Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.

Coil-ring-coil block copolymers as building blocks of supramolecular hollow cylindrical brushes

This work describes the synthesis of a new class of rod-coil block copolymers, oligosubstituted shape persistent macrocycles, (coil-ring-coil block copolymers), and their behavior in solution and in the solid state.The coil-ring-coil block copolymers are formed by nanometer sized shape persistent macrocycles based on the phenyl-ethynyl backbone as rigid block and oligomers of polystyrene or polydimethylsiloxane as flexible blocks. The strategy that has been followed is to synthesize the macrocycles with an alcoholic functionality and the polymer carboxylic acids independently, and then bind them together by esterification. The ester bond is stable and relatively easy to form.The synthesis of the shape persistent macrocycles is based on two separate steps. In the first step the building blocks of the macrocycles are connected by Hagiara-Sogonaschira coupling to form an 'half-ring' as precursor, that contains two free acetylenes. In the second step the half-ring is cyclized by forming two sp-sp bonds via a copper-catalyzed Glaser coupling under pseudo-high-dilution conditions. The polystyrene carboxylic acid was prepared directly by siphoning the living anionic polymer chain into a THF solution, saturated with CO2, while the polydimethylsiloxane carboxylic acid was obtained by hydrosilylating an unsaturated benzylester with an Si-H terminated polydimethylsiloxane, and cleavage of the ester. The carbodiimide coupling was found to be the best way to connect macrocycles and polymers in high yield and high purity.The polystyrene-ring-polystyrene block copolymers are, depending on the molecular weight of the polystyrene, lyotropic liquid crystals in cyclohexane. The aggregation behavior of the copolymers in solution was investigated in more detail using several technique. As a result it can be concluded that the polystyrene-ring-polystyrene block copolymers can aggregate into hollow cylinder-like objects with an average length of 700 nm by a combination of shape complementary and demixing of rigid and flexible polymer parts. The resulting structure can be described as supramolecular hollow cylindrical brush.If the lyotropic solution of the polystyrene-ring-polystyrene block copolymers are dried, they remain birefringent indicating that the solid state has an ordered structure. The polydimethylsiloxane-ring-polydimethylsiloxane block copolymers are more or less fluid at room temperature, and are all birefringent (termotropic liquid crystals) as well. This is a prove that the copolymers are ordered in the fluid state. By a careful investigation using electron diffraction and wide-angle X-ray scattering, it has been possible to derive a model for the 3D-order of the copolymers. The data indicate a lamella structure for both type of copolymers. The macrocycles are arranged in a layer of columns. These crystalline layers are separated by amorphous layers which contain the polymers substituents.

The shaping of foreign policy: Vietnamese grand strategy after the Cold War

This study examines the case of Vietnam and uses the method of process tracing to explore the sources of foreign policy choice and change. Foreign policy is derived from grand strategy, which refers to the full package of a state’s domestic and foreign policies. I argue that a state’s grand strategy results from the interaction of four factors—its society’s historical experience, social motivation, international power, and political contest among domestic groups. Grand strategies emerge as a response to perceived shifts in the balance of international economic, political, and military power. However, this is not to say that international pressures and incentives are translated into foreign policy. Rather, pressures and incentives are given meaning by worldviews, which reflect a society’s historical experiences of its place in the international system at traumatic junctures of its encounter with the outside world. Strategic changes in foreign policy follow what I call the “strategic algorithm,” which incorporates four major mechanisms—balancing against threat, bandwagoning with power, learning, and survival by transformation. This case study generates hypotheses for a theory of strategic choice, a theory of foreign policy transformation, and a theory of grand strategy emergence.

