A Chlamydia trachomatis strain with a chemically generated amino acid substitution (P370L) in the cthtrA gene shows reduced elementary body production

Background Chlamydia (C.) trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness. Genetic approaches to investigate C. trachomatis have been only recently developed due to the organism’s intracellular developmental cycle. HtrA is a critical stress response serine protease and chaperone for many bacteria and in C. trachomatis has been previously shown to be important for heat stress and the replicative phase of development using a chemical inhibitor of the CtHtrA activity. In this study, chemically-induced SNVs in the cthtrA gene that resulted in amino acid substitutions (A240V, G475E, and P370L) were identified and characterized. Methods SNVs were initially biochemically characterized in vitro using recombinant protein techniques to confirm a functional impact on proteolysis. The C. trachomatis strains containing the SNVs with marked reductions in proteolysis were investigated in cell culture to identify phenotypes that could be linked to CtHtrA function. Results The strain harboring the SNV with the most marked impact on proteolysis (cthtrAP370L) was detected to have a significant reduction in the production of infectious elementary bodies. Conclusions This provides genetic evidence that CtHtrA is critical for the C. trachomatis developmental cycle.

Hyaluronic acid enhances the mechanical properties of tissue-engineered cartilage constructs

There is a need for materials that are well suited for cartilage tissue engineering. Hydrogels have emerged as promising biomaterials for cartilage repair, since, like cartilage, they have high water content, and they allow cells to be encapsulated within the material in a genuinely three-dimensional microenvironment. In this study, we investigated the mechanical properties of tissue-engineered cartilage constructs using in vitro culture models incorporating human chondrocytes from osteoarthritis patients. We evaluated hydrogels formed from mixtures of photocrosslinkable gelatin-methacrylamide (Gel-MA) and varying concentrations (0–2%) of hyaluronic acid methacrylate (HA-MA). Initially, only small differences in the stiffness of each hydrogel existed. After 4 weeks of culture, and to a greater extent 8 weeks of culture, HA-MA had striking and concentration dependent impact on the changes in mechanical properties. For example, the initial compressive moduli of cell-laden constructs with 0 and 1% HA-MA were 29 and 41 kPa, respectively. After 8 weeks of culture, the moduli of these constructs had increased to 66 and 147 kPa respectively, representing a net improvement of 69 kPa for gels with 1% HA-MA. Similarly the equilibrium modulus, dynamic modulus, failure strength and failure strain were all improved in constructs containing HA-MA. Differences in mechanical properties did not correlate with glycosaminoglycan content, which did not vary greatly between groups, yet there were clear differences in aggrecan intensity and distribution as assessed using immunostaining. Based on the functional development with time in culture using human chondrocytes, mixtures of Gel-MA and HA-MA are promising candidates for cartilage tissue-engineering applications.

The three-dimensional hydrogen-bonded structures in the ammonium and sodium salt hydrates of 4-aminophenylarsonic acid

The structures of two hydrated salts of 4-aminophenylarsonic acid (p-arsanilic acid), namely ammonium 4-aminophenylarsonate monohydrate, NH4(+)·C6H7AsNO3(-)·H2O, (I), and the one-dimensional coordination polymer catena-poly[[(4-aminophenylarsonato-κO)diaquasodium]-μ-aqua], [Na(C6H7AsNO3)(H2O)3]n, (II), have been determined. In the structure of the ammonium salt, (I), the ammonium cations, arsonate anions and water molecules interact through inter-species N-H...O and arsonate and water O-H...O hydrogen bonds, giving the common two-dimensional layers lying parallel to (010). These layers are extended into three dimensions through bridging hydrogen-bonding interactions involving the para-amine group acting both as a donor and an acceptor. In the structure of the sodium salt, (II), the Na(+) cation is coordinated by five O-atom donors, one from a single monodentate arsonate ligand, two from monodentate water molecules and two from bridging water molecules, giving a very distorted square-pyramidal coordination environment. The water bridges generate one-dimensional chains extending along c and extensive interchain O-H...O and N-H...O hydrogen-bonding interactions link these chains, giving an overall three-dimensional structure. The two structures reported here are the first reported examples of salts of p-arsanilic acid.

