Novel Functions of (p)ppGpp and Cyclic di-GMP in Mycobacterial Physiology Revealed by Phenotype Microarray Analysis of Wild-Type and Isogenic Strains of Mycobacterium smegmatis

The bacterial second messengers (p)ppGpp and bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulate important functions, such as transcription, virulence, biofilm formation, and quorum sensing. In mycobacteria, they regulate long-term survival during starvation, pathogenicity, and dormancy. Recently, a Pseudomonas aeruginosa strain lacking (p) ppGpp was shown to be sensitive to multiple classes of antibiotics and defective in biofilm formation. We were interested to find out whether Mycobacterium smegmatis strains lacking the gene for either (p)ppGpp synthesis (Delta rel(Msm)) or c-di-GMP synthesis (Delta dcpA) would display similar phenotypes. We used phenotype microarray technology to compare the growth of the wild-type and the knockout strains in the presence of several antibiotics. Surprisingly, the Delta rel(Msm) and Delta dcpA strains showed enhanced survival in the presence of many antibiotics, but they were defective in biofilm formation. These strains also displayed altered surface properties, like impaired sliding motility, rough colony morphology, and increased aggregation in liquid cultures. Biofilm formation and surface properties are associated with the presence of glycopeptidolipids (GPLs) in the cell walls of M. smegmatis. Thin-layer chromatography analysis of various cell wall fractions revealed that the levels of GPLs and polar lipids were reduced in the knockout strains. As a result, the cell walls of the knockout strains were significantly more hydrophobic than those of the wild type and the complemented strains. We hypothesize that reduced levels of GPLs and polar lipids may contribute to the antibiotic resistance shown by the knockout strains. Altogether, our data suggest that (p)ppGpp and c-di-GMP may be involved in the metabolism of glycopeptidolipids and polar lipids in M. smegmatis.

B-Spline potential function for maximum a-posteriori image reconstruction in fluorescence microscopy

An iterative image reconstruction technique employing B-Spline potential function in a Bayesian framework is proposed for fluorescence microscopy images. B-splines are piecewise polynomials with smooth transition, compact support and are the shortest polynomial splines. Incorporation of the B-spline potential function in the maximum-a-posteriori reconstruction technique resulted in improved contrast, enhanced resolution and substantial background reduction. The proposed technique is validated on simulated data as well as on the images acquired from fluorescence microscopes (widefield, confocal laser scanning fluorescence and super-resolution 4Pi microscopy). A comparative study of the proposed technique with the state-of-art maximum likelihood (ML) and maximum-a-posteriori (MAP) with quadratic potential function shows its superiority over the others. B-Spline MAP technique can find applications in several imaging modalities of fluorescence microscopy like selective plane illumination microscopy, localization microscopy and STED. (C) 2015 Author(s).

Observation of coherent population trapping in a V-type two-electron system

We observe coherent population trapping (CPT) in a two-electron atom-Yb-174-using the S-1(0), F= 0 -> P-3(1), F `= 1 transition. CPT is not possible for such a transition according to one-electron theory because the magnetic sublevels form a V-type system, but in a two-electron atom like Yb, the interaction of the electrons transforms the level structure into a V-type system, which allows the formation of a dark state and hence the observation of CPT. Since the two levels involved are degenerate, we use a magnetic field to lift the degeneracy. The single fluorescence dip then splits into five dips-the central unshifted one corresponds to coherent population oscillation, while the outer four are due to CPT. The linewidth of the CPT resonance is about 300 kHz and is limited by the natural linewidth of the excited state, which is to be expected because the excited state is involved in the formation of the dark state.

Nanocomposite Made of an Oligo(p-phenylenevinylene)-Based Trihybrid Thixotropic Metallo(organo)gel Comprising Nanoscale Metal-Organic Particles, Carbon Nanohorns, and Silver Nanoparticles

A silver ion (Ag+)-triggered thixotropic metallo(organo)gel of p-pyridyl-appended oligo(p-phenylenevinylene) derivatives (OPVs) is reported for the first time. Solubilization of single-walled carbon nanohorns (SWCNHs) in solutions of the pure OPVs as well as in the metallogels mediated by pi-pi interactions has also been achieved. In situ fabrication of silver nanoparticles (AgNPs) in the SWCNH-doped dihybrid gel leads to the formation of a trihybrid metallogel. The mechanical strength of the metallogels could be increased step- wise in the order: freshly prepared gel pic studies of the trihybrid gel indicate the formation of three distinct morphologies, that is, nanoscale metal organic particles (NMOPs), flowerlike aggregates of SWCNHs and AgNPs, and also their integration with each other. Detailed studies suggest lamellar organizations of the linear metal ligand complexes in the NMOPs, which upon association create a three-dimensional network that eventually immobilizes the solvent molecules.

