Beyond race: towards a whole-genome perspective on human populations and genetic variation

The renewed emphasis on population-specific genetic variation, exemplified most prominently by the International HapMap Project, is complicated by a longstanding, uncritical reliance on existing population categories in genetic research. Race and other pre-existing population definitions (ethnicity, religion, language, nationality, culture and so on) tend to be contentious concepts that have polarized discussions about the ethics and science of research into population-specific human genetic variation. By contrast, a broader consideration of the multiple historical sources of genetic variation provides a whole-genome perspective on the ways i n which existing population definitions do, and do not, account for how genetic variation is distributed among individuals. Although genetics will continue to rely on analytical tools that make use of particular population histories, it is important to interpret findings in a broader genomic context.

Ethical issues in environmental health research

Environmental health research encompasses a wide range of investigational topics, study designs, and empirical methodologies. As that arm of public health research concerned with understanding the health effects of the many environments in which humans live and work, the field is intimately connected with social concerns about environmental quality and disparities of power and privilege that place differential burdens upon members of underserved communities. Environmental health researchers thus engage many ethical and social issues in the work they do. These issues relate to the choice of research topics to study, the methods employed to examine these topics, the communication of research findings to the public, and the involvement of scientific experts in the shaping of environmental policy and governmental regulation. These and other topics are reviewed in this article. These ethical, legal, and social issues are becoming increasingly more complex as new genetic and molecular techniques are used to study environmental toxicants and their potential influence on human and ecologic health.

Environmental, occupational, and genetic risk factors for alpha-1 antitrypsin deficiency

Alpha-1 antitrypsin (AAT) deficiency is an inherited genetic disorder currently diagnosed in approximately 5,000 people in the United States. Although some individuals with AAT deficiency are asymptomatic, the condition often leads to deterioration of lung function in adults and is associated with emphysema, asthma, chronic obstructive pulmonary disease, and other respiratory diseases. In children, AAT deficiency can result in severe liver disease, including fatal cirrhosis in newborn infants. Although much is known about the clinical pathology of AAT deficiency, researchers are just beginning to characterize environmental, occupational, and genetic modifiers affecting the onset and progression of diseases related to AAT deficiency. On 19 August 2002, a group of basic scientists, clinicians, environmental health researchers, and public interest groups gathered at the National Institute of Environmental Health Sciences in Research Triangle Park, North Carolina, to discuss ongoing research on these topics. The goals of this workshop were to a) assess the present state of knowledge regarding environmental and occupational risk factors contributing to AAT deficiency morbidity and mortality, b) define future research needs in this area, and c) explore collaborative opportunities to advance understanding of risk factors affecting the progression of AAT deficiency-related disease. Participants agreed that new research initiatives in these areas represent an opportunity to benefit both basic science, through enhanced understanding of gene-environment interaction, and the AAT deficiency patient community, through innovative new approaches to disease management and treatment.

Ethical issues in international environmental health research

Environmental health problems are among the world's most significant health concerns. Although environmental risks are experienced disproportionately by people in developing countries, environmental health research (EHR) is conducted primarily in developed countries. Human subjects participate in five main types of EHR: (1) documentation and quantification of exposure to potentially hazardous substances; (2) elucidation of biological responses to these materials; (3) characterization and measurement of susceptibility to harmful effects of hazardous materials; (4) trials involving environmental interventions to reduce risk; and (5) documentation and measurement of various manifestations of disease putatively linked to environmental exposures. Although existing frameworks for the ethics of international clinical research are generally relevant to EHR, they currently lack the specificity necessary to confront three inherent problems in EHR, namely under-determination in EHR findings, the unavoidable nature of some environmental hazards, and environmental justice implications. We examine these issues as they relate to community partnership, risk assessment, and the assessment and management of economic and political interests in EHR. We believe that there are 3 general features of ethical EHR, it has health promoting value, the populations studied are not restricted in their ability to avoid environmental hazards by economic or political repression, and the justification for conducting EHR on populations with known exposure to environmental hazards gets stronger as the limits on populations to reduce the hazards or remove themselves from them becomes greater, as long as the first and second conditions are also met.

Race, ethnicity, and genomics: social classifications as proxies of biological heterogeneity

Over the past century, genetics has experienced a tension between the view that racial and ethnic categories are biologically meaningful and the view that these social classifications have little or no biological significance. That tension continues to inform genomics and is evident in the assembly of biological collections and sequence databases that seek to approximate the genetic variation found in human populations. Although social identities can be useful and convenient proxies of some biological features, for example, in ensuring that genomic resources capture a range of genetic variants found in most human populations, the ways in which geneticists conceptualize the relationship between racial and ethnic identities and genetic variation can be problematic. Inclusion of racial and ethnic identifiers in genomic resources can create risks for all members of those identified populations and influence lay perceptions of the nature of racial and ethnic groups. Thus, the burden of showing the scientific utility of racial and ethic identities in the construction and analysis of genomic resources falls on researchers. This requires that genetic researchers pay as much attention to the social constitution of human populations as presently is paid to their genetic composition.