Functionalization of hyperbranched polycarbosilanes - block copolymers and electrochemistry

Polycarbosilanes are a class of polymers at the interface between organic and inorganic chemistry. They are characterized by a high thermal and chemical inertness and high flexibility, especially pronounced for branched structures. Linear polycarbosilanes are well known as precursors for the preparation of SiCx ceramics. Additionally, more sophisticated architectures like dendrimers, hyperbranched polymers or block copolymers have been the subject of research for more than a decade. The scope of this work was to expand the properties and fields of application for polycarbosilane-containing structures. Thus, the work is divided in two major parts. The first part covers the synthesis and characterization of hyperbranched polycarbosilanes containing organometallic moieties. Hyperbranched poly-carbosilanes were synthesized using hydrosilylation of diallylmethylsilane and methyldiundecenylsilane. The degree of branching for polydiallymethylsilane was determined using standard 1H-NMR spectroscopy. The functional building blocks ferrocenyldimethylsilane and diferrocenylmethylsilane were synthesized which contain an isolated ferrocene unit or two ferrocenes bridged by silicon, respectively. Hyperbranched polycarbosilanes functionalized with ferrocenyl moieties were synthesized by modification of preformed polymers or by copolymerization of AB2 carbosilane monomers with AX-type ferrocenylsilanes. Polymers with Mn = 2500-9000g/mol and ferrocene contents of up to 67wt% were obtained. Electrochemical characterization by cyclic voltammetry revealed that polymers functionalized with isolated ferrocene units showed a single reversible oxidation wave, while voltammograms for polymers functionalized with diferrocenyl silane exhibited two well-separated reversible oxidation-reduction waves. This shows that the polymer bound ferrocenes bridged by silicon are electronically communicating and thus oxidation of the first ferrocene shifts the oxidation potential for the adjacent one. The polymers were utilized successfully for the preparation of modified electrodes with persistent and reproducible electrochemical response in organic solvents as well as in aqueous solution. The presented work has proven that ferrocenyl-functionalized hyperbranched polymers exhibit similar electrochemical properties as the analogous dendrimers. In a further approach it was shown that hyperbranched polymers containing organometallic moieties can be synthesized by polymerization of a new ferrocene-containing AB2 monomer - diallylferrocenylsilane. The second part of this work is dedicated to the preparation of core-functional hyperbranched polycarbosilanes. Low molecular weight ambifunctional molecules were synthesized that contain double bonds for the attachment of a polycarbosilane polymer as well as a second functionality available for further reaction and modification. Reactive vinyl groups in the core molecule allow an efficient attachment of hyperbranched polycarbosilane which was proven by MALDI-ToF and GPC. In combination with slow monomer addition techniques molecular weight and polydispersity of the polymers were controlled successfully. Core-functional polymers were characterized by NMR-spectroscopy, MALDI-ToF and GPC. Polymers with polydispersities <2 and molecular weights up to 5300g/mol were obtained. Transformation of the double bonds of the carbosilane was demonstrated with various silanes using hydrosilylation reaction or hydrogenation. Additionally, the core-functionality was varied resulting in polymers with bromo-, phthalimide-, amine- or azide moieties. Thus, a versatile synthetic strategy was developed that allows the synthesis of tailor-made polymers.A promising approach is the application of the polymer building blocks in copolymer synthesis. Bisglycidolization of amine-functional polycarbosilanes produces macro-initiators that are suitable for the multibranching-ring opening polymerization of glycidol. This experiments lead to the first example of hyperbranched-hyperbranched amphiphilic block copolymers, hb-PG-b-hb-PCS. Furthermore, the implementation of copper-catalyzed cycloaddition between azide-functional polycarbosilane and alkyne-functional poly(ethoxyethyl glycidylether) resulted in linear-hyperbranched block copolymers. The facile removal of acetal protecting groups provided convenient access to lin-PG-b-hb-PCS.

Novel cell-free strategy for therapeutic angiogenesis: in vitro generated conditioned medium can replace progenitor cell transplantation

