This review provides a current perspective on the insertion of genes into plants. Some of the knowledge on the structure and control of plant genes gained recently from genetic engineering approaches is described, together with developments that can be expected to emerge from further exploitation of gene transfer techniques.

New possibilities to modify function and direct repair in the central nervous system (CNS) have been established by the merger of gene transfer technology with neural transplantation. Rapid advances in viral‐mediated DNA‐delivery procedures permit the study of novel gene expression in neurons and glial cells. Foreign genes, transferred by a virus vector, can be used to generate new cell lines, identify transplanted cells, and express growth factors or enzymes for neurotransmitter synthesis. In addition to CNS cell types, (...) non‐neural cells are also being studied with transgene technology in the nervous system. Functional effects have been obtained with grafts of genetically modified cells in animal models of several nervous system disorders, and the recent results set the stage for potential application of these techniques to human CNS gene therapy. (shrink)

In discussions of the ethics of human gene therapy, it has become standard to draw a distinction between the use of human gene transfer techniques to treat health problems and their use to enhance or improve normal human traits. Some dispute the normative force of this distinction by arguing that it is undercut by the legitimate medical use of human gene transfer techniques to prevent disease - such as genetic engineering to bolster immune (...) function, improve the efficiency of DNA repair, or add cellular receptors to capture and process cholesterol. If disease prevention is a proper goal of medicine, these critics argue, and the use of gene transfer techniques to enhance human health maintenance capacities will help achieve that goal, then the “treatment/enhancement‘ distinction cannot define the limits of legitimate gene therapy. In this paper, I argue that a line can be drawn between prevention and enhancement for gene therapy (and thus between properly medical and nonmedical uses of gene therapy), but only if one is willing to accept two rather old-fashioned claims: 1) Some health problems are best understood as if they were entities in their own right, reifiable as processes or parts in a biological system, with at least as much ontological objectivity and theoretical significance as the functions that they inhibit. 2) Legitimate preventive genetic health care should be limited to efforts to defend people from attack by these more robust pathological entities, rather than changing their bodies to evade social injustices. (shrink)

Subjects enrolled in studies testing high risk interventions for incurable or progressive brain diseases may be vulnerable to deficiencies in informed consent, such as the therapeutic misconception. However, the definition and measurement of the therapeutic misconception is a subject of continuing debate. Our qualitative pilot study of persons enrolled in a phase I trial of gene transfer for Parkinson disease suggests potential avenues for both measuring and preventing the therapeutic misconception. Building on earlier literature on the topic, we (...) developed and tested an interview guide that focuses on how the subjects decided to participate, emphasizing the integration of subjects’ various statements that are relevant to assessing the therapeutic misconception, rather than evaluating them as isolated statements. The results indicate that a subject’s understanding of the purpose of research is best explored in juxtaposition to the subject’s motivation for participating. (shrink)

The concept of human gene therapy came on the heels of fundamental discoveries on the nature and working of the gene. However, realistic prospects to correct the underlying cause of recessive genetic disorders through the transfer of wild‐type alleles of defective genes had to wait for the arrival of recombinant DNA technology. These techniques permitted the isolation and insertion of genes into the first recombinant delivery systems. The realization that viruses are natural gene carriers provided (...) inspiration for gene therapy and, as engineered vectors, viruses became prominent gene delivery vehicles. Nonetheless, when put in the context of human and non‐human primate studies, all vectors fell short of success regardless of their viral or non‐viral origin. Recognition of issues such as inefficient gene transfer and short‐lived or scant expression in the relevant cell type(s) prompted researchers to refine and develop several gene delivery systems, in particular those based on retroviruses, adeno‐associated viruses and adenoviruses. Concomitantly, available technology was deployed to tackle disorders that require few genetically corrected cells to attain therapy. BioEssays 27: 506–517, 2005. © 2005 Wiley periodicals, Inc. (shrink)

