Crystal structure of ammonium (3,5-dichlorophenoxy)acetate hemihydrate

In the structure of the title hydrated salt, NH4+·C8H5Cl2O3-·0.5H2O, where the anion derives from (3,5-di­chloro­phen­oxy)acetic acid, the ammonium cation is involved in extensive N-H...O hydrogen bonding with both carboxyl­ate and ether O-atom acceptors giving sheet structures lying parallel to (100). The water mol­ecule of solvation lies on a crystallographic twofold rotation axis and is involved in intra-sheet O-H...Ocarboxyl­ate hydrogen-bonding inter­actions. In the anion, the oxoacetate side chain assumes an antiperiplanar conformation with the defining C-O-C-C torsion angle = -171.33 (15)°.

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.

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.

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.

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).

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.

X-ray Structure of Gelonin at 1.8 Å Resolution

Gelonin is a single chain ribosome inactivating protein (RIP) with potential application in the treatment of cancer and AIDS. Diffraction quality crystals grown using PEG3350, belong to the space group P2(1), with it a = 49.4 Angstrom b = 44.9 Angstrom, c = 137.4 Angstrom and beta = 98.4 degrees, and contain two molecules in the asymmetric unit. Diffraction data collected to 1.8 Angstrom resolution has a R(m) value of 7.3%. Structure of gelonin has been solved by the molecular replacement method, using ricin A chain as the search model. Crystallographic refinement using X-PLOR resulted in a model for which the r.m.s deviations from ideal bond lengths and bond angles are 0.012 Angstrom and 2.7 degrees, respectively The final R-factor is 18.4% for 39,806 reflections for which I > 1.0 sigma(I).The C-alpha atoms of the two molecules in the asymmetric unit superpose to within 0.38 Angstrom for 247 atom pairs. The overall fold of gelonin is similar to that of other RIPs such as ricin A chain and alpha-momorcharin, the r.m.s.d. for C-alpha superpositions being 1.3 and 1.4 Angstrom, respectively The-catalytic residues (Glu166, Arg169 and Tyr113) in the active site form a hydrogen bond scheme similar to that observed in other RIPs. The conformation of Tyr74 in the active site, however, is significantly different from that in alpha-momorcharin. Three well defined water molecules are located in the active site cavity and one of them, X319, superposes to within 0.2 Angstrom of a corresponding water molecule in the structure of alpha-momorcharin. Any of the three could be the substrate water molecule in the hydrolysis reaction catalysed by gelonin.Difference electron density for a N-linked sugar moiety has been observed near only one of the two potential glycosylation sites in the sequence. The amino acid at position 239 has been established as Lys by calculation of omit electron density maps.The two cysteine residues in the sequence, Cys44 and Cys50, form a disulphide bond, and are therefore not available for disulphide conjugation with antibodies. Based on the structure, the region of the molecule that is involved in intradimer interactions is suggested to be suitable for introducing a Cys residue for purposes of conjugation with an antibody to produce useful immunotoxins.

Solute induced liquid crystalline behaviour of a quaternary ammonium salt and its application to structure determination

A new liquid crystalline phase, induced by the addition of small amounts of a non-mesogenic solute (such as dimethyl sulphoxide or methyl iodide) to a quaternary ammonium salt, N-methyl-N,N,N-trioctadecylammonium iodide (MTAI), has been detected by NMR and optical microscopic studies. In some cases, there is a coexistence of nematic and smectic phases. Information on the ordering of the phases in the magnetic field of the spectrometer has been derived from NMR spectra of a dissolved molecule, C-13-enriched methyl iodide. The low order parameter of the pure thermotropic nematic phase of the salt provides first-order spectra of the dissolved oriented molecules. Analyses of spectra of cis,cis-mucononitrile exemplifies the utility of the MTAI nematic phase in the determination of structural parameters of the solute.

