Computational identification of self-inhibitory peptides from envelope proteins

Fusion process is known to be the initial step of viral infection and hence targeting the entry process is a promising strategy to design antiviral therapy. The self-inhibitory peptides derived from the enveloped (E) proteins function to inhibit the proteinprotein interactions in the membrane fusion step mediated by the viral E protein. Thus, they have the potential to be developed into effective antiviral therapy. Herein, we have developed a Monte Carlo-based computational method with the aim to identify and optimize potential peptide hits from the E proteins. The stability of the peptides, which indicates their potential to bind in situ to the E proteins, was evaluated by two different scoring functions, dipolar distance-scaled, finite, ideal-gas reference state and residue-specific all-atom probability discriminatory function. The method was applied to a-helical Class I HIV-1 gp41, beta-sheet Class II Dengue virus (DENV) type 2 E proteins, as well as Class III Herpes Simplex virus-1 (HSV-1) glycoprotein, a E protein with a mixture of a-helix and beta-sheet structural fold. The peptide hits identified are in line with the druggable regions where the self-inhibitory peptide inhibitors for the three classes of viral fusion proteins were derived. Several novel peptides were identified from either the hydrophobic regions or the functionally important regions on Class II DENV-2 E protein and Class III HSV-1 gB. They have potential to disrupt the proteinprotein interaction in the fusion process and may serve as starting points for the development of novel inhibitors for viral E proteins. 

The geometry of unstented and stented pig common carotid artery bypass grafts

The long-term success of arterial bypass grafting with autologous saphenous veins is limited by neointimal hyperplasia (NIH), which seemingly develops preferentially at sites where hydrodynamic wall shear is low. Placement of a loose-fitting, porous stent around end-to-end, or end-to-side, autologous saphenous vein grafts on the porcine common carotid artery has been found significantly to reduce NIH, but the mechanism is unclear. In a preliminary study, we implanted autologous saphenous vein grafts bilaterally on the common carotid arteries of pigs, placing a stent around one graft and leaving the contralateral graft unstented. At sacrifice 1 month post implantation, the grafts were pressure fixed in situ and resin casts were made. Unstented graft geometry was highly irregular, with non-uniform dilatation, substantial axial lengthening, curvature, kinking, and possible long-pitch helical distortion. In contrast, stented grafts showed no major dilatation, lengthening or curvature, but there was commonly fine corrugation, occasional slight kinking or narrowing of segments, and possible long-pitch helical distortion. Axial growth of grafts against effectively tethered anastomoses could account for these changes. CFD studies are planned, using 3D MR reconstructions, on the effects of graft geometry on the flow. Abnormality of the flow could favour the development of vascular pathology, including NIH.

Split-Ring FSS Spiral Phase Plate

This letter gives the first report of a planar phase plate structure based on frequency selective surface (FSS) technology for the generation of helical far-field radiation patterns with circular polarization properties.The unit cell of the structure comprises two orthogonal split-ring resonators designed to ensure 180$^{\circ}$ phase shift between orthogonal transmission coefficients. This property is exploited to obtain progressive rotational phase shift within the structure and thus synthesize 360$^{\circ}$ spiral phase profile. Measured far-field radiation patterns demonstrate spiral phase front generation for 10-GHz circularly polarized waves transmitted through the structure.

IQ-motif peptides as novel anti-microbial agents

The IQ-motif is an amphipathic, often positively charged, a-helical, calmodulin binding sequence found in a number of eukaryote signalling, transport and cytoskeletal proteins. They share common biophysical characteristics with established, cationic a-helical antimicrobial peptides, such as the human cathelicidin LL-37. Therefore, we tested eight peptides encoding the sequences of IQ-motifs derived from the human cytoskeletal scaffolding proteins IQGAP2 and IQGAP3. Some of these peptides were able to inhibit the growth of Escherichia coli and Staphylococcus aureus with minimal inhibitory concentrations (MIC) comparable to LL-37. In addition some IQ-motifs had activity against the fungus Candida albicans. This antimicrobial activity is combined with low haemolytic activity (comparable to, or lower than, that of LL-37). Those IQ-motifs with anti-microbial activity tended to be able to bind to lipopolysaccharide. Some of these were also able to permeabilise the cell membranes of both Gram positive and Gram negative bacteria. These results demonstrate that IQ-motifs are viable lead sequences for the identification and optimisation of novel anti-microbial peptides. Thus, further investigation of the anti-microbial properties of this diverse group of sequences is merited.

