Monoclonal antibody screening of a phage-displayed random peptide library reveals mimotopes of chemokine receptor CCR5: Implications for the tertiary structure of the receptor and for an n-terminal binding site for HIV-1 gp120

The chemokine receptor CCR5 contains seven transmembrane-spanning domains. It binds chemokines and acts as co-receptor for macrophage (m)-tropic (or R5) strains of HIV-1. Monoclonal antibodies (mAb) to CCR5, 3A9 and 5C7, were used for biopanning a nonapeptide cysteine (C)-constrained phage-displayed random peptide library to ascertain contact residues and define tertiary structures of possible epitopes on CCR5. Reactivity of antibodies with phagotopes was established by enzyme-linked immunosorbent assay (ELISA). mAb 3A9 identified a phagotope C-HASIYDFGS-C (3A9/1), and 5C7 most frequently identified C-PHWLRDLRV-C (5C7/1). Corresponding peptides were synthesized. Phagotopes and synthetic peptides reacted in ELISA with corresponding antibodies and synthetic peptides inhibited antibody binding to the phagotopes. Reactivity by immunofluorescence of 3A9 with CCR5 was strongly inhibited by the corresponding peptide. Both mAb 3A9 and 5C7 reacted similarly with phagotopes and the corresponding peptide selected by the alternative mAb. The sequences of peptide inserts of phagotopes could be aligned as mimotopes of the sequence of CCR5. For phage 3A9/1, the motif SIYD aligned to residues at the N terminus and FG to residues on the first extracellular loop; for 5C7/1, residues at the N terminus, first extracellular loop, and possibly the third extracellular loop could be aligned and so would contribute to the mimotope. The synthetic peptides corresponding to the isolated phagotopes showed a CD4-dependent reactivity with gp120 of a primary, m-tropic HIV-1 isolate. Thus reactivity of antibodies raised to CCR5 against phage-displayed peptides defined mimotopes that reflect binding sites for these antibodies and reveal a part of the gp120 binding sites on CCR5.

Climbing skill and complexity of climbing wall design: Assessment of jerk as a novel indicator of performance fluency

This study investigated a new performance indicator to assess climbing fluency (smoothness of the hip trajectory and orientation of a climber using normalized jerk coefficients) to explore effects of practice and hold design on performance. Eight experienced climbers completed four repetitions of two, 10-m high routes with similar difficulty levels, but varying in hold graspability (holds with one edge vs holds with two edges). An inertial measurement unit was attached to the hips of each climber to collect 3D acceleration and 3D orientation data to compute jerk coefficients. Results showed high correlations (r = .99, P < .05) between the normalized jerk coefficient of hip trajectory and orientation. Results showed higher normalized jerk coefficients for the route with two graspable edges, perhaps due to more complex route finding and action regulation behaviors. This effect decreased with practice. Jerk coefficient of hip trajectory and orientation could be a useful indicator of climbing fluency for coaches as its computation takes into account both spatial and temporal parameters (ie, changes in both climbing trajectory and time to travel this trajectory)

Analysis of effects of axial shortening of steel columns in frame structure

Steel columns in frame structure always carry heavy upcoming compressive forces. As a consequence, axial shortening becomes a common phenomenon in a multistoried steel structure. A 100 storied steel structure is analyzed in SAP2000 to study the magnitude overall effects of column shortening. It was found from the study that the maximum axial shortening occurs at the columns of top storey of the steel structure and at the columns of bottom storey, the axial deformation is negligible. The increasing rate of axial shortening is significant at the initial levels. However, at the upper levels, the amount of axial shortening in steel columns differs insignificantly. In the selected rigid frame structure, the axial shortening of adjacent steel columns is found to influence significantly the differential shortening of the structure. The consequent effect of differential shortening leads to develop excessive stress in the corner joints which ultimately hamper the normal behavior of the structural systems. The results are discussed elaborately in the paper.