A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC

Membrane proteins play important roles in many biochemical processes and are also attractive targets of drug discovery for various diseases. The elucidation of membrane protein types provides clues for understanding the structure and function of proteins. Recently we developed a novel system for predicting protein subnuclear localizations. In this paper, we propose a simplified version of our system for predicting membrane protein types directly from primary protein structures, which incorporates amino acid classifications and physicochemical properties into a general form of pseudo-amino acid composition. In this simplified system, we will design a two-stage multi-class support vector machine combined with a two-step optimal feature selection process, which proves very effective in our experiments. The performance of the present method is evaluated on two benchmark datasets consisting of five types of membrane proteins. The overall accuracies of prediction for five types are 93.25% and 96.61% via the jackknife test and independent dataset test, respectively. These results indicate that our method is effective and valuable for predicting membrane protein types. A web server for the proposed method is available at http://www.juemengt.com/jcc/memty_page.php

Inhibition by poly(acrylic acid) and morphological changes in calcium carbonate and calcium carbonate/calcium sulfate crystallization on silica fibers

An intrinsic exposed core optical fiber sensor (IECOFS) made from fused silica was used to monitor the crystallization of calcium carbonate (CaCO3) and CaCO3/calcium sulfate (CaSO4) composite at 100 and 120 °C in the absence and presence of low-molar-mass (Mn ≤ 2000) poly(acrylic acid) (PAA) with different end groups. The IECOFS responded only to deposition and growth processes on the fiber surface rather than changes occurring in the bulk of the solution. Hexyl isobutyrate-terminated PAA (Mn = 1400) and hexadecyl isobutyrate-terminated PAA (Mn = 1700) were the most effective species in preventing CaCO3 deposition. Phase transformation from vaterite to aragonite/calcite decreased with increasing hydrophobicity of the PAA end group. Low-molar-mass PAA at 10 ppm showed very significant inhibition of CaCO3/CaSO4 composite formation for all end groups investigated.

Two-dimensional coordination polymeric structures in caesium complexes with ring-substituted phenoxyacetic acids

The two-dimensional polymeric structures of the caesium complexes with the phenoxyacetic acid analogues (4-fluorophenoxy)acetic acid, (3-chloro-2-methylphenoxy)acetic acid and the herbicidally active (2,4-dichlorophen­oxy)acetic acid (2,4-D), namely poly[[5-(4-fluorophenoxy)acetato][4-(4-fluorophenoxy)acetato]dicaesium], [Cs2(C8H6FO3)2]n, (I), poly[aqua[5-(3-chloro-2-methylphenoxy)acetato]caesium], [Cs(C9H8ClO3)(H2O)]n, (II), and poly[[7-(2,4-di­chlorophenoxy)acetato][(2,4-dichlorphenoxy)acetic acid]caesium], [Cs(C8H5Cl2O3)(C8H6Cl2O3)]n, (III), are described. In (I), the Cs+ cations of the two individual irregular coordination polyhedra in the asymmetric unit (one CsO7 and the other CsO8) are linked by bridging carboxylate O-atom donors from the two ligand molecules, both of which are involved in bidentate chelate Ocarboxy,Ophenoxy interactions, while only one has a bidentate carboxylate O,O'-chelate inter­action. Polymeric extension is achieved through a number of carboxylate O-atom bridges, with a minimum CsCs separation of 4.3231 (9) Å, giving layers which lie parallel to (001). In hydrated complex (II), the irregular nine-coordination about the Cs+ cation comprises a single monodentate water molecule, a bidentate Ocarboxy,Ophenoxy chelate interaction and six bridging carboxylate O-atom bonding interactions, giving a CsCs separation of 4.2473 (3) Å. The water mol­ecule forms intralayer hydrogen bonds within the two-dimensional layers, which lie parallel to (100). In complex (III), the irregular centrosymmetric CsO6Cl2 coordination environment comprises two O-atom donors and two ring-substituted Cl-atom donors from two hydrogen bis[(2,4-dichlorophenoxy)acetate] ligand species in a bidentate chelate mode, and four O-atom donors from bridging carboxyl groups. The duplex ligand species lie across crystallographic inversion centres, linked through a short O-HO hydrogen bond involving the single acid H atom. Structure extension gives layers which lie parallel to (001). The present set of structures of Cs salts of phenoxyacetic acids show previously demonstrated trends among the alkali metal salts of simple benzoic acids with no stereochemically favourable interactive substituent groups for formation of two-dimensional coordination polymers.