In 1969, the field of human genetics was in its infancy. Amniocentesis was a new technique for prenatal diagnosis, and a newborn genetic screening program had been established in one state. There were also concerns about the potential hazards of genetic engineering. A research group at the Hastings Center and Paul Ramsey pioneered in the discussion of genetics and bioethics. Two principal techniques have emerged as being of enduring importance: human gene transfer research and genetic testing and (...) screening. This essay tracks the development and use of these techniques and considers the ethical issues that they raise. (shrink)

Kenneth Waters and Marcel Weber argue that the joint use of distinct gene concepts and the transfer of knowledge between classical and molecular analyses in contemporary scientific practice is possible because classical and molecular concepts of the gene refer to overlapping chromosomal segments and the DNA sequences associated with these segments. However, while pointing in the direction of coreference, both authors also agree that there is a considerable divergence between the actual sequences that count as genes in (...) classical genetics and molecular biology. The thesis advanced in this paper is that the referents of classical and molecular gene concepts are coextensive to a higher degree than admitted by Waters and Weber, and therefore coreference can provide a satisfactory account of the high level of integration between classical genetics and molecular biology. In particular, I argue that the functional units/cistrons identified by classical techniques overlap with functional elements entering the composition of molecular transcription units, and that the precision of this overlap can be improved by conducting further experimentation. (shrink)

The February 1997 announcement of the birth of Dolly, the sheep cloned from a mammary cell of an adult ewe, has drawn attention to the growing ability to select, alter, or otherwise manipulate the genome of offspring. Prior to Dolly, ethical discussion of genes in reproduction had focused on negative selection: carrier screening, prenatal diagnosis, and abortion or embryo discard. After Dolly, ethical debate will have to consider the direct or positive use of genetic selection or alteration technology.The principal use (...) of genetic selection techniques in human reproduction likely will be to treat or prevent disease in offspring. In the future, however, such techniques might also be used to enhance or even diminish expected characteristics of progeny. Techniques to accomplish these goals are likely to include: selection of the nuclear genome, as occurs in somatic cell cloning; chromosomal transplants; or direct insertion or deletion of specific genes. (shrink)

Doping can be both of chemical and protein nature or may involve prohibited methods, such as illegal blood transfusions. The rapidly increasing number of genetic therapies as a promising new branch of regular medicine, has raised the issue whether these techniques might be abused in the field of sports. The risks involved in gene doping are several, and are related both to the vector protein used (DNA, chemical, viral) and to the encoded transgene. A concern in the athletic (...) community is that no one knows how easily gene doping can be detected. The DNA used for gene transfer is of human origin, and not different from that of the person applying gene doping. A combination of developing detection methods based on gene arrays or proteomics and a clear education program on the associated risks seems to be the most promising preventive method to counteract the possible application of gene doping. (shrink)

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural (...) phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available—polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis—could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for ‘shadow microbes’ (heretofore unrecognized ‘alien’ forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as ‘biological’ or ‘nonbiological’. Ó 2007 Elsevier Ltd.. (shrink)

Over the past several decades, geneticists have succeeded in identifying the genetic mutations associated with disease. New strategies for treatment, including gene transfer and gene therapy, are under development. Although genetic science has been welcomed for its potential to predict and treat disease, interventions may become ethically objectionable if they threaten to alter characteristics that are distinctively human. Before we can determine whether or not a genetic technique carries this risk, we must clarify what it means to (...) be “human”. This paper inquires how “humanness” has been defined within various academic fields. The views of several legal theoreists, scientists, bioethicists, psychologists, philosophers and anthropologists whose works seem to best reflect how “humanness” is understood in their respective fields of study are considered. Our survey attempts to chart a path for a more detailed study on the meaning of “humanness” in the future. (shrink)

Recent results confirm that long‐term expression of therapeutic transgenes can be achieved by using a transposon‐based system in primary stem cells and in vivo. Transposable elements are natural DNA transfer vehicles that are capable of efficient genomic insertion. The latest generation, Sleeping Beauty transposon‐based hyperactive vector (SB100X), is able to address the basic problem of non‐viral approaches – that is, low efficiency of stable gene transfer. The combination of transposon‐based non‐viral gene transfer with the latest (...) improvements of non‐viral delivery techniques could provide a long‐term therapeutic effect without compromising biosafety. The new challenges of pre‐clinical research will focus on further refinement of the technology in large animal models and improving the safety profile of SB vectors by target‐selected transgene integration into genomic “safe harbors.” The first clinical application of the SB system will help to validate the safety of this approach. (shrink)

