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Essays on deregulation in the electricity generation sectorAjayi, Victor A. January 2017 (has links)
Over that past three decades, power sector reform has been a key pillar of policy agendas in more than half of the countries across the world. This thesis specifically concerns the empirical investigation of the economic performance of the international electricity generation industry. Drawing on the stochastic frontier analysis techniques, the thesis considers the influence of reform as exogenous factors in shifting frontier technology as well as shaping inefficiency function directly -determinants and heteroscedasticity variables. The first essay uses an extensive panel dataset of 91 countries over the period 1980 to 2010 to measure the impact of deregulation on efficiency and total productivity growth using stochastic input distance frontier (SIDF). Three specific issues are addressed in the first essay: (1) the relationship between deregulation and technical efficiency, (2) the extent of the rank correlation of the country intercepts with deregulation via their position on the frontier, (3) the trend of total factor productivity and its components. We establish a positive impact of deregulation on efficiency and some compelling evidence suggesting that the country intercepts equally account for the influence of deregulation aside efficiency. In particular, the technical efficiency index from the first paper reveals that most OECD European countries are consistently efficient. Building on this finding, the second essay investigates the performance in term of cost efficiency for electricity generation in OECD power sector while accounting for the impact of electricity market product regulatory indicators. Empirical models are developed for the cost function as a translog form and analysed using panel data of 25 countries during the period 1980 to 2009. We show that it is necessary to model latent country-specific heterogeneity in addition to time-varying inefficiency. The estimated economies of scale are adjusted to take account of the importance of the quasi-fixed capital input in determining cost behaviour, and adjusted economies of scale are verified for the OECD generation sector. The findings suggest there is a significant impact of electricity market regulatory indicators on cost. Cost complementarity between generation and emissions found to be significant, indicating the possibility of reducing emissions without necessarily reducing electricity generation. Finally, the third essay examines the performance of electric power industry s using consistent state-level electricity generation dataset for the US contiguous states from 1998-2014. We estimate stochastic production frontier for five competing models in order to identify the determinants of technical inefficiency and marginal effects. We find evidence of positive impacts of deregulation on technical efficiency across the models estimated. Our preferred model shows that deregulated states are more efficient in electricity generation than non-deregulated states. The result of the marginal effects shows that deregulation has a positive and monotonic effect on the technical efficiency.
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Current challenges in legal and political thought / Los retos actuales del pensamiento jurídico-políticoRubio Castro, Ana María 10 April 2018 (has links)
The article analyses the theoretical debates on equality and justice that represent the structural and institutional dimension of politics within the framework of a rigid constitutionality of fundamental rights as well as the changes in process to which law and politics are subject in Spain as a consequence of the globalization of economic production and of culture. The actions carried out by the Spanish government in recent years justify us in speaking about the return of the old socio-economic hierarchies and of the clear obstacles to the development of alternative legal-political thinking. For these reasons, the article defends the need to redefine the collective political subject (to construct a new us) and to develop a new model of the state which gives priority to solidarity against fear and security. / En el artículo se analizan los debates teóricos sobre la igualdad y la justicia que representa la dimensión estructural e institucional de la política en el marco de una constitucionalidad rígida de los derechos fundamentales, así como los cambios en proceso a los que están sometidos el derecho y la política en España como consecuencia de la globalización de la producción económica y de la cultura. Las actuaciones realizadas por el ejecutivo español en los últimos años permiten hablar del retorno de las viejas jerarquías socio-económicas y de claros obstáculos al desarrollo de un pensamiento jurídico-político alternativo. Por estas razones se defiende la necesidad de redefinir el sujeto político colectivo (construir un nuevo nosotros) y de desarrollar un nuevo modelo de Estado en el que prime la solidaridad frente al miedo y la seguridad.
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'n Vervoerlogistieke benadering tot die hervestiging van verspreidingsentra in die lig van deregulasie van padvervoerWiggins, Henry Owen 06 1900 (has links)
Text in Afrikaans, abstract in Afrikaans and English / In the case of an economical activity such as a distribution system, the distribution depot
normally forms the nucleus of the network. The market place that is being served is not static
and with the passing of time, due to the change in demand together with the change in the
product range which is being offered, a tendency develops for the distribution point to move
away from the nucleus of the network, thereby not representing the optimal location anymore.