Community involvement in the ethical review of genetic research: lessons from American Indian and Alaska Native populations

The National Bioethics Advisory Commission has proposed that regulatory oversight for research with human subjects be extended beyond the protection of individual research participants to include the protection of social groups. To accomplish this, the commission recommends that investigators and ethics review boards a) work directly with community representatives to develop study methods that minimize potential group harms, b) discuss group implications as part of the informed consent process, and c) consider group harms in reporting research results. We examine the utility of these recommendations in the context of research with American Indian and Alaska Native communities. Because much attention has been given to the question of how best to consult with members of these communities in the design and conduct of research, we believe it behooves investigators to consider the lessons to be learned from research involving American Indians and Alaska Natives. After describing several difficulties surrounding the application of the commission's approach to these research contexts, we propose a research agenda to develop best practices for working with local communities in the ethical assessment of epidemiologic and environmental health research.

An analysis of research guidelines on the collection and use of human biological materials from American Indian and Alaskan Native communities

American Indian and Alaskan Native communities have expressed concern about the use of human biological materials in research. These concerns have prompted research sponsors and professional organizations to develop guidelines for investigators working with these communities. This paper reviews research guidelines and presents recommendations that reflect "best practices" for working with North American indigenous communities in the collection, storage, and distribution of human biological materials for research. These recommendations strike a reasonable balance between three imperatives in research: (1) minimizing harm, (2) treating sample contributors with respect, and (3) promoting intellectual freedom to pursue a range of research questions. The recommendations can be used in designing appropriate methods of collecting and using human biological materials from members of American Indian and Alaskan Native communities and will likely be applicable to other historically disadvantaged communities as well.

Restoring and preserving trust in biomedical research

Recent media depictions of the dangers of biomedical research have fueled public and regulatory scrutiny of academic research institutions. The authors argue that if these institutions are to preserve the trust that the public has historically bestowed upon them, they must go beyond mere compliance with regulatory mandates. Several steps are suggested that institutions can take to strengthen and supplement ongoing compliance efforts, steps the authors believe will bolster the public's confidence in the integrity of academic research institutions. These steps grow out of the authors' analysis of three key components of institutional trustworthiness: (1) shared goals between research institutions and the communities they serve, (2) robust institutional oversight of research activities, and (3) training programs that build professional character. The authors' recommendations include the use of research advisory councils to assure the public that research goals reflect community interests, more collaborative relationships between institutional review boards and members of investigative teams, and educational programs that emphasize the importance of professional integrity in biomedical research. These efforts will help preserve public confidence that an institution's research priorities are appropriate and that the research it conducts is ethical. Preserving this public trust is central to the long-term success of biomedical research and the institutions in which such research takes place.

Pharmacogenetics, race, and ethnicity: social identities and individualized medical care

Social categories such as race and ethnicity have long been used in interpreting patient symptoms, diagnosing disease, and predicting therapeutic response. DNA-based diagnostic tests and pharmacogenetic screens could make these uses of social categories largely irrelevant by allowing clinicians to base diagnosis and treatment decisions on the unique genetic features of individual patients. Despite this attractive vision of individualized care, however, social categories are likely to continue playing a significant role in the coming era of genetic medicine. Current uses of social categories in pharmacogenetic research, for example, illustrate how drug development and marketing will perpetuate the use of social categories such as race and ethnicity. Those uses may unintentionally blunt the precision of genetic technologies and pose new threats to socially identifiable populations. These implications suggest the need for greater caution in using social categories as indicators for specific tests or therapies and for federal legislation to protect against discriminatory uses of individuals' genetic information. In addition, more precise social classifications than those presently in use may allow us to realize the full potential of DNA-based technologies, thus minimizing social disparities in health care. Those more precise social classifications should reflect extended patient pedigrees and not the self-reported claims of racial and/or ethnic affiliation.

Applying genomic technologies in environmental health research: challenges and opportunities

Recent discoveries in molecular biology and genetics have made it possible for environmental health researchers to examine how genetic characteristics affect response to environmental exposures. Understanding such gene-environment interactions offers exciting possibilities for the prevention and control of environmentally induced diseases. Despite these potential benefits, the collection and analysis of genetic information in environmental health research presents many of the same ethical, legal, and social (ELSI) challenges found in other types of genetic research. In this article, we describe a number of ELSI challenges in environmental genomic research and the opportunities and responsibilities that accompany this research.

