Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.     

N‐bromo‐hydantoin grafted polystyrene beads: Synthesis and nano‐micro beads characteristics for achieving controlled release of active oxidative bromine and extended microbial inactivation efficiency

N‐bromo‐hydantoin and N‐bromo‐5,5′‐dimethylhydantoin conjugated polystyrene beads were synthesized from chloromethyl polystyrene beads which differ in their particles size, crosslinking, nano‐micro porosity, and tunnels size on the surface, in order to study the effect of these parameters on oxidative halogen release and resultant activity, for water purification applications. The synthesized beads were characterized using elemental analysis, FT‐IR, solid state ¹³C‐NMR, and scanning electron microscope (SEM). The conjugation yield and kinetics in different solvents and bromine loading capacity were studied. The N‐bromoamine polystyrene beads were tested for water decontamination according to NSF 231 protocol. The release of active bromine was analyzed by spectrophotometer using a DPD‐1 kit and also studied the antimicrobial activity against Escherichia coli and MS2 phages. Bead's nano‐micro characteristics were found critical for oxidative halogen release control: rate stabilization and modulation, extension and also influences antimicrobial activity. The synthesized beads exhibited extended and stable release of bromine, 6 and 4 log reduction for E. coli and MS2, respectively for 250 L of passing contaminated water. Thus, N‐halamine hydantoins conjugated polystyrenes, chemically or kinetically release modified should have applications as disinfectants in water purification systems as well as medical field. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 596–610     

Cannabis-Derived Compounds Cannabichromene and Δ9-Tetrahydrocannabinol Interact and Exhibit Cytotoxic Activity against Urothelial Cell Carcinoma Correlated with Inhibition of Cell Migration and Cytoskeleton Organization

Cannabis sativa contains more than 500 constituents, yet the anticancer properties of the vast majority of cannabis compounds remains unknown. We aimed to identify cannabis compounds and their combinations presenting cytotoxicity against bladder urothelial carcinoma (UC), the most common urinary system cancer. An XTT assay was used to determine cytotoxic activity of C. sativa extracts on T24 and HBT-9 cell lines. Extract chemical content was identified by high-performance liquid chromatography (HPLC). Fluorescence-activated cell sorting (FACS) was used to determine apoptosis and cell cycle, using stained F-actin and nuclei. Scratch and transwell assays were used to determine cell migration and invasion, respectively. Gene expression was determined by quantitative Polymerase chain reaction (PCR). The most active decarboxylated extract fraction (F7) of high-cannabidiol (CBD) C. sativa was found to contain cannabichromene (CBC) and Δ9-tetrahydrocannabinol (THC). Synergistic interaction was demonstrated between CBC + THC whereas cannabinoid receptor (CB) type 1 and type 2 inverse agonists reduced cytotoxic activity. Treatments with CBC + THC or CBD led to cell cycle arrest and cell apoptosis. CBC + THC or CBD treatments inhibited cell migration and affected F-actin integrity. Identification of active plant ingredients (API) from cannabis that induce apoptosis and affect cell migration in UC cell lines forms a basis for pre-clinical trials for UC treatment.     

Electrical properties study of multi-walled carbon nanotubes/hybrid-glass nanocomposites

Electrical properties of multi-walled carbon nanotubes (MWNTs)/hybrid-glass nanocomposites prepared by the fast-sol–gel reaction were investigated in light of percolation theory. A good correlation was found between the experimental results and the theory. We obtained a percolation threshold ? _c  = 0.22 wt%, and a critical exponent of t = 1.73. These values are reported for the first time for a silica-based system. The highest conductivity measured on the MWNT/hybrid-glass nanocomposites was σ ≈ 10^?3(Ω cm)^?1 for 2 wt% carbon nanotube (CNT) loading. The electrical conductivity was at least 12 orders of magnitude higher than that of pure silica. Electrostatic force microscopy and conductive-mode atomic force microscopy studies demonstrated conductivity at the micro-level, which was attributed to the CNT dispersed in the matrix. It appears that the dispersion in our MWNT/hybrid-glass system yields a particularly low percolation threshold compared with that of a MWNT/silica-glass system. Materials with electrical conductivities described in this work can be exploited for anti-static coating.     

