Occurrence and Function of Hoogsteen Base Pairs in Nucleic Acids

Nucleic acids (DNA and RNA) play essential roles in the central dogma of biology for the storage and transfer of genetic information. The unique chemical and conformational structures of nucleic acids – the double helix composed of complementary Watson-Crick base pairs, provide the structural basis to carry out their biological functions. DNA double helix can dynamically accommodate Watson-Crick and Hoogsteen base-pairing, in which the purine base is flipped by ~180° degrees to adopt syn rather than anti conformation as in Watson-Crick base pairs. There is growing evidence that Hoogsteen base pairs play important roles in DNA replication, recognition, damage or mispair accommodation and repair. Here, we constructed a database for existing Hoogsteen base pairs in DNA duplexes by a structure-based survey from the Protein Data Bank, and structural analyses based on the resulted Hoogsteen structures revealed that Hoogsteen base pairs occur in a wide variety of biological contexts and can induce DNA kinking towards the major groove. As there were documented difficulties in modeling Hoogsteen or Watson-Crick by crystallography, we collaborated with the Richardsons’ lab and identified potential Hoogsteen base pairs that were mis-modeled as Watson-Crick base pairs which suggested that Hoogsteen can be more prevalent than it was thought to be. We developed solution NMR method combined with the site-specific isotope labeling to characterize the formation of, or conformational exchange with Hoogsteen base pairs in large DNA-protein complexes under solution conditions, in the absence of the crystal packing force. We showed that there are enhanced chemical exchange, potentially between Watson-Crick and Hoogsteen, at a sharp kink site in the complex formed by DNA and the Integration Host Factor protein. In stark contrast to B-form DNA, we found that Hoogsteen base pairs are strongly disfavored in A-form RNA duplex. Chemical modifications N1-methyl adenosine and N1-methyl guanosine that block Watson-Crick base-pairing, can be absorbed as Hoogsteen base pairs in DNA, but rather potently destabilized A-form RNA and caused helix melting. The intrinsic instability of Hoogsteen base pairs in A-form RNA endows the N1-methylation as a functioning post-transcriptional modification that was known to facilitate RNA folding, translation and potentially play roles in the epitranscriptome. On the other hand, the dynamic property of DNA that can accommodate Hoogsteen base pairs could be critical to maintaining the genome stability.

Best Practices: Lessons Learned by a South Florida Non-Profit Community Based Organization while Designing and Implementing a Career Exploration Evidence Informed Framework in Urban Communities

All A’s was designed to support of the agency’s family strengthening initiatives in South Florida. All A’s uses evidence informed strategies poised to be an inclusive curriculum that teaches self-determination and adaptive behavior skills. The framework incorporates problem based learning and adult learning theory and follows the Universal Design for Learning. Since 2012, the agency has served over 8500 youth and 4,000 adults using the framework. The framework addresses educational underachievement and career readiness in at risk populations. It is used to enhance participants AWARENESS of setting SMART goals to achieve future goals and career aspirations. Participants are provided with ACCESS to resources and opportunities for creating and implementing an ACTION plan as they pursue and ACHIEVE their goals. All A’s promotes protective factors and expose youth to career pathways in Science, Technology, Engineering and Math (STEM) related fields. Youth participate in college tours, job site visits, job shadowing, high school visits, online college and career preparation assistance, service learning projects, STEM projects, and the Winning Futures© mentoring program. Adults are assisted with résumé development; learn job search strategies, interview techniques, job shadowing experiences, computer and financial literacy programs. Adults and youth are also given the opportunity to complete industry-recognized certifications in high demand industries (food service, general labor, and construction), and test preparation for the General Educational Development Test.

Sustentabilidade das empresas associadas à REDEPETRO-RN

The present study investigated the management of social, environmental and economic sustainability practices employed by 72 oil companies in Rio Grande do Norte state in Brazil associated to Joint Business Network for Enhancing the Competitive Ability of Suppliers of Goods and Services to the Gas and Oil Industry in Rio Grande do Norte (REDEPETRO-RN). Thus, our investigation aimed to determine the extent to which sustainability practices of companies associated to REDEPETRO-RN are developed through their own efforts or influenced by the Triple Helix interorganizational arrangement (governamental organizations, education and research institutions, and industries). The research instrument used was a questionnaire in order to map and characterize the sustainability practices. The research subjects were business owners and managers. The data collected supported the descriptive, correspondence and correlation analyzes. Were identified a greater emphasis of the companies surveyed in developing sustainability practices and greater economic influence of business organizations in the construction of sustainability status. It was concluded with confirmation of thesis of the REDEPETRO-RN arrangement exhibits the characteristics and functioning of a common Interorganizational Cooperative Arrangement, not those of a triple helix interorganizational arrangement, given that the influences exerted for the development of social, environmental and economical sustainability on the part of teaching and research institutions, and government and business organizations do not interact with one another sufficiently to create a virtuous circle of cooperation among the associated companies. By contrast, the Interorganizational Cooperative Arrangement plays an important role in strengthening the competitiveness of companies affiliated to REDEPETRO-RN, by combining different competencies in an attempt at supporting the adoption of sustainability practices, a role reinforced by the scope of PETROBRAS, which, due to its economic importance, has considerable weight in the managerial decisions of associated companies