The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück’s phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA, genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due (...) to the availability of specific RNases, enzymes used as chemical tools to analyse RNA. Finally, RNA phages provided scientists with a pure source of mRNA to investigate the genetic code, genes and even a genome sequence. This paper focuses on Walter Fiers’ laboratory at Ghent University and their work on the RNA phage MS2. When setting up his Laboratory of Molecular Biology, Fiers planned a comprehensive study of the virus with a strong emphasis on the issue of structure. In his lab, RNA sequencing, now a little-known technique, evolved gradually from a means to solve the genetic code, to a tool for completing the first genome sequence. Thus, I follow the research pathway of Fiers and his ‘RNA phage lab’ with their evolving experimental system from 1960 to the late 1970s. This study illuminates two decisive shifts in post-war biology: the emergence of molecular biology as a discipline in the 1960s in Europe and of genomics in the 1990s. (shrink)

We present an annotated bibliography of peer reviewed scientific research highlighting the human health, animal welfare, and environmental risks associated with genetic modification. Risks associated with the expression of the transgenic material include concerns over resistance and non-target effects of crops expressing Bt toxins, consequences of herbicide use associated with genetically modified herbicide-tolerant plants, and transfer of gene expression from genetically modified crops through vertical and horizontal gene transfer. These risks are not connected to the technique (...) of genetic modification as such, but would be present for any conventionally produced crops with the same heritable traits. In contrast, other risks are a direct consequence of the method used in gene manipulation. These come about because of the unstable nature of the transgene and vectors used to insert it, and because of unpredictable interactions between the transgene and the host genome. The debate over the release of genetically modified organisms is not merely a scientific one; it encompasses economics, law, ethics, and policy. Any discussion on these levels does, however, need to be informed by sound science. We hope that the scientific references provided here will provide a useful starting point for further debate. (shrink)

Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications (...) landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of media coverage. (shrink)

The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In (...) addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology (...) and computational science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

In this article I argue that the proper subjects of intangible property claims include medical records, genetic profiles, and gene enhancement techniques. Coupled with a right to privacy these intangible property rights allow individuals a zone of control that will, in most cases, justifiably exclude governmental or societal invasions into private domains. I argue that the threshold for overriding privacy rights and intangible property rights is higher, in relation to genetic enhancement techniques and sensitive personal information, than (...) is commonly suggested. Once the bar is raised, so‐to‐speak, the burden of overriding it is formidable. Thus many policy decisions that have been recently proposed or enacted – citywide audio and video surveillance, law enforcement DNA sweeps, genetic profiling, national bans on genetic testing and enhancement of humans, to name a few – will have to be backed by very strong arguments. (shrink)

Clinical gene transfer research has both a unique history and a complex and layered system of research oversight, featuring a unique review body, the Recombinant DNA Advisory Committee. This paper briefly describes the process of decision-making about clinical GTR, considers whether the questions, problems, and issues raised in clinical GTR are unique, and concludes by examining whether the RAC's oversight is a useful model that should be reproduced for other similar areas of clinical research.Clinical GTR is governed by (...) the same oversight system as most clinical trials, with a significant addition: the RAC. Like other research with human subjects, GTR, if it is affiliated with a federally funded institution, must be approved by an institutional review board whose activities are governed by the common rule, that is, the federal regulations for protection of human subjects in research. Like other research intended to produce a drug, device, or biologic to be marketed in the United States, GTR is also overseen by the Food and Drug Administration. (shrink)

