Label-free detection of nanomolar unmodified single- and double-stranded dna by using surface-enhanced raman spectroscopy on Ag and Au colloids

Unlabelled single- and double-stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations =10-9?M by surface-enhanced Raman spectroscopy. Under appropriate conditions the sequences spontaneously adsorbed to the surface of both Ag and Au colloids through their nucleobases; this allowed highly reproducible spectra with good signal-to-noise ratios to be recorded on completely unmodified samples. This eliminated the need to promote absorption by introducing external linkers, such as thiols. The spectra of model ssDNA sequences contained bands of all the bases present and showed systematic changes when the overall base composition was altered. Initial tests also showed that small but reproducible changes could be detected between oligonucleotides with the same bases arranged in a different order. The spectra of five ssDNA sequences that correspond to different strains of the Escherichia coli bacterium were found to be sufficiently composition-dependent so that they could be differentiated without the need for any advanced multivariate data analysis techniques.

Comparative validation of c-kit exon 11 mutation analysis on cytology samples and corresponding surgical resections of gastrointestinal stromal tumours

Objective:

Combined studies of DFT atomistic modelling and in situ FTIR spectroscopy on surface oxidants and CO oxidation at Ru electrodes

We report the combined studies of density functional theory (DFT) calculations and electrochemical in situ FTIR spectroscopy on surface oxidants and mechanisms of CO oxidation at the Ru(0001) electrodes. It is shown that CO can co-adsorb with both O and OH species at lower potential region where a low coverage of the (2 x 2)-O/OH adlayer formed; the oxidation of CO adsorbates takes place at higher potentials where a high coverage of the (1 x 1)-O/OH adlayer formed. Surface O species are not the active oxidants under all coverages studied, due to the high reaction barriers between CO and O (>1 eV). However, surface OH species with higher coverage are identified as the active oxidants, and CO oxidation takes place via a two-steps' mechanism of CO + 3OH -> COOH + 2OH -> CO2 + H2O + OH, in which three nearby OH species are involved in the CO2 formation: CO reacts with OH, forming COOH; COOH then transfers the H to a nearby OH to form H2O and CO2, at the same time, another H in the H2O transfers to a nearby OH to form a weak adsorbed H2O and a new OH. The reaction barrier of these processes is reduced significantly to around 0.50 eV. These new results not only provide an insight into surface active oxidants on Ru, which is directly relevant to fuel cell catalysis, but also reveals the extra complexity of catalytic reactions taking place at solid/liquid electrochemical interface in comparison to the relatively simpler ones at solid/gas phase. 

The human micro-vascular enclothelial cells in vitro interaction with atomic-nitrogen-doped diamond-like carbon thin films

This paper reports the initial response of atomic nitrogen doped diamond like carbon (DLC) to endothelial cells in vitro. The introduction of nitrogen atoms/molecules to the diamond like carbon structures leads to an atomic structural change favorable to the attachment of human micro-vascular enclothelial cells. Whilst the semi-conductivity induced by nitrogen in DLC is thought to play a part, the increase in the inion-bonded N atoms and N-2 molecules in the atomic doped species (with the exclusion of the charged species) seems to contribute to the improved attachment of human microvascular endothelial cells. The increased endothelial attachment is associated with a lower work function and slightly higher water contact angle in the atomic doped films, where the heavy charged particles are excluded. The films used in the study were synthesized by the RF PECVD technique followed by post deposition doping with nitrogen, and afterwards the films were characterized by XPS, Raman spectroscopy, SIMS and Kelvin probe. The water contact angles were measured, and the counts of the adherent endothelial cells on the samples were carried out. This study is relevant and contributory to improving biocompatibility of surgical implants and prostheses.

The Influence of Aspect on the Biological Colonization of Stone in Northern Ireland.

