Current knowledge of gene flow in plants: implications for transgene flow

Plant evolutionary biologists' view of gene flow and hybridization has undergone a revolution. Twenty-five years ago, both were considered rare and largely inconsequential. Now gene flow and hybridization are known to be idiosyncratic, varying with the specific populations involved. Gene flow typically occurs at evolutionarily significant rates and at significant distances. Spontaneous hybridization occasionally has important applied consequences, such as stimulating the evolution of more aggressive invasives and increasing the extinction risk for rare species. The same problems have occurred for spontaneous hybridization between crops and their wild relatives. These new data have implications for transgenic crops: (i) for most crops, gene flow can act to introduce engineered genes into wild populations; (ii) depending on the specific engineered gene(s) and populations involved, gene flow may have the same negative impacts as those observed for traditionally improved crops; (iii) gene flow's idiosyncratic nature may frustrate management and monitoring attempts; and (iv) intercrop transgene flow, although rarely discussed, is equally worthy of study.     

Assessing risks and benefits of floral supplements in conservation biological control

The use of flowering field margins is often proposed as a method to support biological control in agro-ecosystems. In addition to beneficial insects, many herbivores depend on floral food as well. The indiscriminate use of flowering species in field margins can therefore lead to higher pest numbers. Based on results from field observations and laboratory experiments we assessed risks as well as benefits associated with the provision of nectar plants in field margins, using Brussels sprouts as a model system. Results show that Brussels sprouts bordered by nectar plants suitable for the cabbage white Pieris rapae L., suffered higher infestation levels by this herbivore. In contrast, nectar plants providing accessible nectar for the diamondback moth Plutella xylostella L., did not raise densities of P. xylostella larvae in the Brassica crop. Margins with Anethum graveolens L., selected on the basis of its suitability as nectar plant for parasitoids, significantly increased the number of adult Diadegma semiclausum Hellén in the crop. This didn’t translate into enhanced parasitism rates, as parasitism of P. xylostella by D. semiclausum exceeded 65 % in all treatments, irrespective of the plants in the field margin. Our findings emphasize the importance of taking a multitrophic approach when choosing flowering field margin plants for biocontrol or other ecosystem services.     

Assessing and managing methylmercury risks associated with power plant mercury emissions in the United States

Until the Clean Air Mercury Rule was signed in March 2005, coal-fired electric utilities were the only remaining, unregulated major source of industrial mercury emissions in the United States. Proponents of coal-burning power plants assert that methylmercury is not a hazard at the current environmental levels, that current technologies for limiting emissions are unreliable, and that reducing mercury emissions from power plants in the United States will have little impact on environmental levels. Opponents of coal-burning plants assert that current methylmercury exposures from fish are damaging to the developing nervous system of infants, children, and the fetus; that current technology can significantly limit emissions; and that reducing emissions will reduce exposure and risk. One concern is that local mercury emissions from power plants may contribute to higher local exposure levels, or "hot spots." The impact of the Mercury Rule on potential hot spots is uncertain due to the highly site-specific nature of the relationship between plant emissions and local fish methylmercury levels. The impact on the primary source of exposure in the United States, ocean fish, is likely to be negligible due to the contribution of natural sources and industrial sources outside the United States. Another debate centers on the toxic potency of methylmercury, with the scientific basis of the US Environmental Protection Agency's (EPA's) recommended exposure limit questioned by some and defended by others. It is likely that the EPA's exposure limit may be appropriate for combined exposure to methylmercury and polychlorinated biphenyls (PCBs), but may be lower than the available data suggest is necessary to protect children from methylmercury alone. Mercury emissions from power plants are a global problem. Without a global approach to developing and implementing clean coal technologies, limiting US power plant emissions alone will have little impact.     

Fluid flow in a spiral device used for irradiation of biological fluids

The manufacture of plasma‐derived therapeutics includes dedicated viral inactivation steps to minimize the risk of infection. Traditional viral inactivation methods are effective for the removal and inactivation of enveloped viruses, but less effective against small nonenveloped viruses. UV‐C irradiation has been demonstrated to be an effective means of inactivating such viruses. The UVivatec lab system consists of a spiral tube around an UV‐C irradiation source. Flow of a solution through the chamber generates and ensures controlled mixing and uniform exposure to irradiation. A detailed assessment of the effect of flow rate, alternate cross sectional design and scale up of the irradiation chamber on Dean vortices was performed using the smoothed particle hydrodynamics method. The aim was to provide a basis for setting flow rate limits and using a laboratory scale apparatus to model viral inactivation in larger manufacturing scale equipment. The effect of flow rate related changes on the fluence rate was also investigated through chemical actinometry studies. The data were consistent with the simulations indicating that Dean vortices were present at low flow rates, but dissipated at higher flow rates through the spiral chamber. Importantly, this work also allowed a correlation between the small system and large scale system to be established. This will greatly facilitate process development and viral validation studies. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29: 359–367, 2013     

