation for the apparent extreme virulence of the German outbreak strain. It comments that there are three copies of particular virulence related genes that encode for a secreted toxin system that goes under the acronym SPATE. This is an unusually large number of SPATE toxin genes for enteroaggregative E. coli. It seems possible that part of the virulence capabilities that the outbreak strain has acquired is an increased range of SPATE toxins, adding to the damage that could be caused by Shiga toxin.

The bottom line is the German outbreak was caused by a horizontal gene movement of extra virulence genes into a enteroaggregative E. coli and this gene movement added to the virulence capabilities of the strain leading to the relatively recent emergence of a new form of HUS disease. The mechanisms by which this evolution occurred were very similar to genetic changes frequently seen in other strains of E. coli, and such horizontal gene movement in bacteria is wholly unsurprising from a biological point of view, despite the fact that the emergence of new forms of disease caused by new germs is a dreadful shock to the health system and the food supply.

Comment on:
Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

David A. Rasko, Ph.D., Dale R. Webster, Ph.D., Jason W. Sahl, Ph.D., Ali Bashir, Ph.D., Nadia Boisen, Ph.D., Flemming Scheutz, Ph.D., Ellen E. Paxinos, Ph.D., Robert Sebra, Ph.D., Chen-Shan Chin, Ph.D., Dimitris Iliopoulos, Ph.D., Aaron Klammer, Ph.D., Paul Peluso, Ph.D., Lawrence Lee, Ph.D., Andrey O. Kislyuk, Ph.D., James Bullard, Ph.D., Andrew Kasarskis, Ph.D., Susanna Wang, B.S., John Eid, Ph.D., David Rank, Ph.D., Julia C. Redman, Ph.D., Susan R. Steyert, Ph.D., Jakob Frimodt-Møller, M.Sc.Eng., Carsten Struve, Ph.D., Andreas M. Petersen, Ph.D., Karen A. Krogfelt, Ph.D., James P. Nataro, M.D., Ph.D., M.B.A., Eric E. Schadt, Ph.D., and Matthew K. Waldor, M.D., Ph.D.
July 27, 2011 (10.1056/NEJMoa1106920)

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

A wonderful colorful and readable booklet about the success of Bt cotton in India has been made available from the ISAAA website for India.
A sample table from this booklet tells the story of the massive expansion of cotton output over the last 10 years.

Indian cotton production statistics this last decade

“Amidst the oilseed crisis, cotton is the only oilseeds crop that has shown a remarkable progress after the introduction of Bt cotton hybrids in 2002. In the last nine years, cottonseed has become an important source of oilseeds in the country. The production of cotton oil registered a three-fold increase from 0.46 million tons in 2002-03 to 1.20 million tons in 2010-11 (Table 3). “

Summary.
In this decade, 2002 to 2011, Bt cotton has been successfully used as a multiple purpose crop in three ways: in the form of edible oil as food for human consumption; de-oiled cake as an animal feed; and kapas for fiber. The production of cotton seed, and its byproducts as oil and meal, has increased manifold from 0.46 million tons in 2002-03 to 1.20 million tons in 2010-11. As a result, Bt cotton meal (de-oiled cake) contributes one third of the country’s total demand for animal feed, whereas cotton oil contributes 13.7% of total edible oil production for human consumption in the country – a significant contribution which offsets more than half of the import bill for edible oil valued at US$6.5 billion annually. Increased production of Bt cotton oil could be one of the important strategies to substitute for edible oil imports which constitute more than 50% of the total edible oil consumption in the country. In 2009-10 India, for the first time ever, imported more edible oil, 8.80 million tons, than the 7.88 million tons it produced domestically. Due to the high nutritional content of cotton oil, Bt cotton oil is marketed after blending it with different edible oils. India is becoming increasingly dependent on expensive imports of vegetable oil, which is a valid strategic concern, and biotech Bt cotton and its second generation of stacked products, as a multipurpose crop for oil, fiber and feed, can play a critical role in Indian agriculture in the near, mid and long term future (James, 2010).

It is noteworthy that the by-products of Bt cotton, have been safely consumed as food and feed in India for nine years, without incident. Given this unblemished record, which is consistent with experience of more than 10 other countries world-wide, now maybe is the time for India to benefit from the application of the well-tested Bt technology in other crops.

