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Dec 27, 2008

Asilomar and Recombinant DNA

by Paul Berg
1980 Nobel Laureate in Chemistry

Introduction


Advances in the life sciences, particularly in biomedicine, are increasingly being scrutinized and their acceptance questioned. Novel technologies and ideas that impinge on human biology and their perceived impact on human values have renewed strains in the relationship between science and society. Thirty years ago, nations were engaged in debates about whether recombinant DNA research, also referred to as gene splicing and genetic engineering, was too dangerous to be allowed to continue. Fears of creating new kinds of plagues or of altering human evolution or of irreversibly altering the environment were only some of the concerns that were rampant. Lingering doubts and concerns still persist about the use of that technology in the development of genetically modified plants and animals used as food. Notably, some nations have enacted legislation that prohibits genetically-modified plants and animals from entering into their food supply. Paradoxically, no such embargo exists for the drugs and therapies that have revolutionized the treatment of serious diseases although many of them were created with the same technologies.


Today, it is research with human embryonic stem cells and attempts to prepare cloned stem cells for research and medical therapies that are being disavowed as being ethically unacceptable. As with the GM food controversy and other cases where science and public policy clash, there are repeated calls to convene an "Asilomar Conference" to examine and resolve the policy controversies.


Unique Conference


The lofty status of the Asilomar Conference and the deliberative process it spawned stems from its success in identifying, evaluating and ultimately mitigating the perceived risks of recombinant DNA. Looking back now, this unique conference marked the beginning of an exceptional era for science and for the public discussion of science policy. Its success permitted the then contentious technology of recombinant DNA to emerge and flourish. Now the use of the recombinant DNA technology dominates research in biology. It has altered both the way questions are formulated and the way solutions are sought. The isolation of genes from any organism on our planet, alive or dead, is now routine. Furthermore, the construction of new variants of genes, chromosomes and viruses is standard practice in research laboratories as is the introduction of genes into microbes, plants and experimental animals. Without the tools of recombinant DNA there would be no human or any other genome sequence. Equally profound is the influence it has had in many related fields. Even a brief look at journals in such diverse fields as chemistry, evolutionary biology, paleontology, anthropology, linguistics, psychology, medicine, plant science, and, surprisingly, forensics, information theory and computer science shows the pervasive influence of this new paradigm.



Additional testimony to the conference's success are the frequent calls to resurrect the "Asilomar Process" to resolve the ethical dilemmas posed by newly emerging ideas and technologies, most recently human embryonic stem cell research. Whether the Asilomar Conference model can duplicate its achievement for current conflicts is problematic. But in acknowledging its thirtieth anniversary, it is worth examining the circumstances that gave birth to the conference and how the outcome permitted the then contentious recombinant DNA technology to emerge and flourish.


Time and faulty memory have obscured some of the circumstances and events that led to the scientific breakthrough and the path to Asilomar. The emergence of a new paradigm in any field of science generates, along with the excitement of a new frontier and perspective, an uncertainty about its full implications. This was especially true for the geneticists that fueled the emergence of the recombinant DNA technology during the 1970s.


Voluntary Moratorium


The concerns about recombinant DNA had their antecedent in the creation of a DNA molecule containing the entire Simian Virus 40 genome joined to a segment of DNA containing three genes responsible for galactose metabolism in Escherichia coli.1 But improvements in the technology, most notably the ability to clone DNA segments from virtually any organism on our planet,2 triggered a new level of concern which culminated in mid-1974 with a call for a voluntary moratorium on certain recombinant DNA experiments.3 This unprecedented action by a group of American scientists echoed reservations expressed at a conference on nucleic acids during the previous summer.4 Both groups acknowledged that the new technology created extraordinary novel avenues for genetics and could ultimately provide exceptional opportunities for medicine, agriculture and industry. Nevertheless, there were concerns that unfettered pursuit of this research might engender unforeseen and damaging consequences for human health and the Earth's ecosystems. In spite of widespread consternation among many scientists about the proscriptions, the validity of the concerns, and the manner in which they were announced, the moratorium was universally observed. One goal of the moratorium was to provide time for a conference that would evaluate the state of the new technology and the risks, if any, associated with it.