There is therefore a constant need for companies to determine whether their distribution
system is suitable for their present, as well as their future trading circumstances. This factor
together with the normal endeavour to minimise physical distribution costs, results in the need
for a sophisticated approach to the whole problem of relocating distribution networks.
The aim of this study is therefore to develop a basic model which will set out guidelines for the
relocation of distribution centres.
With the above mentioned in mind, the first step is a study of the theory to highlight and
analyse applicable techniques and methods that could possibly be used in this model. The
accent throughout this section is placed on well known and proven theories and techniques.
The second part of this research focuses on the empirical study that forms the basis for the
building of a relocation model. With the help of practical examples it is shown how to apply
the model and each step is being highlighted and illustrated.
The model that has been designed in this study clearly outlines the steps that enable the user to undertake and optimally apply a relocation study. Its application does not necessarily require
highly trained personnel or complicated programming. It is therefore recommended that this
model be applied in the case of the relocation of distribution centres. / In die geval van ekonomiese aktiwiteite soos 'n distribusiesisteem, vorm die verspreidingsdepot
gewoonlik die kernpunt van die netwerk. Die markplek wat bedien word is egter nie staties nie
en met die verloop van tyd, as gevolg van die verandering in die aanvraag tesame met die
verandering in die produkreeks wat aangebied word, ontstaan daar 'n neiging dat die
oorsponklike verspreidingspunt weg beweeg vanaf die kernpunt van die netwerk en dus nie
meer die optimale liggging verteenwoordig nie. Daar is dus 'n konstante behoefte by
maatskappye om te bepaal of hulle distribusiesisteme geskik is vir hulle huidige, sowel as
toekomstige handelsomstandighede. Hierdie faktor, tesame met die normale strewe na
minimalisering van fisiese distribusiekoste, het tot gevolg dat daar 'n behoefte bestaan aan 'n
gesofistikeerde benadering tot die hele problematiek van vestiging van verspreidingsnetwerke.
Die studie het dus ten doel die ontwikkeling van 'n basiese model wat riglyne daarstel vir die
hervestiging van verspreidingsentra.
Met bogenoemde in gedagte, is daar in die eerste plek 'n teoretiese studie onderneem wat
toepaslike tegnieke en metodes wat moonlik in hierdie model opgeneem kon word, uitgelig en
geanaliseer het. In hierdie gedeelte word die aksent deurentyd op bekende en bewese teoriee
geplaas.
Die tweede gedeelte van die navorsing fokus op die empiriese studie wat met die bou van 'n hervestigingsmodel gepaard gaan. Daar word aangetoon hoe om die model toe te pas en elke
stap word met behulp van praktiese voorbeelde toegelig en verduidelik.
Die model wat hier ontwikkel is le duidelike riglyne neer wat die verbruiker in staat stel om 'n
hervestigingstudie aan te pak en optimaal toe te pas. Die toepassing daarvan vereis nie
noodwendig hoogsopgeleide personeel of ingewikkelde programering nie en word daar
gevolglik aanbeveel dat hierdie model toegepas word in die geval van die hervestiging van
verspreidingsentra. / Business Management / D. Comm.
