Visualising single molecules of HIV-1 and miRNA nucleic acids

Background
The scarcity of certain nucleic acid species and the small size of target sequences such as miRNA, impose a significant barrier to subcellular visualization and present a major challenge to cell biologists. Here, we offer a generic and highly sensitive visualization approach (oligo fluorescent in situ hybridization, O-FISH) that can be used to detect such nucleic acids using a single-oligonucleotide probe of 19–26 nucleotides in length.

Results
We used O-FISH to visualize miR146a in human and avian cells. Furthermore, we reveal the sensitivity of O-FISH detection by using a HIV-1 model system to show that as little as 1–2 copies of nucleic acids can be detected in a single cell. We were able to discern newly synthesized viral cDNA and, moreover, observed that certain HIV RNA sequences are only transiently available for O-FISH detection.

Conclusions
Taken together, these results suggest that the O-FISH method can potentially be used for in situ probing of, as few as, 1–2 copies of nucleic acid and, additionally, to visualize small RNA such as miRNA. We further propose that the O-FISH method could be extended to understand viral function by probing newly transcribed viral intermediates; and discern the localisation of nucleic acids of interest. Additionally, interrogating the conformation and structure of a particular nucleic acid in situ might also be possible, based on the accessibility of a target sequence.

Three-dimensional atom probe analysis of solute distribution in thermomechanically processed TRIP steels

Complex multiphase microstructures were obtained in transformation induced plasticity C–Mn–Si–(Nb–Al–Mo) steels by simulated controlled thermomechanical processing. These microstructures were characterized using transmission electron microscopy, X-ray diffraction and three-dimensional atom probe tomography (APT), which was used to determine the partitioning of elements between different phases and microconstituents. The measured carbon concentration (not, vert, similar0.25 at%) in the ferrite of carbide-free bainite was higher than expected from para-equilibrium between the austenite and ferrite, while the concentrations of substitutional elements were the same as in the parent austenite suggesting that incomplete bainite transformation occurred. In contrast, the distribution of substitutional elements between the ferrite lath and austenite in carbide-containing bainite indicated a complete bainite reaction. The average carbon content in the retained austenite (3.2 ± 1.6 at%) was somewhat higher than the T0 limit. On the basis of the APT measured composition, the calculated Ms temperatures for retained austenite were above room temperature, indicating its low chemical stability.

Precipitate characterisation of an advanced high-strength low-alloy (HSLA) steel using atom probe tomography

Increased fuel economy, combined with the need for the improved safety has generated the development of new hot-rolled high-strength low-alloy (HSLA) and multiphase steels such as dual-phase or transformation-induced plasticity steels with improved ductility without sacrificing strength and crash resistance. However, the modern multiphase steels with good strength-ductility balance showed deteriorated stretch-flangeability due to the stress concentration region between the soft ferrite and hard martensite phases [1]. Ferritic, hot-rolled steels can provide good local elongation and, in turn, good stretch-flangeability [2]. However, conventional HSLA ferritic steels only have a tensile strength of not, vert, similar600 MPa, while steels for the automotive industry are now required to have a high tensile strength of not, vert, similar780 MPa, with excellent elongation and stretch-flangeability [1]. This level of strength and stretch-flangeability can only be achieved by precipitation hardening of the ferrite matrix with very fine precipitates and by ferrite grain refinement. It has been suggested that Mo [3] and Ti [4] should be added to form carbides and decrease the coiling temperature to 650 °C since only a low precipitation temperature can provide the precipitation refinement [4]. These particles appeared to be (Ti, Mo)C, with a cubic lattice and a parameter of 0.433 nm, and they were aligned in rows [4]. It was reported [4] that the formation of these very fine carbides led to an increase in strength of not, vert, similar300 MPa. However, the detailed analysis of these particles has not been performed to date due to their nanoscale size. The aim of this work was to carry out a detailed investigation using atom probe tomography (APT) of precipitates formed in hot-rolled low-carbon steel containing additions Ti and Mo.

