Thermodynamic basis of the enhanced specificity of structured DNA probes

Molecular beacons are DNA probes that form a stem-and-loop structure and possess an internally quenched fluorophore. When they bind to complementary nucleic acids, they undergo a conformational transition that switches on their fluorescence. These probes recognize their targets with higher specificity than probes that cannot form a hairpin stem, and they easily discriminate targets that differ from one another by only a single nucleotide. Our results show that molecular beacons can exist in three different states: bound to a target, free in the form of a hairpin structure, and free in the form of a random coil. Thermodynamic analysis of the transitions between these states reveals that enhanced specificity is a general feature of conformationally constrained probes.

Design of polyzinc finger peptides with structured linkers

Zinc finger domains are perhaps the most versatile of all known DNA binding domains. By fusing up to six zinc finger modules, which normally recognize up to 18 bp of DNA, designer transcription factors can be produced to target unique sequences within large genomes. However, not all continuous DNA sequences make good zinc finger binding sites. To avoid having to target unfavorable DNA sequences, we designed multizinc finger peptides with linkers capable of spanning long stretches of nonbound DNA. Two three-finger domains were fused by using either transcription factor IIIA for the Xenopus 5S RNA gene (TFIIIA) finger 4 or a non-sequence-specific zinc finger as a “structured” linker. Our gel-shift results demonstrate that these peptides are able to bind with picomolar affinities to target sequences containing 0–10 bp of nonbound DNA. Furthermore, these peptides display greater sequence selectivity and bind with higher affinity than similar six-finger peptides containing long, flexible linkers. These peptides are likely to be of use in understanding the behavior of polydactyl proteins in nature and in the targeting of human, animal, or plant genomes for numerous applications. We also suggest that in certain polydactyl peptides an individual finger can “flip” out of the major groove to allow its neighbors to bind shorter, nontarget DNA sequences.

RAD51 supports spontaneous non-homologous recombination in mammalian cells, but not the corresponding process induced by topoisomerase inhibitors

The RAD51 protein has been shown to participate in homologous recombination by promoting ATP-dependent homologous pairing and strand transfer reactions. In the present study, we have investigated the possible involvement of RAD51 in non-homologous recombination. We demonstrate that overexpression of CgRAD51 enhances the frequency of spontaneous non-homologous recombination in the hprt gene of Chinese hamster cells. However, the rate of non-homologous recombination induced by the topoisomerase inhibitors campothecin and etoposide was not altered by overexpression of RAD51. These results indicate that the RAD51 protein may perform a function in connection with spontaneous non-homologous recombination that is not essential to or not rate-limiting for non-homologous recombination induced by camptothecin or etoposide. We discuss the possibility that the role played by RAD51 in non-homologous recombination observed here may not be linked to non-homologous end-joining.

Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications

Variability in population growth rate is thought to have negative consequences for organism fitness. Theory for matrix population models predicts that variance in population growth rate should be the sum of the variance in each matrix entry times the squared sensitivity term for that matrix entry. I analyzed the stage-specific demography of 30 field populations from 17 published studies for pattern between the variance of a demographic term and its contribution to population growth. There were no instances in which a matrix entry both was highly variable and had a large effect on population growth rate; instead, correlations between estimates of temporal variance in a term and contribution to population growth (sensitivity or elasticity) were overwhelmingly negative. In addition, survivorship or growth sensitivities or elasticities always exceeded those of fecundity, implying that the former two terms always contributed more to population growth rate. These results suggest that variable life history stages tend to contribute relatively little to population growth rates because natural selection may alter life histories to minimize stages with both high sensitivity and high variation.