Information and communication technologies , with their increasing and widespread utilization in daily life, may exert an important impact on brain performances. The development of their use for improving several cerebral processes, by abolishing the brain/machine interface, is envisaged and is subject to debate. The scientific research on brain implants and brain gene transfer aiming to restore central nervous system functions, altered by disease or trauma, may contribute to this debate. Indeed, the advances that are enabling non drug-mediated (...) approaches for direct interventions on the brain are raising the possibility not only of restoring neural functions for therapeutic purposes, but also of monitoring, controlling and ultimately modifying from the outside these functions for enhancement. This paper gives an overview of the state of the art of brain implants and brain gene transfer for neurological diseases with a particular emphasis on Parkinson’s disease and a forecast on their possible application for other conditions. In doing so, the authors, who are neuroscientists working in the field of gene transfer for neuropsychiatric diseases, aim to establish a scientifically, medically and technically realistic framework to open up discussion on relevant ethical issues in this domain. (shrink)

In a recent BioEssays paper [W. F. Martin, BioEssays 2017, 39, 1700115], William Martin sharply criticizes evolutionary interpretations that involve lateral gene transfer into eukaryotic genomes. Most published examples of LGTs in eukaryotes, he suggests, are in fact contaminants, ancestral genes that have been lost from other extant lineages, or the result of artefactual phylogenetic inferences. Martin argues that, except for transfers that occurred from endosymbiotic organelles, eukaryote LGT is insignificant. Here, in reviewing this field, we seek to (...) correct some of the misconceptions presented therein with regard to the evidence for LGT in eukaryotes. A recent paper dismisses claims of lateral gene transfer into eukaryotic genomes. We counter the arguments made in that paper and discuss the extensive evidence for LGT in eukaryotes. (shrink)

Attentional focus is an area that has garnered considerable attention in the sport psychology and motor performance literature. This is unsurprising given that attentional focus has been directly linked to performance outcomes and is susceptible to coaching input. While research has amassed supporting benefits of an external focus of attention on motor performance using verbal instruction, other studies have challenged the notion that an EFA is more beneficial than an internal focus of attention for sport-related performance. Further, it is unclear (...) what type of instructions may serve to direct an athlete to an EFA and, in particular, if coaching can utilize imagery to orient an athlete toward an EFA. In the present exploratory study, we evaluate the effectiveness of instruction to improve free-throw shooting performance with an emphasis on an EFA brought about by implementing techniques borrowed from the imagery literature. This was tested relative to an alternate approach with an IFA induced through an emphasis on technique, devised to more closely resemble input typical of coach-to-athlete instruction. Twenty-five male and female university basketball players completed both conditions in a fully counterbalanced within-subject design. Results confirmed that participants in the EFA imagery condition had greater shooting accuracy than in the IFA technique condition. The study provides initial evidence that EFA coaching can borrow from imagery techniques, though future research should elucidate the underlying mechanisms of the effect. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Kennedy Institute of Ethics Journal 10.2 (2000) 171-174 [Access article in PDF] Bioethics Inside the Beltway The Oversight of Human Gene Transfer Research LeRoy Walters Jesse Gelsinger's death last September in a gene transfer study being conducted at the University of Pennsylvania has helped to spark a national debate. In part, this debate parallels the broader discussion of how human subjects research should be reviewed (...) and regulated in the United States. However, human gene transfer research is one of a handful of biomedical technologies that seem to deserve special attention, at least in the early years of their development.The major participants in the national debate on human gene transfer include the National Institutes of Health (NIH), the Food and Drug Administration (FDA), the National Bioethics Advisory Commission, members of Congress, biotechnology and pharmaceutical companies, disease-oriented advocacy groups, reporters, and academics. At the December 1999 meeting of the NIH Recombinant DNA Advisory Committee (RAC), the protocol that involved Jesse Gelsinger was a central focus of discussion, but other topics emerged as well. One ad hoc panel reviewed adverse events that had occurred in other research protocols using adenovirus vectors, while a second proposed changes in the general system for reporting adverse events to NIH and the RAC.During the first several months of the year 2000, the United States Congress also became involved in the human gene transfer debate. In February, Senator Bill Frist (R-TN) convened a hearing to which Jesse Gelsinger's father, representatives of NIH and FDA, and several other witnesses were invited. At approximately the same time, the House Commerce Committee and its Subcommittee on Oversight and Investigations initiated their own inquiries, asking the Office of Inspector General at the Department of Health and Human Services to review the oversight roles of NIH and FDA. In March and April, the House committee also wrote directly to the NIH Director, the FDA Commissioner, and the President of the University of Pennsylvania, requesting extensive documentation on gene transfer, in general, and the trial in which Jesse Gelsinger was involved, in particular. Congressman Henry Waxman (D-CA) and Senator Edward Kennedy (D-MA) have also raised questions and proposed solutions in multiple letters to the NIH Director and the Secretary of Health and Human Services. [End Page 171]The major general questions that have emerged from this discussion are the following:(1) What kinds of information about adverse events should be reported by researchers or sponsors during the course of human gene transfer trials?(2) To what group or groups should adverse-event information be reported? How often and in what ways should the information be analyzed?(3) Should the information about adverse events remain confidential, or should it be discussed publicly?(4) How can the disclosure and consent process in gene transfer trials be improved?(5) Which federal agency should have primary responsibility for overseeing human gene transfer research, and how can it best fulfill its oversight role?How these questions are answered will have immediate relevance to the field of human gene transfer research as it enters into its next phase. At the same time, the models that are created for this important cutting-edge field also may be useful in other complex or controversial arenas of biomedical research, for example, xenotransplantation or human embryonic stem-cell research. In addition, the lessons learned from this one important area of human subjects research may suggest ways to improve protections for all the volunteers who make clinical research--and medical progress--possible.In the remainder of this article, I will turn from reporting, in as objective a way as possible, on the status of the public policy debate about human gene transfer research to suggesting measures for improving the current oversight system for such research. My initial general recommendation is that we should not expect a single regulatory agency to be solely responsible for a field as large and dynamic as human gene transfer research. Rather, there should be some helpful redundancy or, to change the metaphor, checks and balances in the public oversight of this field. Thus, an... (shrink)