The investigated low-carbon steel, containing Fe–0.1C–1.24Mn–0.03Si–0.11Cr–0.11Mo–0.09Ti–0.091Al at.%, was produced by hot rolling. The processing route has been described in detail elsewhere [5] European Patent Application, 1616970 A1, 18.01.2006.[5]. The microstructure was characterised by transmission electron microscopy (TEM) on a Philips CM 20, operated at 200 kV using thin foil and carbon replica techniques. Qualitative energy dispersive X-ray spectroscopy (EDXS) was used to analyse the chemical composition of particles. The atomic level of particle characterisation was performed at the University of Sydney using a local electrode atom probe [6]. APT was carried out using a pulse repetition rate of 200 kHz and a 20% pulse fraction on the sample with temperature of 80 K. The extent of solute-enriched regions (radius of gyration) and the local solute concentrations in these regions were estimated using the maximum separation envelope method with a grid spacing of 0.1 nm [7]. A maximum separation distance between the atoms of interest of dmax = 1 nm was used.

The microstructure of the steel consisted of two types of fine ferrite grains: (i) small recrystallised grains with an average grain size of 1.4 ± 0.2 μm; and (ii) grains with a high dislocation density (5.8 ± 1.4 × 1014 m−2) and an average grain size of 1.9 ± 0.1 μm in thickness and 2.7 ± 0.1 μm in length (Fig. 1a). Some grains with high dislocation density displayed an elongated shape with Widmanstätten side plates and also the formation of cells and subgrains (Fig. 1a). The volume fraction of recrystallised grains was 34 ± 8%.

Emotional habituation to filmed violence employing the startle probe response

This thesis reports on research examining the habituation of emotional variables to filmed violence. The following subjective emotional variables were assessed: positive feelings, anxiety, disgust, entertainment and anger. In addition, an objective measure of emotional response was recorded physiologically, using the startle eyeblink response. The mediating influence of personality, individual differences and contextual features on an individuals’ perception of and reaction to filmed violence were also explored. Study one was exploratory in nature served to identify and select the film stimuli to be employed in the subsequent studies. The primary aim of the study was to allow for the identification of violent stimuli considered to be most socially and culturally relevant. The present research builds on existing scientific literature which has began to appreciate that differences in the context of a portrayal holds important implications for its impact on viewers. Thus, a secondary and more specific desire of study one was to obtain an evaluation of the contextual features of the violent film segments. A sample of 30 participants viewed and rated the film stimuli on the variables of realism, fantasy and violence. From this exploratory study four violent film stimuli were subsequently employed. Study 2 used the eyeblink startle response proposed by Vrana, Spence and Lang (1988) to explore the habituation of emotional variables to a realistic depiction of filmed violence. Emotional response was assessed both objectively, using the eyeblink startle response and subjectively through individuals self-reports. In addition the study investigated the significance of individual differences as mediators of emotional response. Questionnaire and physiological data were obtained from 30 participants. Overall, repeated exposure to filmed violence resulted in a decline in both objective and subjective emotional response. Differences were identified in the manner in which men and women responded to the film. Women reacted initially and over time with more intense physiological and psychological reactions to the violent film than males. Specifically, men displayed more curiosity and reported greater entertainment and positive feelings in response to the film, whilst women found the violence more disgusting and reported higher levels of anger and anxiety. It was found that the eyeblink startle magnitude paralleled the subjective emotional processing of the violent film, thus providing further confirmatory evidence of its validity in the investigation of emotional reactions to a stimulus. Personality factors were found to mediate emotional response to filmed violence, with neuroticism most powerfully implicated. High levels of neuroticism were found to be associated with greater anger and anxiety and less positive feelings whilst viewing violent film. A high score on extraversion was correlated with higher levels of anger and lower levels of curiosity and entertainment. Whilst the aims of study 3 were identical to that of study 2, a variation in the contextual feature of the violent film stimuli under investigation was the distinguishing and pertinent feature. Study 2 provided data on the habituation of emotional response to a realistic depiction of filmed violence. Study 3 was concerned with emotional response over repeated exposure to a fantasized violent depiction. Therefore, allowing for a comparison regarding the effects of context on emotional response. The results of study 3, with respect to habituation of emotional response, personality and individual differences, were similar to that obtained in study 2. A comparison of the two studies, however, revealed that individuals responded significantly different to the contextual features of the violent portrayal. Compared to the fantasised portrayal the realistic film stimulus was reported to be more digusting, anxiety provoking and less entertaining. In addition, and not surprisingly respondents reported that the realistic portrayal resulted in the production of more anger and less positive feelings.