BACKGROUND: Current evidence suggests that endothelial progenitor cells (EPC) contribute to ischemic tissue repair by both secretion of paracrine factors and incorporation into developing vessels. We tested the hypothesis that cell-free administration of paracrine factors secreted by cultured EPC may achieve an angiogenic effect equivalent to cell therapy. METHODOLOGY/PRINCIPAL FINDINGS: EPC-derived conditioned medium (EPC-CM) was obtained from culture expanded EPC subjected to 72 hours of hypoxia. In vitro, EPC-CM significantly inhibited apoptosis of mature endothelial cells and promoted angiogenesis in a rat aortic ring assay. The therapeutic potential of EPC-CM as compared to EPC transplantation was evaluated in a rat model of chronic hindlimb ischemia. Serial intramuscular injections of EPC-CM and EPC both significantly increased hindlimb blood flow assessed by laser Doppler (81.2+/-2.9% and 83.7+/-3.0% vs. 53.5+/-2.4% of normal, P<0.01) and improved muscle performance. A significantly increased capillary density (1.62+/-0.03 and 1.68+/-0.05/muscle fiber, P<0.05), enhanced vascular maturation (8.6+/-0.3 and 8.1+/-0.4/HPF, P<0.05) and muscle viability corroborated the findings of improved hindlimb perfusion and muscle function. Furthermore, EPC-CM transplantation stimulated the mobilization of bone marrow (BM)-derived EPC compared to control (678.7+/-44.1 vs. 340.0+/-29.1 CD34(+)/CD45(-) cells/1x10(5) mononuclear cells, P<0.05) and their recruitment to the ischemic muscles (5.9+/-0.7 vs. 2.6+/-0.4 CD34(+) cells/HPF, P<0.001) 3 days after the last injection. CONCLUSIONS/SIGNIFICANCE: Intramuscular injection of EPC-CM is as effective as cell transplantation for promoting tissue revascularization and functional recovery. Owing to the technical and practical limitations of cell therapy, cell free conditioned media may represent a potent alternative for therapeutic angiogenesis in ischemic cardiovascular diseases.

Achieving a more realistic assessment of rockfall hazards by coupling three-dimensional process models and field-based tree-ring data

Sound knowledge of the spatial and temporal patterns of rockfalls is fundamental for the management of this very common hazard in mountain environments. Process-based, three-dimensional simulation models are nowadays capable of reproducing the spatial distribution of rockfall occurrences with reasonable accuracy through the simulation of numerous individual trajectories on highly-resolved digital terrain models. At the same time, however, simulation models typically fail to quantify the ‘real’ frequency of rockfalls (in terms of return intervals). The analysis of impact scars on trees, in contrast, yields real rockfall frequencies, but trees may not be present at the location of interest and rare trajectories may not necessarily be captured due to the limited age of forest stands. In this article, we demonstrate that the coupling of modeling with tree-ring techniques may overcome the limitations inherent to both approaches. Based on the analysis of 64 cells (40 m × 40 m) of a rockfall slope located above a 1631-m long road section in the Swiss Alps, we illustrate results from 488 rockfalls detected in 1260 trees. We illustrate that tree impact data cannot only be used (i) to reconstruct the real frequency of rockfalls for individual cells, but that they also serve (ii) the calibration of the rockfall model Rockyfor3D, as well as (iii) the transformation of simulated trajectories into real frequencies. Calibrated simulation results are in good agreement with real rockfall frequencies and exhibit significant differences in rockfall activity between the cells (zones) along the road section. Real frequencies, expressed as rock passages per meter road section, also enable quantification and direct comparison of the hazard potential between the zones. The contribution provides an approach for hazard zoning procedures that complements traditional methods with a quantification of rockfall frequencies in terms of return intervals through a systematic inclusion of impact records in trees.

The quintuple way: cognitive Strategies - transformation strategies

In this work five different ways of intervention, strategically articulated, on the social world, are established. And it includes two approaches regarding the realm of knowledge and that of social change. In the second approach, five basic categories are proposed: society, State, economy, poverty and power, which work as basic a framework understand society and to serve as an orientation to carry out the necessary change. This approach to fundamental problems in our society can be applied both to world order conflicts as well as to regional and local ones. The five-fold way embodies the set of strategic packages that make it possible to understand social life and to transform it.

The quintuple way: cognitive Strategies - transformation strategies

In this work five different ways of intervention, strategically articulated, on the social world, are established. And it includes two approaches regarding the realm of knowledge and that of social change. In the second approach, five basic categories are proposed: society, State, economy, poverty and power, which work as basic a framework understand society and to serve as an orientation to carry out the necessary change. This approach to fundamental problems in our society can be applied both to world order conflicts as well as to regional and local ones. The five-fold way embodies the set of strategic packages that make it possible to understand social life and to transform it.