Polygalacturonase Gene Expression in Ripe Melon Fruit Supports a Role for Polygalacturonase in Ripening-Associated Pectin Disassembly

Ripening-associated pectin disassembly in melon is characterized by a decrease in molecular mass and an increase in the solubilization of polyuronide, modifications that in other fruit have been attributed to the activity of polygalacturonase (PG). Although it has been reported that PG activity is absent during melon fruit ripening, a mechanism for PG-independent pectin disassembly has not been positively identified. Here we provide evidence that pectin disassembly in melon (Cucumis melo) may be PG mediated. Three melon cDNA clones with significant homology to other cloned PGs were isolated from the rapidly ripening cultivar Charentais (C. melo cv Reticulatus F1 Alpha) and were expressed at high levels during fruit ripening. The expression pattern correlated temporally with an increase in pectin-degrading activity and a decrease in the molecular mass of cell wall pectins, suggesting that these genes encode functional PGs. MPG1 and MPG2 were closely related to peach fruit and tomato abscission zone PGs, and MPG3 was closely related to tomato fruit PG. MPG1, the most abundant melon PG mRNA, was expressed in Aspergillus oryzae. The culture filtrate exponentially decreased the viscosity of a pectin solution and catalyzed the linear release of reducing groups, suggesting that MPG1 encodes an endo-PG with the potential to depolymerize melon fruit cell wall pectin. Because MPG1 belongs to a group of PGs divergent from the well-characterized tomato fruit PG, this supports the involvement of a second class of PGs in fruit ripening-associated pectin disassembly.

Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation

Modification of damaged replication forks is emerging as a crucial factor for efficient chromosomal duplication and the avoidance of genetic instability. The RecG helicase of Escherichia coli, which is involved in recombination and DNA repair, has been postulated to act on stalled replication forks to promote replication restart via the formation of a four-stranded (Holliday) junction. Here we show that RecG can actively unwind the leading and lagging strand arms of model replication fork structures in vitro. Unwinding is achieved in each case by simultaneous interaction with and translocation along both the leading and lagging strand templates at a fork. Disruption of either of these interactions dramatically inhibits unwinding of the opposing duplex arm. Thus, RecG translocates simultaneously along two DNA strands, one with 5′-3′ and the other with 3′-5′ polarity. The unwinding of both nascent strands at a damaged fork, and their subsequent annealing to form a Holliday junction, may explain the ability of RecG to promote replication restart. Moreover, the preferential binding of partial forks lacking a leading strand suggests that RecG may have the ability to target stalled replication intermediates in vivo in which lagging strand synthesis has continued beyond the leading strand.

Extending the chemistry that supports genetic information transfer in vivo: phosphorothioate DNA, phosphorothioate RNA, 2'-O-methyl RNA, and methylphosphonate DNA.

DNA and RNA are the polynucleotides known to carry genetic information in life. Chemical variants of DNA and RNA backbones have been used in structure-function and biosynthesis studies in vitro, and in antisense pharmacology, where their properties of nuclease resistance and enhanced cellular uptake are important. This study addressed the question of whether the base(s) attached to artificial backbones encodes genetic information that can be transferred in vivo. Oligonucleotides containing chemical variants of DNA or RNA were used as primers for site-specific mutagenesis of bacteriophage f1. Progeny phage were scored both genetically and physically for the inheritance of information originally encoded by bases attached to the nonstandard backbones. Four artificial backbone chemistries were tested: phosphorothioate DNA, phosphorothioate RNA, 2'-O-methyl RNA and methylphosphonate DNA. All four were found capable of faithful information transfer from their attached bases when one or three artificial positions were flanked by normal DNA. Among oligonucleotides composed entirely of nonstandard backbones, only phosphorothioate DNA supported genetic information transfer in vivo.

Interaction of GroEL with a highly structured folding intermediate: iterative binding cycles do not involve unfolding.

The GroE proteins are molecular chaperones involved in protein folding. The general mechanism by which they facilitate folding is still enigmatic. One of the central open questions is the conformation of the GroEL-bound nonnative protein. Several suggestions have been made concerning the folding stage at which a protein can interact with GroEL. Furthermore, the possibility exists that binding of the nonnative protein to GroEL results in its unfolding. We have addressed these issues that are basic for understanding the GroE-mediated folding cycle by using folding intermediates of an Fab antibody fragment as molecular probes to define the binding properties of GroEL. We show that, in addition to binding to an early folding intermediate, GroEL is able to recognize and interact with a late quaternary-structured folding intermediate (Dc) without measurably unfolding it. Thus, the prerequisite for binding is not a certain folding stage of a nonnative protein. In contrast, general surface properties of nonnative proteins seem to be crucial for binding. Furthermore, unfolding of a highly structured intermediate does not necessarily occur upon binding to GroEL. Folding of Dc in the presence of GroEL and ATP involves cycles of binding and release. Because in this system no off-pathway reactions or kinetic traps are involved, a quantitative analysis of the reactivation kinetics observed is possible. Our results indicate that the association reaction of Dc and GroEL in the presence of ATP is rather slow, whereas in the absence of ATP association is several orders of magnitude more efficient. Therefore, it seems that ATP functions by inhibiting reassociation rather than promoting release of the bound substrate.