Prediction of the fate of oxytetracycline and oxolinic acid in a fish pond using simulation model: A preliminary study

The fate of two popular antibiotics, oxytetracycline and oxolinic acid, in a fish pond were simulated using a computational model. The VDC model, which is designed based on a model for predicting pesticide fate and transport in paddy fields, was modified to take into account the differences between the pond and the paddies as well as those between the fish and the rice plant behaviors. The pond conditions were set following the typical practice in South East Asia aquaculture. The two antibiotics were administered to the animal in the pond through medicated feed during a period of 5 days as in actual practice. Concentrations of oxytetracycline in pond water were higher than those of oxolinic acid at the beginning of the simulation. Dissipation rate of oxytetracycline is also higher as it is more readily available for degradation in the water. For the long term, oxolinic acid was present at higher concentration than oxytetracycline in pond water as well as pond sediment. The simulated results were expected to be conservative and can be useful for the lower tier assessment of exposure risk of veterinary medicine in aquaculture industry but more data are needed for the complete validation of the model.

Crystal structures and hydrogen bonding in the morpholinium salts of four phenoxyacetic acid analogues

The anhydrous salts morpholinium (tetrahydro-2-H-1,4-oxazine) phenxyacetate, C4H10NO+ C8H7O3- (I), (4-fluorophenoxy)acetate, C4H10NO+ C8H6FO3- (II) and isomeric morpholinium (3,5-dichlorophenoxy)acetate (3,5-D) (III) and morpholinium (2,4-dichlorophenoxy)acetate (2,4-D), C4H10NO+ C8H5Cl2O3- (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation-anion N-H...O,O' R2/1(4) hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N---H...O interaction is linear. In the structures of (I), (II) and (III), the second N-H...O(carboxyl) hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N-H...O hydrogen bonds [graph set R2/4(8)], giving a cyclic heterotetrameric structure.

X-ray studies on crystalline complexes involving amino acids and peptides. XXXIII. Crystal structures of L- and DL-arginine complexed with oxalic acid and a comparative study of amino acid oxalic acid complexes

The DL- and L-arginine complexes of oxalic acid are made up of zwitterionic positively charged amino acid molecules and semi-oxalate ions. The dissimilar molecules aggregate into separate alternating layers in the former. The basic unit in the arginine layer is a centrosymmetric dimer, while the semi-oxalate ions form hydrogen-bonded strings in their layer. In the L-arginine complex each semi-oxalate ion is surrounded by arginine molecules and the complex can be described as an inclusion compound. The oxalic acid complexes of basic amino acids exhibit a variety of ionization states and stoichiometry. They illustrate the effect of aggregation and chirality on ionization state and stoichiometry, and that of molecular properties on aggregation. The semi-oxalate/oxalate ions tend to be planar, but large departures from planarity are possible. The amino acid aggregation in the different oxalic acid complexes do not resemble one another significantly, but the aggregation of a particular amino acid in its oxalic acid complex tends to have similarities with its aggregation in other structures. Also, semi-oxalate ions aggregate into similar strings in four of the six oxalic acid complexes. Thus, the intrinsic aggregation propensities of individual molecules tend to be retained in the complexes.

Adenosine-5'-carboxylic Acid

The two molecules in the asymmetric unit of adenosine-5'-carboxylic acid, C10H11N5O5, exist as zwitterions with N1 protonated and the carboxyl groups ionized. Both molecules are in an anti conformation with glycosyl torsion angles of -161.4(3) and -155.5(3)degrees. The ribose moieties adopt a C3-endo-C2-exo twist conformation. The pseudo-rotation parameters are P = 0.01(1) and 6.58(1)degrees, and tau(m) = 36.2(2) and 34.6(2)degrees, for molecules A and B, respectively. The carboxyl groups of A and B are not in the standard g(+), g(-) or t conformations. Both Watson-Crick sites, N1 and N6, of the adenine bases are involved in a pair of hydrogen bonds with the dissociated carboxyl groups, forming a cyclic tetramer. The adenine base of molecule A stacks on the ribose O4' atom of a symmetry-related B molecule at a distance of 2.88 Angstrom; the adenine base of B stacks in an analogous way at a distance of 2.91 Angstrom.

