Improved assay-dependent searching of nucleic acid sequence databases

Nucleic acid-based biochemical assays are crucial to modern biology. Key applications, such as detection of bacterial, viral and fungal pathogens, require detailed knowledge of assay sensitivity and specificity to obtain reliable results. Improved methods to predict assay performance are needed for exploiting the exponentially growing amount of DNA sequence data and for reducing the experimental effort required to develop robust detection assays. Toward this goal, we present an algorithm for the calculation of sequence similarity based on DNA thermodynamics. In our approach, search queries consist of one to three oligonucleotide sequences representing either a hybridization probe, a pair of Padlock probes or a pair of PCR primers with an optional TaqMan™ probe (i.e. in silico or ‘virtual’ PCR). Matches are reported if the query and target satisfy both the thermodynamics of the assay (binding at a specified hybridization temperature and/or change in free energy) and the relevant biological constraints (assay sequences binding to the correct target duplex strands in the required orientations). The sensitivity and specificity of our method is evaluated by comparing predicted to known sequence tagged sites in the human genome. Free energy is shown to be a more sensitive and specific match criterion than hybridization temperature

A qualitative study into the use of formal services for dementia by carers from culturally and linguistically diverse (CALD) communities.

BACKGROUND: People with dementia and their family carers need to be able to access formal services in the community to help maintain their wellbeing and independence. While knowing about and navigating one's way through service systems is difficult for most people, it is particularly difficult for people from culturally and linguistically diverse (CALD) communities. This study addresses a lack of literature on the use of formal services for dementia by people from CALD backgrounds by examining the experiences and perceptions of dementia caregiving within four CALD communities - Italian, Chinese, Spanish and Arabic-speaking - in south western Sydney, Australia. METHODS: The study used a qualitative design and the methods included focus groups with family carers and one-to-one interviews with bilingual/bicultural community workers, bilingual general practitioners and geriatricians. A total of 121 family carers participated in 15 focus groups and interviews were held with 60 health professionals. All fieldwork was audiotaped, transcribed and subjected to thematic analysis. RESULTS: People from CALD communities are often unfamiliar with the concept of formal services and there may be strong cultural norms about maintaining care within the family, rather than relying on external services. CALD communities often have limited knowledge of services. There is a preference for services that will allow families to keep their relative at home, for safety as well as cultural reasons, and they are particularly reluctant to use residential care. While there is a preference for ethno-specific or multicultural services, mainstream services also need to ensure they are more flexible in providing culturally appropriate care. Positive outcomes occur when ethno-specific services work in partnership with mainstream programs. Dementia service providers need to develop a trusting relationship with their local CALD communities and promote their services in a way that is understandable and culturally acceptable to members of these communities. CONCLUSIONS: While members of CALD communities may have difficulties accessing formal services, they will use them if they are culturally and linguistically appropriate and can meet their needs. There are a number of ways to improve service provision to CALD communities and the responsibility for this needs to be shared by a range of stakeholders

Robustness and modularity properties of a non-covalent DNA catalytic reaction

The biophysics of nucleic acid hybridization and strand displacement have been used for the rational design of a number of nanoscale structures and functions. Recently, molecular amplification methods have been developed in the form of non-covalent DNA catalytic reactions, in which single-stranded DNA (ssDNA) molecules catalyze the release of ssDNA product molecules from multi-stranded complexes. Here, we characterize the robustness and specificity of one such strand displacement-based catalytic reaction. We show that the designed reaction is simultaneously sensitive to sequence mutations in the catalyst and robust to a variety of impurities and molecular noise. These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks

Hachimoji DNA and RNA: A genetic system with eight building blocks

Reported here are DNA and RNA-like systems built from eight (hachi-) nucleotide letters (-moji) that form four orthogonal pairs. This synthetic genetic biopolymer meets the structural requirements needed to support Darwinism, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to double the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos

In Situ Assembly of Well-Defined MoS2 Slabs on Shape-Tailored Anatase TiO2 Nanostructures: Heterojunctions Role in Phenol Photodegradation

MoS2/TiO2-based nanostructures have attracted extensive attention due to their high performance in many fields, including photocatalysis. In this contribution, MoS2 nanostructures were prepared via an in situ bottom-up approach at the surface of shape-controlled TiO2 nanoparticles (TiO2 nanosheets and bipyramids). Furthermore, a multi-technique approach by combining electron microscopy and spectroscopic methods was employed. More in detail, the morphology/structure and vibrational/optical properties of MoS2 slabs on TiO2 anatase bipyramidal nanoparticles, mainly exposing {101} facets, and on TiO2 anatase nanosheets exposing both {001} and {101} facets, still covered by MoS2, were compared. It was shown that unlike other widely used methods, the bottom-up approach enabled the atomic-level growth of well-defined MoS2 slabs on TiO2 nanostructures, thus aiming to achieve the most effective chemical interactions. In this regard, two kinds of synergistic heterojunctions, namely, crystal face heterojunctions between anatase TiO2 coexposed {101} and {001} facets and semiconductor heterojunctions between MoS2 and anatase TiO2 nanostructures, were considered to play a role in enhancing the photocatalytic activity, together with a proper ratio of (101), (001) coexposed surfaces

