Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. (c) 2012 Wiley Periodicals, Inc.

High-temperature kinetics of the reaction between CN and hydrocarbons using a novel high-enthalpy flow tube

More than 70 molecules of varied nature have been identified in the envelopes of carbon-rich stars through their spectral fingerprints in the microwave or far infrared regions. Many of them are carbon chain molecules and radicals, and a significant number are unique to the circumstellar medium. The determination of relevant laboratory kinetics data is critical to keep up with the development of the high spectral and spatial resolution observations and of the refinement of chemical models. Neutralneutral reactions of the CN radical with unsaturated hydrocarbons could be a dominant route in the formation of cyanopolyynes, even at low temperatures and deserve a detailed laboratory investigation. The approach we have developed aims to bridge the temperature gap between resistively heated flow tubes and shock tubes. The present kinetic measurements are obtained using a new reactor combining a high-enthalpy source with a flow tube and a pulsed laser photolysislaser-induced fluorescence system to probe the undergoing chemical reactions. The high-enthalpy flow tube has been used to measure the rate constant of the reaction of the CN radical with propane (C3H8), propene (C3H6), allene (C3H4), 1,3-butadiene (1,3-C4H6), and 1-butyne (C4H6) over a temperature range extending from 300 to 1200 K. All studied reactions of CN with unsaturated hydrocarbons are rapid, with rate coefficients greater than 10-10 cm3 center dot molecule-1 center dot s-1 and exhibit slight negative temperature dependence above room temperature. (c) 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 753766, 2012

Acyclic Edge Coloring of Triangle-Free Planar Graphs

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a'(G). It was conjectured by Alon, Sudakov and Zaks (and much earlier by Fiamcik) that a'(G) ? ? + 2, where ? = ?(G) denotes the maximum degree of the graph. If every induced subgraph H of G satisfies the condition |E(H)| ? 2|V(H)|-1, we say that the graph G satisfies Property A. In this article, we prove that if G satisfies Property A, then a'(G) ? ? + 3. Triangle-free planar graphs satisfy Property A. We infer that a'(G) ? ? + 3, if G is a triangle-free planar graph. Another class of graph which satisfies Property A is 2-fold graphs (union of two forests). (C) 2011 Wiley Periodicals, Inc. J Graph Theory

LbL-coated microcapsules as systems for encapsulation of optical brightening agent

We report the encapsulation of optical brightening agent (OBA) into hollow microcapsules prepared by the controlled Layer- by-Layer (LbL) self-assembly process, achieved by the sequential adsorption of oppositely charged polyelectrolytes using negatively charged silica template. Loading takes place by spontaneous deposition method which was proved by confocal laser scanning microscopy (CLSM) using rhodamine 6G (Rd6G) as a fluorescent probe. The loading of the OBA into the microcapsules was found to be dependent on the feeding concentration, pH of the medium, and loading temperature. The encapsulation efficiency of OBA decreased on increasing feeding concentration. Maximum loading was observed at pH 4 and amount of OBA loaded decreased with increase in pH. The loaded OBA was released in a sustained manner for 8 h. No degradation of the OBA was observed during the process of encapsulation and release. Polyelectrolyte capsules potentially offer an innovative way of encapsulating large amounts of active materials for a variety of applications. (c) 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 127: 1609-1614, 2013

Adsorption of anionic dyes on a reversibly swelling cationic superabsorbent polymer

A cationic monomer 2-(methacryloyloxy)ethyl]trimethylammonium chloride was polymerized using N,N'-methylenebisacrylamide as the crosslinker to obtain a cationic superabsorbent polymer (SAP). This SAP was characterized by Fourier transform-infrared spectroscopy, and the equilibrium swelling capacity was determined by swelling in water. The SAP was subjected to cyclic swelling/deswelling in water and NaCl solution. The conductivity of the swelling medium was monitored during the swelling/deswelling and was related to the swelling/deswelling characteristics of the SAP. The adsorption of five anionic dyes of different classes on the SAP was carried out and was found to follow the first-order kinetics. The Langmuir adsorption isotherms were found to fit the equilibrium adsorption data. The dye adsorption capacity of the SAP synthesized in this study was higher than that obtained for other hydrogels reported in the literature. (c) 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013

In vitro bioactivity and cytocompatibility properties of spark plasma sintered HA-Ti composites