As relações da tríplice hélice no setor da carcinicultura do Rio Grande do Norte: uma análise a partir das abordagens da imersão social e da dependência de recursos

This work consists in a study of the Shrimp Industry in the state of Rio Grande do Norte, whose central issue relates to the understanding of how the Triple Helix (University, Government and the productive sector) interrelationship limits or expands the industry s innovation process. The study aims to understand how the Triple Helix relationship interferes in the innovation process of shrimp in Rio Grande do Norte. As the knowledge becomes the resource key for production methods, the generation of new technologies, new products and processes which demands joint and integrated action of the institutions comprising the Triple Helix: University, Government and productive sector, which possess the essential resources to innovate the process and can be maximized from cooperative relationships between the referred Institutions. Thus, in this work, it was sharply used the pioneering studies of Sabato and Botana (1968) regarding the cooperation relationship between the scientific-technological sphere, the governmental and the productive base, and studies on the Triple Helix approach, proposed by Etzkowitz and Leydesdorff (2000), in which the university has a key role in the process of technological and innovative development of countries and regions, and under which it is assigned to the very University - the character of the entrepreneurial institution, through the concept of entrepreneurial University. Aiming to overcome the criticism of Cooke (2005), regarding the limitations of the Triple Helix approach, in this study it was used - as analytical perspectives - the perspective of social immersion (Granovetter, 1985, 2005) and the theory of resources dependence (PFEFFER; SALANCIK, 1978). The analytical perspectives presented in here, despite of the different assumptions, are essential to eliminate the bias that one only approach can lead (ASTLEY; VAN DE VEM; 2007). The authors arguments focus on the fact that the integration is possible if the researcher acknowledged that different perspectives may have different descriptions of the same phenomenon. As a research strategy, this study is characterized as a study case, along with the proposed objectives - the qualitative method was used as an approach and, depending on the gathering of the sector s historical, a sectional longitudinal view approach was applied (VIEIRA, 2004). The primary and secondary data were used in order to understand the sector s evolutionary process and its inter-institutional relations - regarding the shrimp culture in Rio Grande do Norte - to promote the development, as the content was used for the technical analysis (BARDIN, 1977). The approach of social immersion and resources addiction dependence made it possible to understand that relationships are established within and between each sphere (university, government and productive sector) characterizing a network of low density relationships and strongly internal and external dependence. Based on the speech of Etzkowitz and Mello (2006), a successful Triple Helix strategy of innovation requires not only the involvement and commitment of the parts, within the institutional sphere and among them, but also the development of mechanisms to coordinate the multiple and complex interactions and interfaces, focusing on promoting both environment and context for innovation and learning; it can be acknowledge from study results that the shrimp in the State of the RN, although there are several institutional mechanisms to promote greater integration and technological development, has been presented disjointed - both internally and between the spheres - and under no legitimate practice when facing the innovational promotion and integration institutions. Due to those factors, the central institutions of the network are crucial to the promotion of innovations, spreading through their direct contacts the importance factor of the sustainable competitive activity in the world market and on the national level. However, it may be concluded, from the data, that the Triple Helix relations are interfering in a negative way on what concerns the promotion of innovations in the shrimp industry in RN

A história da ciência como subsídio para a construção do conhecimento do conceito da dupla hélice

Acompanha: Dupla-hélice: a construção de um conhecimento

Na granicy Unii Europejskiej – pozycja europejskich terytoriów autonomicznych w dobie globalizacji i integracji. Przypadek Wysp Alandzkich