The rate and type of biological colonization of stone is influenced by a wide array of environmental factors in addition to substrate characteristics. A series of experiments was designed to compare the rate and type of biological colonization of stone at varying locations over a 21-month time period. Exposure
trials were set up at nine different sites across Northern Ireland that covered a wide variety of environmental conditions. To determine aspect-related differences in colonization, blocks of Peakmoor sandstone and Portland limestone were placed on the north- and south-facing sides of purpose-designed exposure racks. Colorimetry and visual analysis were carried out on collected samples at increasing time intervals. Results showed significantly different rates of darkening and greening over time between north-facing and south-facing blocks, for both sandstone and limestone. This difference is likely to be representative of the fact that in Northern Ireland’s wet climate and northern-latitude position, the north face of a building will receive less direct sunlight. Therefore north-facing blocks, once wet, will remain damp for much longer than blocks on other façades. This slow-drying phenomenon is much more hospitable for biological colonization and continued growth than the hostile environment of rapid wetting and drying cycles experienced on the south face.

Guest sorption and desorption in the metal-organic framework [Co(INA)(2)] (INA = isonicotinate) - evidence of intermediate phases during desorption

The metal-organic framework [Co(INA)(2)].0.5EtOH (INA = isonicotinate, NC5H4-4-CO2-), 1 was synthesised under solvothermal conditions. Its X-ray crystal structure shows channels containing ethanol guests which are hydrogen-bonded to carboxylate oxygens of the framework. The pyridyl rings of the framework alternate between `open' and `closed' positions along the channels resulting in large variation in the channel cross-sectional area from ca. 1.4 by 2.3 at the narrowest point to 4.9 by 5.3 at the widest. Despite the very small windows, the ethanol guests (of van der Waals diameter ca. 4.2-6.1 Angstrom) may be reversibly desorbed and sorbed into the structure quantitatively, as shown by in situ variable-temperture IR spectroscopy and XRPD. The single-crystal structure of the desolvated form [Co(INA)(2)]2 shows that there is no change in the overall connectivity on desolvation, but the rotational positions of the pyridine rings are altered. This suggests that pyridyl rotation may occur to allow guests to pass in and out. When the synthesis was conducted in 1-propanol solvent [Co(INA)(2)].0.5Pr(n)OH.H2O 3, was obtained, and a single-crystal X-ray structure revealed the same overall connectivity as in 1 but with pyridine rings disordered over closed and open positions. There was no evidence of included guests from X-ray crystallography, suggesting that they are also highly disordered. Variable-temperature XRPD performed on bulk samples showed peaks which were unsymmetrical and exhibited shoulders, suggesting that for each pattern obtained the material actually consisted of several closely-related phases. The movements of the peaks during desolvation showed the presence of intermediate phases before the final desolvated product was formed. The peak positions of the intermediate phases matched more closely with the calculated pattern for 3 than with 1 or 2, suggesting that they may have disordered structures similar to 3. The results also suggest that the intermediate phase represents an initial increase in volume before a larger decrease in volume occurs to give the final desolvated material.

Report of the workshop for life detection in samples from Mars

The question of whether there is or was life on Mars has been one of the most pivotal since Schiaparellis' telescopic observations of the red planet. With the advent of the space age, this question can be addressed directly by exploring the surface of Mars and by bringing samples to Earth for analysis. The latter, however, is not free of problems. Life can be found virtually everywhere on Earth. Hence the potential for contaminating the Mars samples and compromising their scientific integrity is not negligible. Conversely, if life is present in samples from Mars, this may represent a potential source of extraterrestrial biological contamination for Earth. A range of measures and policies, collectively termed ‘planetary protection’, are employed to minimise risks and thereby prevent undesirable consequences for the terrestrial biosphere. This report documents discussions and conclusions from a workshop held in 2012, which followed a public conference focused on current capabilities for performing life-detection studies on Mars samples. The workshop focused on the evaluation of Mars samples that would maximise scientific productivity and inform decision making in the context of planetary protection. Workshop participants developed a strong consensus that the same measurements could be employed to effectively inform both science and planetary protection, when applied in the context of two competing hypotheses: 1) that there is no detectable life in the samples; or 2) that there is martian life in the samples. Participants then outlined a sequence for sample processing and defined analytical methods that would test these hypotheses. They also identified critical developments to enable the analysis of samples from Mars.