The present study reports the results of the detailed in vitro bioactivity and cytocompatibility properties of the hydroxyapatite (HA) and the HA-titanium (HA-Ti) composite with varying amount of Ti (5, 10, and 20 wt %), densified using spark plasma sintering process (SPS). Using this technique and tailoring suitable processing parameters, it has been possible to retain both HA and Ti in the sintered ceramics. Importantly, the uniquely designed SPS processing with suitably chosen parameters enables in achieving better mechanical properties, such as higher indentation fracture toughness (similar to 1.5 MPa m1/2) in HA-Ti composites compared with HA. X-ray diffraction and scanning electron microscopic (SEM) observations reveal good bioactivity of the HA-Ti composites with the formation of thick, flaky, and porous apatite layer when immersed in simulated body fluid at 37 degrees C and pH of 7.4. Atomic absorption spectroscopic analysis of the simulated body fluid solution reveals dynamic changes in Ca+2 ion concentration with more dissolution of Ca+2 ion from the HA-20Ti composite. However, the measurements with inductively coupled plasma spectrometer do not record dissolution of Ti+4 ions. Transmission electron microscopic analysis indicates weak crystalline nature of the apatite and confirms the formation of fine-scale apatite crystals. MTT assay, fluorescence, and SEM study demonstrate good cell viability and cell adhesion/proliferation of the Saos -2 cells, cultured on the developed composites under standard culture condition, and the difference in cell viability has been discussed in reference to substrate composition and roughness. Overall, HA-Ti composites exhibit comparable and even better in vitro bioactivity and cytocompatibility properties than HA. (c) 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2013.

Stiffness- and wettability-dependent myoblast cell compatibility of transparent poly(vinyl alcohol) hydrogels

This study reports the in vitro compatibility of muscle cells (C2C12 mouse myoblast cell line) with the transparent poly(vinyl alcohol) (PVA) hydrogels and the results are explained on the basis of surface wettability, crystallinity, and nanoscale elastic stiffness property. Nanoindentation was carried out with a maximum load of 100 mu N for all the hydrogel compositions and the properties such as elastic stiffness, hardness and total work done during indentation were computed. The difference in cell viability as well as adhesion of cultured myoblast cells on the investigated hydrogel substrates were discussed in reference to the difference in the nanoscale elastic properties, crystallinity, and surface wettability. An important result has been that both elastic stiffness and surface wettability synergistically influence myoblast viability/adhesion on PVA hydrogels. (c) 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2013.

Current trends in modeling hostpathogen interactions

The rapid emergence of infectious diseases calls for immediate attention to determine practical solutions for intervention strategies. To this end, it becomes necessary to obtain a holistic view of the complex hostpathogen interactome. Advances in omics and related technology have resulted in massive generation of data for the interacting systems at unprecedented levels of detail. Systems-level studies with the aid of mathematical tools contribute to a deeper understanding of biological systems, where intuitive reasoning alone does not suffice. In this review, we discuss different aspects of hostpathogen interactions (HPIs) and the available data resources and tools used to study them. We discuss in detail models of HPIs at various levels of abstraction, along with their applications and limitations. We also enlist a few case studies, which incorporate different modeling approaches, providing significant insights into disease. (c) 2013 Wiley Periodicals, Inc.

Identification of mycobacterial lectins from genomic data

Sixty-four sequences containing lectin domains with homologs of known three-dimensional structure were identified through a search of mycobacterial genomes. They appear to belong to the -prism II, the C-type, the Microcystis virdis (MV), and the -trefoil lectin folds. The first three always occur in conjunction with the LysM, the PI-PLC, and the -grasp domains, respectively while mycobacterial -trefoil lectins are unaccompanied by any other domain. Thirty heparin binding hemagglutinins (HBHA), already annotated, have also been included in the study although they have no homologs of known three-dimensional structure. The biological role of HBHA has been well characterized. A comparison between the sequences of the lectin from pathogenic and nonpathogenic mycobacteria provides insights into the carbohydrate binding region of the molecule, but the structure of the molecule is yet to be determined. A reasonable picture of the structural features of other mycobacterial proteins containing one or the other of the four lectin domains can be gleaned through the examination of homologs proteins, although the structure of none of them is available. Their biological role is also yet to be elucidated. The work presented here is among the first steps towards exploring the almost unexplored area of the structural biology of mycobacterial lectins. Proteins 2013. (c) 2012 Wiley Periodicals, Inc.

