Nucleic acid crystallography: a view from the nucleic acid database

What are the future directions of the field of nucleic acid crystallography? Although there have been many duplex structures determined, the sample is still relatively small. This is especially true if one wants to derive enough information about the relationships between sequence and structure. Indeed, there are data for all the possible 10 dimer steps, but for some steps it is very limited. If the structural code resides in trimers or tetrad steps then there is simply not enough data to do meaningful statistical analyses. So the first direction that needs to be explored is the determination of more structures with more varied sequences. The other noticeable thing about the data is the shortness of the strands. While it is probably true that attempts to crystallize very long sequences will not meet with success, the idea of crystallizing sequences engineered to fit together via sticky ends such as has been done for the CAP-DNA complex (Schultz et al., 1990) should give data about the behavior of much longer stretches of DNA. The question of the effects of environment on the structure of DNA continues to be a very important one to address since DNA is rarely alone. The preliminary data we have analysed from the current sample shows that the conformation of some steps are very sensitive to packing type. Numerous studies of the hydration around DNA shows that there is a real synergy between the hydration structure and the base conformation. More data will allow further quantitation of these observations. RNA structure is the next very exciting frontier. The emerging structures of duplexes with internal loops, the two hammerhead ribozyme structures and the group I intron ribozyme have given us a glimpse of the complexity and elegance of this class of molecules. With the technology now in place to allow the determination of the structures of these molecules, the expectation is that now we will see a large increase in the number of these structures in the NDB.     

Phosphorus magnetic resonance spectroscopic imaging using flyback echo planar readout trajectories

Object

To present and evaluate a fast phosphorus magnetic resonance spectroscopic imaging (MRSI) sequence using echo planar spectroscopic imaging with flyback readout gradient trajectories.

Materials and Methods

Waveforms were designed and implemented using a 3 Tesla MRI system. ³¹P spectra were acquired with 2 × 2 cm² and 3 × 3 cm² resolution over a 20- and 21-cm field of view and spectral bandwidths up to 1923 Hz. The sequence was first tested using a 20-cm-diameter phosphate phantom, and subsequent in vivo tests were performed on healthy human calf muscles and brains from five volunteers.

Results

Flyback EPSI achieved 10× and 7× reductions in acquisition time, with 68.0 ± 1.2 and 69.8 ± 2.2% signal-to-noise ratio (SNR) per unit of time efficiency (theoretical SNR efficiency was 74.5 and 76.4%) for the in vivo experiments, compared to conventional phase-encoded MRSI for the 2 × 2 cm² and 3 × 3 cm² resolution waveforms, respectively. Statistical analysis showed no difference in the quantification of most metabolites. Time savings and SNR comparisons were consistent across phantom, leg and brain experiments.

Conclusion

EPSI using flyback readout trajectories was found to be a reliable alternative for acquiring ³¹P-MRSI data in a shorter acquisition time.

     

Mapping the structure of a liquid spray by means of neural networks

This paper presents the results of a study aimed at mapping the structure of a liquid spray system along the spray cone. Experimental results obtained by phase-Doppler anemometry (PDA) consisted of the number distributions of droplet size, velocity, and interparticle arrival time at different locations within the spray cone. The experimental data were analyzed by means of multivariate statistical techniques, in order to identify different regimes in the spray. Neural network models (NN) were fitted to the experimental data, resulting in good agreement between experimental and calculated results for most locations within the spray cone. However, in some parts of the cone the agreement was poor, and the general trends could not be well predicted by the NN models. The mismatch is due to unsteady spray conditions or incomplete atomization (e.g. existence of non-spherical particles). This fact was adopted as a criterion to identify the regions where the spray is fully established, corresponding to the regions of the spray where PDA measurements can be successfully performed. This criterion has been applied along the spray cone for different operating conditions, and can be used as a tool to map the fluid dynamic characteristics in liquid sprays.     