The model of autonomy developed by the Aland Isles can provide a number of interesting solutions applicable in other territories. Territorial autonomy as a manner of ensuring the political and economic rights of the minority involves facing up to the challenges of European integration and globalization. It seems that the Aland Isles have successfully coped with this challenge. Firstly, they were able to present and promote their own interests during the accession negotiations in an efficient manner. Secondly, they maintained (and additionally strengthened by including it in the aquis communitaire) their separate, autonomous status and the guarantees of identity protection by virtue of limiting the rights of persons without domicile rights to purchase land and run business activity. Thirdly, they managed to obtain a special status excluding them from the process of indirect tax harmonization, thus ensuring considerable economic benefits. Fourthly, both Finland and the European Union confirmed their autonomy, demilitarization and neutrality allowing the Isles to retain their former status under the new circumstances. Fifthly, they obtained representation in the Committee of the Regions and a defined position on European matters in Finland. The skillful application of the existing solutions and the winning of an advantageous set of derogations and exceptions strengthened the position of the Isles both with respect to Finland and the international surroundings. The Isles’ economic, cultural and political protection was augmented. Alongside their participation in international organizations, such as The Nordic Board, the Aland Isles have remained active and discernible on the international arena.

Sustentabilidade das empresas associadas à REDEPETRO-RN

The present study investigated the management of social, environmental and economic sustainability practices employed by 72 oil companies in Rio Grande do Norte state in Brazil associated to Joint Business Network for Enhancing the Competitive Ability of Suppliers of Goods and Services to the Gas and Oil Industry in Rio Grande do Norte (REDEPETRO-RN). Thus, our investigation aimed to determine the extent to which sustainability practices of companies associated to REDEPETRO-RN are developed through their own efforts or influenced by the Triple Helix interorganizational arrangement (governamental organizations, education and research institutions, and industries). The research instrument used was a questionnaire in order to map and characterize the sustainability practices. The research subjects were business owners and managers. The data collected supported the descriptive, correspondence and correlation analyzes. Were identified a greater emphasis of the companies surveyed in developing sustainability practices and greater economic influence of business organizations in the construction of sustainability status. It was concluded with confirmation of thesis of the REDEPETRO-RN arrangement exhibits the characteristics and functioning of a common Interorganizational Cooperative Arrangement, not those of a triple helix interorganizational arrangement, given that the influences exerted for the development of social, environmental and economical sustainability on the part of teaching and research institutions, and government and business organizations do not interact with one another sufficiently to create a virtuous circle of cooperation among the associated companies. By contrast, the Interorganizational Cooperative Arrangement plays an important role in strengthening the competitiveness of companies affiliated to REDEPETRO-RN, by combining different competencies in an attempt at supporting the adoption of sustainability practices, a role reinforced by the scope of PETROBRAS, which, due to its economic importance, has considerable weight in the managerial decisions of associated companies

Glutathione Transferases as Detoxification Agents: Structural and Functional Studies

Glutathione transferases (GSTs) are a diverse family of enzymes that catalyze the glutathione-dependent detoxification of toxic compounds. GSTs are responsible for the conjugation of the tripeptide glutathione (GSH) to a wide range of electrophilic substrates. These include industrial pollutants, drugs, genotoxic carcinogen metabolites, antibiotics, insecticides and herbicides. In light of applications in biomedicine and biotechnology as cellular detoxification agents, detailed structural and functional studies of GSTs are required. Plant tau class GSTs play crucial catalytic and non-catalytic roles in cellular xenobiotic detoxification process in agronomically important crops. The abundant existence of GSTs in Glycine max and their ability to provide resistance to abiotic and biotic stresses such as herbicide tolerance is of great interest in agriculture because they provide effective and suitable tools for selective weed control. Structural and catalytic studies on tau class GST isoenzymes from Glycine max (GmGSTU10-10, GmGSTU chimeric clone 14 (Sh14), and GmGSTU2-2) were performed. Crystal structures of GmGSTU10-10 in complex with glutathione sulfenic acid (GSOH) and Sh14 in complex with S-(p-nitrobenzyl)-glutathione (Nb-GSH) were determined by molecular replacement at 1.6 Å and 1.75 Å, respectively. Major structural variations that affect substrate recognition and catalytic mechanism were revealed in the upper part of helix H4 and helix H9 of GmGSTU10-10. Structural analysis of Sh14 showed that the Trp114Cys point mutation is responsible for the enhanced catalytic activity of the enzyme. Furthermore, two salt bridges that trigger an allosteric effect between the H-sites were identified at the dimer interface between Glu66 and Lys104. The 3D structure of GmGSTU2-2 was predicted using homology modeling. Structural and phylogenetic analysis suggested GmGSTU2-2 shares residues that are crucial for the catalytic activity of other tau class GSTs–Phe10, Trp11, Ser13, Arg20, Tyr30, Leu37, Lys40, Lys53, Ile54, Glu66 and Ser67. This indicates that the catalytic and ligand binding site in GmGSTU2-2 are well-conserved. Nevertheless, at the ligandin binding site a significant variation was observed. Tyr32 is replaced by Ser32 in GmGSTU2-2 and thismay affect the ligand recognition and binding properties of GmGSTU2-2. Moreover, docking studies revealed important amino acid residues in the hydrophobic binding site that can affect the substrate specificity of the enzyme. Phe10, Pro12, Phe15, Leu37, Phe107, Trp114, Trp163, Phe208, Ile212, and Phe216 could form the hydrophobic ligand binding site and bind fluorodifen. Additionally, side chains of Arg111 and Lys215 could stabilize the binding through hydrogen bonds with the –NO2 groups of fluorodifen. GST gene family from the pathogenic soil bacterium Agrobacterium tumefaciens C58 was characterized and eight GST-like proteins in A. tumefaciens (AtuGSTs) were identified. Phylogenetic analysis revealed that four members of AtuGSTs belong to a previously recognized bacterial beta GST class and one member to theta class. Nevertheless, three AtuGSTs do not belong to any previously known GST classes. The 3D structures of AtuGSTs were predicted using homology modeling. Comparative structural and sequence analysis of the AtuGSTs showed local sequence and structural characteristics between different GST isoenzymes and classes. Interactions at the G-site are conserved, however, significant variations were seen at the active site and the H5b helix at the C-terminal domain. H5b contributes to the formation of the hydrophobic ligand binding site and is responsible for recognition of the electrophilic moiety of the xenobiotic. It is noted that the position of H5b varies among models, thus providing different specificities. Moreover, AtuGSTs appear to form functional dimers through diverse modes. AtuGST1, AtuGST3, AtuGST4 and AtuGST8 use hydrophobic ‘lock–and–key’-like motifs whereas the dimer interface of AtuGST2, AtuGST5, AtuGST6 and AtuGST7 is dominated by polar interactions. These results suggested that AtuGSTs could be involved in a broad range of biological functions including stress tolerance and detoxification of toxic compounds.