The quintuple way: cognitive Strategies - transformation strategies

In this work five different ways of intervention, strategically articulated, on the social world, are established. And it includes two approaches regarding the realm of knowledge and that of social change. In the second approach, five basic categories are proposed: society, State, economy, poverty and power, which work as basic a framework understand society and to serve as an orientation to carry out the necessary change. This approach to fundamental problems in our society can be applied both to world order conflicts as well as to regional and local ones. The five-fold way embodies the set of strategic packages that make it possible to understand social life and to transform it.

Uncoupling signal transducers from oncogenic MET mutants abrogates cell transformation and inhibits invasive growth

The assumption that genes encoding tyrosine kinase receptors could play a role in human cancers has been confirmed by the identification of oncogenic mutations in the kinase domain of RET and KIT. Recently, homologous residues were found mutated in MET, in papillary renal carcinomas (PRCs). The link coupling these genetic lesions to cellular transformation is still unclear. METPRC mutations result in increased kinase activity and—in some instances, i.e., M1250T substitution—in changes in substrate specificity. A direct correlation occurs between the transforming potential of METPRC mutants and their ability to constitutively associate with signal transducers through two phosphorylated tyrosines (Y1349VHVNATY1356VNV) located in the receptor tail. Substitution of these “docking tyrosines” with phenylalanines leaves unaffected the altered properties of the kinase but abrogates transformation and invasiveness in vitro. Uncoupling the receptor from signal transducers with a tyrosine-phosphorylated peptide derivative (YpVNV) inhibits invasive growth induced by METPRC mutants. These data indicate that constitutive receptor coupling to downstream signal transducers is a key mechanism in neoplastic transformation driven by mutated MET and suggest a therapeutic strategy to target neoplastic diseases associated with this oncogene.

Identification and characterization of a RING zinc finger gene (C-RZF) expressed in chicken embryo cells.

To identify changes in gene expression that occur in chicken embryo brain (CEB) cells as a consequence of their binding to the extracellular matrix molecule cytotactin/tenascin (CT/TN), a subtractive hybridization cloning strategy was employed. One of the cDNA clones identified was predicted to encode 381 amino acids and although it did not resemble any known sequences in the nucleic acid or protein data bases, it did contain the sequence motif for the cysteine-rich C3HC4 type of zinc finger, also known as a RING-finger. This sequence was therefore designated the chicken-RING zinc finger (C-RZF). In addition to the RING-finger, the C-RZF sequence also contained motifs for a leucine zipper, a nuclear localization signal, and a stretch of acidic amino acids similar to the activation domains of some transcription factors. Southern analysis suggested that C-RZF is encoded by a single gene. Northern and in situ hybridization analyses of E8 chicken embryo tissues indicated that expression of the C-RZF gene was restricted primarily to brain and heart. Western analysis of the nuclear and cytoplasmic fractions of chicken embryo heart cells and immunofluorescent staining of chicken embryo cardiocytes with anti-C-RZF antibodies demonstrated that the C-RZF protein was present in the nucleus. The data suggest that we have identified another member of the RING-finger family of proteins whose expression in CEB cells may be affected by CT/TN and whose nuclear localization and sequence motifs predict a DNA-binding function in the nucleus.

A general strategy for producing conditional alleles of Src-like tyrosine kinases.

The Src-like tyrosine kinases require membrane localization for transformation and probably for their normal role in signal transduction. We utilized this characteristic to prepare Src-like tyrosine kinases that can be readily activated with the rationally designed chemical inducer of dimerization FK1012. Dimerization of cytoplasmic Src-like tyrosine kinases was not sufficient for signaling, but their recruitment to the plasma membrane led to the rapid activation of transcription factors identical to those regulated by crosslinking the antigen receptor. Moreover, recruitment of activated Src-like kinases to the membrane replaced signaling by the T-lymphocyte antigen receptor complex, leading to the activation of both the Ras/protein kinase C and Ca2+/calcineurin pathways normally activated by antigen receptor signaling. Since these chemical inducers of dimerization are cell permeable, this approach permits the production of conditional alleles of any of the Src-like tyrosine kinases, thereby allowing a delineation of their developmental roles.