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Rota de colisão: a cultura da Varig Grande e a aviação civil brasileira em meio à globalização / Route of collision: the culture of "Big Varig" and the brazilian civil aviation during globalizationSandra Regina de Oliveira 22 July 2009 (has links)
Esta dissertação de História tem por objetivo demonstrar a estreita relação existente entre a crise da VARIG e a mudança de paradigma do governo brasileiro com relação à aviação civil e, conseqüentemente, com relação às empresas nacionais de aviação, a partir da década de 1980, através da adoção dos preceitos neoliberais que marcaram a desregulamentação da aviação civil no mercado doméstico norte-americano. Desta forma, a partir do momento que o Estado brasileiro passou oficialmente a adotar políticas para o mercado da aviação, cujas diretrizes foram traçadas nos Estados Unidos da América, foi possível associar o estudo da história da aviação n acional à história da política governamental no que tange às suas relações com a política internacional, levando-nos a traçar um paralelo entre a política externa brasileira e a política externa dos EUA, tal a grande influência deste país no desenvolvimento da aviação civil no Brasil, principalmente após a Segunda Guerra Mundial, até as mudanças neoliberais das últimas décadas. Pôde-se, assim, observar em que grau a política externa norte-americana conseguiu influenciar a evolução da aviação no Brasil, em função da maior ou menor autonomia dos diversos governos brasileiros a esta política específica. Para demonstrar a relação existente entre a crise da VARIG e esta mudança de paradigma, foi necessário estudar os aspectos relacionais externos da empresa, o quanto o lema VARIG Grande se atrelava à política econômica de um BRASIL Grande, concebido durante o chamado Milagre Brasileiro, isto é, o quanto sua política empresarial esteve associada à política nacional- desenvolvimentista do Estado, que ao entrar em crise desestabilizou a histórica estratégia da VARIG, principalmente após a década de 1990, quando os espaços de interlocução entre a burocracia estatal e as empresas privadas se reduziram ao extremo. No caso da VARIG, foi preciso também analisar os seus aspectos relacionais internos, construídos ao longo de seus mais de oitenta anos de história, com práticas institucionais bastante próximas às das em presas estatais. Na conclusão, será demonstrada a co-responsabilidade do Estado na formação, no crescimento, no início da crise e na intensificação do processo de queda da empresa , através de atuações determinantes, em momentos diferentes da história do país.
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A desregulamentação e o desempenho do complexo sucroalcooleiro no Brasil.Baccarin, José Giacomo 28 June 2005 (has links)
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TeseJGB.pdf: 1513867 bytes, checksum: 9b43d49293d7da266f4d2953d6f0bc6a (MD5)
Previous issue date: 2005-06-28 / This work analyzed the evolution of the relation between the sugar and alcohol complex and the State from 1975 to 2002, when there was a change from public intervention, marked by Proálcool , to a new situation, in which deregulation is proposed. We attempted to interpret the main political and economical stipulators of the process, as well as describe the way it happened and how the structure and performance of the process were affected. It is assumed that since 1985 the possibilities of an orchestration of social and economical interests allowing the maintenance of a national, public and continuous
program to support the sugar and alcohol complex have narrowed. The financial crisis of the Brazilian State and the adoption of liberal politic orientation, the prevailing conditions
of the oil market and the resistance of Petrobrás to the increase of alcohol production have contributed to this situation, as well as the little interest of car makers to develop ethanolpowered engines in the 1990 s. It is also assumed that the political pressure strength of sugar and alcohol complex representatives and the specific formal relations established with the federal administrative machine throughout decades have made the sugar and alcohol deregulation differentiated and marked by compensation policies. From 1975 to 1985, the complex counted on favored public policies that resulted in great increase of the production capacity, consumption and production of fuel ethanol. Since 1986, the price fixation policy for sugar and alcohol products was more unfavorable, resulting in production settling until 1990. The extinction of the Sugar and Alcohol Institute (IAA), in 1990, formally gave birth to deregulation, marked by constant tension between government and millers. The elimination of the public monopoly on sugar exportation and the
defrosting of sugarcane, sugar and alcohol prices in 1999 are noticeable. In compensation,
the addition of 20% to 24% of anhydrous ethanol to gasoline became obligatory; the gasoline was overtaxed in benefit of alcohol, and a specific source of production and buildup financing for sugar and alcohol was created. From 1990 to 2002, while alcohol production remained still, there was an increase of sugar production aiming the world market. Crop and industry yield did not show higher increase with deregulation. However, the work productivity did. The sugarcane production tended to concentrate in the centersouth, instead of the north-northeast. There was a considerable decrease in the number of mills, but the remaining became bigger. It can be concluded that in fact there was no
complete deregulation, but actually a change resulting in a new regulation. We suggest that
the public intervention should not be attached to opportunist interests, but a public/private