The impact of accretion disc winds on the optical spectra of cataclysmic variables

Many high-state non-magnetic cataclysmic variables (CVs) exhibit blueshifted absorption or P-Cygni profiles associated with ultraviolet (UV) resonance lines. These features imply the existence of powerful accretion disc winds in CVs. Here, we use our Monte Carlo ionization and radiative transfer code to investigate whether disc wind models that produce realistic UV line profiles are also likely to generate observationally significant recombination line and continuum emission in the optical waveband. We also test whether outflows may be responsible for the single-peaked emission line profiles often seen in high-state CVs and for the weakness of the Balmer absorption edge (relative to simple models of optically thick accretion discs). We find that a standard disc wind model that is successful in reproducing the UV spectra of CVs also leaves a noticeable imprint on the optical spectrum, particularly for systems viewed at high inclination. The strongest optical wind-formed recombination lines are H alpha and He ii lambda 4686. We demonstrate that a higher density outflow model produces all the expected H and He lines and produces a recombination continuum that can fill in the Balmer jump at high inclinations. This model displays reasonable verisimilitude with the optical spectrum of RW Trianguli. No single-peaked emission is seen, although we observe a narrowing of the double-peaked emission lines from the base of the wind. Finally, we show that even denser models can produce a single-peaked H alpha line. On the basis of our results, we suggest that winds can modify, and perhaps even dominate, the line and continuum emission from CVs.

Alpha particles induce pan-nuclear phosphorylation of H2AX in primary human lymphocytes mediated through ATM

The use of high linear energy transfer radiations in the form of carbon ions in heavy ion beam lines or alpha particles in new radionuclide treatments has increased substantially over the past decade and will continue to do so due to the favourable dose distributions they can offer versus conventional therapies. Previously it has been shown that exposure to heavy ions induces pan-nuclear phosphorylation of several DNA repair proteins such as H2AX and ATM in vitro. Here we describe similar effects of alpha particles on ex vivo irradiated primary human peripheral blood lymphocytes. Following alpha particle irradiation pan-nuclear phosphorylation of H2AX and ATM, but not DNA-PK and 53BP1, was observed throughout the nucleus. Inhibition of ATM, but not DNA-PK, resulted in the loss of pan-nuclear phosphorylation of H2AX in alpha particle irradiated lymphocytes. Pan-nuclear gamma-H2AX signal was rapidly lost over 24h at a much greater rate than foci loss. Surprisingly, pan-nuclear gamma-H2AX intensity was not dependent on the number of alpha particle induced double strand breaks, rather the number of alpha particles which had traversed the cell nucleus. This distinct fluence dependent damage signature of particle radiation is important in both the fields of radioprotection and clinical oncology in determining radionuclide biological dosimetry and may be indicative of patient response to new radionuclide cancer therapies.

Microbial community of black band disease on infection, healthy and dead part of scleractinian Montipora sp. colony at Seribu islands, Indonesia

It is crucial to understand the microbial community associated with the host when attempting to discern the pathogen responsible for disease outbreaks in scleractinian corals. This study determines changes in the bacterial community associated with Montipora sp. in response to black band disease in Indonesian waters. Healthy, diseased, and dead Montipora sp. (n = 3 for each sample type per location) were collected from three different locations (Pari Island, Pramuka Island, and Peteloran Island). DGGE (Denaturing Gradient Gel Electrophoresis) was carried out to identify the bacterial community associated with each sample type and histological analysis was conducted to identify pathogens associated with specific tissues. Various Desulfovibrio species were found as novelty to be associated with infection samples, including Desulfovibrio desulfuricans, Desulfovibrio magneticus, and Desulfovibrio gigas, Bacillus benzoevorans, Bacillus farraginis in genus which previously associated with pathogenicity in corals. Various bacterial species associated with uninfected corals were lost in diseased and dead samples. Unlike healthy samples, coral tissues such as the epidermis, endodermis, zooxanthellae were not present on dead samples under histological observation. Liberated zooxanthellae and cyanobacteria were found in black band diseased Montipora sp. samples.