Citrate synthase from the liver fluke Fasciola hepatica

Citrate synthase catalyses the first step of the Krebs' tricarboxylic acid cycle. A sequence encoding citrate synthase from the common liver fluke, Fasciola hepatica, has been cloned. The encoded protein sequence is predicted to fold into a largely a-helical protein with high structural similarity to mammalian citrate synthases. Although a hexahistidine-tagged version of the protein could be expressed in Escherichia coli, it was not possible to purify it by nickel-affinity chromatography. Similar results were obtained with a version of the protein which lacks the putative mitochondrial targeting sequence (residues 1 to 29). However, extracts from bacterial cells expressing this version had additional citrate synthase activity after correcting for the endogenous, bacterial activity. The apparent K m for oxaloacetate was found to be 0.22 mM, which is higher than that observed in mammalian citrate synthases. Overall, the sequence and structure of F. hepatica citrate synthase are similar to ones from other eukaryotes, but there are enzymological differences which merit further investigation.

Chemical tuning of the interlayer magnetic coupling in TlCo2Se2-xSx

The system TlCo2Se2-xSx has been thoroughly investigated by neutron powder diffraction and SQUID magnetometry. TlCo2Se2-xSx is a layered tetragonal structure containing atomic cobalt layers separated by a distance of 6.4 angstrom in the sulphide and 6.8 angstrom in the selenide. The solid solubility of isovalent selenium and sulphur atoms in the structure makes it possible to continuously vary the interlayer distance and thereby tune the magnetic coupling between the Co-layers. At low temperatures, the Co-atoms are ferromagnetically ordered within the layers and magnetic moments lie in the ab-plane. However, these Co-moments form a helical magnetic structure that prevails for 0 <= x <= 1.5 with a gradual decrease of the angle between adjacent Co-layers from 122 degrees to 39 degrees. For x >= 1.75, a collinear ferromagnetic structure is stable. The relationship between the coupling angle and the Co-interlayer separation shows an almost linear behaviour. The helical phase contains no net spontaneous magnetic moment up to TlCo2SeS, where a small net magnetic moment appears that increases until the ferromagnetic structure is found for 1.75 <= x <= 2.0. (C) 2005 Elsevier B.V. All rights reserved.

Identification of a suitable sterilisation method for collagen derived from a marine Demosponge

Collagen is widely used as a biomedical material, and its importance is likely to grow as research and understanding progresses in this field. As a biomedical material, ensuring the sterility of collagen before use as, or incorporation into, a medical device is paramount. However, common sterilisation techniques can induce changes in the physical structure and protein chemistry of collagen, potentially affecting the performance. In this preliminary study, the influence of autoclaving, gamma irradiation and ethylene oxide gas sterilisation on the denaturation temperature and helical content of the collagen was evaluated using differential scanning calorimetry and Fourier transform infrared spectroscopy. Early results indicate that all sterilisation techniques affect collagen properties but suggest that the least damaging of the techniques investigated was y irradiation.

Studies in the use of magnetic microspheres for immunoaffinity extraction of paralytic shellfish poisoning toxins from shellfish

Paralytic shellfish poisoning (PSP) is a potentially fatal human health condition caused by the consumption of shellfish containing high levels of PSP toxins. Toxin extraction from shellfish and from algal cultures for use as standards and analysis by alternative analytical monitoring methods to the mouse bioassay is extensive and laborious. This study investigated whether a selected MAb antibody could be coupled to a novel form of magnetic microsphere (hollow glass magnetic microspheres, brand name Ferrospheres-N) and whether these coated microspheres could be utilized in the extraction of low concentrations of the PSP toxin, STX, from potential extraction buffers and spiked mussel extracts. The feasibility of utilizing a mass of 25 mg of Ferrospheres-N, as a simple extraction procedure for STX from spiked sodium acetate buffer, spiked PBS buffer and spiked mussel extracts was determined. The effects of a range of toxin concentrations (20-300 ng/mL), incubation times and temperature on the capability of the immuno-capture of the STX from the spiked mussel extracts were investigated. Finally, the coated microspheres were tested to determine their efficiency at extracting PSP toxins from naturally contaminated mussel samples. Toxin recovery after each experiment was determined by HPLC analysis. This study on using a highly novel immunoaffinity based extraction procedure, using STX as a model, has indicated that it could be a convenient alternative to conventional extraction procedures used in toxin purification prior to sample analysis.