Expression of Connexin43 Stimulates Endothelial Angiogenesis Independently of Gap Junctional Communication In Vitro

Connexins (Cx) form gap junctions (GJ) and allow for intercellular communication. However, these proteins also modulate gene expression, growth, and cell migration. The downregulation of Cx43 impairs endothelial cell migration and angiogenetic potential. Conversely, endothelial Cx43 expression is upregulated in an in vivo angiogenesis model relying on hemodynamic forces. We studied the effects of Cx43 expression on tube formation and proliferation in HUVECs and examined its dependency on GJ communication. Expectedly, intercellular communication assessed by dye transfer was linked to Cx43 expression levels in HUVECs and was sensitive to a GJ blockade by the Cx43 mimetic peptide Gap27. The proliferation of HUVECs was not affected by Cx43 overexpression using Cx43 cDNA transfection, siRNA-mediated knockdown of Cx43, or the inhibition of GJ compared to the controls (transfection of an empty vector, scrambled siRNA, and the solvent). In contrast, endothelial tube and sprout formation in HUVECs was minimized after Cx43 knockdown and significantly enhanced after Cx43 overexpression. This was not affected by a GJ blockade (Gap27). We conclude that Cx43 expression positively modulates the angiogenic potential of endothelial cells independent of GJ communication. Since proliferation remained unaffected, we suggest that Cx43 protein may modulate endothelial cell migration, thereby supporting angiogenesis. The modulation of Cx43 expression may represent an exploitable principle for angiogenesis induction in clinical therapy.     

A comparative study of the electrical and mechanical properties of epoxy nanocomposites reinforced by CVD- and arc-grown multi-wall carbon nanotubes

In this study, three different types of multi-wall carbon nanotubes (MWCNTs) were compared as nanostructured reinforcements in epoxy polymers: commercially available CVD-MWCNTs, synthesised in an industrial process, aligned-CVD-MWCNTs and arc-grown MWCNTs, both obtained from a lab-scale processes. The nanocomposite properties were characterised by means of electron microscopy, rheological, electrical and mechanical methods. Industrial CVD-MWCNTs are favourable for the implication of an electrical conductivity in the epoxy due to their high tendency to form conducting networks. The less entangled structure of aligned-CVD-MWCNTs turns out to be favourable for an easy dispersion and low viscosity in epoxy at similar conductivities compared to the CVD-MWCNTs. Additionally, they provide the highest increase in fracture toughness (∼17%). Arc-grown MWCNTs do not offer any electrical conductivity in epoxy without sufficient purification methods. Their high level of impurities and short length further complicate the transfer of their good electrical and mechanical properties into the nanocomposite.     

Slip Control System for a Deep-Sea Mining Machine

Tracked vehicles capable of locomotion in the deep sea are used for manganese nodule mining. This requires specific technical solutions in various respects. Locomotion in the soft sea bed is one of them. For the Crawler to safely maneuver, an automatic drive mode with slip control of the driving tracks is essential. Based on experimental studies at IKS, University of Siegen, slip control for the NIOT-IKS mining machine has been developed and implemented. The experimental setup for the development of the slip control along with the logic of the automatic driving mode is described. The system is critically discussed and the test results and future work are briefly outlined. Note to Practitioners-The work is carried out as part of the polymetallic nodule mining program of the Government of India. The technique of slip control is a specific requirement for a tracked vehicle used in the deep sea. Slip is common in many vehicles-tracked and otherwise. Examples are steam engines in the early days and ordinary cars while negotiating slush or snow/ice and dozers working in soft soil. While these are manually controlled by drivers who have firsthand knowledge of the environmental conditions, in the case of a mining machine in deep sea, it has to be completely automatic and, hence, is challenging. The knowledge generated in this work could be effectively used by practitioners in other related areas of automobile engineering for updating their expertise. Also, similar techniques may be used for maneuvering vehicles sent to other planets