A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge (...) networks by fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. (shrink)

During evolution, the genomes of eukaryotic cells have undergone major restructuring to meet the new regulatory challenges associated with compartmentalization of the genetic material in the nucleus and the organelles acquired by endosymbiosis (mitochondria and plastids). Restructuring involved the loss of dispensable or redundant genes and the massive translocation of genes from the ancestral organelles to the nucleus. Genomics and bioinformatic data suggest that the process of DNA transfer from organelles to the nucleus still continues, providing raw material for (...) evolutionary tinkering in the nuclear genome. Recent reconstruction of these events in the laboratory has provided a unique tool to observe genome evolution in real time and to study the molecular mechanisms by which plastid genes are converted into functional nuclear genes. Here, we summarize current knowledge about plastid‐to‐nuclear gene transfer in the context of genome evolution and discuss new insights gained from experiments that recapitulate endosymbiotic gene transfer in the laboratory. BioEssays 30:556–566, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Horizontal gene transfer (HGT) is a major mechanism responsible for the spread of antibiotic resistance. Conversely, it is often assumed that antibiotics promote HGT. Careful dissection of the literature, however, suggests a lack of conclusive evidence supporting this notion in general. This is largely due to the lack of well‐defined quantitative experiments to address this question in an unambiguous manner. In this review, we discuss the extent to which HGT is responsible for the spread of antibiotic resistance and (...) examine what is known about the effect of antibiotics on the HGT dynamics. We focus on conjugation, which is the dominant mode of HGT responsible for spreading antibiotic resistance on the global scale. Our analysis reveals a need to design experiments to quantify HGT in such a way to facilitate rigorous data interpretation. Such measurements are critical for developing novel strategies to combat resistance spread through HGT. -/- . (shrink)

The most common form of the CO2‐fixing enzyme rubisco is a form I enzyme, heretofore found universally in oxygenic phototrophs (cyanobacteria and plastids) and widely in proteobacteria. Two groups(1–4), however, now report that in dinoflagellate plastids the usual form I rubisco has been replaced by the distantly related form II enzyme, known previously only from anaerobic proteobacteria. This raises the important question of how such an oxygensensitive rubisco could function in an aerobic organism. Moreover, the dinoflagellate rubisco has unusual molecular (...) properties: it is encoded as a polyprotein, by nuclear (rather than plastid) genes, and these genes contain noncanonical spliceosomal introns. The nuclear location and alphaproteobacterial affinity of dinoflagellate rubisco genes hint at a possible mitochondrial origin and highlight the extraordinary richness of lateral gene transfers, both between and within organisms, that have occurred during rubisco evolution. (shrink)