In vitro cytocompatibility assessment of amorphous carbon structures using neuroblastoma and Schwann cells

The development of scaffolds for neural tissue engineering application requires an understanding of cell adhesion, proliferation, and migration of neuronal cells. Considering the potential application of carbon as scaffold materials and the lack of understanding of compatibility of amorphous carbon with neuronal cells, the carbon-based materials in the forms of carbon films and continuous electrospun carbon nanofibers having average diameter of approximate to 200 nm are being investigated with or without ultraviolet (UV) and oxy-plasma (OP) treatments for cytocompatibility property using mouse Neuroblastoma (N2a) and rat Schwann cells (RT4-D6P2T). The use of Raman spectroscopy in combination with Fourier transform infrared (FTIR) and X-ray diffraction establishes the amorphous nature and surface-bonding characteristics of the studied carbon materials. Although both UV and OP treatments make carbon surfaces more hydrophilic, the cell viability of N2a cells is statistically more significant on OP treated fibers/films compared to UV fiber/film substrates after 4 days in culture. The electrospun carbon fibrous substrate provides the physical guidance to the cultured Schwann cells. Overall, the experimental results of this study demonstrate that the electrospun amorphous carbon nanofibrous scaffolds can be used as a suitable biomaterial substrate for supporting cell adhesion and proliferation of neuronal cells in the context of their applications as artificial nerve implants. (c) 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2013.

Structure-property correlation in BaO-TiO2-B2O3 glasses: glass stability, optical, hydrophobic, and dielectric properties

Glasses in the x(BaO-TiO2)-B2O3 (x = 0.25, 0.5, 0.75, and 1 mol.) system were fabricated via the conventional melt-quenching technique. Thermal stability and glass-forming ability as determined by differential thermal analysis (DTA) were found to increase with increasing BaO-TiO2 (BT) content. However, there was no noticeable change in the glass transition temperature (T-g). This was attributed to the active participation of TiO2 in the network formation especially at higher BT contents via the conversion of the TiO6 structural units into TiO4 units, which increased the connectivity and resulted in an increase in crystallization temperature. Dielectric and optical properties at room temperature were studied for all the glasses under investigation. Interestingly, these glasses were found to be hydrophobic. The results obtained were correlated with different structural units and their connectivity in the glasses.

Single-step synthesis of internally functionalizable hyperbranched polyethers

Radical catalyzed thiol-ene reaction has become a useful alternative to the Huisgen-type azide-yne click reaction as it helps expand the variability in reaction conditions as well as the range of clickable entities. In this study, the direct generation of a hyperbranched polyether (HBPE) having decyl units at the periphery and a pendant allyl group on every repeat unit of the polymer backbone is described; the allyl groups serve as a reactive handle for postpolymerization modifications and permits the generation of a variety of internally functionalized HBPEs. In this design, the AB(2) monomer carries two decylbenzyl ether units (B-functionality), an aliphatic OH (A-functionality) and a pendant allyl group within the spacer segment; polymerization of the monomer readily occurs at 150 degrees C via melt transetherification process by continuous removal of 1-decanol under reduced pressure. The resulting HBPE has a hydrophobic periphery due to the presence of numerous decyl chains, while the allyl groups that remain unaffected during the melt polymerization provides an opportunity to install a variety of functional groups within the interior; thiol-ene click reaction with two different thiols, namely 3-mercaptopropionic acid and mercaptosuccinic acid, generated interesting amphiphilic structures. Preliminary field emission scanning electron microscope (FESEM) and Atomic Force Microscopy (AFM) imaging studies reveal the formation of fairly uniform spherical aggregates in water with sizes ranging from 200 to 400 nm; this suggests that these amphiphilic HBPs is able to reconfigure to generate jellyfish-like conformations that subsequently aggregate in an alkaline medium. The internal allyl functional groups were also used to generate intramolecularly core-crosslinked HBPEs, by the use of dithiol crosslinkers; gel permeation chromatography traces provided clear evidence for reduction in the size after crosslinking. In summary, we have developed a simple route to prepare core-clickable HBPEs and have demonstrated the quantitative reaction of the allyl groups present within the interior of the polymers; such HB polymeric systems that carry numerous functional groups within the core could have interesting applications in analyte sequestration and possibly sensing, especially from organic media. (c) 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 4125-4135