agenda that contributes to the maintenance of the complex and guarantees alcohol supply to
the society as an energy source. / O tema do trabalho foi a análise da evolução da relação do complexo sucroalcooleiro com o Estado, entre 1975 e 2002, em que houve a passagem de uma situação com forte intervenção pública, marcada pelo Proálcool, para outra, em que se
propunha sua desregulamentação. Procurou-se interpretar os principais condicionantes políticos e econômicos do processo, descrever a forma como ele se deu e como foram afetados a estrutura e o desempenho do complexo. Assume-se que, desde 1985, foram-se estreitando as possibilidades de uma orquestração de interesses sociais e econômicos que permitisse a manutenção de um programa público contínuo e nacional de sustentação do complexo sucroalcooleiro. Contribuíram para isso a crise fiscal do Estado Brasileiro e a adoção de orientação política liberal, as condições prevalecentes no mercado do petróleo e a resistência da Petrobrás ao aumento da produção de álcool, bem como o pouco interesse
da indústria automobilística no desenvolvimento de motores a álcool na década de 1990. Assume-se também que o poder de pressão política dos representantes do complexo e as relações formais específicas que se estabeleceram com a máquina administrativa federal, ao longo de décadas, fizeram com que a desregulamentação sucroalcooleira fosse diferenciada e marcada por políticas de compensação. De 1975 a 1985, o complexo contou com políticas públicas favorecidas, que levaram à grande expansão da capacidade produtiva, da produção e do consumo de álcool carburante. A partir de 1986, a política de fixação de preços dos produtos sucroalcooleiros foi mais desfavorável, conduzindo à estagnação da produção setorial, até 1990. A extinção do Instituto do Açúcar e do Álcool (IAA), em 1990, deu
início, formalmente, à desregulamentação sucroalcooleira, marcada por uma constante
tensão entre Governo e empresários. Merecem destaque a eliminação do monopólio público na exportação de açúcar e a liberação de preços da cana-de-açúcar, do açúcar e do álcool, encerrada em 1999. Em compensação, instituiu-se a obrigatoriedade de adição entre 20% e 24% de álcool anidro à gasolina, sobre taxou-se a gasolina em benefício do álcool e criouse fonte específica de financiamento da produção e estocagem alcooleira. Entre 1990 e 2002, enquanto mantinha-se estagnada a produção de álcool, a de açúcar crescia visando o mercado externo. Os rendimentos cultural e agroindustrial não apresentaram crescimento maior na desregulamentação, ao contrário da produtividade do trabalho. A produção
canavieira tendeu a se concentrar no Centro-Sul em detrimento do Norte-Nordeste. Houve diminuição considerável do número de groindústrias e crescimento de seu tamanho médio. Conclui-se que, de fato, não houve uma desregulamentação completa, mas uma mudança em sua forma, constituindo-se uma nova regulamentação. Sugere-se que a intervenção pública não se prenda a interesses oportunistas, mas que se estabeleça uma agenda pública/privada que contribua para a manutenção do complexo sucroalcooleiro e que dê
garantia à sociedade quanto ao fornecimento do álcool, enquanto fonte energética.
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Rota de colisão: a cultura da Varig Grande e a aviação civil brasileira em meio à globalização / Route of collision: the culture of "Big Varig" and the brazilian civil aviation during globalizationSandra Regina de Oliveira 22 July 2009 (has links)
Esta dissertação de História tem por objetivo demonstrar a estreita relação existente entre a crise da VARIG e a mudança de paradigma do governo brasileiro com relação à aviação civil e, conseqüentemente, com relação às empresas nacionais de aviação, a partir da década de 1980, através da adoção dos preceitos neoliberais que marcaram a desregulamentação da aviação civil no mercado doméstico norte-americano. Desta forma, a partir do momento que o Estado brasileiro passou oficialmente a adotar políticas para o mercado da aviação, cujas diretrizes foram traçadas nos Estados Unidos da América, foi possível associar o estudo da história da aviação n acional à história da política governamental no que tange às suas relações com a política internacional, levando-nos a traçar um paralelo entre a política externa brasileira e a política externa dos EUA, tal a grande influência deste país no desenvolvimento da aviação civil no Brasil, principalmente após a Segunda Guerra Mundial, até as mudanças neoliberais das últimas décadas. Pôde-se, assim, observar em que grau a política externa norte-americana conseguiu influenciar a evolução da aviação no Brasil, em função da maior ou menor autonomia dos diversos governos brasileiros a esta política específica. Para demonstrar a relação existente entre a crise da VARIG e esta mudança de paradigma, foi necessário estudar os aspectos relacionais externos da empresa, o quanto o lema VARIG Grande se atrelava à política econômica de um BRASIL Grande, concebido durante o chamado Milagre Brasileiro, isto é, o quanto sua política empresarial esteve associada à política nacional- desenvolvimentista do Estado, que ao entrar em crise desestabilizou a histórica estratégia da VARIG, principalmente após a década de 1990, quando os espaços de interlocução entre a burocracia estatal e as empresas privadas se reduziram ao extremo. No caso da VARIG, foi preciso também analisar os seus aspectos relacionais internos, construídos ao longo de seus mais de oitenta anos de história, com práticas institucionais bastante próximas às das em presas estatais. Na conclusão, será demonstrada a co-responsabilidade do Estado na formação, no crescimento, no início da crise e na intensificação do processo de queda da empresa , através de atuações determinantes, em momentos diferentes da história do país.