Germany's energy transformation: difficult beginnings. OSW Report, March 2013

Initiated in May 2011, several months after the Fukushima nuclear disaster, Germany’s energy transformation (Energiewende) has been presented as an irrevocable plan, and – due to the speed of change required – it represents a new quality in Germany’s energy strategy. Its main objectives include: nuclear energy being phased out by 2022, the development of renewable energy sources (OZE), the expansion of transmission networks, the construction of new conventional power plants and an improvement in energy efficiency.The cornerstone of the strategy is the development of renewable energy. Under Germany's amended renewable energy law, the proportion of renewable energy in electricity generation is supposed to increase steadily from the current level of around 20% to approximately 38% in 2020. In 2030, renewable energy is expected to account for 50% of electricity generation. This is expected to increase to 65% in 2040 and to as much as 80% in 2050. The impact of the Energiewende is not limited to the sphere of energy supplies. In the medium and long term, it will change not only to the way the German economy operates, but also the functioning of German society and the state. Facing difficulties with the expansion of transmission networks, the excessive cost of building wind farms, and problems with the stability of electricity supplies, especially during particularly cold winters, the federal government has so far tended to centralise power and limit the independence of the German federal states with regard to their respective energy policies, justifying this with the need for greater co-ordination. The Energiewende may also become the beginning of a "third industrial revolution", i.e. a transition to a green economy and a society based on sustainable development. This will require a new "social contract" that will redefine the relations between the state, society and the economy. Negotiating such a contract will be one of the greatest challenges for German policy in the coming years.

Capitalism without Capitalists? A Bottom-Up View of Industrial Transformation in East Germany. CES Germany & Europe Working Papers, No. 00.1, 1999

Research on the industrial transition in East Germany and its outcomes has long focused on the strategy of the Treuhand­ anstalt (IHA). According to institutionalists, David Stark and Lazlo Brust!: (1998), the powerful position of the German privatization agency was not only a result of German unification but also a function of a pathway rooted in the institutional peculiarities of the East German economy before 1989. This paper shows that neither a simple top-down perspective nor the pathway approach, as Stark and Brust!: suggested, are adequate for explaining the internal dynamic of enterprise transformation as well as the outcomes of this process. First of all, the dissolution of the former organizational structures and hierarchies was less coordinated by the 1HA than is often assumed. Often Kombinates fell apart more quickly from below than they could be dismantled from above since enterprises or their units chose the exit­ option and had good reasons to do so. Secondly, although the privatization by the 1HA resulted in the clear dominance of Western investors, the new ownership structure of East German industry as a whole could be characterized as a "capitalism without (East German) capitalists." In fact, what exists in East Germany is rather a kind of "small business capitalism" (KleinbetriebsknpitalifmllS) in which small-and medium-sized producers dominate the landscape. Finally, there was no single starting point in 1989. Two different industrial orders shaped the industrial history of the East German regions which were not destroyed between 1945-89, but rather transformed into the state socialist production system. It can be shown that these older historical patterns are relevant for transition and their outcomes as well.

Functional promoter analysis using an approach based on an in vitro evolution strategy

In vitro evolution imitates the natural evolution of genes and has been very successfully applied to the modification of coding sequences, but it has not yet been applied to promoter sequences. We propose an alternative method for functional promoter analysis by applying an in vitro evolution scheme consisting of rounds of error-prone PCR, followed by DNA shuffling and selection of mutant promoter activities. We modified the activity in embryogenic sugarcane cells of the promoter region of the Goldfinger isolate of banana streak virus and obtained mutant promoter sequences that showed an average mutation rate of 2.5% after applying one round of error-prone PCR and DNA shuffling. Selection and sequencing of promoter sequences with decreased or unaltered activity allowed us to rapidly map the position of one cis-acting element that influenced promoter activity in embryogenic sugarcane cells and to discover neutral mutations that did not affect promoter Junction. The selective-shotgun approach of this promoter analysis method immediately after the promoter boundaries have been defined by 5' deletion analysis dramatically reduces the labor associated with traditional linker-scanning deletion analysis to reveal the position of functional promoter domains. Furthermore, this method allows the entire promoter to be investigated at once, rather than selected domains or nucleotides, increasing the, prospect of identifying interacting promoter regions.