Electronic Structure of Vacancy Ordered Spinels, $GaMo_{4}S_{8}$ and $GaV_{4}S_{8}$, from ab Initio Calculations

We report ab initio calculations for the band dispersions and total as well as partial densities of states for vacancy ordered, clustered spinels, GaMo4S8 and GaV4S8. Results are presented for the high temperature cubic phase for both compounds. Additionally, we discuss results of similar calculations for GaMo4S8 in an idealized cubic structure, as well as the nonmagnetic and the ferromagnetic states of the low temperature rhombohedral structure. Comparison of these results allows us to discuss the unusual aspects of the electronic structure of this interesting class of compounds, and provide estimates of the crystal-field and exchange splitting strengths.

Crystal structure of morpholin-4-ium cinnamate

In the anhydrous salt formed from the reaction of morpholine with cinnamic acid, C4H10NO+ C9H7O2-, the acid side chain in the trans-cinnamate anion is significantly rotated out of the benzene plane [C-C-C-C torsion angle = 158.54(17)deg. In the crystal, one of the the aminium H atoms is involved in a asymmetric three-centre cation-anion N-H...(O,O') R2/1(4) hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. The second aminium H atom forms an inter-species N-H...O(carboxyl) hydrogen bond, generating a one-dimensional chain structure extending along [100]. Chains are linked by C-H...O interactions forming a supramolecular layer parallel to (01-1).

Structure of KNb0.5OPO4, a KTiOPO4 analog

The crystal structure of KNb0.5V0.5OPO4, a new KTiOPO4 isomorph, has been refined from powder X-ray diffraction data by Rietveld refinement. The structure is orthorhombic, space group Pna2(1), with a = 12.933(1), b = 6.4713(8), and c = 10.7273(6) Angstrom, Z = 8. There is a preferential distribution of Nb(V) and V(III) atoms in the octahedral M(1) [0.806Nb, 0.194V] and M(2) [0.194Nb, 0.806V] sites, the M(1)O-6 octahedra being more distorted than the M(2)O-6 octahedra. The results are compared with other KTiOPO4 derivatives.

Structure of the benzene center dot center dot center dot ICI complex: A UVPES and ab initio molecular orbital study

UVPES studies and ab initio and DFT computations have been done on the benzene...ICl complex; electron spectral data and computed orbital energies show that donor orbitals are stabilized and acceptor orbitals are destabilized due to complexation. Calculations predict an oblique structure for the complex in which the interacting site is a C=C bond center in the donor and iodine atom in the acceptor, in full agreement with earlier experimental reports. BSSE-corrected binding energies closely match the enthalpy of complexation reported, and the NBO analysis clearly reveals the involvement of the pi orbital of benzene and the sigma* orbital of ICl in the complex.

Evolution of electronic structure with dimensionality in divalent nickelates

We investigate the evolution of electronic structure with dimensionality (d) of Ni-O-Ni connectivity in divalent nickelates, NiO (3-d), La2NiO4, Pr2NiO4 (2-d), Y2BaNiO5 (1-d) and Lu2BaNi5 (0-d), by analyzing the valence band and the Ni 2p core-level photoemission spectra in conjunction with detailed many-body calculations including full multiplet interactions. Experimental results exhibit a reduction in the intensity of correlation-induced satellite features with decreasing dimensionality. The calculations based on the cluster model, but evaluating both Ni 3d and O 2p related photoemission processes on the same footing, provide a consistent description of both valence-band and core-level spectra in terms of various interaction strengths. While the correlation-induced satellite features in NiO is dominated by poorly screened d(8) states as described in the existing literature, we find that the satellite features in the nickelates with lower dimensional Ni-O-Ni connectivity are in fact dominated by the over-screened d(10)L(2) states. It is found that the changing electronic structure with the dimensionality is primarily driven by two factors: (i) a suppression of the nonlocal contribution to screening; and (ii) a systematic decrease of the charge-transfer energy Delta driven by changes in the Madelung potential. [S0163-1829(99)09619-8].