Recent developments in studies of sperm‐mediated gene transfer (SMGT) now provide solid ground for the notion that sperm cells can act as vectors for exogenous genetic sequences. A substantive body of evidence indicates that SMGT is potentially useable in animal transgenesis, but also suggests that the final fate of the exogenous sequences transferred by sperm is not always predictable. The analysis of SMGT‐derived offspring has shown the existence of integrated foreign sequences in some cases, while in others stable (...) modifications of the genome are difficult to detect. The appearance of SMGT‐derived modified offspring on the one hand and, on the other hand, the rarity of actual modification of the genome, suggest inheritance as extrachromosomal structures. Several specific factors have been identified that mediate distinct steps in SMGT. Among those, a prominent role is played by an endogenous reverse transcriptase of retrotransposon origin. Mature spermatozoa are naturally protected against the intrusion of foreign nucleic acid molecules; however, particular environmental conditions, such as those occurring during human assisted reproduction, can abolish this protection. The possibility that sperm cells under these conditions carry genetic sequences affecting the integrity or identity of the host genome should be critically considered. These considerations further suggest the possibility that SMGT events may occasionally take place in nature, with profound implications for evolutionary processes. BioEssays 27: 551–562, 2005. © 2005 Wiley periodicals, Inc. (shrink)

This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a (...) phylogenetic tree will split differently than if the identity of an organism does not survive the fission process. (shrink)

In contrast to bilaterian animals, non‐bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of (...) the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter‐domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA. (shrink)

We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other hand, taxonomic (...) patterns in microbial phylogenies might also be created through biased gene transfer. The agreement between different molecular phylogenies has encouraged interpretation of the consensus signal as reflecting organismal history or as the tree of cell divisions; however, to date the extent to which the consensus reflects shared organismal ancestry and to which it reflects highways of gene sharing and biased gene transfer remains an open question. Preferential patterns of gene exchange act as a homogenizing force in creating and maintaining microbial groups, generating taxonomic patterns that are indistinguishable to those created by shared ancestry. To understand the evolution of higher bacterial taxonomic units, concepts usually applied in population genetics need to be applied. (shrink)

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the (...) latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution.Editor's suggested further reading in BioEssaysLinguistic evidence supports date for Homeric epics Abstract. (shrink)

In the early 1970s, the major industrial states were preparing to shift to nuclear fission as their principal source of electrical power. But that change has not occurred. In part, this is due to a growing public recognition that techniques and institutions for management of spent nuclear fuel, separated plutonium, and long-lived radioactive wastes are not yet fully developed. The consequent pressures for resolution have spurred a series of often ill-defined and sometimes contradictory attempts to promote international cooperation and (...) control of hazardous activities. How are these varied suggestions to be compared and evaluated? By what criteria can plans be selected that are likely to be both effective and negotiable? In this study, Gene I. Rochlin, physicist and social scientist, explores the technical, political, and institutional aspects of international nuclear export and fuel cycle policies. He categorizes existing proposals and suggests way to develop new ones that better promote both national and international goals. Dr. Rochlin argues neither for nor against the use of nuclear power or plutonium fuels. Instead, he addresses the question of how international arrangements could be reached that might jointly satisfy the objective of the several key nations, yet not be too difficult to negotiate. He concludes that a major fault has been the tendency to improvise arrangements for specific technical or industrial operations. As a result, overall social and political goals have become the bargaining points for compromise. Yet attempts to simultaneously resolve all problems are unlikely to prove fruitful. Dr. Rochlin suggests instead the formation of institutions organized around more limited social, political, and technical objectives, even at the expense of excluding some nations or omitting some aspects of the nuclear fuel cycle. Only by so doing, he argues, can immediate agreements be reached that preserve the potential for more comprehensive future arrangements without sacrificing industrial, environmental, or nonproliferation goals. This important book will be of interest to scientists, social scientists, government officials, and others concerned with the problems of plutonium management and nuclear wastes. (shrink)