Advanced tissue engineering scaffold design for regeneration of the complex hierarchical periodontal structure

AIM: This study investigated the ability of an osteoconductive biphasic scaffold to simultaneously regenerate alveolar bone, periodontal ligament and cementum. MATERIALS AND METHODS: A biphasic scaffold was built by attaching a fused deposition modelled bone compartment to a melt electrospun periodontal compartment. The bone compartment was coated with a calcium phosphate (CaP) layer for increasing osteoconductivity, seeded with osteoblasts and cultured in vitro for 6 weeks. The resulting constructs were then complemented with the placement of PDL cell sheets on the periodontal compartment, attached to a dentin block and subcutaneously implanted into athymic rats for 8 weeks. Scanning electron microscopy, X-ray diffraction, alkaline phosphatase and DNA content quantification, confocal laser microscopy, micro computerized tomography and histological analysis were employed to evaluate the scaffold's performance. RESULTS: The in vitro study showed that alkaline phosphatase activity was significantly increased in the CaP-coated samples and they also displayed enhanced mineralization. In the in vivo study, significantly more bone formation was observed in the coated scaffolds. Histological analysis revealed that the large pore size of the periodontal compartment permitted vascularization of the cell sheets, and periodontal attachment was achieved at the dentin interface. CONCLUSIONS: This work demonstrates that the combination of cell sheet technology together with an osteoconductive biphasic scaffold could be utilized to address the limitations of current periodontal regeneration techniques.

Free-standing alumina nanobottles and nanotubes pre-integrated into nanoporous alumina membranes

A novel interfacial structure consisting of long (up to 5 μm), thin (about 300 nm), highly-ordered, free-standing, highly-reproducible aluminum oxide nanobottles and long tubular nanocapsules attached to a rigid, thin (less than 1 μm) nanoporous anodic alumina membrane is fabricated by simple, fast, catalyst-free, environmentally friendly voltage-pulse anodization. A growth mechanism is proposed based on the formation of straight channels in alumina membrane by anodization, followed by neck formation due to a sophisticated voltage control during the process. This process can be used for the fabrication of alumina nanocontainers with highly controllable geometrical size and volume, vitally important for various applications such as material and energy storage, targeted drug and diagnostic agent delivery, controlled drug and active agent release, gene and biomolecule reservoirs, micro-biologically protected platforms, nano-bioreactors, tissue engineering and hydrogen storage.

Microporous bamboo biochar for lithium-sulfur batteries

Being simple, inexpensive, scalable and environmentally friendly, microporous biomass biochars have been attracting enthusiastic attention for application in lithium-sulfur (Li-S) batteries. Herein, porous bamboo biochar is activated via a KOH/annealing process that creates a microporous structure, boosts surface area and enhances electronic conductivity. The treated sample is used to encapsulate sulfur to prepare a microporous bamboo carbon-sulfur (BC-S) nanocomposite for use as the cathode for Li-S batteries for the first time. The BC-S nanocomposite with 50 wt.% sulfur content delivers a high initial capacity of 1,295 mA·h/g at a low discharge rate of 160 mA/g and high capacity retention of 550 mA·h/g after 150 cycles at a high discharge rate of 800 mA/g with excellent coulombic efficiency (⩾95%). This suggests that the BC-S nanocomposite could be a promising cathode material for Li-S batteries.

Single-walled carbon nanotube-based polymer monoliths for the enantioselective nano-liquid chromatographic separation of racemic pharmaceuticals

Many protocols have been used for extraction of DNA from Thraustochytrids. These generally involve the use of CTAB, phenol/chloroform and ethanol. They also feature mechanical grinding, sonication, N2 freezing or bead beating. However, the resulting chemical and physical damage to extracted DNA reduces its quality. The methods are also unsuitable for large numbers of samples. Commercially-available DNA extraction kits give better quality and yields but are expensive. Therefore, an optimized DNA extraction protocol was developed which is suitable for Thraustochytrids to both minimise expensive and time-consuming steps prior to DNA extraction and also to improve the yield. The most effective method is a combination of single bead in TissueLyser (Qiagen) and Proteinase K. Results were conclusive: both the quality and the yield of extracted DNA were higher than with any other method giving an average yield of 8.5 µg/100 mg biomass.