Citation: Choudhary, B. and Gaur, K. (2011). Bt cotton in India: A multipurpose crop, ISAAA Biotech Information Centre, ISAAA, New Delhi, India

Update:

10 Years of Bt in India: Biotech Seeds Save Indian Market  
By K.R. Kranthi May 1, 2011 Cotton 24-7
Part II: 10 Years of Bt in India
By K.R. Kranthi May 1, 2011 Cotton 24-7

Other relevant posts at GMO Pundit (see also the “Cotton” and “India” tags)

Fluffy revolution
Financial Chronicle, India Sep 23 2009

For several years before the introduction of the new variety, cotton exports from India fluctuated between few thousands bales and one lakh bales. Within three years, exports moved to 5.8 million bales, peaking at 8.5 million in 2007-08 and earning foreign exchange worth Rs 8,366 crore. Compared with the other two top producers of cotton in the world, India’s performance is even more impressive. In 2002, the United States produced 17.2 million bales and China 25.2 million bales, according to figures published by the US department of agriculture. The spurt in India’s cotton production took it to 29 million bales in 2008-09, while the US declined to 13.52 million bales, having peaked at 23.89 in 2005-06. China produced 36. 5 million. From producing around 40 per cent of what China did, India has now touched a level of almost 70 per cent. Against the US, India’s output was 61 per cent

Roundup of Indian cotton statistics

International Food Policy Research Institute study on the possible connection between Bt cotton and farmer suicides in India
We first show that there is no evidence in available data of a “resurgence” of farmer suicides in India in the last five years. Second, we find that Bt cotton technology has been very effective overall in India. However, the context in which Bt cotton was introduced has generated disappointing results in some particular districts and seasons. Third, our analysis clearly shows that Bt cotton is neither a necessary nor a sufficient condition for the occurrence of farmer suicides. In contrast, many other factors have likely played a prominent role.

Related posts about Indian cotton:

Cotton farmer suicide linked to export controls?

Millions of poisonings avoided

Reduction in market share

The early years of the fluffy revolution

Doubly insect protected cotton expands in India.

The push from Indian Bt cotton

Maintaining the status quo not good enough for human development

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

Greenpeace's own photo of their criminal activity in destroying the wheat trial in ACT, Australia

Greenpeace recently enlisted Vandana Shiva to protest on their behalf about GM wheat trials underway in Australia. Vandana Shiva endorses criminal arson as direct action against scientific laboratories she disproves (explicit video interview).

Now Greenpeace — by their own self-acknowledged vandalism — are following Vandana Shiva (Sydney Peace [sic] Prize recipient)  into the cesspool of criminality.

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Greenpeace destroys GM wheat
Jessica Nairn, ABC Radio 666 Canberra
Updated July 14, 2011 11:08:36

Greenpeace protesters have broken into a CSIRO experimental farm in Canberra to destroy a crop of genetically modified wheat.

In the early hours of this morning a group of Greenpeace protesters scaled the fence of the CSIRO experimental station at Ginninderra in the capital’s north.

Greenpeace says activists were wearing Hazmat protective clothing and were equipped with weed string trimmers.

They say the entire crop of genetically modified wheat has been destroyed.

About half a hectare of GM wheat is being grown on the site, as part of Australia’s first outdoor trials.

No genetically modified wheat strain had ever been approved for cropping in Australia before.
Last month the CSIRO received permission to conduct Australia’s first trial in which humans will eat GM wheat.

The wheat’s genes have been modified to lower the glycemic index and increase fibre to create a product which will improve bowel health and increase nutritional value.

Animal feeding trials of up to three months have been conducted, with human trials at least six months away.

Greenpeace says it has taken action because of concerns over health, cross-contamination and the secrecy surrounding the experiments.

Campaigner Laura Kelly says the Federal Government needs to put an end to testing GM wheat in Australia.

She says parts of the United States and many countries throughout Europe have already rejected the crop, and Australia should do the same.

“No one is looking after the health of Australians. Julia Gillard isn’t standing up to foreign GM countries to protect our daily bread so Greenpeace has to,” she said.

ACT Greens MLA Shane Rattenbury used to work for Greenpeace and says he is not surprised the group has taken such action.

“It’s always very controversial these sorts of actions, but you have to stand up for what you believe in sometimes,” he said.

