Linking number analysis of a self-assembled lemniscular Möbius-metallamacrocycle

A 26 membered, 24π-electron metallamacrocycle containing two Ag(I) centers is shown to be a double-twist Möbius cycle by a linking number analysis.

Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation

pBR322 form V DNA is a highly torsionally strained molecule with a linking number of zero. We have used sequence- specific DNA methylases as probes for B-DNA in this molecule, exploiting the inability of methylases to methylate single-stranded DNA and Z-DNA, both of which are known to occur in form V DNA. Some sequences in form V DNA were shown to be totally in the B-form, others were totally in an altered, unmethylatable conformation, while still other sites appeared to exist partly in altered and partly in normal B-conformation. Some potential Z-forming sequences (alternating pyrimidine/purine) of less than seven base-pairs were not in the Z conformation in form V DNA, whereas others did adopt an altered structure, indicating a modulating influence of flanking sequences. Furthermore, regions of imperfect alternating pyrimidine/purine structure were sometimes capable of adopting an altered structure. In addition, some regions of altered structure had no apparent Z-forming sequences, nor were they in polypurine stretches, which have also been proposed to form left-handed DNA. These non-B-DNA conformations may represent novel left-handed helical structures or sequences that become single stranded under torsional strain. Long regions of either altered (unmethylatable) DNA or B-DNA were not always observed. In fact, one region showed three transitions between B-like DNA and altered structure within 26 base-pairs.

Unwinding of heterologous DNA by RecA protein during the search for homologous sequences

The search for homologous sequences promoted by RecA protein in vitro involves a presynaptic filament and naked duplex DNA, the multiple contacts of which produce nucleoprotein networks or coaggregates. The single-stranded DNA within the presynaptic filaments, however, is extended to an axial spacing 1.5 times that of B-form DNA. To investigate this paradoxical difference between the spacing of bases in the RecA presynaptic filament versus the target duplex DNA, we explored the effect of heterologous contacts on the conformation of DNA, and vice versa. In the presence of wheat germ topoisomerase I, RecA presynaptic filaments induced a rapid, limited reduction in the linking number of heterologous circular duplex DNA. This limited unwinding of heterologous duplex DNA, termed heterologous unwinding, was detected within 30 seconds and reached a steady state within a few minutes. Presynaptic filaments that were formed in the presence of ATP?S and separated from free RecA protein by gel filtration also generated a ladder of topoisomers upon incubation with relaxed duplex DNA and topoisomerase. The inhibition of heterologous contacts by 60 mImage -NaCl or 5 mImage -ADP resulted in a corresponding decrease in heterologous unwinding. In reciprocal fashion, the stability or number of heterologous contacts with presynaptic filaments was inversely related to the linking number of circular duplex DNA. These observations show that heterologous contacts with the presynaptic filament cause a limited unwinding of the duplex DNA, and conversely that the ability of the DNA to unwind stabilizes transient heterologous contacts.

Étude des transitions de phases dans le modèle de Higgs abélien en (2+1) dimensions et l'effet du terme de Chern-Simons

Nous avons investigué, via les simulations de Monte Carlo, les propriétés non-perturbatives du modèle de Higgs abélien en 2+1 dimensions sans et avec le terme de Chern-Simons dans la phase de symétrie brisée, en termes de ses excitations topologiques: vortex et anti-vortex. Le but du présent travail est de rechercher les phases possibles du système dans ce secteur et d'étudier l'effet du terme de Chern-Simons sur le potentiel de confinement induit par les charges externes trouvé par Samuel. Nous avons formulé une description sur réseau du modèle effectif en utilisant une tesselation tétraédrique de l'espace tridimensionnel Euclidien pour générer des boucles de vortex fermées. En présence du terme de Chern-Simons, dans une configuration donnée, nous avons formulé et calculé le nombre d'enlacement entre les différentes boucles de vortex fermées. Nous avons analysé les propriétés du vide et calculé les valeurs moyennes de la boucle de Wilson, de la boucle de Polyakov à différentes températures et de la boucle de 't Hooft en présence du terme de Chern-Simons. En absence du terme de Chern-Simons, en variant la masse des boucles de vortex, nous avons trouvé deux phases distinctes dans le secteur de la symétrie brisée, la phase de Higgs habituelle et une autre phase caractérisée par l'apparition de boucles infinies. D'autre part, nous avons trouvé que la force entre les charges externes est écrantée correpondant à la loi périmètre pour la boucle de Wilson impliquant qu'il n'y a pas de confinement. Cependant, après la transition, nous avons trouvé qu'il existe toujours une portion de charges externes écrantée, mais qu'après une charge critique, l'énergie libre diverge. En présence du terme de Chern-Simons, et dans la limite de constante de couplage faible de Chern-Simons nous avons trouvé que les comportements de la boucle de Wilson et de la boucle de 't Hooft ne changent pas correspondants à une loi périmètre, impliquant qu'il n'y a pas de confinement. De plus, le terme de Chern-Simons ne contribue pas à la boucle de Wilson.