Diagnosis of {alpha}+-thalassemias by determining the ratio of the two {alpha}-globin gene copies by oligonucleotide hybridization and melting curve analysis

Most cases of {alpha}-thalassemia result from large deletions at the {alpha}-globin locus (1). The {alpha}-globin gene cluster contains a tandem array of 2 nearly identical {alpha}-globin genes (HBA; Fig. 1A ) (2). The {alpha}0-thalassemias are characterized by deletions that inactivate both {alpha}-globin genes of a given chromosome, whereas in {alpha}+-thalassemias, one gene remains functional. The most widespread {alpha}+-thalassemias are those designated –{alpha}3.7 and –{alpha}4.2, according to the lengths of the deleted fragments (3).

Concept design of a novel tactile probe tip for down scaled 3D CMMs

Although coordinate metrology has reached a very high state of development concerning versatility and accuracy for common engineering parts, a high precision capability with nano scale resolution and accuracy is often hard to achieve when it is required to measure very small parts and features. The limiting component is the bulky probing system of traditional CMMs (coordinate measuring machines). In order to satisfy increasing demand for highly accurate geometrical measurements on small parts and small structures, a new measuring probe of high sensitivity and small geometrical dimension with low contact forces needs to be developed. In this paper, a novel probing system, which combines a FBG (Fibre Bragg Grating) embedded optical fibre tactile probe with an optical sensing technique, has been proposed. With the sensor elements integrated into the probe tip directly, the system sensitivity can be increased significantly. A preliminary theoretical analysis of the sensitivity of the FBG fibre sensor under axial and lateral end point loading has been presented and the results show that this micro scale probe has great potential to realize a resolution of 1nanometer on geometrical measurement of small parts.

Atom probe tomography of solute distributions in mg-based alloys

Atom probe tomography (APT) has been carried out on three magnesium-based alloys: M1 (Mg-1 wt pct Mn), AZ31(Mg-3 pct Al-1 pct Zn), and ME10 (Mg-1 pct Mn- 0.4 pct misch metal). The aims of this experiment were to measure the composition of the matrix and to investigate solute clustering in the matrix of the three different alloys. For AZ31, the matrix composition was variable but close to the bulk composition. For ME10 and M1, the matrix was depleted in alloying additions, with the remainder residing in precipitates. Most alloying additions were found to exhibit clustering to some extent, with misch metal having the strongest partitioning behavior to clusters. Solute clusters did not appear to affect mechanical twinning. It has been proposed that the clustering behavior of misch metal contributes to its ability to modify the recrystallization texture.

Development of a contact probe incorporating a bragg grating strain sensor for nano coordinate measuring machines

This paper presents a novel optical fibre based micro contact probe system with high sensitivity and repeatability. In this optical fibre probe with a fused spherical tip, a fibre Bragg grating has been utilized as a strain sensor in the probe stem. When the probe tip contacts the surface of the part, a strain will be induced along the probe stem and will produce a Bragg wavelength shift. The contact signal can be issued once the wavelength shift signal is produced and demodulated. With the fibre grating sensor element integrated into the probe directly, the probe system shows a high sensitivity. In this work, the strain distributions along the probe stem with the probe under axial and lateral load are analysed. A simulation of the strain distribution was performed using the finite element package ANSYS 11. Performance tests using a piezoelectric transducer stage with a displacement resolution of 1.5 nm yielded a measurement resolution of 60 nm under axial loading.