Investigating the Potential Impact of Four-dimensional Computed Tomography (4DCT) on Toxicity, Outcomes and Dose Escalation for Radical Lung Cancer Radiotherapy

AIMS: To investigate the potential dosimetric and clinical benefits predicted by using four-dimensional computed tomography (4DCT) compared with 3DCT in the planning of radical radiotherapy for non-small cell lung cancer.

MATERIALS AND METHODS:
Twenty patients were planned using free breathing 4DCT then retrospectively delineated on three-dimensional helical scan sets (3DCT). Beam arrangement and total dose (55 Gy in 20 fractions) were matched for 3D and 4D plans. Plans were compared for differences in planning target volume (PTV) geometrics and normal tissue complication probability (NTCP) for organs at risk using dose volume histograms. Tumour control probability and NTCP were modelled using the Lyman-Kutcher-Burman (LKB) model. This was compared with a predictive clinical algorithm (Maastro), which is based on patient characteristics, including: age, performance status, smoking history, lung function, tumour staging and concomitant chemotherapy, to predict survival and toxicity outcomes. Potential therapeutic gains were investigated by applying isotoxic dose escalation to both plans using constraints for mean lung dose (18 Gy), oesophageal maximum (70 Gy) and spinal cord maximum (48 Gy).

RESULTS:
4DCT based plans had lower PTV volumes, a lower dose to organs at risk and lower predicted NTCP rates on LKB modelling (P < 0.006). The clinical algorithm showed no difference for predicted 2-year survival and dyspnoea rates between the groups, but did predict for lower oesophageal toxicity with 4DCT plans (P = 0.001). There was no correlation between LKB modelling and the clinical algorithm for lung toxicity or survival. Dose escalation was possible in 15/20 cases, with a mean increase in dose by a factor of 1.19 (10.45 Gy) using 4DCT compared with 3DCT plans.

CONCLUSIONS:
4DCT can theoretically improve therapeutic ratio and dose escalation based on dosimetric parameters and mathematical modelling. However, when individual characteristics are incorporated, this gain may be less evident in terms of survival and dyspnoea rates. 4DCT allows potential for isotoxic dose escalation, which may lead to improved local control and better overall survival.

Effective cutting of a quantum spin chain by bond impurities

Spin chains are promising media for short-haul quantum communication. Their usefulness is manifested in all those situations where stationary information carriers are involved. In the majority of the communication schemes relying on quantum spin chains, the latter are assumed to be finite in length, with well-addressable end-chain spins. In this paper we propose that such a configuration could actually be achieved by a mechanism that is able to effectively cut a spin ring through the insertion of bond defects. We then show how suitable physical quantities can be identified as figures of merit for the effectiveness of the cut. We find that, even for modest strengths of the bond defect, a ring is effectively cut at the defect site. In turn, this has important effects on the amount of correlations shared by the spins across the resulting chain, which we study by means of a scattering-based mechanism of a clear physical interpretation. © 2013 American Physical Society.

Failed filament eruption inside a coronal mass ejection in active region 11121

Aims. We study the formation and evolution of a failed filament eruption observed in NOAA active region 11121 near the southeast
limb on November 6, 2010.
Methods. We used a time series of SDO/AIA 304, 171, 131, 193, 335, and 94 Å images, SDO/HMI magnetograms, as well as ROSA
and ISOON Hα images to study the erupting active region.
Results. We identify coronal loop arcades associated with a quadrupolar magnetic configuration, and show that the expansion and
cancellation of the central loop arcade system over the filament is followed by the eruption of the filament. The erupting filament
reveals a clear helical twist and develops the same sign of writhe in the form of inverse γ-shape.
Conclusions. The observations support the “magnetic breakout” process in which the eruption is triggered by quadrupolar reconnection
in the corona. We propose that the formation mechanism of the inverse γ-shape flux rope is the magnetohydrodynamic helical
kink instability. The eruption has failed because of the large-scale, closed, overlying magnetic loop arcade that encloses the active
region