Equilibrium distributions of topological states in circular DNA: Interplay of supercoiling and knotting

Two variables define the topological state of closed double-stranded DNA: the knot type, K, and ΔLk, the linking number difference from relaxed DNA. The equilibrium distribution of probabilities of these states, P(ΔLk, K), is related to two conditional distributions: P(ΔLk|K), the distribution of ΔLk for a particular K, and P(K|ΔLk) and also to two simple distributions: P(ΔLk), the distribution of ΔLk irrespective of K, and P(K). We explored the relationships between these distributions. P(ΔLk, K), P(ΔLk), and P(K|ΔLk) were calculated from the simulated distributions of P(ΔLk|K) and of P(K). The calculated distributions agreed with previous experimental and theoretical results and greatly advanced on them. Our major focus was on P(K|ΔLk), the distribution of knot types for a particular value of ΔLk, which had not been evaluated previously. We found that unknotted circular DNA is not the most probable state beyond small values of ΔLk. Highly chiral knotted DNA has a lower free energy because it has less torsional deformation. Surprisingly, even at |ΔLk| > 12, only one or two knot types dominate the P(K|ΔLk) distribution despite the huge number of knots of comparable complexity. A large fraction of the knots found belong to the small family of torus knots. The relationship between supercoiling and knotting in vivo is discussed.

Functional analysis of DNA bending and unwinding by the high mobility group domain of LEF-1

LEF-1 (lymphoid enhancer-binding factor 1) is a cell type-specific member of the family of high mobility group (HMG) domain proteins that recognizes a specific nucleotide sequence in the T cell receptor (TCR) α enhancer. In this study, we extend the analysis of the DNA-binding properties of LEF-1 and examine their contributions to the regulation of gene expression. We find that LEF-1, like nonspecific HMG-domain proteins, can interact with irregular DNA structures such as four-way junctions, albeit with lower efficiency than with specific duplex DNA. We also show by a phasing analysis that the LEF-induced DNA bend is directed toward the major groove. In addition, we find that the interaction of LEF-1 with a specific binding site in circular DNA changes the linking number of DNA and unwinds the double helix. Finally, we identified two nucleotides in the LEF-1-binding site that are important for protein-induced DNA bending. Mutations of these nucleotides decrease both the extent of DNA bending and the transactivation of the TCRα enhancer by LEF-1, suggesting a contribution of protein-induced DNA bending to the function of TCRα enhancer.

Temperature, template topology, and factor requirements of archaeal transcription

Although Archaea are prokaryotic and resemble Bacteria morphologically, their transcription apparatus is remarkably similar to those of eukaryotic cell nuclei. Because some Archaea exist in environments with temperatures of around 100°C, they are likely to have evolved unique strategies for transcriptional control. Here, we investigate the effects of temperature and DNA template topology in a thermophilic archaeal transcription system. Significantly, and in marked contrast with characterized eucaryal systems, archaeal DNA template topology has negligible effect on transcription levels at physiological temperatures using highly purified polymerase and recombinant transcription factors. Furthermore, archaeal transcription does not require hydrolysis of the β-γ phosphoanhydride bond of ATP. However, at lower temperatures, negatively supercoiled templates are transcribed more highly than those that are positively supercoiled. Notably, the block to transcription on positively supercoiled templates at lowered temperatures is at the level of polymerase binding and promoter opening. These data imply that Archaea do not possess a functional homologue of transcription factor TFIIH, and that for the promoters studied, transcription is mediated by TATA box-binding protein, transcription factor TFB, and RNA polymerase alone. Furthermore, they suggest that the reduction of plasmid linking number by hyperthermophilic Archaea in vivo in response to cold shock is a mechanism to maintain gene expression under these adverse circumstances.