Is there an association between angiotensin-converting enzyme gene variants and chronic nonproductive cough?

Background: It is unclear why some patients develop a chronic nonproductive cough. Angiotensin-converting enzyme (ACE) inactivates tussive peptides in the airways such as bradykinin and tachykinins. An insertion/deletion polymorphism in the ACE gene accounts for variation in ACE levels, and patients with the II genotype have lowest serum ACE levels compared with ID and DD genotypes. We hypothesized that the II genotype would be associated with increased risk of developing a chronic cough.

Materials and methods: We recruited 47 patients (33 women), referred for evaluation of cough (median cough duration, 24 months; range, 2 to 240 months). Cough patients were evaluated using a comprehensive diagnostic protocol, and cough reflex sensitivity was measured using a capsaicin inhalation challenge. ACE genotyping was performed on DNA samples from patients using the polymerase chain reaction followed by agarose gel electrophoresis. ACE genotypes in patients with chronic cough were compared with those in 199 healthy control subjects. Serum ACE levels were determined using a colorimetric assay.

Results: Genotype frequencies for the ACE gene were similar between patients and control subjects. There was no correlation between capsaicin sensitivity and ACE genotypes or serum ACE levels.

Conclusion: Susceptibility to develop chronic cough is not associated with ACE genotype.

High-precision radiocarbon measurements of contemporaneous tree-ring wood from the British Isles and New Zealand: AD 1850-950.

The University of Waikato, Hamilton, New Zealand and The Queen's University of Belfast, Northern Ireland radiocarbon dating laboratories have undertaken a series of high-precision measurements on decadal samples of dendrochronologically dated oak (Quercus petraea) from Great Britain and cedar (Libocedrus bidwillii) and silver pine (Lagarostrobos colensoi) from New Zealand. The results show an average hemispheric offset over the 900 yr of measurement of 40±13 yr. This value is not constant but varies with a periodicity of about 130 yr. The Northern Hemisphere measurements confirm the validity of the Pearson et al. (1986) calibration dataset.

Calibration of the Radiocarbon Time Scale for the Southern Hemisphere: AD 1850-950

We have conducted a series of radiocarbon measurements on decadal samples of dendrochronologically dated wood from both hemispheres, spanning 1000 years (McCormac et al. 1998; Hogg et al. this issue). Using the data presented in Hogg et al., we show that during the period AD 950-1850 the 14C offset between the hemispheres is not constant, but varies periodically (~130 yr periodicity) with amplitudes varying between 1 and 10‰ (i.e. 8-80 yr), with a consequent effect on the 14C calibration of material from the Southern Hemisphere. A large increase in the offset occurs between AD 1245 and 1355. In this paper, we present a Southern Hemisphere high-precision calibration data set (SHCal02) that comprises measurements from New Zealand, Chile, and South Africa. This data, and a new value of 41 ± 14 yr for correction of the IntCal98 data for the period outside the range given here, is proposed for use in calibrating Southern Hemisphere 14C dates.

Development of a technique to measure the residual strength of woodworm infested timber

This paper presents a study of the residual strength of Pinus sylvestris, which has been subject to attack by the furniture beetle (Anobium punctatum). It is relatively easy to stop the infestation, but difficult to assess the structural soundness of the remaining timber. Removal and replacement of affected structural elements is usually difficult and expensive, particularly in buildings of historic interest. Current on-site assessment procedures are limited. The main object of the study was to develop an on-site test of timber quality: a test which can be carried out on the surface and also at varying depths into the timber. It is based on a probe pull-out technique using a portable load-measuring device. Pull-out force values have been correlated with both strength and energy absorbed as measured by compression testing on laboratory samples of both sound and infested timber. These two relationships are significant and could be used to assess whether remedial work is needed. In addition, work on the use of artificial borings to simulate the natural worming of timber is presented and the findings discussed.