Antimicrobial silica particles loaded with quaternary ammonium polyethyleneimine network

Silica particles functionalized with quaternary ammonium groups were prepared by interpenetrating polyethylenimine (PEI) into silica particles and crosslinking with diiodopentane, followed by octyliodide alkylation and methyliodide quaternarization (S‐QA‐PEI). The synthesized S‐QA‐PEI particles were identified with a slight particle size increase of 2–3 µm. Different ratios of PEI:silica particles were prepared and analyzed. While silica particles are negatively charged, ?16.7 ± 5.11 mV, the prepared S‐QA‐PEI particles are positively charged, +50–60 mV. These particles were embedded in poly(ethylene vinyl acetate) and poly(ethylene methacrylic acid) coatings which exhibited strong antibacterial activity. Copyright © 2014 John Wiley & Sons, Ltd.     

Adductor spasmodic dysphonia: case reports withacoustic analysis following botulinum toxin injection and acupuncture

We analyzed frequency and duration parameters of voice and speech in two men with adductor spasmodic dysphonia (SD). One was treated with botulinum toxin injection; the other received acupuncture therapy. Im provement after acupuncture therapy in terms of standard deviation of fundamental frequency, acoustic perturbation measurements, durational measurements of voice and speech, and spectrographic analysis was comparable to the results achieved with botulinum toxin injection. Voice and speech parameters were stable I year after acupuncture therapy.     

Propagation of avalanches in Mn12-acetate: magnetic deflagration

Local time-resolved measurements of fast reversal of the magnetization of single crystals of Mn12-acetate indicate that the magnetization avalanche spreads as a narrow interface that propagates through the crystal at a constant velocity that is roughly 2 orders of magnitude smaller than the speed of sound. We argue that this phenomenon is closely analogous to the propagation of a flame front (deflagration) through a flammable chemical substance.     

Inter-particle spin-polarized tunneling in arrays of magnetite nanocrystals

Inter-particle spin-polarized tunneling was measured in an organically capped magnetite nanocrystal (NC) array deposited between 30 nm spaced gold electrodes. Magnetoresistance (MR) measurements performed around the blocking temperature (T_b) of the magnetic moments of the particles in the array, which was relatively high (220 K), yielded negative MR values of the order of 10-25% under moderate magnetic fields of several kOe. The field dependence of the MR followed closely the square of the film's magnetization and its voltage dependence indicated maximal spin polarization around the Fermi level. These findings suggested that the measured MR is the result of spin-polarized tunneling between individual magnetite NCs acting as superparamagnetic spin polarizers.     

Computer Mediated Learning: An Example of an Approach

There are several possible approaches in which dynamic computerized environments play a significant, and possibly unique, role in supporting innovative learning trajectories in mathematics in general, and particularly in geometry. These approaches are influenced by the way one views mathematics and mathematical activity.In this paper we briefly describe an approach based on a problem situation and our experiences using it with students and teachers. This leads naturally to a discussion of some of the ways in which parts of the mathematics curriculum, classroom practice, and student learning may differ from the traditional approach.This revised version was published online in September 2005 with corrections to the Cover Date.     

Antibacterial effect of composite resins containing quaternary ammonium polyethyleneimine nanoparticles

Quaternary ammonium polyethyleneimine (QA-PEI)-based nanoparticles were synthesized by crosslinking with dibromopentane followed by N-alkylation with various alkyl halides and further N-methylation with methyl iodide. Insoluble pyridinium-type particles were prepared by suspension polymerization of 4-vinyl pyridine followed by N-alkylation with alkyl halides. Polyamine-based nanoparticles embedded in restorative composite resin at 1% w/w were tested for antibacterial activity against Streptococcus mutans using direct contact test. Activity analysis revealed that the alkyl chain length of the QA-PEI nanoparticles plays a significant role in antibacterial activity of the reagent. The most potent compound was octyl-alkylated QA-PEI embedded in restorative composite resin at 1% w/w that totally inhibited S. mutans growth in 3-month-aged samples. This data indicates that restorative composite resin with antibacterial properties can be produced by the incorporation of QA-PEI nanoparticles.