Pre-lithiation of onion-like carbon/MoS2 nano-urchin anodes for high-performance rechargeable lithium ion batteries

Hybrid urchin-like nanostructures composed of a spherical onion-like carbon (OLC) core and MoS2 nanoleaves were synthesized by a simple solvothermal method followed by thermal annealing treatment. Compared to commercial MoS2 powder, MoS2/OLC nanocomposites exhibit enhanced electrochemical performance as anode materials of lithium-ion batteries (LIBs) with a specific capacity of 853 mA h g−1 at a current density of 50 mA g−1 after 60 cycles, and a moderate initial coulombic efficiency of 71.1%. Furthermore, a simple pre-lithiation method based on direct contact of lithium foil with MoS2/OLC nano-urchins was used to achieve a very high coulombic efficiency of 97.6% in the first discharge/charge cycle, which is at least 26% higher compared to that of pristine MoS2/OLC nano-urchins. This pre-lithiation method can be generalized to develop other carbon-metal sulfide nanohybrids for LIB anode materials. These results may open up a new avenue for the development of the next-generation high-performance LIBs.

Optimizing the quantum dot: Plasmon interaction in a nano gap waveguide

Spontaneous emission (SE) of a Quantum emitter depends mainly on the transmission strength between the upper and lower energy levels as well as the Local Density of States (LDOS)[1]. When a QD is placed in near a plasmon waveguide, LDOS of the QD is increased due to addition of the non-radiative decay and a plasmonic decay channel to free space emission[2-4]. The slow velocity and dramatic concentration of the electric field of the plasmon can capture majority of the SE into guided plasmon mode (Гpl ). This paper focused on studying the effect of waveguide height on the efficiency of coupling QD decay into plasmon mode using a numerical model based on finite elemental method (FEM). Symmetric gap waveguide considered in this paper support single mode and QD as a dipole emitter. 2D simulation models are done to find normalized Гpl and 3D models are used to find probability of SE decaying into plasmon mode ( β) including all three decay channels. It is found out that changing gap height can increase QD-plasmon coupling, by up to a factor of 5 and optimally placed QD up to a factor of 8. To make the paper more realistic we briefly studied the effect of sharpness of the waveguide edge on SE emission into guided plasmon mode. Preliminary nano gap waveguide fabrication and testing are already underway. Authors expect to compare the theoretical results with experimental outcomes in the future

Secondary structure element alignment kernel method for prediction of protein structural classes

In this paper, we aim at predicting protein structural classes for low-homology data sets based on predicted secondary structures. We propose a new and simple kernel method, named as SSEAKSVM, to predict protein structural classes. The secondary structures of all protein sequences are obtained by using the tool PSIPRED and then a linear kernel on the basis of secondary structure element alignment scores is constructed for training a support vector machine classifier without parameter adjusting. Our method SSEAKSVM was evaluated on two low-homology datasets 25PDB and 1189 with sequence homology being 25% and 40%, respectively. The jackknife test is used to test and compare our method with other existing methods. The overall accuracies on these two data sets are 86.3% and 84.5%, respectively, which are higher than those obtained by other existing methods. Especially, our method achieves higher accuracies (88.1% and 88.5%) for differentiating the α + β class and the α/β class compared to other methods. This suggests that our method is valuable to predict protein structural classes particularly for low-homology protein sequences. The source code of the method in this paper can be downloaded at http://math.xtu.edu.cn/myphp/math/research/source/SSEAK_source_code.rar.

Multipurpose nanoporous alumina-carbon nanowall bi-dimensional nano-hybrid platform via catalyzed and catalyst-free plasma CVD

Simple, rapid, plasma-assisted synthesis of large-area arrays of vertically-aligned carbon nanowalls on highly-porous, transparent bare and gold-coated alumina membranes with the two pore sizes is reported. It is demonstrated that the complex patterns of vertically aligned nanowalls can nucleate and form different morphologies in the low-temperature plasmas. The process is stable, and the twofold change in the gas flow (10 and 20 sccm) does not noticeably influence the morphology of the nanowall pattern. Application of a thin (5 nm) gold layer to nanoporous membrane prior to the nanowall growth allows controlling the network morphology.