That conference, held at the Asilomar Conference Center on California's Monterey peninsula in the USA, included scientists from throughout the world, lawyers, members of the press and government officials.5,6 One aim of the meeting was to consider whether to lift the voluntary moratorium and, if so, under what conditions the research could proceed safely. Although there were few data on which to base a scientifically defensible judgment the conference concluded, not without outspoken opposition from some of its more notable participants, that recombinant DNA research should proceed but under strict guidelines.7 Such guidelines were subsequently promulgated by the National Institutes of Health8 and by comparable bodies in other countries.9,10


The primary motivation for the prompt actions taken by scientists and governments in the period 1973-1976 was to protect laboratory personnel, the general public, and the environment from any hazards that might be directly generated by the experiments. In particular, there were speculations that normally innocuous microbes could be changed into human pathogens by introducing genes that rendered them resistant to then available antibiotics, or enabled them to produce dangerous toxins, or transformed them into cancer causing agents. The uncertainties stimulated occasionally turbulent debates. Public fear was fanned by the popularity of visions of "The Andromeda Strain" and the myriad of 'what ifs' floated by both serious and demagogic commentators. Some scientists, and public officials as well, were certain that recombinant DNA research was flirting with disaster and that lifting the moratorium was a blunder. Others, reflecting their intuition and expertise, argued that such cells, viruses and recombinant DNAs posed no risk at all. The overwhelming assessment today is that the latter view was correct. Literally hundreds of millions of experiments, many inconceivable in 1975, have been carried out in the last 30 years without incident. No documented hazard to public health has been attributable to the applications of recombinant DNA technology. Moreover, the concern of some that moving DNA among species would breach customary breeding barriers and have profound effects on natural evolutionary processes has substantially disappeared as the science revealed that such exchanges occur in nature.



Recombinant DNA Technology


At the time of Asilomar, scientists optimistically predicted that the recombinant DNA methods would soon yield important drugs, industrial products and improved agricultural varieties. In fact, such developments took longer than anticipated. Some have never been realized because learning how to manipulate genes for useful purposes presented unexpected difficulties. Since the mid-1980s, however, the number of products has increased continually. Hormones, vaccines, therapeutic agents and diagnostic tools are enhancing medical practice. The production and consumption of genetically engineered food plants are realities although their dissemination has been limited. A thriving biotechnology industry has created products, interesting jobs and wealth for scientists and others. In retrospect, very few of those attending the Asilomar Conference foresaw the pervasive, complex, robust, and rich ramifications of recombinant DNA technology. Nor could most have predicted the pace at which fundamental understanding of biology has deepened.


Frequently heard in the 1970s were criticisms of scientists for assuming leadership in formulating policies that were matters of public concern. This led some scientists to believe that the public debate itself was a great threat and that the fallout of claim and counterclaim would bring debilitating restrictions or even prohibitions on molecular biological research. In truth, many scientists grew impatient with the time-consuming, contentious debates. Yet the effort to inform the public also encouraged responsible public discussion that succeeded in developing a consensus for the measured approach that many scientists supported. Restrictive national legislation was avoided, and in the long run, scientists benefited from their forthrightness and prudent actions in the face of uncertainty.


Ethical and Legal Implications


An often-voiced criticism of the Asilomar Conference discussions was the failure to consider the ethical and legal implications of genetic engineering of plants, animals and humans. Did the organizers and participants of the Asilomar conference deliberately limit the scope of the concerns? The participants were scored for ignoring the increased perils of biological warfare made possible by the development of the new recombinant technology. Others have been critical of the conference because it did not confront the potential misuse of the recombinant DNA technology or the ethical dilemmas that would arise from applying the technology to genetic screening and somatic and germ line gene therapy, or the environmental consequences arising from the creation of genetically modified food plants.10 It should not be forgotten that these possibilities were still far in the future and the more immediate issue confronting the Asilomar organizers and participants was the one the scientists had raised: the potential risks to human health and the environment posed by the expanding recombinant DNA technology. We could not avoid the question of whether there were serious health hazards associated with going forward with the experiments that were being planned. In short, the agenda for the three-day meeting had to focus on an assessment of the risks and how to eliminate or reduce the risks that seemed plausible. We accepted that the other issues would be dealt with as they became imminent and estimable.



