Agricultural biotechnology (GM food) (French, Italian, Spanish)
Gene therapy and stem cells: How are they related?
Gene therapy in China (Chinese)
Miscellaneous (other books, web sites, comments)
Posts in my Musings newsletter. Also see next section.
+ New 5/16/16, 7/15/16, 12/9/16, 2/27/17
Recent items, briefly noted. Also see previous section.
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Why are GM foods and gene therapy shown as one topic? Because they are fundamentally the same. Both involve the intentional and directed modification of an organism's genome.
In general, one might carry out such a modification either by changing a gene within the organism, or by delivering a new gene to the organism. In the latter case, the new gene may either replace an original version of the gene that was within the organism, or may add into the genome.
Most work on genetic modification of higher organisms is currently done by adding a gene, rather than changing or replacing.
Why do these genetic modifications? One major use is in research. Such genetic modifications have long been used to help us understand gene function in microbes. The techniques were then extended to study gene function in some higher organisms. Now we are in the era of practical genetic modifications -- where the intent is to create a modified organism. One class of such modifications is to make crop plants with "improved" properties (such as resistance to a pest). Another class is to repair a defect in an organism -- to treat a disease. The use of gene therapy to treat a disease in humans, such as SCID (severe combined immune deficiency), is an example.
A "knockout mouse".
In all seriousness, knockout mice are important research tools. Techniques have been developed that allow one to change a particular gene in the mouse genome. One type of change that is often made is simply to inactivate (knock out) the gene. Mice are then grown without this gene product. This is one useful tool for figuring out what the function of a gene is. Unfortunately, the techniques for doing this have not been widely adapted for other organisms.
(Figure source lost. Anyone have any information?)
|For a general description of how to make knockout mice, see http://www.bio.davidson.edu/courses/genomics/method/homolrecomb.html. Caution... it is rather complex! (This is from Malcolm Campbell's site, which is listed as a general BITN resource for molecular biology methods, under Web sites.)|
|The 2007 Nobel prize in Medicine or Physiology was awarded to Mario R Capecchi, Martin J Evans and Oliver Smithies "for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells" -- that is, for their pioneering work in developing the knockout mouse and related procedures. Nobel site: http://www.nobelprize.org/nobel_prizes/medicine/laureates/2007/index.html.|
One other distinction among types of genetic modification is important. Some modifications are hereditary, and will be passed on to the offspring of the individual that was treated. Some are not hereditary, and will affect only the treated individual. The former is called "germ line" treatment, and the latter "somatic" (body) treatment. All work with human gene therapy is somatic at this time. (The use of knockout mice, above, leads to germ line treatment.)
What is controversial? The heart of the controversy is evaluation of what the benefits and risks are of making such modifications. For example, I suggested above that a pest-resistant plant would be an "improvement". That statement is subject to debate about how much or how useful an improvement it is, and we need to consider what the risks are. In the field of human gene therapy, a current clinical trial involving treating SCID seemed to be showing benefit to the patients. Then it was found that two of the patients have developed leukemia, quite possibly a side effect of the gene therapy.
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This topic was discussed in the BITN class, Fall 2003. This overview section summarizes the class presentation. The original web materials were designed as a supplement to that class presentation.
Genetic modification. We will discuss some general background, on mutations and recombination. This will lead to work on genetically modified plants and animals -- and gene therapy for humans.
We began to talk about gene modification. We started with the natural processes of mutation and recombination. The former creates new genetic information and the latter rearranges existing information. A generic procedure for gene modification involves getting (finding or making) a new gene, getting it into the desired cell, and getting it to function. All of these steps have many variations, depending both on the specific goal and the organism being modified. I showed examples involving bacteria, tobacco and mice. I showed slides which are equivalent to Figures 7-4, 8-36, and 8-38 from Lodish et al, Molecular Cell Biology (4th edition, 2000). A link to a very nice animation of part of the recombination process is below under New Links.
The 4th edition of the Lodish book is available online at the PubMed Bookshelf: https://www.ncbi.nlm.nih.gov/sites/entrez?db=Books. The Figures I mention above are available there. Also relevant is: Fig 8-34 (General procedure for producing gene-targeted knockout mice). For more about this site, which includes a number of free books, see my Internet - Misc; Books section. (If you are already at the PubMed site, choose Books.)