As new biotechnologies are developed, the parallels with GM crops are often drawn. In this paper, I consider GM animals and contrast them with GM crops. I use a systems of innovation perspective to consider innovation, product markets and regulatory systems and suggest that whilst there are some parallels between GM crops and animals there are also clear differences. There are differences in the techniques used, the availability of single genes useful for transfer and the acceptability of 'failures'. (...) Existing animal breeding techniques are competitive with GM technologies and dissemination of GM animals into a population is difficult and time consuming. The structure of the industry is different between crops and livestock with large multinational companies largely absent in the production of farm livestock for breeding. Additionally animal welfare and ethical aspects are widely recognised as important in the context of GM animals, but the likely impacts of welfare and ethicsbased regulation on any GM animal production is not clear. All these differences are potentially important for the future trajectory of the technology. I also suggest that at present, the development of GM animals is being pulled in different directions by the opening up of technological possibilities and the emphasis on animal welfare and notions of animal integrity. (shrink)

Presented in six principal analytic chapters with supporting appendices, this book explores the role of Islam in precipitating Europe's twelfth century commercial renaissance. Employing the classic analytic techniques of economics, Gene Heck determines that medieval Europe's feudal interregnum was largely caused by indigenous governmental business regulation and not by shifts in international trade patterns. He then proceeds by demonstrating how Islamic economic precepts provided the ideological rationales that empowered medieval Europe to escape its three-centuries-long experiment in "Dark Age (...) economics" ― in the process, providing the West with its archetypic tools of capitalism. While treatises such as Maxime Rodinson's excellent book, Islam and Capitalism, document the capitalistic nature of the Islamic economic system, in applying modern economic method to medieval orientalist historiography, this work is unique in capturing both the evolution and the impact of the system's role in forging medieval history. (shrink)

DNA methylation constitutes one of the pillars of epigenetics, relying on covalent bonds for addition and/or removal of chemically distinct marks within the major groove of the double helix. DNA methyltransferases, enzymes which introduce methyl marks, initially evolved in prokaryotes as components of restriction‐modification systems protecting host genomes from bacteriophages and other invading foreign DNA. In early eukaryotic evolution, DNA methyltransferases were horizontally transferred from bacteria into eukaryotes several times and independently co‐opted into epigenetic regulatory systems, primarily via establishing connections (...) with the chromatin environment. While C5‐methylcytosine is the cornerstone of plant and animal epigenetics and has been investigated in much detail, the epigenetic role of other methylated bases is less clear. The recent addition of N4‐methylcytosine of bacterial origin as a metazoan DNA modification highlights the prerequisites for foreign gene co‐option into the host regulatory networks, and challenges the existing paradigms concerning the origin and evolution of eukaryotic regulatory systems. (shrink)

The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), (...) and their associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity. (shrink)

Background: “Therapeutic misconception” arises when human subjects interpret a clinical trial as aimed primarily at therapy rather than producing knowledge. Therapeutic misconceptions may be more prevalent in trials enrolling gravely ill subjects or involving novel and well publicised investigational agents.Objective: To examine the extent to which investigators express therapeutic optimism in phase 1 human gene transfer consent documents, whether highly active gene transfer researchers are more prone to expressing therapeutic optimism, and whether consent forms have grown (...) more optimistic in their descriptions of personal benefit over the last decade.Design: Content analysis was performed on 277 consent documents to measure the number of sentences describing possibility of benefit, terminology used for experimental agents, the proportion of statements describing personal versus societal benefits, and whether investigators attempted to thwart therapeutic misconceptions.Results: Consent forms generally used therapeutic terminology to describe study agents, devoted more sentences to describing possible personal benefits than to describing benefits to society, and infrequently explained that a particular benefit was unlikely. Consent documents used by highly active gene transfer researchers tended to portray significantly greater optimism about personal benefit than less active investigators, though they were also significantly more cautious with agent terminology. Finally, therapeutic optimism expressed in consent forms has declined over the past decade.Conclusions: Consent documents used in phase 1 gene transfer trials, although increasingly attentive to possible therapeutic misconceptions, are inappropriately optimistic about direct benefits of trial participation. Such optimism is expressed more emphatically in trials involving highly active gene transfer researchers as principal investigators. (shrink)