The alpha 5 beta 1 integrin supports survival of cells on fibronectin and up-regulates Bcl-2 expression.

Anchorage-dependent cells that are prevented from attaching to an extracellular matrix substrate stop proliferating and may undergo apoptosis. Cell adhesion to a substrate is mediated by the integrin family of cell surface receptors, which are known to elicit intracellular signals upon cell adhesion. We show here that Chinese hamster ovary cells expressing the alpha 5 beta 1 integrin, which is a fibronectin receptor, do not undergo apoptosis upon serum withdrawal when the cells are plated on fibronectin. However, the alpha v beta 1 integrin, which is also a fibronectin receptor and binds fibronectin on the same RGD motif as alpha 5 beta 1, did not prevent apoptosis on fibronectin of the same cells. The cytoplasmic domain of the integrin alpha 5 subunit was required for the alpha 5 beta 1-mediated cell survival on fibronectin. The fibronectin-mediated survival effect appeared to be independent of the level of tyrosine phosphorylation of the focal adhesion kinase, which is induced by integrin-mediated cell attachment. The expression of the Bcl-2 protein, which counteracts apoptosis, was elevated in cells attaching to fibronectin through alpha 5 beta 1; cells attaching through alpha v beta 1 survived only if exogenous Bcl-2 was provided. Thus, alpha 5 beta 1, but not the closely related alpha v beta 1 integrin, appears to suppress apoptotic cell death through the Bcl-2 pathway.

Sentidos de família construídos por profissionais de saúde na estratégia de saúde da família

Na construção de políticas sociais atribuiu-se um papel central à família na proteção social e no cuidado com os seus membros. Na saúde, a família assume essa centralidade na Estratégia de Saúde da Família (ESF), sendo compreendida como objeto da atenção em saúde. Essa centralidade se deu a partir de uma pretensão de mudança no modelo assistencial que visasse a integralidade do cuidado e um olhar para as condições de vida como fundamentais no processo saúde-doença. Tais transformações nos sentidos e práticas de saúde têm sido desafiadoras. A partir da perspectiva Construcionista Social, que orienta esse estudo, compreendemos que os sentidos são construídos nas interações entre as pessoas e que esses configuram práticas sociais. Diante deste quadro de desafios na ESF e a partir da perspectiva adotada, temos como objetivo compreender os sentidos produzidos por profissionais de equipes de saúde sobre famílias em contextos de reuniões de discussão de família/caso na ESF, buscando analisar como esses configuram a produção de práticas de cuidado e também como se dá a dinâmica de construção desses sentidos a partir das negociações entre os participantes. A constituição do corpus foi feita a partir da observação e registros em áudio de 16 reuniões de duas equipes de saúde da família, contando com 26 participantes, dentre eles profissionais e estagiários de diferentes especialidades. A análise foi feita a partir da perspectiva das práticas discursivas, com os seguintes passos: 1) transcrição do material; 2) leitura intensiva e organização do material; 3) construção de sentidos sobre a família, e análise dos repertórios interpretativos, discursos usados, e implicações para ação; e 4) narrativa ilustrativa da dinâmica dos sentidos. Os sentidos construídos na análise foram: a) Família como pessoas que moram juntas: os repertórios usados descreviam os modos de ser família a partir do ambiente em que ela vive, entendendo a família como informante e cuidadora dos seus membros; b) Família como responsável pelo cuidado: repertórios de família como aquela que dá suporte aos seus membros e é responsável por eles; e, por vezes, está sobrecarregada com esses cuidados; c) Família como problema: repertórios que configuravam a família como aquela que é responsável pelo problema de saúde dos seus membros, como aquela que funciona como um estressor para eles ou como aquela que está em situação de risco; e d) Família como rede de relações, sentido que foi usado, mais comumente, em conversas sobre casos complexos, com discussões voltadas para configurações, estruturas e dinâmicas familiares. A partir da análise do processo de discussão da equipe em torno de um \"caso\", foi possível ilustrar o dinamismo desses sentidos nas conversas e como esses são negociados a todo momento. A análise nos permite considerar que há esforços dos profissionais em voltar a atenção do cuidado para a família, porém ainda são comuns práticas centradas no indivíduo e pouco pautadas no contexto e nas condições de vida das famílias. Compreendemos que dar visibilidade a esses diferentes sentidos e seu uso permite reflexões sobre como cada forma de descrever as famílias possibilita a construção de práticas distintas, o que pode contribuir para uma maior reflexão dos profissionais de saúde sobre sua prática cotidiana (Apoio Capes e Fapesp- 2014/08618-6).