Public Trust


What did the actions taken by the scientific community achieve? First and foremost, we gained the public's trust, for it was the very scientists who were most involved in the work and had every incentive to be left free to pursue their dream that called attention to the risks inherent in the experiments they were doing. Aside from unprecedented nature of that action, the scientists' call for a temporary halt to the experiments that most concerned them and the assumption of responsibility for assessing and dealing with those risks was widely acclaimed as laudable ethical behavior. If the Asilomar exercise was a success, it was because scientists took the initiative in raising the issue rather than having it raised against them; that initiative engendered considerable credibility instead of cynical suspicion of what was to follow. The public's trust was undeniably increased by the fact that more than 10% of the participants were from the news media. They were free to describe, comment on and criticize the discussions and conclusions at the end of the conference. All the deliberations, bickering, bitter accusations, wavering views and the arrival at a consensus were widely chronicled by the reporters that attended and subsequently by the rest of the media and subsequent commentators.5,9,10


Moving Science Forward


Is "the Asilomar model" appropriate for resolving or contributing to some of the "hot button" issues confronting scientists and the public today? For example, are the deep divisions about fetal tissue and embryonic stem cell research, somatic and germ-line gene therapy and directed genetic modification of food crops amenable to deliberation and resolution? I believe the Asilomar model would not succeed in dealing with those issues today to the extent it did 30 years ago with recombinant DNA for the following reasons. First, the public's awareness of the recombinant DNA breakthrough was sudden and unanticipated. It was more than just another interesting scientific advance because it brought with it potential dangers to public health. Furthermore, the implications of risk came from the scientists conducting that research, not from some investigative reporter or disaffected scientist; that was most unusual, even historic. There seemed to be an urgent need for consensus on how to proceed and a plausible plan on how to deal with issues, both of which were provided by the scientific community. Action was prompt and seen by the public to have been achieved by transparent deliberations and with considerable cost to their own scientific interests. The issue and its resolution were complete before an entrenched, intransigent and chronic opposition developed. Attempts to prohibit the research or reverse the actions recommended by the conference threatened but never generated sufficient traction to succeed.

By contrast, the issues that challenge us today are qualitatively different. They are often beset with economic self-interest and increasingly by nearly irreconcilable ethical and religious conflicts and challenges to deeply held social values. An Asilomar type conference trying to contend with such contentious views is, I believe, doomed to acrimony and policy stagnation, neither of which advances the cause of finding a solution. There are many forums for airing opposing views but emerging with an agreed upon solution from such an exercise is elusive and discouraging.


The Asilomar decisions emerged from a consensus of opposing views. Although the recommendations were clearly "inconvenient", the participants had a stake in having the science move forward and not in leaving the rules for conducting the research to be set by others. By contrast, there is little prospect for consensus in our society on the ethical issues concerning fetal tissue and embryonic stem cell research, genetic testing, somatic and germ-line gene therapy, and engineered plant and animal species and hence little incentive to seek a compromise. Compromise in those instances may only be achievable by political means, where majority rule prevails.



Bibliography


1 Jackson, D.A., Symons, R.H. and Berg, P., "Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA containing lambda phage genes and the galactose operon of Escherichia coli," Proc. Nat. Acad. Sci. USA 69, pp. 2904-2909 (1972).

2 Mertz, J.E. and Davis, R.W., "Cleavage of DNA by R1 restriction endonuclease generates cohesive ends," Proc. Nat. Acad. Sci. USA 69, pp. 3370-3374 (1972).

3 Berg, P., Baltimore, D., Boyer, H.W., Cohen, S.N., Davis, R.W., Hogness, D.S., Nathans, D., Roblin, R., Watson, J.D., Weissman, S. and Zinder, N.D., "Biohazards of Recombinant DNA," Science 185, p. 3034, also Science 185, p. 303 (1974).

4 Singer, M.F. and Soll, D., "Guidelines for hybrid DNA molecules," Science 181, p. 1114 (1973).

5 Rogers, M., "Biohazard," Alfred A. Knopf, New York (1977).

6 Fredrickson, D.S., "Asilomar and recombinant DNA: the end of the beginning" in Biomedical Politics, National Academy Press, Washington, D.C., pp. 258-292 (1991).

7 Berg, P., Baltimore, D., Brenner, S., Roblin, R.O. III, Singer, M.F., "Summary statement of the Asilomar Conference on recombinant DNA molecules," Proc. Nat. Acad. Sci. USA 72, pp. 1981-1984 (1975), also Science 188, p. 991 (1975).

8 "Guidelines for research involving recombinant DNA molecules," Federal Register 41, no. 131, pp. 27911-27943 (1976).

9 Fredrickson, D.S., Chapters 1 and 5 in "The recombinant DNA controversy. A memoir," ASM Press, Washington, D.C., p. 388 (2001).