Risk mitigation of genetically modified bacteria and plants designed for bioremediation

While the possible advantages of bioremediation and phytoremediation, by both recombinant microbes and plants, have been extensively reviewed, the biosafety concerns have been less extensively treated. This article reviews the possible risks associated with the use of recombinant bacteria and plants for bioremediation, with particular emphasis on ways in which molecular genetics could contribute to risk mitigation. For example, genetic techniques exist that permit the site-specific excision of unnecessary DNA, so that only the transgenes of interest remain. Other mechanisms exist whereby the recombinant plants or bacteria contain conditional suicide genes that may be activated under certain conditions. These methods act to prevent the spread and survival of the transgenic bacteria or plants in the environment, and to prevent horizontal gene flow to wild or cultivated relatives. Ways in which these genetic technologies may be applied to risk mitigation in bioremediation and phytoremediation are discussed.     

Web-based applications for building, managing and analysing kinetic models of biological systems

Mathematical modelling and computational analysis play an essentialrole in improving our capability to elucidate the functionsand characteristics of complex biological systems such as metabolic,regulatory and cell signalling pathways. The modelling and concomitantsimulation render it possible to predict the cellular behaviourof systems under various genetically and/or environmentallyperturbed conditions. This motivates systems biologists/bioengineers/bioinformaticiansto develop new tools and applications, allowing non-expertsto easily conduct such modelling and analysis. However, amonga multitude of systems biology tools developed to date, onlya handful of projects have adopted a web-based approach to kineticmodelling. In this report, we evaluate the capabilities andcharacteristics of current web-based tools in systems biologyand identify desirable features, limitations and bottlenecksfor further improvements in terms of usability and functionality.A short discussion on software architecture issues involvedin web-based applications and the approaches taken by existingtools is included for those interested in developing their ownsimulation applications.      

Assessing the efficiency of methods for the bioremediation of oil production wastes

The results obtained during the laboratory remediation modeling of oil-containing waste (652 g/kg) and natural radionuclides (Ra²²⁶, Th²³², and K⁴⁰) using the methods of landfarming, biostimulation, and bioaugmentation are given in the article. It is found that landfarming and biostimulation decrease the content of oil products and phytotoxicity of the waste. Landfarming is the most rapid process.     

Assessing and managing breast cancer risk: clinical tools for advising patients

Using breast cancer risk assessment tools and going through the process of assessing breast cancer risk can answer many women's questions about what puts them at relatively higher or lower risk. This effectively engages both the clinician and the patient in a discussion about breast cancer, the chances of getting it, and the family's involvement--making the process as important as the actual tools. Examples of selected case histories demonstrate risk assessment using available tools such as the Gail-NCI and the Claus models. For some women, such as those considering tamoxifen or prophylactic surgeries, it may be desirable to prescreen for the inheritance of hereditary mutations and to follow with genetic testing, if indicated. Testing for mutations of breast cancer susceptibility genes or for their diminished expression adds to our ability to assess breast cancer risk at an individual level. The literature contains general interventions that are widely accepted to reduce the severity and the burden of breast cancer, and these are brought together here. The risk assessment process is an important part of a risk reduction program and can help motivate women to engage in prevention activities. This paper uses 2 hypothetical but fact-based and typical case histories to discuss the utility of risk assessment tools for informing women about their options.     