Dawkins in his The Selfish Gene(1) quite aptly applies the term “selfish” to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as (...) infectiously by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional “tree of life”.(5–10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT. BioEssays 27:741–747, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Traditionally, plant viruses are viewed as harmful, undesirable pathogens. However, their genomes can provide several useful ‘designer functions’ or ‘sequence modules’ with which to tailor future gene vectors for plant or general biotechnology.The majority (77 %) of known plant viruses have single‐stranded RNA of the messenger (protein coding) sense as their genetic material. Over the past 4 years, improved in vitro transcription systems and the construction of partial of fulllength DNA copies of several plant RNA viruses have enhanced our (...) ability to manipulate and study their genomes, particularly in the context of their pathogenic interactions with host plants.Recently, two forms of genetically engineered protection against plant virus infections have been reported. In both, a virus‐related ‘interfering’ molecule was stably introduced into plants via the DNA‐transfer mechanism of Agro‐bacterium tumefaciens. To date, the choice of ‘interfering’ molecule has been guided by empirical field‐observations and each is effective against only a narrow range of closely‐related viruses. As yet, we do not fully understand the molecular mechanism(s) responsible for the observed protection.The ability to manipulate the plant–pathogen relationship is a powerful tool to increase our knowledge and improve future strategies for uncoventional cropprotection by genetic engineering techniques. (shrink)

Passive Cooling addresses all of the existing creative energyless means of keeping buildings cool. Unlike passive heating, which draws on the sun, passive cooling relies on three natural heat sinks - the sky, the atmosphere, and the earth to achieve temperature moderation. This book describes and evaluates mechanisms for coupling buildings to these sinks and ways of integrating multiple strategies into effective passive cooling systems.In "Radiative Cooling," Marlo Martin explains how the sky specifically outer space - acts as the ultimate (...) absorber to balance energy inputs from the sun as well as other sources. "Ventilative Cooling" by Subrato Chandra and "Evaporative Cooling" by John Yellott describe two ways in which the atmosphere can serve as a medium of heat transfer. The third natural heat sink the earth, is evaluated by Kenneth Labs in "Earth Coupling." Gene Clark in "Passive Cooling Systems" explains how each of these cooling resources affects the design of a building in a dramatically different way and shows how they can be combined. And Jeffrey Cook reviews the current state of basic and applied research projects and anticipates promising future directions of study and application.Because passive cooling techniques have a rich and diverse history of worldwide development and application, the editor has taken special care to relate developments in the United States to international practice and research, providing a broad base for professional redirection in building design.Jeffrey Cook is Regents Professor of Architecture at Arizona State University. Passive Cooling is volume 8 in the series Solar Heat Technologies: Fundamentals and Applications, edited by Charles A Bankston. (shrink)

An urgent need for standards and guidelines on genetic testing has arisen because of swift advances in research, facilitated by the Human Genome Project. The goals of the Human Genome Project include the identification of all genes and sequencing of the human genome. The project is currently ahead of schedule and under budget. We can expect an avalanche of genetic information, much of which will be relevant to human disease. In addition to the Human Genome Project, investigator-initiated research projects and (...) commercial biotechnology laboratories are discovering human disease genes at a breathtaking pace. Technology transfer has been rapid and has led to the availability of numerous clinical tests within only a few years since the first disease gene yielded to the technique of positional cloning. Disease genes are selected for study for a number of reasons. Genes for rare diseases may be studied before more common disorders because they elucidate an important area of pathogenesis. Unfortunately, technology transfer to the clinic for rare tests is hindered by several factors. Standards need to be established to assure that genetic tests for rare diseases are not ignored or mismanaged in the rush to commercialize tests for more common human genetic diseases. (shrink)