We discussed the gene therapy trial for X-SCID in some detail. We briefly discussed the nature of the disease, and then the general approach of the gene therapy treatment. The basic result is a very high level of treatment success: most of the treated patients have developed immune systems that seem good, and are now living substantially normally. However, two of the patients developed leukemia. The leukemia itself was treatable, so the benefit seems to outweigh the side effect in this case. The leukemia is now understood to be due to how the gene therapy vector integrated. How to avoid this side effect is a subject of active work. An important question, which can be answered only over time, is whether more patients will develop the leukemia side effect. Despite the side effect, this is the best success for gene therapy so far, after two decades or so of work. Two articles in The Scientist on this gene therapy trial are listed for the topic.
We then discussed some issues of GMO crops. I emphasize that formulating questions is the critical step here; good questions can -- ultimately -- be answered. The big problem is with "uneasy feelings" that are not formulated as answerable questions. I also emphasize that you do not need to accept my "biases" (predicted likely answers) for things that have not yet been tested.
Article mentioned in class, about trying to predict which crop modifications are more or less likely to be environmental problems: J F Hancock, A framework for assessing the risk of transgenic crops. BioScience 53:512; 5/03. In reading this, I think it is more important at this point to follow his general plan, rather than to agree with him on specifics.
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Transgenic crops: An Introduction and resource guide. A wide range of basic information, including many individual projects. For example, there is a section on "golden rice" -- rice with a high content of vitamin A. http://cls.casa.colostate.edu/TransgenicCrops/index.html. Also in Spanish. (This site is not being updated, since December 2004. Nevertheless, it is a fine archive of useful material.)
Maize & Biodiversity - The effects of transgenic maize in Mexico. http://www.cec.org/our-work/independent-reports/maize-and-biodiversity. From the Commission for Environmental Cooperation (CEC) for North America. Also in French & Spanish, reflecting the tri-national nature of the Commission. The CEC site (see "Home page" link at top) includes many issues.
At the heart of this story is a UC Berkeley professor, Dr Ignacio Chapela, of the Department of Environmental Science, Policy and Management. His web site is http://nature.berkeley.edu/chapelalab/. The site includes copies of some key papers and some press releases. It also includes a broader perspective on Chapela's research interests and activities.
European views. There is major resistance to GM foods in Europe, and especially in Britain. It is interesting to watch their attempts to rationally analyze the issue, and to see what impact their work has both on the general public, and ultimately on the regulatory systems.
Farm scale evaluations. Several reports of experimental work on ecological impacts of GM crops, including gene flow, are available from the UK Department for Environment, Food and Rural Affairs (DEFRA). http://webarchive.nationalarchives.gov.uk/20130402151656/http://archive.defra.gov.uk/environment/quality/gm/crops/fse.htm. The reports are mainly from 2002-2005, plus some background materials. These are archived materials.
Public Perceptions of Agricultural Biotechnologies in Europe. European Commission, May 2002. http://csec.lancs.ac.uk/archive/pabe/index.htm. Some documents here are also available in French, Italian.
Africa. R J Blaustein, The green revolution arrives in Africa. BioScience 58:8, 1/08. Article is free online: http://www.bioone.org/doi/abs/10.1641/B580103.
Nature has a web focus site on GM crops. http://www.nature.com/nature/focus/gm/index.html. (October 2003)
The Pew Initiative on Food and Biotechnology, http://www.pewtrusts.org/en/archived-projects/agricultural-biotechnology.Topics include:
* "Issues in Science and Regulation of Transgenic Fish" (January 2003). Transgenic salmon (salmon with modified growth hormone, intended for faster farming production).
* "A Snapshot of Federal Research on Food Allergy: Implications for Genetically Modified Food" (June 2002). Allergens in plants; note that this issue is not restricted to GMOs, but is a general concern.
* "Harvest on the Horizon: Future Uses of Agricultural Biotechnology" (September 2001).
* Monarch butterflies.
* Labeling of GM foods.
The Safety of Genetically Modified Foods Produced Through Biotechnology. A "Position Paper" from the (US) Society of Toxicology. Published in Toxicological Sciences 71:2, 2003. Freely available at: https://academic.oup.com/toxsci/article/71/1/2/1639537/The-Safety-of-Genetically-Modified-Foods-Produced. The tone of the report is generally favorable, but of course there is much meat in it, on issues such as methodology and philosophy of how novel products should be evaluated.