Self-Assembled Discrete Molecules for Sensing Nitroaromatics

Efficient sensing of trace amount nitroaromatic (NAC) explosives has become a major research focus in recent time due to concerns over national security as well as their role as environment pollutants. NO2-containing electron-deficient aromatic compounds, such as picric acid (PA), trinitrotoluene (TNT), and dinitrotoluene (DNT), are the common constituents of many commercially available chemical explosives. In this article, we have summarized our recent developments on the rational design of electron-rich self-assembled discrete molecular sensors and their efficacy in sensing nitroaromatics both in solution as well as in vapor phase. Several p-electron-rich fluorescent metallacycles (squares, rectangles, and tweezers/pincers) and metallacages (trigonal and tetragonal prisms) have been synthesized by means of metal-ligand coordination-bonding interactions, with enough internal space to accommodate electron-deficient nitroaromatics at the molecular level by multiple supramolecular interactions. Such interactions subsequently result in the detectable fluorescence quenching of sensors even in the presence of trace quantities of nitroaromatics. The fascinating sensing characteristics of molecular architectures discussed in this article may enable future development of improved sensors for nitroaromatic explosives.

Panchromatic Borane-aza-BODIPY Conjugate: Synthesis, Intriguing Optical Properties, and Selective Fluorescent Sensing of Fluoride Anions

A new triarylborane-aza-BODIPY conjugate is reported. The compound consists of two blue emissive dimesitylarylborane moieties and a near-infrared (NIR) emissive aza-BOIDPY core and shows panchromatic absorption spanning approximately 300-800 nm. DFT computational studies suggest limited electronic communication between the individual fluorophore units. Hence, the partial energy transfer from blue fluorophore triarylborane to NIR chromophore aza-BODIPY unit leads to a broad dual-emissive feature covering a large part of visible and NIR region. Furthermore, the broadband emissive compound can act as a selective sensor for fluoride anion as a result of fluorescence quenching response in both visible and NIR spectral regions.

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.

Polyfunctional Lewis Acids: Intriguing Solid-State Structure and Selective Detection and Discrimination of Nitroaromatic Explosives

Synthesis and crystal structures of three porphyrin-based polyfunctional Lewis acids 1-3 are reported. Intermolecular HgClHgCl (linear and -type) interactions in the solid state of the peripherally ArHgCl-decorated compound 3 lead to a fascinating 3D supramolecular architecture. Compound3 shows a selective fluorescence quenching response to picric acid and discriminates other nitroaromatic-based explosives. For the first time, an electron-deficient polyfunctional Lewis acid is shown to be useful for the selective detection and discrimination of nitroaromatic explosives. The Stern-Volmer quenching constant and detection limits of compound3 for picric acid are the best among the reported small-molecular receptors for nitroaromatic explosives. The electronic structure, Lewis acidity, and selective sensing characteristics of 3 are well corroborated by DFT calculations.

The X-C---Y (X = O/F, Y = O, S, F, Cl, Br, N, P,) Carbon bond and hydrophobic interactions

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C···Y interaction, which could be called 'carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the 'hydrophobic interactions'.

A Variant of the Hadwiger-Debrunner (p, q)-Problem in the Plane

Let X be a convex curve in the plane (say, the unit circle), and let be a family of planar convex bodies such that every two of them meet at a point of X. Then has a transversal of size at most . Suppose instead that only satisfies the following ``(p, 2)-condition'': Among every p elements of , there are two that meet at a common point of X. Then has a transversal of size . For comparison, the best known bound for the Hadwiger-Debrunner (p, q)-problem in the plane, with , is . Our result generalizes appropriately for if is, for example, the moment curve.

Directional bilateral filters for smoothing fluorescence microscopy images

Images obtained through fluorescence microscopy at low numerical aperture (NA) are noisy and have poor resolution. Images of specimens such as F-actin filaments obtained using confocal or widefield fluorescence microscopes contain directional information and it is important that an image smoothing or filtering technique preserve the directionality. F-actin filaments are widely studied in pathology because the abnormalities in actin dynamics play a key role in diagnosis of cancer, cardiac diseases, vascular diseases, myofibrillar myopathies, neurological disorders, etc. We develop the directional bilateral filter as a means of filtering out the noise in the image without significantly altering the directionality of the F-actin filaments. The bilateral filter is anisotropic to start with, but we add an additional degree of anisotropy by employing an oriented domain kernel for smoothing. The orientation is locally adapted using a structure tensor and the parameters of the bilateral filter are optimized for within the framework of statistical risk minimization. We show that the directional bilateral filter has better denoising performance than the traditional Gaussian bilateral filter and other denoising techniques such as SURE-LET, non-local means, and guided image filtering at various noise levels in terms of peak signal-to-noise ratio (PSNR). We also show quantitative improvements in low NA images of F-actin filaments. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