10 Wright, S., "Molecular Politics: Developing American and British regulatory policy for genetic engineering," U. Chicago Press, p. 592 (1994).

Nov 30, 2008

BioProtocols for Nucleic Acids (DNA-1)

DNA (In Alphabeta)

ABC Random Amplification
Alcohol Precipitation of DNA
AML sample DNA preparation

Agarose gel electrophoresis

Agarose gel electrophoresis

Boomerang DNA Amplification Single primer DNA amplification

cDNA amplification from l-phage library

cDNA library screening

Characterization of DNA

Collection of Materials for DNA Analysis

Colony Hybridization

Colony Hybridization Protocols

Deoxyribose Isolation from DNA Degrasion

DNA Isolation, Purification and Troubleshooting

DNA Labeling Protocols

DNA ligation Protocol

DNA Methods 3

DIG DNA labelling and hybrid detection (Boehringer Mannheim)

Direct Automated Sequencing off Bacterial Genomic DNABruce Rhoe

DNA extraction from agarose (Qiagen)

DNA - dische diphenylamine determination

DNA Fragment Isolation from LM agarose

DNA Ligation

DNA detection
DAPI chromosome identification

DNA preparation by cryostom tissue dissection
DNA labeling by nick translation

Ethanol precipitation of DNA

Extraction of DNA from bovine spleen

Fluorometry

BioProtocols for Nucleic Acids (DNA-2)

FISH

Genome DNA Extraction

Genomic DNA Isolation from Specific Samples

Genomic DNA preparation (plants)
Hybridization

In-Situ hybridization to Embryonic Tissue Section

Large Scale Plasmid Preparation: MGH

Methylene Blue DNA staining protocol

Microsatellites Protocols

Mitochondrial DNA Isolation

Modifications of DNA ends

PCR amplification of DNA

PCR analysis of DNA from Laser Microdissected (LM) Samples - Embryo Genotyping Protocol

PCR product purification (Qiagen)

Perfectly Blunt Cloning of DNA (Novagen)

Phenol/chloroform extraction of DNA

Plasmid midi-prep from bacteria

Plasmid Protocol--(1-10)

Plasmid Protocols--(21-30)

Plasmid Protocols--(31-37)

Preparation of genomic DNA from bacteria

Purification of DNA

Q-PCR

Random Primed labeling of DNA (Prime-It II -Stratagene)

Restriction enzyme digestion of DNA
Southern Hybridization
Stark's Prehybridization Buffer

Sequencing using Sequenase

Southern blot

Tail DNA prep

Wizard Plus Mini-preps (109. Plasmid Mini-prep)

Worm Genomic DNA: MGH

Worm genomic Southern blots: Michael Koelle

BioProtocols for Nucleic Acids (RNA)

RNA (In Alphabeta)

Amino-allyl labeling
BioAnalyzer

C. elegans RNA prep: Michael Koelle

IN VITRO TRANSCRIPTION OF RNA

In vitro transcription reaction

Isolation of poly-A RNA

LiCl RNA Preparation: MGH

Northern blots

Northern Blots: Michael Koelle

Nucleic Acids Research Methods (2)

Nucleotide composition of RNA

Orcinol determination of RNA

Phenol extraction of rRNA (rat liver)

PROTOCOL FOR SINGLE CELL mRNA AMPLIFICATION (REVERSE NORTHERN ANALYSIS)

Protocol: Fluorescence in situ hybridization

Protocols for SiRNA

Reverse Transfection Protocols

RNA amplification
RNA gel electrophoresis

RNA and protein extraction from the same sample

RNA Isolation

RNA MicroArray Protocol

RNA prepararion (from plants tissue)

RNA Preparation: MGH

RNEasy Midi

SELEX—in vitro selection

shRNA Protocols

Spectrophotometric analysis of RNA

Sucrose density fractionation

TRIzol plus RNEasy Mini
TRIzol product insert

Worm RNA Preparation: MGH

Nucleic Acids Research Articles and Protocols

Cell biology (8 Articles)


Chromatin (4 Articles)


Cloning (35 Articles)


Computational methods (92 Articles)


DNA characterisation (96 Articles)


DNA transfer (30 Articles)


Enzyme assays (24 Articles)


Genomics (74 Articles)


Microarray (48 Articles)


Miscellaneous/other (62 Articles)


Monitoring gene expression (63 Articles)


Mutagenesis (42 Articles)