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銀行法規開放與會計穩健性之關聯 / The relation between banking deregulation and accounting conservatism徐筱淳, Hsu, Hsiao Chun Unknown Date (has links)
本研究以美國證券市場為樣本,探討銀行業之法規開放是否對非金融業公司之會計穩健性造成影響。銀行法規開放可使銀行透過併購於州內擴張,借款公司可能面對之銀行議價能力上升,使得銀行要求融資顧客出具高品質之財務報表。另一方面,州際銀行法規開放可能使他州銀行進入本地金融市場,進而提高金融市場之競爭度。由於會計穩健性可降低管理階層與投資人的資訊不對稱,被視為高品質的財務報表,本文推測銀行業法規鬆綁會影響公司會計穩健性。實證結果顯示,州內銀行法規開放與會計穩健性間具有顯著正向關係;然而,州際銀行法規開放與會計穩健性間具有顯著負向關係。額外分析顯示,大型企業更傾向於對銀行法規開放作出反應,而較依賴發行公司債融資方式之公司在面對銀行法規開放時則減少財務報導中認列損失之即時性。 / This study uses US banking deregulation as a research setting to examine whether banking deregulation has an impact on the degree of accounting conservatism of non-financial firms. Since banking deregulation would enable large banks expand within states through merge and acquisition, bank’s bargaining power to lenders may increase. Banks may require their clients to provide higher quality of financial statements. On the other hand, banking deregulation may increase competition in local financial markets by enabling large banks to enter into local markets. As accounting conservatism could alleviate information asymmetry between management and investors, and serves as an indicator of high quality of financial statements, I expect that banking deregulations would have an impact on firms’ reporting conservatism. I find that there is a significantly positive relationship between intrastate banking deregulation and firms’ timely loss recognition. In contrast, interstate banking deregulation has a significantly negative influence on firms’ timely loss recognition. Additional analyses reveal that large firms are more likely to respond to the banking deregulation and that firms that rely more on public debt financing respond to the banking deregulation by decreasing their degree of timely loss recognition in financial reporting.
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Neo-liberal ideas in Social Democratic arguments? : A look at the privatization debate regarding the Swedish railway sectorLarsson, Johan January 2011 (has links)
Privatization is said to be fundamentally a neo-liberal idea and deregulation is one form of privatization. The Swedish railway sector has been deregulated gradually over the years. Some of the policy changes towards more deregulation have been done with the Swedish Social Democrats in government. This thesis analyzes the arguments for and against privatization on two occasions, 2000 and 2009 with the Social Democrats in government and opposition respectively, to see if the party’s argumentation has been influenced by neo-liberal ideas and if that change depending on whether they are in government or not. The analysis shows that there has been influence of neo-liberal ideas on arguments from the Social Democrats and that their view on privatization and deregulation differed depending on whether they were in government or in opposition.