Topological challenges to DNA replication: Conformations at the fork

The unwinding of the parental DNA duplex during replication causes a positive linking number difference, or superhelical strain, to build up around the elongating replication fork. The branching at the fork and this strain bring about different conformations from that of (−) supercoiled DNA that is not being replicated. The replicating DNA can form (+) precatenanes, in which the daughter DNAs are intertwined, and (+) supercoils. Topoisomerases have the essential role of relieving the superhelical strain by removing these structures. Stalled replication forks of molecules with a (+) superhelical strain have the additional option of regressing, forming a four-way junction at the replication fork. This four-way junction can be acted on by recombination enzymes to restart replication. Replication and chromosome folding are made easier by topological domain barriers, which sequester the substrates for topoisomerases into defined and concentrated regions. Domain barriers also allow replicated DNA to be (−) supercoiled. We discuss the importance of replicating DNA conformations and the roles of topoisomerases, focusing on recent work from our laboratory.

The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA

The essential Bacillus subtilis DnaD and DnaB proteins have been implicated in the initiation of DNA replication. Recently, DNA remodeling activities associated with both proteins were discovered that could provide a link between global or local nucleoid remodeling and initiation of replication. DnaD forms scaffolds and opens up supercoiled plasmids without nicking to form open circular complexes, while DnaB acts as a lateral compaction protein. Here we show that DnaD-mediated opening of supercoiled plasmids is accompanied by significant untwisting of DNA. The net result is the conversion of writhe (Wr) into negative twist (Tw), thus maintaining the linking number (Lk) constant. These changes in supercoiling will reduce the considerable energy required to open up closed circular plectonemic DNA and may be significant in the priming of DNA replication. By comparison, DnaB does not affect significantly the supercoiling of plasmids. Binding of the DnaD C-terminal domain (Cd) to DNA is not sufficient to convert Wr into negative Tw, implying that the formation of scaffolds is essential for duplex untwisting. Overall, our data suggest that the topological effects of the two proteins on supercoiled DNA are different; DnaD opens up, untwists and converts plectonemic DNA to a more paranemic form, whereas DnaB does not affect supercoiling significantly and condenses DNA only via its lateral compaction activity. The significance of these findings in the initiation of DNA replication is discussed.

Linking Theory and Practice: Performing a Reality Check on a Model of IS Success

The issue of ‘rigour vs. relevance’ in IS research has generated an intense, heated debate for over a decade. It is possible to identify, however, only a limited number of contributions on how to increase the relevance of IS research without compromising its rigour. Based on a lifecycle view of IS research, we propose the notion of ‘reality checks’ in order to review IS research outcomes in the light of actual industry demands. We assume that five barriers impact the efficient transfer of IS research outcomes; they are lack of awareness, lack of understandability, lack of relevance, lack of timeliness, and lack of applicability. In seeking to understand the effect of these barriers on the transfer of mature IS research into practice, we used focus groups. We chose DeLone and McLean’s IS success model as our stimulus because it is one of the more widely researched areas of IS.

Soil carbon saturation: Linking concept and measurable carbon pools

The soil C saturation concept suggests a limit to whole soil organic carbon (SOC) accumulation determined by inherent physicochemical characteristics of four soil C pools: unprotected, physically protected, chemically protected, and biochemically protected. Previous attempts to quantify soil C sequestration capacity have focused primarily on silt and clay protection and largely ignored the effects of soil structural protection and biochemical protection. We assessed two contrasting models of SOC accumulation, one with no saturation limit (i.e., linear first-order model) and one with an explicit soil C saturation limit (i.e., C saturation model). We isolated soil fractions corresponding to the C pools (i.e., free particulate organic matter POM], microaggregate-associated C, silt- and clay-associated C, and non-hydrolyzable C) from eight long-term agroecosystern experiments across the United States and Canada. Due to the composite nature of the physically protected C pool, we firactioned it into mineral- vs. POM-associated C. Within each site, the number of fractions fitting the C saturation model was directly related to maximum SOC content, suggesting that a broad range in SOC content is necessary to evaluate fraction C saturation. The two sites with the greatest SOC range showed C saturation behavior in the chemically, biochemically, and some mineral-associated fractions of the physically protected pool. The unprotected pool and the aggregate-protected POM showed linear, nonsaturating behavior. Evidence of C saturation of chemically and biochemically protected SOC pools was observed at sites far from their theoretical C saturation level, while saturation of aggregate-protected fractions occurred in soils closer to their C saturation level.