NMR paramagnetic relaxation enhancement: test of the controlling influence of zfs rhombicity for S = 1

Prior theoretical work has predicted that the NMR paramagnetic relaxation enhancement (NMR-PRE) produced by electron spin S = 1 ions is highly sensitive to orthorhombic terms in the static zero field splitting (zfs) tensor. Zfs orthorhombicity (which implies chemical inequivalence of the three principal directions of the zfs-principal axis system and is described by the zfs E-parameter) is predicted to suppress the NMR-PRE profoundly relative to the reference cylindrical zfs-limit situation. This expectation was tested experimentally by a comparison of the zfs-limit NMR-PRE produced by [Ni(II)(en)(3)](2+) (en = ethylenediamine), a trigonal complex which lacks zfs-rhombicity, with the zfs-limit NMR-PRE produced by two orthorhombic complexes, [Ni(II)(en)(2)(H(2)O)(2)](2+) and [Ni(II)(en)(H(2)O)(4)](2+). As predicted, the zfs-limit NMR-PRE produced by the orthorhombic complexes in the proton resonance of a dioxane probe species in the solvent was strongly suppressed (by factors of approximately 5 and 7, respectively) relative to the comparable measurement on the trigonal complex. The suppression of the NMR-PRE due to the orthorhombic zfs terms is counteracted by an applied Zeeman field, leading to a predicted rise in the NMR-PRE with increasing Zeeman field strength; this rise occurs when the Zeeman energy is comparable to the orthorhombic zfs splitting, 2E. This second prediction of theory was likewise confirmed: the expected rhombicity-induced magnetic field dependence in the NMR-PRE was observed for the orthorhombic complexes but not for the trigonal complex.

The environmental genome project: ethical, legal, and social implications

The National Institute of Environmental Health Sciences is supporting a multiyear research initiative examining genetic influences on environmental response. Proponents of this new initiative, known as the Environmental Genome Project, hope that the information learned will improve our understanding of environmentally associated diseases and allow clinicians and public health officials to target disease-prevention strategies to those who are at increased risk. Despite these potential benefits, the project presents several ethical and social challenges. Of immediate concern is the protection of individual research participants. Other ethical issues relate to the application of research results and how study findings could affect social priorities. Clarifying these emerging areas of concern, many of which have not received adequate attention in the existing bioethics literature, is an important step toward minimizing potential research-related risks and defining research needs.

Involving study populations in the review of genetic research

Genetic research can present risks to all members of a study population, not just those who choose to participate in research. The authors suggest that community-based reviews of research protocols can help identify and minimize such research-related risks.

The role of community review in evaluating the risks of human genetic variation research

The practicality and moral value of community review of human genetic research has become a focus of debate. Examples from two Native American communities are used to address four aspects of that debate: (1) the value of community review in larger, geographically dispersed populations; (2) the identification of culturally specific risks; (3) the potential conflict between individual and group assessments of research-related risks; and (4) the confusion of social categories with biological categories. Our experiences working with these two communities suggest that: (1) successful community review may require the involvement of private social units (e.g., families); (2) culturally specific implications of genetic research may be identifiable only by community members and are of valid concern in their moral universes; (3) community concerns can be incorporated into existing review mechanisms without necessarily giving communities the power to veto research proposals; and (4) the conflation of social and biological categories presents recruitment problems for genetic studies. These conclusions argue for the use of community review to identify and minimize research-related risks posed by genetic studies. Community review also can assist in facilitating participant recruitment and retention, as well as in developing partnerships between researchers and communities.

Activity and stability of a recombinant plasmid-borne TCE degradative pathway in biofilm cultures

The activity and stability of the TCE degradative plasmid TOM31c in the transconjugant host Burkholderia cepacia 17616 was studied in selective and non-selective biofilm cultures. The activity of plasmid TOM31c in biofilm cultures was measured by both TCE degradative studies and the expression of the Tom pathway. Plasmid loss was measured using continuous flow, rotating annular biofilm reactors, and various analytical and microbiological techniques. The probability of plasmid loss in the biofilm cultures was determined using a non-steady-state biofilm plasmid loss model that was derived from a simple mass balance, incorporating results from biofilm growth and plasmid loss studies. The plasmid loss model also utilized Andrew's inhibition growth kinetics and a biofilm detachment term. Results from these biofilm studies were compared to similar studies performed on suspended cultures of Burkholderia cepacia 17616-TOM31c to determine if biofilm growth has a significant effect on either plasmid retention or Tom pathway expression (i.e., TCE degradation rates). Results show that the activity and expression of the Tom pathway measured in biofilm cultures was significantly less than that found in suspended cultures at comparable growth rates. The data obtained from these studies fit the plasmid loss model well, providing plasmid loss probability factors for biofilm cultures that were equivalent to those previously found for suspended cultures. The probability of plasmid loss in the B. cepacia 17616-TOM31c biofilm cultures was equivalent to those found in the suspended cultures. The results indicate that biofilm growth neither helps nor hinders plasmid stability. In both the suspended and the biofilm cultures, plasmid retention and expression could be maintained using selective growth substrates and/or an appropriate plasmid-selective antibiotic. Copyright 1998 John Wiley & Sons, Inc.