An Alternating l(p) - l(2) Projections Algorithm (ALPA) for Speech Modeling using Sparsity Constraints

We address the problem of separating a speech signal into its excitation and vocal-tract filter components, which falls within the framework of blind deconvolution. Typically, the excitation in case of voiced speech is assumed to be sparse and the vocal-tract filter stable. We develop an alternating l(p) - l(2) projections algorithm (ALPA) to perform deconvolution taking into account these constraints. The algorithm is iterative, and alternates between two solution spaces. The initialization is based on the standard linear prediction decomposition of a speech signal into an autoregressive filter and prediction residue. In every iteration, a sparse excitation is estimated by optimizing an l(p)-norm-based cost and the vocal-tract filter is derived as a solution to a standard least-squares minimization problem. We validate the algorithm on voiced segments of natural speech signals and show applications to epoch estimation. We also present comparisons with state-of-the-art techniques and show that ALPA gives a sparser impulse-like excitation, where the impulses directly denote the epochs or instants of significant excitation.

QUANTITATIVE OH PLANAR LASER INDUCED FLUORESCENCE DIAGNOSTICS OF SYNGAS AND METHANE COMBUSTION IN A CAVITY COMBUSTOR

The current work reports quantitative OH species concentration in the cavity of a trapped vortex combustor (TVC) in the context of mixing and flame stabilization studies using both syngas and methane fuels. Planar laser induced fluorescence (PLIF) measurements of OH radical obtained using a Nd: YAG pumped dye laser are quantified using a flat flame McKenna burner. The momentum flux ratio (MFR), defined as the ratio of the cavity fuel jet momentum to that of the guide vane air stream, is observed to be a key governing parameter. At high MFRs similar to 4.5, the flame front is observed to form at the interface of the fuel jet and the air jet stream. This is substantiated by velocity vector field measurements. For syngas, as the MFR is lowered to similar to 0.3, the fuel-air mixing increases and a flame front is formed at the bottom and downstream edge of the cavity where a stratified charge is present. This trend is observed for different velocities at similar equivalence ratios. In case of methane combustion in the cavity, where the MFRs employed are extremely low at similar to 0.01, a different mechanism is observed. A fuel-rich mixture is now observed at the center of the cavity and this mixture undergoes combustion. On further increase of the cavity equivalence ratio, the rich mixture exceeds the flammability limit and forms a thin reaction zone at the interface with air stream. As a consequence, a shear layer flame at the top of the cavity interface with the mainstream is also observed. The equivalence ratio in the cavity also determines the combustion characteristics in the case of fuel-air mixtures that are formed as a result of the mixing. Overall, flame stabilization mechanisms have been proposed, which account for the wide range of MFRs and premixing in the mainstream as well.

Unconjugated Bilirubin exerts Pro-Apoptotic Effect on Platelets via p38-MAPK activation

Thrombocytopenia is one of the most frequently observed secondary complications in many pathological conditions including liver diseases, where hyperbilirubinemia is very common. The present study sought to find the cause of thrombocytopenia in unconjugated hyperbilirubinemic conditions. Unconjugated bilirubin (UCB), an end-product of heme catabolism, is known to have pro-oxidative and cytotoxic effects at high serum concentration. We investigated the molecular mechanism underlying the pro-apoptotic effect of UCB on human platelets in vitro, and followed it up with studies in phenylhydrazine-induced hyperbilirubinemic rat model and hyperbilirubinemic human subjects. UCB is indeed found to significantly induce platelet apoptotic events including elevated endogenous reactive oxygen species generation, mitochondrial membrane depolarization, increased intracellular calcium levels, cardiolipin peroxidation and phosphatidylserine externalization (p < 0.001) as evident by FACS analysis. The immunoblots show the elevated levels of cytosolic cytochrome c and caspase activation in UCB-treated platelets. Further, UCB is found to induce mitochondrial ROS generation leading to p38 activation, followed by downstream activation of p53, ultimately resulting in altered expression of Bcl-2 and Bax proteins as evident from immunoblotting. All these parameters conclude that elevated unconjugated bilirubin causes thrombocytopenia by stimulating platelet apoptosis via mitochondrial ROS-induced p38 and p53 activation.