Using polyatomic primary ions to probe an amino acid and a nucleic base in water ice

In this study on pure water ice, we show that protonated water species [H₂O]_nH⁺ are more prevalent than (H₂O)_n⁺ ions after bombardment by Au+ monoatomic and Au₃⁺ and C₆₀⁺ polyatomic projectiles. This data also reveals significant differences in water cluster yields under bombardment by these three projectiles. The amino acid alanine and the nucleic base adenine in solution have been studied and have been shown to have an effect on the water cluster ion yields observed using an Au₃⁺ ion beam.

Positron annihilation lifetime spectroscopy as a probe of free volume in plasticized solid polymer electrolytes

A recent report on the correlation between enhanced polymer mobility and ionic conductivity at room temperature in plasticized polyether-urethane solid polymer electrolytes (Forsyth et al.[1]), has prompted the present investigation. Positron annihilation lifetime spectroscopy (PALS) has been used to study the effect of plasticizer addition on the room temperature free volume characteristics of the crosslinked polyether-urethane. The addition of low molecular weight plasticizers to the polyether-urethane results in a constant or decreasing mean free volume cavity radius, as measured by the orthoPositronium lifetime τ₃, and a decreasing relative concentration of free volume cavities as measured by the ortho-Positronium intensity, I₃. It is postulated that the plasticizers interrupt polymer-polymer interactions by occupying the inter- and intra-chain free volume. The plasticizer structure influences the polymerplasticizer interactions which affect inter- and intra-chain separation and hence the free volume of the system. The decrease in polymer-polymer interaction and the increase in polymer-plasticizer interaction in turn influence the glass transition temperature behaviour.

Atom probe microscopy of self-assembled monolayers : preliminary results

We have achieved three-dimensional imaging of decanethiol self-assembled monolayers (SAMs) on metal surfaces by atom probe tomography (APT). The present Letter provides preliminary results on Ni [001] and Au [111], shows the analytical potential of APT analysis of SAMs, and details developments in specimen preparation and in data-treatment methodologies. Importantly, the investigation of the mass spectra from analysis of the SAMs revealed no combination of sulfur and hydrogen at the interface between the metal substrates and the organic materials, potentially providing insight about the bonding of the thiols on the substrate.

Electrooxidation of [(η5-C5H5)Fe(CO)2]2 as a probe of the nucleophilic properties of ionic liquid anions

The oxidative electrochemistry of [CpFe(CO)2]2, 1 (Cp = [η5-C5H5]–), was examined in detail in ionic liquids (ILs) composed of ions of widely varying Lewis acid−base properties. Cyclic voltammetric responses were strongly dependent on the nucleophilic properties of the IL anion, but all observations are consistent with the initial formation of 1+ followed by attack from the IL anion. In [NTf2]–-based ILs ([NTf2]– = bis(trifluoromethylsulfonyl)amide), the process shows nearly ideal chemical reversibility as the reaction between 1+ and [NTf2]– is very slow. This is highly significant, as 1+ is known to be highly susceptible to nucleophilic attack and its stability indicates a remarkable lack of coordinating ability of these ILs. In 1-methyl-3-butylimidazolium hexafluorophosphate, [bmim][PF6], the oxidation of 1 is still largely reversible, but there is more pronounced evidence of [PF6]– coordination. In contrast, 1 exhibits an irreversible two-electron oxidation process in a dicyanamide-based IL. This overall oxidation process is thought to proceed via an ECE mechanism, details of which are presented. Rate constants were estimated by fitting the experimental data to digital simulations of the proposed mechanism. The use of [NTf2]–-based ILs as a supporting electrolyte in CH2Cl2 was examined by using this solvent/electrolyte as a medium in which to perform bulk electrolyses of 1 and 1*, the permethylated analogue [Cp*Fe(CO)2]2 (Cp* = [η5-C5(CH3)5]–). These cleanly yielded the corresponding binuclear radical-cation species, 1+ and 1*+, which were subsequently characterized by electron paramagnetic resonance (EPR) spectroscopy. In addition to the above oxidation studies, the reduction of 1 was studied in each of the ILs; differences in cathodic peak potentials are attributed, in part, to ion-pairing effects. This study illustrates the wide range of electrochemical environments available with ILs and demonstrates their utility for the investigation of the redox properties of metal carbonyls and other organometallic compounds.