Management of the Diabetic Patient in the Diagnostic Care Pathway

Diabetes is a complex pathology both for the affected patients and for the medical specialists who follow them. Furthermore, since diabetes is a pathology with a high prevalence and incidence, it is essential to intervene effectively in therapeutic actions through the application of common guidelines. Therefore, in order to improve the management of the diabetic patient, the aim of the work is to define a Diagnostic Therapeutic Assistance Pathway (PDTA). A questionnaire-based approach is adopted for data collection from 136 patients at the Clinical Dermatology Unit of the University Hospital “Federico II”. In most cases (64%) the diagnosis was made by the General Practitioner, 15% of patients obtained the diagnosis at the ASL and 12% at the Polyclinic of Naples AOU “Federico II” and the remaining part from the diabetologist specialist. The second access is generally carried out at the “Federico II” AOU (66%), followed by the ASL (17%), by a doctor specialized in diabetology (12%) while no patient has turned to the General Practitioner for the treatment of diabetes. The final visit is carried out at the “Federico II” AOU in almost cases. The data obtained follow the Italian guidelines: the patients get the diagnosis from the Family Doctor and then they are addressed either to ASL or to diabetologists specialists. For the subsequent visits, most of them prefer to turn to the “Federico II” AOU, especially when they have complications associated with the diseases as they are followed in a more careful and satisfying manner

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl

DNA unzipped under a constant force exhibits multiple metastable intermediates

Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the unzipped length as a function of time is characterized by jumps during which the strands separate rapidly, followed by long pauses where the number of separated base pairs remains constant. Here, we report previously uncharacterized observations of this striking behavior carried out on a number of identical single molecules simultaneously. When several single lphage molecules are subject to the same applied force, the pause positions are reproducible in each. This reproducibility shows that the positions and durations of the pauses in unzipping provide a sequence-dependent molecular fingerprint. For small forces, the DNA remains in a partially unzipped state for at least several hours. For larger forces, the separation is still characterized by jumps and pauses, but the double-stranded DNA will completely unzip in less than 30 min

Ex vivo biomechanical evaluation of polyester and polyblend suture techniques to perform equine laryngoplasty

Objective: To validate the use of a polyblend tape suture in equine laryngoplasty (PL). Study design: Experimental study. Animals: Thirty-two cadaveric larynges. Methods: Each larynx was randomly assigned to 1 of 4 groups: PL with polyblend tape suture (TigerTape), without (TT) or with a cannula (TTC) in the muscular process of the arytenoid cartilage, and PL with polyester suture (Ethibond), without (EB) or with a cannula (EBC). Construct stiffness, total migration, creep, and drift values were measured after 3000 cycles. The specimens were then loaded to failure to assess their residual properties: load at failure, total energy, displacement, and 2 stiffness coefficients. Results: After cyclic testing, the total migration and creep were lower in TTC (6.36 ± 1.20 mm; 1.35 ± 0.38 mm/s) than in EB (11.12 ± 4.20 mm; 3.39 ± 2.68 mm/s) and in the TT constructs (11.26 ± 1.49 mm; 3.20 ± 0.54 mm/s); however, no difference was found with EBC (9.19 ± 3.18 mm; 2.14 ± 0.99). A correlation was found between total migration and creep (R =.85). The TTC constructs failed at higher loads (129.51 ± 33.84 N) than EB (93.16 ± 18.21 N) and EBC (81.72 ± 13.26 N) whereas the EB and EBC constructs were less stiff than TT and TTC (P <.001). Conclusion: Biomechanical properties were generally superior for the TTC constructs tested under cyclical loading. The TT and TTC constructs failed at a higher load than EB and EBC constructs. The cannula in TTC and EBC reduced the failure at the muscular process. Clinical significance: These results provide evidence to support the in vivo evaluation of the polyblend tape suture with or without a cannula in the muscular process for laryngoplasty in horses

Supported tris-triazole ligands for batch and continuous-flow copper-catalyzed huisgen 1,3-dipolar cycloaddition reactions

The lack of supported versions of the tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine (TBTA) ligand, suitable for flow-chemistry applications at scale, prompted us to develop a new route for the immobilization of such tris-triazole chelating units on highly cross-linked polystyrene resins. With this aim, the preparation of the known TBTA-type monomer 3 was optimized to develop a high-yield synthetic sequence, devoid of chromatographic purifications at any stage. Then, bead-type (P7) and monolithic (M7) functional resins were obtained by the easy and scalable suspension-or mold-copolymerization of 3 with divinylbenzene. Both types of materials were found to possess a highly porous morphology and specific surface area in the dry state and could be charged with substantial amounts of Cu(I) or Cu(II) salts. After treatment of the latter with a proper reducing agent, the corresponding supported Cu(I) complexes were tested in the copper-catalyzed alkyne-azide cycloaddition reaction (CuAAC). The immobilized catalysts proved active at room temperature and, in batch and with catalyst loadings as low as 0.6 mol%, afforded quantitative conversions within 20 h. Independent of the alkyne structure, extended use of the supported catalyst in flow was also possible. In the reaction of benzylazide and propargyl alcohol, this allowed a total turnover number larger than 400 to be reached