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Seasonal Aggregations of the Florida Manatee (Trichechus manatus latirostris) in the Port Everglades and Intracoastal Regions of Fort Lauderdale, Florida.Goldman, Jaime M. 01 December 2010 (has links)
The Florida manatee (Trichechus manatus latirostris), a subspecies of the West Indian manatee, is one of the most endangered marine mammals in United States waters. The Florida manatee is the only manatee that ranges into subtropical and temperate regions. During the winter months manatees adopt a “refuging strategy” where they aggregate at warm-water sources immediately following decreases in the ambient water temperature to below 20° C (68° F) in order to avoid cold stress syndrome (CSS). During the winter manatees aggregate in warm water refuges, including natural warm water springs and the effluent discharges of power plants.
The purpose of this study was to determine the number of manatees that aggregate and utilize the waters of the Florida Power and Light (FPL) Plant in Port Everglades (PPE), Florida, its effluent canal, and the surrounding Intracoastal Waterway during the winter months. This study documents the importance of Port Everglades as a wintering refuge for the Florida manatee. This study analyzed the inverse relationship between the number of manatees present at a warm water effluent and water temperature.
In this study data were collected over five manatee winter seasons (between 15 November and 31 March) from 1999-2004, from both boat-based and land-based surveys monitoring the presence of manatees in the effluent canal from the FPL electricity generating facility in Port Everglades, FL and the Intracoastal Waterway. Findings indicated that there was an inverse relationship between the number of manatees present and water temperature, where more manatees were present in cooler months, and fewer in warmer months. This study also analyzed the parameters of Catch per Unit Effort (CPUE) as well as heating degree-days and their effect on and relationship to the number of manatees present. The higher the heating degree-days number, the more severe, or cold, winter this indicates. The year with the highest heating degree-days, 24.98, was the 2002-2003 season, which was also the season with the highest number of manatees observed, 393, and the highest CPUE, 10.62 manatees/day.
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Evaluation of Alternate DNA Structures at c-MYC Fragile Region Associated with t(8;14) Translocation And Role of GNG Motifs During G-quadruplex FormationDas, Kohal January 2016 (has links) (PDF)
Watson-Crick paired B-form DNA is the genetic material in most of the biological systems. Integrity of DNA is of utmost importance for the normal functioning of any organism. Various environmental factors, chemicals and endogenous agents constantly challenge integrity of the genome resulting in mutagenesis. Over the past few decades multiple reports suggest that DNA can adopt alternative conformations other than the right handed double helix. Such structures occur within the context of B-DNA as sequence dependent structural variations and are facilitated by free energy derived from negative supercoiling, which may be generated during physiological processes like transcription, replication, etc. or binding of proteins. Multiple groups have shown that these structures render fragility to the genome owing to single-strandedness (presence of unpaired bases). This conformational polymorphism of the DNA is due to the presence of several repetitive elements across the genome. Some of the common non-B DNA structures include Z-DNA, H-DNA (triplex DNA), cruciform DNA, G-quadruplexes and RNA: DNA hybrid (R-loops).
Over the past few decades G-quadruplex structures have gained tremendous importance owing to its role in physiology and pathology. Recently it has been shown that novel sequence motifs, called GNG or bulges can fold into G-quadruplexes, thus increasing the propensity of such structures genome-wide. Neurological diseases, psychiatric diseases and genomic disorders (due to deletions, translocations, duplications and inversions) are some of the consequences of non-B DNA structures in the human genome.
Inadvertent genomic rearrangements in human can lead to different diseases including cancer. Immediate consequence of genomic rearrangement includes structural alteration of genome through joining of distant sequences. t(8;14) translocation is the hallmark of Burkitt’s lymphoma, which results in deregulation of c-MYC gene that may contribute to oncogenic transformation. In the present study, we delineate the causes of fragility within the c-MYC gene. In order to do this, breakpoints at the c-MYC locus from Burkitt’s lymphoma patient sequences reported in database were plotted and analysed. Interestingly, unlike many other translocations, breakpoints at c-MYC locus were widespread, except for a cluster of breakpoints downstream to promoter 2 (P2).