“Greenpeace has clearly formed a view that the best way to both draw attention to this issue and to potentially protect the human food chain in Australia is to take this action.”

Mr Rattenbury says Greenpeace has a track record of breaking the law to highlight problems.
“I’ve certainly been involved in action in the past where Greenpeace has broken the law and that has been necessary to highlight what we’ve considered at the time to be a greater issue than perhaps a simple trespass,” he said.

ACT police have confirmed they are investigating but have not released any further information.

GM crop destroyed
BY STAFF REPORTERS (Canberra Times)
14 Jul, 2011 09:08 AM

…ABC radio reported that the four protesters scaled the fence at the secure facility in Ginninderra wearing full-body Hazmat protective clothing.

Greenpeace have confirmed at least two women scaled the fence, including one mother, Heather McCabe*, who is concerned about her family’s health.

“This GM wheat should never have left the lab,” said Ms McCabe.

“I’m sick of being treated like a dumb Mum* who doesn’t understand the science. As far as I’m concerned, my family’s health is too important. GM wheat is not safe, and if the Government can’t protect the safety of my family, then I will.”

Canberra Greens MLA Shane Rattenbury [Pundit note:former Greenpeacer staffer] this morning condoned the action on ABC Radio, citing Greenpeace’s long-held opposition to GM crops, and saying that sometimes the end justified the means.

The site was being used to grow some of the first outdoor GM wheat crops in Australia, and trials were due to begin on human consumption of the modified wheat.

“We had no choice but to take action to bring an end to this experiment,” said Greenpeace Food campaigner Laura Kelly in a release this morning.

“This is about the protection of our health, the protection of our environment and the protection of our daily bread.

“It is time Julia Gillard stood up to global biotech companies and protected Australia’s daily bread. With public health and our largest food export under threat, this is too big an issue for the Prime Minister to continue to ignore.”

Police are investigating the incident.

Updates:

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Fish by avlxyz via Flickr.

There has been a long and tortuous discussion of Steve Savage’s post  Way Too Much Angst about GMO crops covering many of the usual topics. But among the hundreds of comments there is at last some gold. Fishy smelling gold.

A new paper has been kindly unearthed in the comments by (a commenter): Genetically modified plants as fish feed ingredients by Nini Hedberg Sissener, Monica Sanden, Åshild Krogdahl, Anne-Marie Bakke, Lene Elisabeth Johannessen, and Gro-Ingunn Hemre (2011).

Abstract:

Genetically modified (GM) plants were first grown commercially more than 20 years ago, but their use is still controversial in some parts of the world. Many GM plant varieties are produced in large quantities globally and are approved for use in fish feeds both in Norway and the European Union. European consumers, however, are skeptical to fish produced by means of GM feed ingredients. Concerns have been raised regarding the safety of GM plants, including potential toxicity and (or) allergenicity of the novel protein, potential unintended effects, and risk of horizontal gene transfer to other species. This review will present the current state of knowledge regarding GM plants as fish feed ingredients, focusing on fish performance and health as well as the fate of the GM DNA fragments in the fish, identifying limitations of the current work and areas where further research is needed.

Allan’s comment:

First, I thank (a commenter) for turning us on to a new paper. I’ve downloaded the paper and additionally downloaded many of the references in the paper so that I can check out what the referenced authors are actually saying.