Soil chromium bioremediation: Synergic activity of actinobacteria and plants

The aim of this work was to evaluate a strategy to reduce the bioavailable chromium fraction in soil, using a Cr(VI) resistant microorganism, Streptomyces sp. MC1, under non sterile conditions, with maize plants as bioindicator and/or bioremediator.Soil samples were contaminated with 100, 200 and 400 mg kg⁻¹ of Cr(VI) or Cr(III). Bioavailable chromium (35%) was only detected in samples with Cr(VI). Soil samples with Cr(VI) 200 mg kg⁻¹ were inoculated with Streptomyces sp. MC1, and bioavailable chromium decreased up to 73%.Zea mays seedlings were planted in soil samples contaminated with chromium. Plantlets accumulated chromium mainly as Cr(III), and biomass decreased up to 88%. Streptomyces sp. MC1 was inoculated in soil samples contaminated with 200 mg kg⁻¹ of Cr(VI) and Z.mays seedlings were planted.Streptomyces sp. MC1 caused Z.mays biomass increase (57%), chromium accumulation and bioavailable chromium decreased up to 46% and 96%, respectively.This work constitutes the first contribution of cooperative action between actinobacteria and Z.mays in the bioremediation of Cr(VI) contaminated soil. The large removal capacity of bioavailable chromium by Streptomyces sp. MC1 and Z.mays infers that they could be successfully applied together in bioremediation of soils contaminated with Cr(VI).     

Scientific advances in the analysis of direct risks of weed biological control agents to nontarget plants

Research on host specificity testing protocols over the last 10 years has been considerable. Traditional experimental designs have been refined and interpretation of the results is benefiting from an improved understanding of agent behavior. The strengths, weaknesses, and best practice for the different test types are now quite clearly understood. Understanding the concept of fundamental host range (the genetically determined limits to preference and performance) and using this to maximize reliability in predicting field host specificity following release (behavioral expression of the fundamental host range under particular conditions) are still inconsistently understood or adopted despite having been identified as the critical steps in analyzing the threats posed by biological control agents to the agriculture and biodiversity of novel environments. This needs to be consistently understood and applied so the process of testing can follow a recognized process of risk analysis from hazard identification (identifying life stages of the agent that pose a threat and defining their fundamental host range) to uncertainty analysis based on the magnitude (predicted field host specificity following release) and likelihood of threats (predicted actual damage and impact) to nontargets. Modern molecular techniques are answering questions associated with subspecific variation in biological control agents with respect to host use and the chance of host shifts of agents following release. Guidelines for assessment of nontarget impacts need to recognize and adopt such recent developments and emphasize a general increased understanding of the evolution of host choice and the phylogenetic constraints to shifts in host use. This review covers all these recent advances for the first time in one document, highlighting how inconsistent interpretation by biological control practitioners can be avoided.     

Determination of transgene repeat formation and promoter methylation in transgenic plants

The integration of transgenes into a plant host genome following Agrobacterium tumefaciens-mediated or direct transformation may occur as a single copy or in the form of tandem repeats. The latter has been associated with promoter methylation and silencing of transgenes. Thus, the early screening of such transgenic plants is desirable for ruling out future repeat-dependent transgene instability. We developed a simple PCR-based method in which primer pairs were specifically designed so that amplifications could only be obtained if the transgene was present in the form of multiple inserts in a transgenic line. The method was established using 35S-rolC transgenic aspen lines showing morphologically visible transgenic silencing. Later, it was possible to screen independent transgenic lines showing no visible marker gene expression. Furthermore, a method was developed in which positive PCR amplification was indicative of promoter methylation. The results were consistent and reproducible across different independent transgenic lines. The methods were quick, reliable, consistent and reproducible, and can be useful for routine screening of transgene silencing in lines derived from many different systems.     

Assessing the biosecurity risk from pathogens and herbivores to indigenous plants: lessons from weed biological control

Some potentially invasive herbivores/pathogens in their home range may attack plants originating from another geographic area. Methods are required to assess the risk these herbivores/pathogens pose to these plants in their indigenous ecosystems. The processes and criteria used by weed biological control researchers to assess the impact of potential biological control agents on a plant species in its non-native range provide a possible framework for assessing risks to indigenous plants. While there are similarities between these criteria such as the need for clear objectives, studies in the native range of the herbivore/pathogen, good knowledge of the ecology of the target plant and taxonomy of the plant and herbivore/pathogen, and modelling of the interaction between the two organisms, there are some important differences in approach. These include the need to consider the threat classification of the plant, the likely greater risk from polyphagous herbivores/pathogens than oligophagous or monophagous species, and the need to consider the impact of an additional natural enemy in conjunction with a suite of existing natural enemies. The costs of conducting a risk assessment of a herbivore/pathogen in another country that damages plants indigenous to another geographic area means that criteria will be needed for deciding which foreign herbivore/pathogen species should be assessed. These criteria could include the threat classification of the plant, the amount of damage to the particular plant organs affected, and the importance in key ecosystems.     