Women Leaders Resolving Conflict in Higher Education: A Feminist Epistemological Perspective

In an American postsecondary context, conflict is inherent (Gianneschi & Yanagiura, 2006; Valian, 1999). Successful navigation of conflict in the academy is vital for those who aspire to leadership positions (Nadler & Nadler, 1987; Walters, Stuhlmacher, & Meyer, 1998). Presently, however, women face significant barriers to achieving success in higher education administration, including gender expectations for conflict resolution behavior (Bartunek, 1992; Bowles, Babcock, & McGinn, 2005; Gayle, Preiss, & Allen, 2002). While a considerable body of literature exists for understanding gender negotiation, it remains rooted in a masculine paradigm (Kolb & Putnam, 2006; Shuter & Turner, 1997), and, as such, established theories lack a feminist epistemological perspective. Consequently, my primary research question is, How do women leaders experience and perceive conflict in the higher education work environment? I conduct a qualitative study that examines workplace conflict experiences of 15 women leaders from diverse personal and professional backgrounds. Hartsock's (1983) three-tiered gender-sensitive analysis of power, updated to include multicultural perspectives, serves as my theoretical framework. It is a lens through which I evaluate theories, finding multicultural organizational, higher education conflict, and gender negotiation theories most applicable to this study. The framework also creates the foundation upon which I build my study. Specifically, I determine that a feminist research method is most relevant to this investigation. To analyze data obtained through in depth interviews, I employ a highly structured form of grounded theory called dimensional analysis. Based on my findings, I co-construct with study participants a Feminist Conflict Process Theory and Flowchart in which initially the nature of the relationship, and subsequently the level of risk to the relationship, institution, or self, is evaluated. This study supports that which is observed in the conflict resolution practitioner literature, but is unique in its observation of factors that influence decisions within a dynamic conflict resolution process. My findings are significant to women who aspire to serve in leadership positions in higher education, as well as to the academy as a whole, for it expands our knowledge of women's ontological and epistemological perspectives on resolving conflict in postsecondary education.

Electoral Systems and Ethnic Conciliation: A Structured, Focused Analysis of Vote-Pooling in Northern Ireland Elections 1998-2011

This research project examines the role of electoral system rules in affecting the extent of conciliatory behavior and cross-ethnic coalition making in Northern Ireland. It focuses on the role of the Single Transferable Vote (STV) electoral system in shaping party and voter incentives in a post-conflict divided society. The research uses a structured, focused comparison of the four electoral cycles since the Belfast Agreement of 1998. This enables a systematic examination of each electoral cycle using a common set of criteria focused on conciliation and cross-ethnic coalition making. Whilst preference voting is assumed to benefit moderate candidates, in Northern Ireland centrist and multi-ethnic parties outside of the dominant ethnic communities have received little electoral success. In Northern Ireland the primary effect of STV has not been to encourage inter-communal voting but to facilitate intra-community and intra-party moderation. STV has encouraged the moderation of the historically extreme political parties in each of the ethnic bloc. Patterns across electoral cycles suggest that party elites from the Democratic Unionist Party (DUP) and Sinn Fein have moderated their policy positions due to the electoral system rules. Therefore they have pursued lower-preference votes from within their ethnic bloc but in doing so have marginalized parties of a multi-ethnic or non-ethnic orientation.