Second, I’m detecting a creeping confusion between hazard, risk, and just plain old homeostatic physiological phenomena that are neither adverse effects, hazards, or risks. Specifically, (a commenter) cites Bodner as saying, ““There is no indication that Bt protein (in transgenic plants or in sprays) is harmful to mammals, birds, or fish…”. He indirectly refutes this generality by referring to the review article by Sissener et al. (2011) and then to Sissener’s summary of some of the papers that she reviewed. The quotes in Sissener’s article does not refute Bodner’s statement. The evidence for this can be drawn directly by examining the referenced author’s own words. For example, the longest section in Sissener et al. (2011) that was quoted by (a commenter) refers to a paper by Sagstad et al. (2007). wherein immune system parameters among others was found to differ in a comparison of reference diet-fed fish, GM corn diet-fed fish, and non GM corn-diet fed fish. However, the question is health effects, which is not addressed by examining immune system biomarkers (I’ll come back to what Sagstad et al. (2007) really showed). A better paper, on which Sagstad is an author, is the one by Hemre et al. 2007 in Aquatic Nutrition, in which they conclude the following (from the abstract) : “Based on the present findings, the conclusions made are: Atlantic salmon smolts fed GM maize (event MON810 ), its near-isogenic parental line and suprex maize (Reference diet), all resulted in high growth rates, ADC and feed utilization. Health, when evaluated by means of mortality (low), normal ranges of blood and plasma parameters, except somewhat elevated ASAT values and minor variations in organ sizes, were considered good in all diet groups. The changes in the glucose transport mechanism and intestinal maltase enzyme activity in the gastrointestinal tract warrant further studies.” If the last statement is worrisome, then consider what the conclusion is based on. Whereas the vast majority of comparisons for the measured parameters were made between three treatment groups: a reference diet control, non GM corn, and GM corn, the latter statement is based on an in vitro study of isolated brush border membrane cells but DID NOT INCLUDE the reference diet fish. This is important, because sometimes there might be a difference between non-GM and GM fed group parameters, but the parameters do not differ significantly between the GM and reference diet group.

Now back to the Sagstad et al. 2007 article and those immune system biomarker results for my third point. Here is where you have to actually look at Table 4 to find out the following. First, the data are expressed as the percentage proportion of several different innate immune system cells in the sampled population of white blood cell populations from the reference diet, non-GM corn, and GM corn diet groups. While it is true that some significant differences in proportions of cells amounting to several percent were found when non-GM corn and GM corn were compared, there were no statistical differences between the reference diet and the GM diet fish. So, what does it mean? I argue it does not mean anything other than observation about homeostatic mechanisms owing to differences in environment. What do I mean by differences in environment? Well, you take 45 fish and isolate them from another group of 45 fish and you’ve automatically changed their environment. Don’t think that fish have personalities and quickly establish dominance hierarchies? I suggest you haven’t observed animals enough. (BTW, I can find no indication of fish sexing prior to group establishment. Lack of sexing could be a confounder, maybe.) The bottom line is that WE EXPECT minor differences in biomarkers between groups, whatever the exposure treatment, because by isolating animals we have changed their environment. The fact that SMALL differences in immune cell proportions were reported by Sagstad, with no statistical difference from a reference diet (that contained an equivalent amount of corn starch as the other diets) tells me there is no consistent physiological effect related directly to treatment. Certainly, these data mean NOTHING regarding health. The important conclusion about health is in the Hemre et al. (2007) paper referenced above.

As an aside, lest you think that Monsanto is hiding something and the regulators don’t know about these studies, consider that Monsanto is credited with providing these researchers with MON 810 corn and its isogenic non GM line. Thus, you can bet that Monsanto had the data and furthermore, as required under FIFRA, had to report those results to the EPA. After all, MON 810 is a registered pesticide (the technical term is a PIP, plant incorporated pesticide). Monsanto was not involved in the GM soya feeding studies because those papers did not use an isogenic line. Differences in cultivars will lead to differences in biomarkers, but even then, the researchers did not see any effects on health, broadly defined for their purposes as effects on growth parameters and mortality (lest you get picky, I’m skipping a lot of details here).

Fourth, the weight of the evidence based on examining more fish GM vs. non GM diet papers shows that the small cadre of authors involved in these studies have more often than not concluded no effects of putting large proportions of plant protein in fish food. And this brings me to the conceptualization of risk in this case. The objective of the research reported in these papers is basically two-fold. First, can you substitute a lot of plant protein for fish meal when rearing fish in aquacultural operations? Second, if the fish health is not affected (remember for this case health = growth parameters, mortality, and proximate nutrient content), will having 15-30% of the plant protein content come from GM soy or corn, affect health? Regulatory toxicology relies on the weight of the evidence, and of the perhaps 20 papers I quickly downloaded following (a commenter’s) remarks, I see no concern expressed by these authors about health. Where specific biomarker parameters were different, the authors call for more study, but what bona fide scientist doesn’t call for more study?

Finally, this forum is a lot more fun when people actually discuss the data and don’t react as if personally threatened by every new bit of information.

Note by Anastasia: (a commenter) was used to replace that commenter’s name. Please visit the comment policy forum if you have any questions about comment use. Thanks!

This post was syndicated from GMO Pundit. You may comment here or on the original entry.