New Restriction Enzymes (17 Articles)


Nucleic acid amplification (66 Articles)


Nucleic acid modification (42 Articles)


Nucleic acid structure (20 Articles)


Polymorphism/mutation detection (112 Articles)


Protein-nucleic acid interaction (50 Articles)


Protein-protein interaction (16 Articles)


Recombinant DNA expression (24 Articles)


Recombination (54 Articles)


Repair (20 Articles)


Replication (13 Articles)


RNA characterisation and manipulation (59 Articles)


Targeted inhibition of gene function (14 Articles)

Nov 28, 2008

HHV-6 is Passed to Children Through DNA

Adrienne Dellwo, Fibromyalgia & CFS Blog

ABSTRACT

NEWSBRIEF: A virus suspected of triggering some cases of chronic fatigue syndrome (CFS or ME/CFS) can be passed genetically from parent to child, according to an article published in the journal Pediatrics.

Experts used to believe that mothers passed human herpesvirus 6 (HHV-6) to their babies through blood exchanged during childbirth. HHV-6 causes roseola in infected children. New evidence shows the virus can come from either parent in the genetic material.

Nearly everyone is infected with HHV-6 at some point in their lives, but researchers are now investigating what it means to have a virus integrated into your genetic matter -- whether it can activate and cause problems, or cause an immune response just by being there.

Guide note: Could this be causing a genetic predisposition to chronic fatigue syndrome or autoimmune diseases? If so, genetic testing may someday be able to diagnose the condition and reveal who is at risk for it.

Brief to Genetic Mapping

What is genetic mapping?


Developing new and better tools to make gene hunts faster, cheaper and practical for any scientist was a primary goal of the Human Genome Project (HGP).


One of these tools is genetic mapping, the first step in isolating a gene. Genetic mapping - also called linkage mapping - can offer firm evidence that a disease transmitted from parent to child is linked to one or more genes. It also provides clues about which chromosome contains the gene and precisely where it lies on that chromosome.


Genetic maps have been used successfully to find the single gene responsible for relatively rare inherited disorders, like cystic fibrosis and muscular dystrophy. Maps have also become useful in guiding scientists to the many genes that are believed to interact to bring about more common disorders, such as asthma, heart disease, diabetes, cancer and psychiatric conditions.


How do researchers create a genetic map?


To produce a genetic map, researchers collect blood or tissue samples from family members where a certain disease or trait is prevalent. Using various laboratory techniques, the scientists isolate DNA from these samples and examine it for the unique patterns of bases seen only in family members who have the disease or trait. These characteristic molecular patterns are referred to as polymorphisms, or markers.


Before researchers identify the gene responsible for the disease or trait, DNA markers can tell them roughly where the gene is on the chromosome. This is possible because of a genetic process known as recombination. As eggs or sperm develop within a person's body, the 23 pairs of chromosomes within those cells exchange - or recombine - genetic material. If a particular gene is close to a DNA marker, the gene and marker will likely stay together during the recombination process, and be passed on together from parent to child. So, if each family member with a particular disease or trait also inherits a particular DNA marker, chances are high that the gene responsible for the disease lies near that marker.


The more DNA markers there are on a genetic map, the more likely it is that one will be closely linked to a disease gene - and the easier it will be for researchers to zero-in on that gene. One of the first major achievements of the HGP was to develop dense maps of markers spaced evenly across the entire collection of human DNA.


What are genetic markers?


Markers themselves usually consist of DNA that does not contain a gene, however they can tell a researcher the identity of the person a DNA sample came from. This makes markers extremely valuable for tracking inheritance of traits through generations of a family, and markers have also proven useful in criminal investigations and other forensic applications.


Although there are several different types of genetic markers, the type most used on genetic maps today is known as a microsatellite map. However, maps of even higher resolution are being constructed using single-nucleotide polymorphisms, or SNPs (pronounced "snips"). Both types of markers are easy to use with automated laboratory equipment, so researchers can rapidly map a disease or trait in a large number of family members.


The development of high-resolution, easy-to-use genetic maps, coupled with the HGP's successful sequencing and physical mapping of the entire human genome, has revolutionized genetics research. The improved quality of genetic data has reduced the time required to identify a gene from a period of years to, in many cases, a matter of months or even weeks. Genetic mapping data generated by the HGP's laboratories is freely accessible to scientists through databases maintained by the National Institutes of Health and the National Library of Medicine's National Center for Biotechnology Information.