Activity and stability of a recombinant plasmid-borne TCE degradative pathway in suspended cultures

The retention and expression of the plasmid-borne, TCE degradative toluene-ortho-monooxygenase (TOM) pathway in suspended continuous cultures of transconjugant Burkholderia cepacia 17616 (TOM31c) were studied. Acetate growth and TCE degradation kinetics for the transconjugant host are described and utilized in a plasmid loss model. Plasmid maintenance did not have a significant effect on the growth rate of the transconjugant. Both plasmid-bearing and plasmid-free strains followed Andrews inhibition growth kinetics when grown on acetate and had maximum growth rates of 0.22 h-1. The transconjugant was capable of degrading TCE at a maximum rate of 9.7 nmol TCE/min. mg protein, which is comparable to the rates found for the original plasmid host, Burkholderia cepacia PR131 (TOM31c). The specific activity of the TOM pathway was found to be a linear function of growth rate. Plasmid maintenance was studied at three different growth rates: 0.17/h, 0.1/h, and 0.065/h. Plasmid maintenance was found to be a function of growth rate, with the probability of loss ranging from 0.027 at a growth rate of 0.065/h to 0.034 at a growth rate 0.17/h.

Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli

Populations of Escherichia coli initiated with a single clone and maintained for long periods in glucose-limited continuous culture, become polymorphic. In one population, three clones were isolated and by means of reconstruction experiments were shown to be maintained in stable polymorphism, although they exhibited substantial differences in maximum specific growth rates and in glucose uptake kinetics. Analysis of these three clones revealed that their stable coexistence could be explained by differential patterns of the secretion and uptake of two alternative metabolites acetate and glycerol. Regulatory (constitutive and null) mutations in acetyl-coenzyme A synthetase accounted for different patterns of acetate secretion and uptake seen. Altered patterns in glycerol uptake are most likely explained by mutations which result in quantitative differences in the induction of the glycerol regulon and/or structural changes in glycerol kinase that reduce allosteric inhibition by effector molecules associated with glycolysis. The evolution of resource partitioning, and consequent polymorphisms which arise may illustrate incipient processes of speciation in asexual organisms.

NMR paramagnetic relaxation enhancements due to manganese in the S0 and S 2 states of Photosystem II-enriched membrane fragments and in the detergent-solubilized Photosystem II complex

The NMR paramagnetic relaxation enhancement (NMR-PRE) produced in the solvent proton resonance by manganese in the S0 and S2 states of the oxygen evolving center (OEC) has been recorded for three Photosystem II (PS II)-enriched preparations: (1) PS II-enriched thylakoid membrane fragments (TMF-2 particles); (2) salt-washed (2M NaCl) TMF-2 particles; and (3) the octylglucopyranoside (OGP)-solubilized PS II complex. The second and third preparations, but not the first, are depleted of the peripheral 17 and 23 kD polypeptides associated with the OEC. It has been proposed that depletion of these polypeptides increases the exposure of OEC manganese to the aqueous phase. The NMR-PRE response measures the quantity (T1m+τm)(-1), where T1m is the spin relaxation time and τm is the mean residence time with respect to chemical exchange reactions of solvent protons in the manganese coordination sphere, and, thus, the NMR-PRE provides a direct measure of the solvent proton chemical exchange rate constant τm (-1). This study tested whether the 17 and 23 kD polypeptides shield the OEC from the solvent phase and whether their depletion enhances the S2 and S0 NMR-PRE signals by removing a kinetic barrier to the solvent proton chemical exchange reaction. The amplitude of the S2 NMR-PRE signal, measured in its chemical exchange-limited regime (τm>T1m), is slightly decreased, rather than increased, in preparations (2) and (3) relative to (1), indicating that removal of the 17 and 23 kD polypeptides slightly slows, rather than accelerates, the rate-limiting steps of the solvent proton chemical exchange reactions. In addition, the lifetime of the S2 state was shortened several-fold in the solubilized PS II complex and in salt-washed TMF-2 membranes relative to untreated TMF-2 control samples. The S0 NMR-PRE signal, which is present in TMF-2 suspensions, was not detected in suspensions of the solubilized PS II complex, even though these samples contained high concentrations of active manganese centers (approximately double those of the TMF-2 control) and exhibited an S2 NMR-PRE signal of comparable amplitude to that of the TMF-2 preparation. These results suggest that the 17 and 23 kD extrinsic polypeptides do not shield the NMR-visible water binding site in the OEC from the aqueous phase, although their removal substantially alters the proton relaxation efficiency by shortening T1m.