The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters

Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching complementary sequence and other spots with one or two mismatches: in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.Comment: 31 pages, 5 figure

Direct Observation of Node-to-Node Communication in Zeolitic Imidazolate Frameworks

Zeolitic imidazolate frameworks (ZIFs) with open-shell transition metal nodes represent a promising class of highly ordered light harvesting antennas for photoenergy applications. However, their charge transport properties within the framework, the key criterion to achieve efficient photoenergy conversion, are not yet explored. Herein, we report the first direct evidence of a charge transport pathway through node-to-node communication in both ground state and excited state ZIFs using the combination of paramagnetic susceptibility measurements and time-resolved optical and X-ray absorption spectroscopy. These findings provide unprecedented new insights into the photoactivity and charge transport nature of ZIF frameworks, paving the way for their novel application as light harvesting arrays in diverse photoenergy conversion devices

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

Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes

The thermodynamic contributions of rA·dA, rC·dC, rG·dG and rU·dT single internal mismatches were measured for 54 RNA/DNA duplexes in a 1 M NaCl buffer using UV absorbance thermal denaturation. Thermodynamic parameters were obtained by fitting absorbance versus temperature profiles using the curve-fitting program Meltwin. The weighted average thermodynamic data were fit using singular value decomposition to determine the eight non-unique nearest-neighbor parameters for each internal mismatch. The new parameters predict the ΔG°37, ΔH° and melting temperature (Tm) of duplexes containing these single mismatches within an average of 0.33 kcal/mol, 4.5 kcal/mol and 1.4°C, respectively. The general trend in decreasing stability for the single internal mismatches is rG·dG > rU·dT > rA·dA > rC·dC. The stability trend for the base pairs 5′ of the single internal mismatch is rG·dC > rC·dG > rA·dT > rU·dA. The stability trend for the base pairs 3′ of the single internal mismatch is rC·dG > rG·dC >> rA·dT > rU·dA. These nearest-neighbor values are now a part of a complete set of single internal mismatch thermodynamic parameters for RNA/DNA duplexes that are incorporated into the nucleic acid assay development software programs Visual oligonucleotide modeling platform (OMP) and ThermoBLAST

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

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

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

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

Predicting promoters in phage genomes using machine learning models

The renewed interest in phages as antibacterial agents has led to the exponentially growing number of sequenced phage genomes. Therefore, the development of novel bioinformatics methods to automate and facilitate phage genome annotation is of utmost importance. The most difficult step of phage genome annotation is the identification of promoters. As the existing methods for predicting promoters are not well suited for phages, we used machine learning models for locating promoters in phage genomes. Several models were created, using different algorithms and datasets, which consisted of known phage promoter and non-promoter sequences. All models showed good performance, but the ANN model provided better results for the smaller dataset (92% of accuracy, 89% of precision and 87% of recall) and the SVM model returned better results for the larger dataset (93% of accuracy, 91% of precision and 80% of recall). Both models were applied to the genome of Pseudomonas phage phiPsa17 and were able to identify both types of promoters, host and phage, found in phage genomes.This study was supported by the Portuguese Foundation for Science andTechnology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and theProject POCI-01-0145-FEDER-029628. This work was also supported by BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fundunder the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Plastic Deformation of 2D Crumpled Wires

When a single long piece of elastic wire is injected trough channels into a confining two-dimensional cavity, a complex structure of hierarchical loops is formed. In the limit of maximum packing density, these structures are described by several scaling laws. In this paper it is investigated this packing process but using plastic wires which give origin to completely irreversible structures of different morphology. In particular, it is studied experimentally the plastic deformation from circular to oblate configurations of crumpled wires, obtained by the application of an axial strain. Among other things, it is shown that in spite of plasticity, irreversibility, and very large deformations, scaling is still observed.Comment: 5 pages, 6 figure