Enantioselective Assembly of a Ruthenium(II) Polypyridyl Complex into a Double Helix

Evolution can increase the complexity of matter by self-organization into helical architectures, the best example being the DNA double helix. One common aspect, apparently shared by most of these architectures, is the presence of covalent bonds within the helix backbone. Here, we report the unprecedented crystal structures of a metal complex that self-organizes into a continuous double helical structure, assembled by non-covalent building blocks. Built up solely by weak stacking interactions, this alternating tread stairs-like double helical assembly mimics the DNA double helix structure. Starting from a racemic mixture in aqueous solution, the ruthenium(II) polypyridyl complex forms two polymorphic structures of a left-handed double helical assembly of only the Λ-enantiomer. The stacking of the helices is different in both polymorphs: a crossed woodpile structure versus a parallel columnar stacking.

Influence of strain and polycrystalline ordering on magnetic properties of high moment rare earth metals and alloys

Despite being the most suitable candidates for solenoid pole pieces in state-of-the-art superconductor- based electromagnets, the intrinsic magnetic properties of heavy rare earth metals and their alloys have gained comparatively little attention. With the potential of integration in micro- and nanoscale devices, thin films of Gd, Dy, Tb, DyGd and DyTb were plasma-sputtered and investigated for their in-plane magnetic properties, with an emphasis on magnetisation vs. temperature profiles. Based on crystal structure analysis of the polycrystalline rare earth films, which consist of a low magnetic moment FCC layer at the seed interface topped with a higher moment HCP layer, an experimental protocol is introduced which allows the direct magnetic analysis of the individual layers. In line with the general trend of heavy lanthanides, the saturation magnetisation was found to drop with increasing unit cell size. In-situ annealed rare earth films exceeded the saturation magnetisation of a high-moment Fe65Co35 reference film in the cryogenic temperature regime, proving their potential for pole piece applications; however as-deposited rare earth films were found completely unsuitable. In agreement with theoretical predictions, sufficiently strained crystal phases of Tb and Dy did not exhibit an incommensurate magnetic order, unlike their single-crystal counterparts which have a helical phase. DyGd and DyTb alloys followed the trends of the elemental rare earth metals in terms of crystal structure and magnetic properties. Inter-rare-earth alloys hence present a desirable blend of saturation magnetisation and operating temperature.

The role of salt and shear on the storage and assembly of spider silk proteins

Major ampullate silk fibers of orb web-weaving spiders have impressive mechanical properties due to the fact that the underlying proteins partially fold into helical/amorphous structures, yielding relatively elastic matrices that are toughened by anisotropic nanoparticulate inclusions (formed from stacks of beta-sheets of the same proteins). In vivo the transition from soluble protein to solid fibers involves a combination of chemical and mechanical stimuli (such as ion exchange, extraction of water and shear forces). Here we elucidate the effects of such stimuli on the in vitro aggregation of engineered and recombinantly produced major ampullate silk-like proteins (focusing on structure-function relationships with respect to their primary structures), and discuss their relevance to the storage and assembly of spider silk proteins in vivo. (C) 2009 Elsevier Inc. All rights reserved.

Tool life and hole surface integrity studies for hole-making of Ti6Al4V Alloy

With a significant growth in the use of titanium alloys in the aviation manufacturing industry, the key challenge of making high-quality holes in the aircraft assembly process needs to be addressed. In this work, case studies deploying traditional drilling and helical milling technologies are carried out to investigate the tool life and hole surface integrity for hole-making of titanium alloy. Results show that the helical milling process leads to much longer tool life, generally lower hole surface roughness, and higher hole subsurface microhardness. In addition, no plastically deformed layer or white layer has been observed in holes produced by helical milling. In contrast, a slightly softened region was always present on the drilled surface. The residual stress distributions within the hole surface, including compressive and tensile residual stress, have also been investigated in detail.