Approved GM plants:
* GM Approval Database. A database of GM plants approved in various countries. Indexed by plant, trait and developer as well as country. It is clearly intended to be comprehensive. From the ISAAA (International Service for the Acquisition of Agri-Biotech Applications). http://www.isaaa.org/gmapprovaldatabase/.
* GM Crop Database, including information on their regulatory status in two dozen countries. Includes a bibliographic database. http://www.cera-gmc.org/GMCropDatabase, From the Center for Environmental Risk Assessment (CERA).
Plantstress. A web site on stresses that affect plants, including the use of genetic modification to produce stress-resistant crops: http://www.plantstress.com
Biological Confinement of Genetically Engineered Organisms, a report from the National Academy of Science, 2004. https://www.nap.edu/catalog/10880/biological-confinement-of-genetically-engineered-organisms. One concern with GMO is the spread of engineered genes to the non-engineered relatives in the field. Thus considerable effort is being expended to explore methods to prevent such gene transfer. A simple example is to make the GMO plant sterile, so that it can not cross with its relatives.
The books listed below are also listed on my page Books: Suggestions for general reading.
Book: Pamela G Ronald & Raoul W Adamchak, Tomorrow's Table - Organic farming, genetics, and the future of food. Oxford, 2008. ISBN 978-0-19-530175-5. A little book on the role of genetic engineering -- "GM" (genetic modification) as it is often called -- in organic farming. It is written by a plant geneticist who does GM and an organic farmer -- who are wife/husband. The organic farming movement has typically objected to GM, but the authors here suggest they should be more open to considering it. They suggest that GM is a good tool to achieve the underlying objectives of organic farming. This is a short and sometimes rambling book. It does not really answer questions, but its purpose is more to raise questions, to get people to look anew at the issues of what GM is and what its role might be. Importantly, it emphasizes that each individual use of GM should be considered on its own merit. I certainly encourage those who might be skeptical of GM to try this book -- not to change your mind, but simply as an opener to further discussion.
Book: Nina V Fedoroff & Nancy Marie Brown, Mendel in the Kitchen - A scientist's view of genetically modified foods. Joseph Henry (National Academies Press), 2004. The book can be purchased online, pdf file or print: https://www.nap.edu/catalog/11000/mendel-in-the-kitchen-a-scientists-view-of-genetically-modified; the page also has more information about the book. Fedoroff is a scientist who has worked on GM (biotechnology) foods, so brings some authority and knowledge -- and of course bias -- to the table. One strength of the book is the extensive discussion of conventional plant breeding, including its risks. This is interesting history, and also serves to put modern GM technologies in proper historical perspective. Another strength is that Fedoroff takes the time to analyze several particular cases in some detail, including good analyses of arguments made against specific developments. (Occasionally, I think she spends too much time on some topics -- a minor problem.) A must read if you want to understand the development of GM plants. In controversial areas, no one book can be trusted to provide a complete view, but this one should be one important part of understanding the GM story.
Book: D. Charles, Lords of the harvest - Biotech, big money, and the future of food. Perseus, 2001. ISBN 0-7382-0291-6. (Paperback: ISBN 0-7382-0773-X.) A journalist tells the story of "GMOs" -- the application of biotechnology to agriculture. The book is intended for the general audience, and avoids scientific detail while presenting all the basic logic. The book is widely regarded as being a fair presentation of a range of views on the subject. I enjoyed reading it.
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NIH Genetic Modification Clinical Research Information System (GeMCRIS). This site, from the US National Institutes of Health and cooperating agencies, is a gene therapy database. It gives information on US gene therapy trials. It includes reports of adverse events. http://osp.od.nih.gov/office-biotechnology-activities/biomedical-technology-assessment/hgt/gemcris.
Gene therapy for SCID and other immune disorders. One major story of recent years was the development of a gene therapy treatment that cured (?) several young boys of X-SCID (severe combined immunodeficiency, due to a mutation on the X-chromosome). Some of the boys also developed leukemia (and one died); scientists have come to understand that this was due to certain specifics of the treatment. Good review of this and other developments during the first decade of the century: A Aiuti & M G Roncarolo, Ten years of gene therapy for primary immune deficiencies. Hematology 2009:682, 2009. http://asheducationbook.hematologylibrary.org/content/2009/1/682.abstract.