Structure matters: Adoption of structured classification Approach in the context of cognitive presence classification

Within online learning communities, receiving timely and meaningful insights into the quality of learning activities is an important part of an effective educational experience. Commonly adopted methods – such as the Community of Inquiry framework – rely on manual coding of online discussion transcripts, which is a costly and time consuming process. There are several efforts underway to enable the automated classification of online discussion messages using supervised machine learning, which would enable the real-time analysis of interactions occurring within online learning communities. This paper investigates the importance of incorporating features that utilise the structure of on-line discussions for the classification of "cognitive presence" – the central dimension of the Community of Inquiry framework focusing on the quality of students' critical thinking within online learning communities. We implemented a Conditional Random Field classification solution, which incorporates structural features that may be useful in increasing classification performance over other implementations. Our approach leads to an improvement in classification accuracy of 5.8% over current existing techniques when tested on the same dataset, with a precision and recall of 0.630 and 0.504 respectively.

Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar

TERMINAL EAR1-like (TEL) genes encode putative RNA-binding proteins only found in land plants. Previous studies suggested that they may regulate tissue and organ initiation in Poaceae. Two TEL genes were identified in both Populus trichocarpa and the hybrid aspen Populus tremula × P. alba, named, respectively, PoptrTEL1-2 and PtaTEL1-2. The analysis of the organisation around the PoptrTEL genes in the P. trichocarpa genome and the estimation of the synonymous substitution rate for PtaTEL1-2 genes indicate that the paralogous link between these two Populus TEL genes probably results from the Salicoid large-scale gene-duplication event. Phylogenetic analyses confirmed their orthology link with the other TEL genes. The expression pattern of both PtaTEL genes appeared to be restricted to the mother cells of the plant body: leaf founder cells, leaf primordia, axillary buds and root differentiating tissues, as well as to mother cells of vascular tissues. Most interestingly, PtaTEL1-2 transcripts were found in differentiating cells of secondary xylem and phloem, but probably not in the cambium itself. Taken together, these results indicate specific expression of the TEL genes in differentiating cells controlling tissue and organ development in Populus (and other Angiosperm species).

Integrating LED lighting design strategies with side daylighting systems to improve interior lighting design of office buildings

A high contrast ratio between windows and surrounding walls may lead to office workers visual discomfort that could negatively affect their satisfaction and productivity. Consequently, occupants may try to adapt their working environment by closing blinds and/ or turning on the lights to enhance indoor visual comfort, which can reduce predicted energy savings. The hypothesis of this study is that reducing luminance contrast ratio on the window wall will improve window appearance which potentially will reduce visual discomfort and decrease workers interventions. Thus, this PhD research proposes a simple strategy to diminish the luminance contrast on the window wall by increasing the luminance of the areas surrounding the windows using supplementary light emitting diode (LED) systems. To test the hypothesis, this investigation will involve three experiments in different office layouts with various window types and orientations in Brisbane, Australia. It will assess user preferences for different luminance patterns in windowed offices featuring flexible, lowpower LED lighting installations that allows multiple lighting design options on the window wall. Detailed luminance and illuminance measures will be used to match quantitative lighting design assessment to user preferences.

X-Ray Studies On The Bilayer Structure Of Trypsin-Treated Rat-Brain Myelin

Trypsin-treated rat brain myelin was subjected to biochemical and X-ray studies. Untreated myelin gave rise to a pattern of three rings with a fundamental repeat period of 155 Angstrom consisting of two bilayers per repeat period, whereas myelin treated with trypsin showed a fundamental repeat period of 75 Angstrom with one bilayer per repeat period. The integrated raw intensity of the h=4 reflection with respect to the h=2 reflection is 0.38 for untreated myelin. The corresponding value reduced to 0.23, 0.18, 0.17 for myelin treated with 5, 10, 40 units of trypsin per mg of myelin, respectively, for 30 min at 30 degrees C. The decrease in relative raw intensity of the higher-order reflection relative to the lower-order reflection is suggestive of a disordering of the phosphate groups upon trypsin treatment or an increased mosaicity of the membrane or a combination of both these effects, However, trypsin treatment does not lead to a complete breakdown of the membrane, The integrated intensity of the h=1 reflection, though weak, is above the measurable threshold for untreated myelin, whereas the corresponding intensity is below the measurable threshold for trypsin-treated myelin, indicating a possible asymmetric to symmetric transition of the myelin bilayer structure about its centre after trypsin treatment.