In vitro and in vivo characterization of designed immunogens derived from the CD-helix of the stem of influenza hemagglutinin

The conserved stem domain of influenza virus hemagglutinin (HA) is a target for broadly neutralizing antibodies and a potential vaccine antigen for induction of hetero-subtypic protection. The epitope of 12D1, a previously reported bnAb neutralizing several H3 subtype influenza strains, was putatively mapped to residues 76-106 of the CD-helix, also referred to as long alpha helix (LAH) of the HA stem. A peptide derivative consisting of wt-LAH residues 76-130 conjugated to keyhole limpet hemocyanin was previously shown to confer robust protection in mice against challenge with influenza strains of subtypes H3, H1, and H5 which motivated the present study. We report the design of multiple peptide derivatives of LAH with or without heterologous trimerization sequences and show that several of these are better folded than wt-LAH. However, in contrast to the previous study immunization of mice with wt-LAH resulted in negligible protection against a lethal homologous virus challenge, while some of the newly designed immunogens could confer weak protection. Combined with structural analysis of HA, our data suggest that in addition to LAH, other regions of HA are likely to significantly contribute to the epitope for 12D1 and will be required to elicit robust protection. In addition, a dynamic, flexible conformation of isolated LAH peptide may be required for eliciting a functional anti-viral response. Proteins 2013; 81:1759-1775. (c) 2013 Wiley Periodicals, Inc.

MRT Letter: Light Sheet Based Imaging Flow Cytometry on a Microfluidic Platform

We propose a light sheet based imaging flow cytometry technique for simultaneous counting and imaging of cells on a microfluidic platform. Light sheet covers the entire microfluidic channel and thus omits the necessity of flow focusing and point scanning based technology. Another advantage lies in the orthogonal detection geometry that totally cuts-off the incident light, thereby substantially reducing the background in the detection. Compared to the existing state-of-art techniques the proposed technique shows marked improvement. Using fluorescently-coated Saccharomyces cerevisiae cells we have recorded cell counting with throughput as high as 2,090 cells/min in the low flow rate regime and were able to image the individual cells on-the-go. Overall, the proposed system is cost-effective and simple in channel geometry with the advantage of efficient counting in operational regime of low laminar flow. This technique may advance the emerging field of microfluidic based cytometry for applications in nanomedicine and point of care diagnostics. Microsc. Res. Tech. 76:1101-1107, 2013. (c) 2013 Wiley Periodicals, Inc.

Steric and Electronic Interactions Controlling the cis/trans Isomer Equilibrium at X-Pro Tertiary Amide Motifs in Solution

A systematic understanding of the noncovalent interactions that influence the structures of the cis conformers and the equilibrium between the cis and the trans conformers, of the X-Pro tertiary amide motifs, is presented based on analyses of H-1-, C-13-NMR and FTIR absorption spectra of two sets of homologous peptides, X-Pro-Aib-OMe and X-Pro-NH-Me (where X is acetyl, propionyl, isobutyryl and pivaloyl), in solvents of varying polarities. First, this work shows that the cis conformers of any X-Pro tertiary amide motif, including Piv-Pro, are accessible in the new motifs X-Pro-Aib-OMe, in solution. These conformers are uniquely observable by FTIR spectroscopy at ambient temperatures and by NMR spectroscopy from temperatures as high as 273 K. This is made possible by the persistent presence of n(i-1i)* interactions at Aib, which also influence the disappearance of steric effects at these cis X-Pro rotamers. Second, contrary to conventional understanding, the energy contribution of steric effects to the cis/trans equilibrium at the X-Pro motifs is found to be nonvariant (0.54 +/- 0.02 kcal/mol) with increase in steric bulk on the X group. Third, the current studies provide direct evidence for the weak intramolecular interactions namely the n(i-1i)*, the N-Pro center dot center dot center dot Hi+1 (C(5)a), and the C-7 hydrogen bond that operate and influence the structures, stabilities, and dynamics between different conformational states of X-Pro tertiary amide motifs. NMR and IR spectral data suggest that the cis conformers of X-Pro motifs are ensembles of short-lived rotamers about the C-X-N-Pro bond. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 66-77, 2014.