As relações da tríplice hélice no setor da carcinicultura do Rio Grande do Norte: uma análise a partir das abordagens da imersão social e da dependência de recursos

This work consists in a study of the Shrimp Industry in the state of Rio Grande do Norte, whose central issue relates to the understanding of how the Triple Helix (University, Government and the productive sector) interrelationship limits or expands the industry s innovation process. The study aims to understand how the Triple Helix relationship interferes in the innovation process of shrimp in Rio Grande do Norte. As the knowledge becomes the resource key for production methods, the generation of new technologies, new products and processes which demands joint and integrated action of the institutions comprising the Triple Helix: University, Government and productive sector, which possess the essential resources to innovate the process and can be maximized from cooperative relationships between the referred Institutions. Thus, in this work, it was sharply used the pioneering studies of Sabato and Botana (1968) regarding the cooperation relationship between the scientific-technological sphere, the governmental and the productive base, and studies on the Triple Helix approach, proposed by Etzkowitz and Leydesdorff (2000), in which the university has a key role in the process of technological and innovative development of countries and regions, and under which it is assigned to the very University - the character of the entrepreneurial institution, through the concept of entrepreneurial University. Aiming to overcome the criticism of Cooke (2005), regarding the limitations of the Triple Helix approach, in this study it was used - as analytical perspectives - the perspective of social immersion (Granovetter, 1985, 2005) and the theory of resources dependence (PFEFFER; SALANCIK, 1978). The analytical perspectives presented in here, despite of the different assumptions, are essential to eliminate the bias that one only approach can lead (ASTLEY; VAN DE VEM; 2007). The authors arguments focus on the fact that the integration is possible if the researcher acknowledged that different perspectives may have different descriptions of the same phenomenon. As a research strategy, this study is characterized as a study case, along with the proposed objectives - the qualitative method was used as an approach and, depending on the gathering of the sector s historical, a sectional longitudinal view approach was applied (VIEIRA, 2004). The primary and secondary data were used in order to understand the sector s evolutionary process and its inter-institutional relations - regarding the shrimp culture in Rio Grande do Norte - to promote the development, as the content was used for the technical analysis (BARDIN, 1977). The approach of social immersion and resources addiction dependence made it possible to understand that relationships are established within and between each sphere (university, government and productive sector) characterizing a network of low density relationships and strongly internal and external dependence. Based on the speech of Etzkowitz and Mello (2006), a successful Triple Helix strategy of innovation requires not only the involvement and commitment of the parts, within the institutional sphere and among them, but also the development of mechanisms to coordinate the multiple and complex interactions and interfaces, focusing on promoting both environment and context for innovation and learning; it can be acknowledge from study results that the shrimp in the State of the RN, although there are several institutional mechanisms to promote greater integration and technological development, has been presented disjointed - both internally and between the spheres - and under no legitimate practice when facing the innovational promotion and integration institutions. Due to those factors, the central institutions of the network are crucial to the promotion of innovations, spreading through their direct contacts the importance factor of the sustainable competitive activity in the world market and on the national level. However, it may be concluded, from the data, that the Triple Helix relations are interfering in a negative way on what concerns the promotion of innovations in the shrimp industry in RN