Self-assembly of indole-2-carboxylic acid at graphite and gold surfaces

Model systems are critical to our understanding of self-assembly processes. As such, we have studied the surface self-assembly of a small and simple molecule, indole-2-carboxylic acid (I2CA). We combine density functional theory gas-phase (DFT) calculations with scanning tunneling microscopy to reveal details of I2CA assembly in two different solvents at the solution/solid interface, and on Au(111) in ultrahigh vacuum (UHV). In UHV and at the trichlorobenzene/highly oriented pyrolytic graphite (HOPG) interface, I2CA forms epitaxial lamellar structures based on cyclic OH⋯O carboxylic dimers. The structure formed at the heptanoic acid/HOPG interface is different and can be interpreted in a model where heptanoic acid molecules co-adsorb on the substrate with the I2CA, forming a bicomponent commensurate unit cell. DFT calculations of dimer energetics elucidate the basic building blocks of these structures, whereas calculations of periodic two-dimensional assemblies reveal the epitaxial effects introduced by the different substrates.

Two-dimensional self-assembly of a symmetry-reduced tricarboxylic acid

Investigations of the self-assembly of simple molecules at the solution/solid interface can provide useful insight into the general principles governing supramolecular chemistry in two dimensions. Here, we report on the assembly of 3,4′,5-biphenyl tricarboxylic acid (H3BHTC), a small hydrogen bonding unit related to the much-studied 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), which we investigate using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. STM images show that H3BHTC assembles by itself into an offset zigzag chain structure that maximizes the surface molecular density in favor of maximizing the number density of strong cyclic hydrogen bonds between the carboxylic groups. The offset geometry creates “sticky” pores that promote solvent coadsorption. Adding coronene to the molecular solution produces a transformation to a high-symmetry host–guest lattice stabilized by a dimeric/trimeric hydrogen bonding motif similar to the TMA flower structure. Finally, we show that the H3BHTC lattice firmly immobilizes the guest coronene molecules, allowing for high-resolution imaging of the coronene structure.

Measurement of Partition Coefficients of Substituted Benzoic Acids between Two Immiscible Solvents by Hyper-Rayleigh Scattering

We demonstrate that the hyper-Rayleigh scattering technique can be employed to measure the partition coefficient (k(p)) of a solute in a mixture of two immiscible solvents. Specifically, partition coefficients of six substituted benzoic acids in water/toluene (1:1 v/v) and water/chloroform (1:1 v/v) systems have been measured. Our values compare well with the k(p) values measured earlier by other techniques, The advantages offered by this technique are also discussed.

Ultrasonic Degradation of Poly(acrylic acid)

The ultrasonic degradation of poly(acrylic acid), a water-soluble polymer, was studied in the presence of persulfates at different temperatures in binary solvent Mixtures of methanol and water. The degraded samples were analyzed by gel permeation chromatography for the time evolution of the molecular weight distributions. A continuous distribution kinetics model based on midpoint chain scission was developed, and the degradation rate coefficients were determined. The decline in the rate of degradation of poly(acrylic acid) with increasing temperature and with an increment in the methanol content in the binary solvent mixture of methanol and water was attributed to the increased vapor pressure of the solutions. The experimental data showed an augmentation of the degradation rate of the polymer with increasing oxidizing agent (persulfate) concentrations. Different concentrations of three persulfates-potassium persulfate, ammonium persulfate, and sodium persulfate-were used. It was found that the ratio of the polymer degradation rate coefficient to the dissociation rate constant of the persulfate was constant. This implies that the ultrasonic degradation rate of poly(acrylic acid) can be determined a priori in the presence of any initiator.