Previous studies indicate that the translocation breakpoint clusters often correlate with formation of non-B DNA structures. The entire breakpoint cluster downstream of P2 was divided into Region 1, Region 2 and Region 3. Interestingly, in silico analysis of the breakpoint clusters revealed no evidence for predictive classic non-B DNA motifs in Region
2; whereas Region 1 harboured a G-quadruplex motif on the template strand and Region 3 had two short inverted repeats. Intriguingly, as the nontemplate strand of Region 2 was G skewed with a good number of AID binding motifs, we tested the MYC breakpoint Region 2 for its potential to form R-loop due to binding of nascent RNA to template DNA. Our results showed that MYC Region 2 can form RNA-DNA hybrid in a transcription dependent manner in physiological orientation. Observed structure was sensitive to RNase H. We showed Region 2 hindered action of Dpn I upon transcription confirming formation of R-loop structure. Owing to single strandedness, Region 2 R-loop was shown to be sensitive to P1 nuclease as opposed to the untranscribed control. The single strandedness of the Region 2 R-loop was characterized at a single molecule level through bisulfite modification assay. The assay corroborated formation of R-loop along with providing snapshots of various length R-loops formed upon Region 2 transcription. Besides, various biophysical and biochemical assays showed the complementary region (template strand) to be single-stranded in stretches, upon transcription. Length of RNA within the R-loop was within a range of 75 to 250 nt. To delineate the mechanism of R-loop formation we tested the sensitivity of R-loop formation to RNase A during and post transcription; and found that R-loop formation was abrogated in presence of RNase A during transcription suggesting that R-loop formation followed a “thread back model”.
Intriguingly we observed that two short regions of the template strand exhibited high degree of single strandedness. To investigate the reason for such unusual single strandedness, oligonucleotides spanning the region was designed and subjected for CD and EMSA studies. EMSA showed robust intramolecular G-quadruplex structure formation in presence of KCl, whereas CD confirmed that both regions formed parallel G-quadruplexes. We also showed the precise involvement of guanines in structure formation through DMS protection assay. Further, the region of interest was cloned into appropriate vectors and primer extension assays were performed in presence of G-quadruplex stabilizing agents like TMPyP4 and KCl.
Increasing concentration of these stabilizing agents enhanced the formation of G-quadruplexes in a double stranded context, which hindered polymerase progression. Since these G-quadruplex structures utilized sequences which are deviant to the consensus of G-quadruplex motifs, non-B DNA predicting tools were unable to score them. On closer analysis of the sequences we found that, these G-quadruplexes involve duplex hairpin and GNG motifs during structure formation. Besides, both the G-quadruplexes were highly thermostable and were able to fold back upon renaturation.
Till recently, it has been believed that G-quadruplex structures are formed using a minimum of four, 3 guanine tracts, with connecting loops ranging from one to seven. Recent studies have reported deviation from this general convention. One such deviation is the involvement of bulges in the guanine tracts. In the present study, guanines along with GNG motifs have been extensively studied using recently reported HOX11 breakpoint fragile region I as a model template. By strategic mutagenesis approach we show that the core elements of a G-quadruplex are not equally important in structure formation when flanked by GNG motifs. Importantly, the positioning and number of GNG/GNGNG can dictate the formation of G-quadruplexes. In addition to HOX11 fragile region, GNG motifs of HIF1-alpha can fold into intramolecular G-quartet. However, GNG motifs in mutant VEGF sequence could not participate in structure formation, suggesting that the usage of GNG is context dependent. Importantly, we show that when two stretches of guanines are flanked by two independent GNG motifs in a naturally occurring sequence (SHOX), it can fold into an intramolecular G-quadruplex. Interestingly, intra molecular GNG G-quadruplexes were able to fold back after complete denaturation of the oligonucleotides. Besides one of the intra molecular GNG G-quadruplexes was purified and confirmed for parallel conformation. Finally, we show the specific binding of G-quadruplex binding protein, Nucleolin and G-quadruplex antibody BG4
to SHOX G-quadruplex through EMSA studies. Thus, the study provides novel insights into the role of GNG motifs in G-quadruplex structure formation, which may have both physiological and pathological implications.
In conclusion, we show formation of transcription dependent R-loop and G-quadruplex structures at the c-MYC gene locus in a mutually exclusive manner. The data presented here, in conjunction with studies from other laboratories suggests that these structures could impart fragility within the c-MYC gene locus during t(8;14) translocation. Besides, we characterised unusual G-quadruplexes harbouring GNG motifs. We find that positioning and number of GNG can dictate the formation of G-quadruplexes and is context dependent.
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