Benefits and risks of exotic biological control agents

The use of exotic (=alien) arthropods in classical and augmentative biological control programs has yielded huge economic and ecological benefits. Exotic species of arthropods have contributed to the suppression of key pests in agriculture and forestry or have aided in restoring natural systems affected by adventive species. However, adverse non-target effects of exotic biological control agents have been observed in a number of projects. Non-target effects range from very small effects, e.g. 2% parasitization on a non-target insect on a local level, to massive effects on a large scale. Until now, no consensus on how to judge the magnitude of non-target effects and whether these effects can be tolerated or are unacceptable has emerged. In this paper, we briefly review both the benefits of biological control as well as the associated risks including to human and animal health, plant health and particularly the environment. We also make an attempt at identifying the major challenges for assessing risks and for balancing benefits and risks. There is general agreement that sound risk assessment procedures should precede the release of exotic invertebrate biological control agents and a recent shift??especially for arthropod biological control??from introductions done without meaningful risk assessment studies to projects conducting thorough host range testing can be observed. However, overly stringent regulations that would preclude promising agents from being developed must be avoided.     

Isolation and characterization of a Scenedesmus acutus strain to be used for bioremediation of urban wastewater

Green microalgae, due to their short growth cycle and to their ability to photosynthetically fix carbon dioxide producing an oil-rich biomass, have been proposed as an attractive alternative feedstock for the production of “second generation” biofuels. However, it has been anticipated that owing to their ability to colonize very different environments characterized by high levels of nitrogen, they can also be good candidates for bioremediation, thus integrating environmental protection with sustainable biomass production. We have isolated a strain belonging to Scenedesmus genus from urban wastewater. This isolate, Scenedesmus acutus PVUW12, was tested for its ability to grow and actively deplete eutrophicating inorganic molecules present in wastewater. In order to test its biomass productivity, the PVUW12 strain was grown in a vertical-column photobioreactor using standard growth medium obtaining a maximal productivity of 0.3?g dry weight L^?1?d. When the same strain was grown in the photobioreactor filled with wastewater collected from the final step of the local urban purifier plant containing 18.8?mg?L^?1 nitrate, we observed complete nitrogen removal coupled with a biomass production of about 0.74?g dry weight L^?1 within 3 days. After 10?days, the recovered biomass was analyzed for triglyceride content which was found to be 9.3% of the dry biomass. However, when algal cells were left for additional 10?days in static conditions the triglyceride content increased to 28.8%. These data show that this Scenedesmus strain can be used for wastewater bioremediation producing a biomass suitable for energy production.     

Evaluation of health risks from a buried mass of diesel fuel before and after bioremediation

Plans are being formulated for in situ bioremediation of a subsurface plume of diesel fuel No. 2 that resulted from an accidental fuel release. Raoult's law and the aqueous solubilities of the toxic components were used to estimate organic contaminant concentrations in leachate from the untreated fuel mass. Carcinogenic risks and noncarcinogenic hazard indices were calculated for undiluted leachate. An 80% decrease in hydrocarbon mass and increases in the average molecular weights of the component fractions were assumed to result from the treatment. Sample calculations are provided to show how to evaluate results of analyses for petroleum hydrocarbons after bioremediation.     

Targeting transgene expression in research,agricultural, and environmental applications: Promoters used in plant transformation

Summary Plant genetic engineering has contributed substantially to the understanding of gene regulation and plant development, in the generation of transgenic organisms for widespread usage in agriculture, and has increased the potential uses of crops for industrial and pharmaceutical purposes. As the application of geneticallly engineered plants has widened, so has the need to develop methods to fine-tune control of transgene expression. The availability of a broad spectrum of promoters that differ in their ability to regulate the temporal and spatial expression patterns of the transgene can dramatically increase the successful application of transgenic technology. Indeed, a variety of promoters in necessary at all levels of genetic engineering in plants, from basic research discoveries, concepts and question to development of economically viable crops and plant commodities, to addressing legitimate concerns raised about the safety and containment of transgenic plants in the environment. This review covers the characterization and usage of a broad range of promoters employed in plant genetic engineering, including the widespread use of plant promoters with viral and plant origin that drive constitutive expression. Also covered are selected tissue-specific promoters from fruit, seed and grain, tubers, flowers, pistils, anther and pollen, roots and root nodules, and leaves and green tissue. Topics also include organellar promoters, and those found in specific cell types, as well as the development and evaluation of inducible (endogenous and exogenous origin) and synthetic plant promoter systems. Discussions on the relevance and potential pitfalls within specific applications are included.