Quality of child abuse information in emergency department injury surveillance data : linking hospital and child welfare data

Emergency departments (EDs) are often the first point of contact with an abused child. Despite legal mandate, the reporting of definite or suspected abusive injury to child safety authorities by ED clinicians varies due to a number of factors including training, access to child safety professionals, departmental culture and a fear of ‘getting it wrong’. This study examined the quality of documentation and coding of child abuse captured by ED based injury surveillance data and ED medical records in the state of Queensland and the concordance of these data with child welfare records. A retrospective medical record review was used to examine the clinical documentation of almost 1000 injured children included in the Queensland Injury Surveillance Unit database (QISU) from 10 hospitals in urban and rural centres. Independent experts re-coded the records based on their review of the notes. A data linkage methodology was then used to link these records with records in the state government’s child welfare database. Cases were sampled from three sub-groups according to the surveillance intent codes: Maltreatment by parent, Undetermined and Unintentional injury. Only 0.1% of cases coded as unintentional injury were recoded to maltreatment by parent, while 1.2% of cases coded as maltreatment by parent were reclassified as unintentional and 5% of cases where the intent was undetermined by the triage nurse were recoded as maltreatment by parent. Quality of documentation varied across type of hospital (tertiary referral centre, children’s, urban, regional and remote). Concordance of health data with child welfare data varied across patient subgroups. Outcomes from this research will guide initiatives to improve the quality of intentional child injury surveillance systems.

Conceptual model linking knowledge management with organisational performance

Better management of knowledge assets has the potential to improve business processes and increase productivity. This fact has led to considerable interest in recent years in the knowledge management (KM) phenomenon, and in the main dimensions that can impact on its application in construction. However, a lack of a systematic way of assessing KM initia-tives’ contribution towards achieving organisational business objectives is evident. This paper describes the first stage of a research project intended to develop, and empirically test, a KM input-process-output framework comprising unique and well-defined theoretical constructs representing the KM process and its internal and external determinants in the context of con-struction. The paper presents the underlying principles used in operationally defining each construct through the use of extant KM literature. The KM process itself is explicitly mod-elled via a number of clearly articulated phases that ultimately lead to knowledge utilisation and capitalisation, which in turn adds value or otherwise to meeting defined business objec-tives. The main objective of the model is to reduce the impact of subjectivity in assessing the contribution made by KM practices and initiatives toward achieving performance improvements.

Linking client and employee perceptions of the organization: A study of client satisfaction with health care services

Client satisfaction with health care services has usually been researched in terms of socio-demographic and predispositional characteristics associated with the client. The present study included organizational characteristics as predictors of client satisfaction with health care services. Participants in the research were clients and employees of an Australian public-sector health care organization who responded to separate client and employee questionnaires. Hierarchical regression analyses indicated that, after controlling for a number of client characteristics, organizational characteristics, as perceived by employees, accounted for a significant proportion of additional variance in client satisfaction with health care services. Results of the present study provided some support for the proposition that employee perceptions of the working environment should be considered in a more comprehensive understanding of client satisfaction with health care services. Limitations of the study highlight practical difficulties in the assessment of client outcomes and methodological complexities in linking individual and organizational processes.

Dance teacher education in the 21st century : Linking cultural and aesthetic practice

This paper describes the implementation of the recommendations of a series of research projects, within an undergraduate dance teacher-training course, into the training of collaborative, empathetic, ethical and creative dance teachers. Banks’s Dimensions for Multicultural Education (Banks, 1993) was used as a lens to analyze the design and delivery of cultural dance activities within a university dance-teaching unit, implemented in Australia and Timor Leste, and to reflect on the adaptability of the Performance in Context Model (Stevens & Huddy, in press) across different cultural contexts. Content and contextual knowledge, transformational learning pedagogy, teaching for equity and empathy development were explored through a culturally responsive teaching and learning unit, supported by critical analysis and reflection. This analysis identified a number of key understandings in relation to the design and delivery of cultural dance activities.