Los conceptos de autonomía y democracia universitaria en la universidad pública colombiana, en el marco de la globalización y a través de la educación por competencias. 1992 - 2013

El interés de esta monografía es analizar la influencia de la globalización como proceso mundial y el neoliberalismo como política económica frente a la definición de políticas educativas. Tiene como objetivo analizar la manera en que se han modificado los conceptos de autonomía y democracia universitaria en la universidad pública colombiana, en el marco de la globalización y a través de la educación por competencias desde 1992 hasta el 2013. Con base en una aproximación conceptual de los términos de autonomía y democracia universitaria a través de elementos teóricos e históricos, se analizará como el actual sistema educativo colombiano y la educación por competencias ha modificado los conceptos de autonomía y democracia universitaria en la universidad pública colombiana.

TFEC is a macrophage-restricted member of the microphthalmia-TFE subfamily of basic helix-loop-helix leucine zipper transcription factors

The murine homologue of the TFEC was cloned as part of an analysis of the expression of the microphthalmia-TFE (MiT) subfamily of transcription factors in macrophages. TFEC, which most likely acts as a transcriptional repressor in heterodimers with other MiT family members, was identified in cells of the mononuclear phagocyte lineage, coexpressed,vith all other known MiT subfamily members (Mitf, TFE3, TFEB), Northern blot analysis of several different cell lineages indicated that the expression of murine TFEC (mTFEC) was restricted to macrophages. A 600-bp fragment of the TATA-less putative proximal promoter of TFEC shares features with many known macrophage-specific promoters and preferentially directs luciferase expression in the RAW264.7 macrophage cell line in transient transfection assays. Five of six putative Ets motifs identified in the TFEC promoter bind the macrophage-restricted transcription factor PU,I under in vitro conditions and in transfected 3T3 fibroblasts; the minimal luciferase activity of the TFEC promoter could be induced by coexpression of PU.1 or the related transcription factor Ets-2. The functional importance of the tissue-restricted expression of TFEC and a possible role in macrophage-specific gene regulation require further investigation, but are likely to be linked to the role of the other MiT family members in this lineage.

Winning the war for talent: Does CSR matter in the recruitment process?

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

The disadvantage of winning an election

This paper analyzes the problem that an incumbent faces during the legislature when deciding how to react to popular initiatives or policy proposals coming from different sources. We argue that this potential source of electoral disadvantage that the incumbent obtains after being elected can jeopardize the reelection possibilities of the incumbent. We analyze the decision of the incumbent when facing reelection and we characterize the conditions under which the advantages that the incumbent obtains can overcome the disadvantages. Finally, we use the results of this analysis to discuss some implications of the use of mechanisms of direct democracy like referenda and popular assemblies on electoral competition.

Solid-phase synthesis and NMR studies of modified oligonucleotides forming triplex helix and of oligonucleopeptides mimicking the topoisomerase I-DNA covalent complex

Report for the scientific sojourn carried out at the Institut de Biologia Molecular de Barcelona of the CSIC –state agency – from april until september 2007. Topoisomerase I is an essential nuclear enzyme that modulates the topological status of DNA, facilitating DNA helix unwinding during replication and transcription. We have prepared the oligonucleotide-peptide conjugate Ac-NLeu-Asn-Tyr(p-3’TTCAGAAGC5’)-LeuC-CONH-(CH2)6-OH as model compound for NMR studies of the Topoisomerase I- DNA complex. Special attention was made on the synthetic aspects for the preparation of this challenging compound especially solid supports and protecting groups. The desired peptide was obtained although we did not achieve the amount of the conjugate needed for NMR studies. Most probably the low yield is due to the intrinsic sensitive to hydrolysis of the phosphate bond between oligonucleotide and tyrosine. We have started the synthesis and the structural characterization of oligonucleotides carrying intercalating compounds. At the present state we have obtained model duplex and quadruplex sequences modified with acridine and NMR studies are underway. In addition to this project we have successfully resolved the structure of a fusion peptide derived from hepatitis C virus envelope synthesized by the group of Dr. Haro and we have synthesized and started the characterization of a modified G-quadruplex.