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The short answer is that they are distinct techniques, but they can be combined. Gene therapy involves changing the genetic information in a cell. Stem cells are cells that can divide and differentiate into the desired cell type. It is possible to do gene therapy on stem cells. One approach used in the work on treating muscular dystrophy in dogs was of this type. That work is described on my stem cell page: Muscular dystrophy in dogs.
This section is included on both my pages for stem cells and for gene therapy (this page).
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China has launched gene therapy products aimed at cancer treatment. Cultural and language barriers mean that we know relatively little of the details. Science ran a "news focus" on gene therapy in China -- an interesting article. J Guo & H Xin, Chinese gene therapy: Splicing out the west? Science 314:1232, 11/24/06. Online at http://science.sciencemag.org/content/314/5803/1232.summary.
The article referred to (in the above Science article) as an English-language summary of the Chinese work is: Z Peng, Current status of gendicine in China: Recombinant human Ad-p53 agent for treatment of cancers. Human Gene Therapy 16:1016-1027, 9/05. Online at http://online.liebertpub.com/doi/abs/10.1089/hum.2005.16.1016. It is accompanied by an editorial: J M Wilson, Gendicine: The first commercial gene therapy product. Human Gene Therapy 16:1014, 9/05. Online at http://online.liebertpub.com/doi/abs/10.1089/hum.2005.16.1014. The editorial is also available there in Chinese.
There is more in the October 2006 issue of Human Gene Therapy, focusing on regulation and approval. Article: H Yin, Regulations and procedures for new drug evaluation and approval in China. Human Gene Therapy 17:970-974, 10/06. Online at http://online.liebertpub.com/doi/abs/10.1089/hum.2006.17.970. Accompanying editorial: J M Wilson, Regulation of gene therapy in China. Human Gene Therapy 17:969, 10/06. Online at http://online.liebertpub.com/doi/abs/10.1089/hum.2006.17.969.
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The Electronic Journal of Biotechnology (EJB). See more detailed information on the EJB.
Recombination. Animated gif. Recombination is one of the underlying processes in genetics -- both natural and lab work. The page listed here shows what we think is happening with one of the best understood recombination processes, in the bacterium Escherichia coli. Nice picture! And it illustrates the idea of molecular motors. The protein is moving along the DNA, fueled by ATP. For details and link, see my page of Molecular Biology - Internet Resources, for the Recombination chapter.
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Also see next section.
There are many posts in my Musings newsletter on agricultural biotechnology
and gene therapy issues. Here are some of them. Each listed here links to related posts.
* Added February 27, 2017. Improving photosynthesis by better adaptation to changing light levels (February 27, 2017).
* Added December 9, 2016. Alternative microbial sources of insecticidal proteins (December 9, 2016).
* Added July 15, 2016. Resistance to Bt toxin: What next? (July 15, 2016).
* Added May 16, 2016. How to administer Bt toxin to people? (May 16, 2016).
* Organ transplantation: from pig to human -- a status report (November 23, 2015).
* How rice leads to global warming, and what we might do about it (September 2, 2015).
* Who's been genetically engineering the sweet potatoes? (June 28, 2015).
* CRISPR and editing of the human germline: the ethical line? (May 4, 2015).
* Could a common food plant be used to make rubber? (March 27, 2015).
* CRISPR: an overview (February 15, 2015).
* A step towards correcting mutant genes with CRISPR (October 7, 2014).
* Development of insects resistant to Bt toxin from "genetically modified" corn (April 19, 2014).
* Rotavirus: passive immunization via food (January 10, 2014). This involves a rice that has been modified to produce an antibody against the virus.
* Down syndrome: Could we turn off the extra chromosome? (November 15, 2013).
* Exploiting the bacterial immune system as a tool for genetic engineering: The Caribou approach (May 4, 2013).
* Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).
* Genetically modified crops and the fate of the monarch butterfly (April 1, 2012).
* Gene therapy: Could we now treat Queen Victoria's sons? The FIX Fix. (January 6, 2012).
* Gene therapy: Curing an animal using a ZFN (August 9, 2011)
* Breeding plants to be more nutritious (May 11, 2010)
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CAUTION. A single report does not a truth make. People are trying various things. I will note here some interesting reports. But these are not final answers. Sometimes such reports turn out to not be reproducible, or not due to what the original authors thought. Or even if true, they may not work in humans. Etc etc. This is all part of the normal process of developing new things. Each breakthrough begins with a simple preliminary step. Some of these hold up, some do not. So, here are some news stories -- of various steps along the way.
Also see previous section.
"Targeting DNA -- After 20 years of high-profile failure, gene therapy is finally well on its way to clinical approval." A nice overview of the encouraging recent work on gene therapy. J Akst, The Scientist, June 2012, p 36. http://www.the-scientist.com/?articles.view/articleNo/32141/title/Targeting-DNA/.
High-calcium carrots. A Texas group has genetically modified carrots to take up calcium better. In the new work, reported here, they show that the higher calcium content of the carrots is indeed bioavailable, for both mice and humans. This is an example of modifying a food crop for an improvement in a nutritional characteristic. In this case, if further work shows this works well, consumption of high-calcium carrots could allow reduced consumption of dairy products. News story: Scientists unveil 'supercarrot'. January 2008. http://news.bbc.co.uk/2/hi/health/7188969.stm. The paper is: J Morris et al, Nutritional impact of elevated calcium transport activity in carrots. PNAS 105(5):1431-5, 2/15/08. Online at: http://www.pnas.org/content/105/5/1431.abstract.
Parkinson's disease. A gene therapy trial for Parkinson's disease was just reported. It was a small Phase I trial; the main purpose of this stage is to look for general safety, and the trial is not blinded. The main conclusion, then, is that the treatment seemed quite safe; some patients have been followed for over three years so far. Intriguingly, there were signs of efficacy, with most patients showing some improvement. Clearly, this work deserves follow-up. News story from Cornell: First gene therapy clinical trial for Parkinson's disease improves patients' motor skills with no major side effects, 8/8/07. http://www.news.cornell.edu/stories/2007/08/parkinsons-gene-therapy-trial-results-promising-wcmc-team-says. The paper is M G Kaplitt et al, Safety and tolerability of gene therapy with an adeno-associated virus (AAV) borne GAD gene for Parkinson's disease: an open label, phase I trial. Lancet 369:2097, 6/23/07. There is an accompanying commentary, on p 2056; this is probably a good place to start.
Making cottonseed non-toxic. Gossypol is a toxic polyphenol terpenoid found in cotton plants. The high levels of this toxic compound in the seed limit the use of this abundant resource for human food. Previously, scientists were able to develop mutant cotton plants that lack gossypol; the problem was that they were highly susceptible to insects, thus showing the natural protective role of this chemical. Now, K S Rathore and colleagues at Texas A&M have developed a cotton that lacks gossypol only in the seeds, but has normal levels elsewhere. The basic strategy for doing this makes use of two kinds of knowledge. First, they develop a RNAi (interfering RNA) that is specific for a key gene needed for making gossypol. Second, they target this RNAi to the seed, by using a seed-specific promoter. The results are encouraging, suggesting that the plant makes enough gossypol to protect itself, yet produces seeds that contain minimal levels of the toxic compound. A news story: "Toxic seed becomes hope for the hungry. Scientists reengineer cottonseed. Now, they aim to turn more poisonous plants into human food." November 27, 2006. http://www.csmonitor.com/2006/1127/p03s02-usgn.html. The paper is G Sunilkumar et al, Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol. PNAS 103:18054-9, 11/29/06. Online at: http://www.pnas.org/content/103/48/18054.abstract. For some background on RNAi, see my section RNAi (RNA interference or silencing).
Selenium decontamination. UC Berkeley scientists, headed by Dr Norman Terry, have been studying decontamination of soils that contain high levels of selenium. They have developed GM plants with enhanced ability to decontaminate such soils. A news story about a field trial of these plants was in the Feb 3, 2005, issue of the Berkeleyan. "New GMO technique really cuts the mustard. Engineered to absorb high levels of selenium, and tested with great caution, these plants may aid in toxic cleanup." Online at: http://www.berkeley.edu/news/berkeleyan/2005/02/02_GMO.shtml.
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