Low-temperature polycrystalline silicon waveguides for low loss transmission in the near-to-mid-infrared region.

Low-temperature deposited polycrystalline silicon waveguides are emerging as a flexible platform that allows for dense optoelectronic integration. Here, the optical transmission properties of poly-silicon waveguides have been characterized from the near-to-mid-infrared wavelength regime, extending the optical transmission well beyond previous reports in the telecom band. The poly-Si waveguides with a dimension of 3 µm × âˆ¼0.6 µm have been produced from pre-patterned amorphous silicon waveguides that are post-processed through laser melting, reflowing, and crystallization using a highly localized laser induced heat treatment at a wavelength of 532 nm. Low optical transmission losses (<3 dB cm-1) have been observed at 1.55 µm as well as across the wavelength range of 2-2.25 µm, aided by the relatively large waveguide heights that are enabled by the deposition process. The results demonstrate the suitability of low-temperature poly-silicon waveguides to find wide ranging applications within integrated mid-infrared systems.

Computational studies to identify the common type-I and type-II inhibitors against the CDK8 enzyme.

In this study, multicomplex-based pharmacophore modeling was conducted on the structural proteome of the two states of CDK8 protein, that is, DMG-in and out. Three pharmacophores having six, five, and four features were selected as the representative models to conduct the virtual screening process using the prepared drug-like natural product database. The screened candidates were subjected to molecular docking studies on DMG-in (5XS2) and out (4F6U) conformation of the CDK8 protein. Subsequently, the common four docked candidates of 5XS2 and 4F6U were selected to perform the molecular dynamics simulation studies. Apart from one of the complexes of DMG-in (5XS2-UNPD163102), all other complexes displayed stable dynamic behavior. The interaction and stability studies of the docked complexes were compared with the references selected from the two conformations (DMG-in and out) of the protein. The current work leads to the identification of three common DMG-in and out hits with diverse scaffolds which can be employed as the initial leads for the design of the novel CDK8 inhibitors.

Noise in supercontinuum generated using PM and non-PM tellurite glass all-normal dispersion fibers.

Intensity fluctuations in supercontinuum generation are studied in polarization-maintaining (PM) and non-PM all-normal dispersion tellurite photonic crystal fibers. Dispersive Fourier transformation is used to resolve the shot-to-shot spectra generated using 225-fs pump pulses at 1.55 µm, with experimental results well reproduced by vector and scalar numerical simulations. By comparing the relative intensity noise for the PM and non-PM cases, supported by simulations, we demonstrate the advantage of the polarization-maintaining property of the PM fibers in preserving low-noise dynamics. We associate the low-noise in the PM case with the suppression of polarization modulation instability.

Cross-phase modulation instability in PM ANDi fiber-based supercontinuum generation.

We demonstrate broadband supercontinuum generation in an all-normal dispersion polarization-maintaining photonic crystal fiber and report the observation of a cross-phase modulation instability sideband generated outside of the supercontinuum bandwidth. We demonstrate that this sideband is polarized on the slow axis and can be suppressed by pumping on the fiber's fast axis. We theoretically confirm and model this nonlinear process using phase-matching conditions and numerical simulations, obtaining good agreement with the measured data.

Computational image analysis of the baseplate-tail complex of O1 ElTor vibriophage M4.

We performed an in-depth computational image analysis of the baseplate-tail complex of the M4 vibriophage and identified seven major densities in its baseplate, which notably share structural similarities with baseplate modules of a number of other bacteriophages belonging to different species. Employing computational analysis, we explained the helical organization of the sheath protein, wrapping the tail tube. Based on the results obtained in this work along with the proteomics information published previously, we are able to decipher the plausible roles assigned to the different components of the M4 baseplate during infection of the host.

Nested capillary anti-resonant silica fiber with mid-infrared transmission and low bending sensitivity at 4000 nm.

We report a silica glass nested capillary anti-resonant nodeless fiber with transmission and low bending sensitivity in the mid-infrared around 4000 nm. The fiber is characterized in terms of transmission over 1700-4200 nm wavelengths, revealing a mid-infrared 3500-4200 nm transmission window, clearly observable for a 12 m long fiber. Bending loss around 4000 nm is 0.5 dB/m measured over three full turns with 40 mm radius, going up to 5 dB/m for full turns with 15 mm radius. Our results provide experimental evidence of hollow-core silica fibers in which nested, anti-resonant capillaries provide high bend resistance in the mid-infrared. This is obtained for a fiber with a large core diameter of over 60 µm relative to around 30 µm capillaries in the cladding, which motivates its application in gas fiber lasers or fiber-based mid-infrared spectroscopy of COx or NxO analytes.

Nanoimprinting and tapering of chalcogenide photonic crystal fibers for cascaded supercontinuum generation.

Improved long-wavelength transmission and supercontinuum (SC) generation is demonstrated by antireflective (AR) nanoimprinting and tapering of chalcogenide photonic crystal fibers (PCFs). Using a SC source input spanning from 1 to 4.2 µm, the total transmission of a 15 µm core diameter PCF was improved from ∼53% to ∼74% by nanoimprinting of AR structures on both input and output facets of the fiber. Through a combined effect of reduced reflection and redshifting of the spectrum to 5 µm, the relative transmission of light >3.5 µm in the same fiber was increased by 60.2%. Further extension of the spectrum to 8 µm was achieved using tapered fibers. The spectral broadening dynamics and output power were investigated using different taper parameters and pulse repetition rates.

Correction to: Structural analysis and proteomics studies on the Myoviridae vibriophage M4.

Unfortunately, the original article was published with an incorrect figure. Figure 11 contains errors and needs to be withdrawn.

Structural analysis and proteomics studies on the Myoviridae vibriophage M4.

Bacteriophages play a crucial role in tracking the spread of bacterial epidemics. The frequent emergence of antibiotic-resistant bacterial strains throughout the world has motivated studies on bacteriophages that can potentially be used in phage therapy as an alternative to conventional antibiotic treatment. A recent outbreak of cholera in Haiti took many lives due to a rapid development of resistance to the available antibiotics. The properties of vibriophages, bacteriophages that infect Vibrio cholerae, are therefore of practical interest. A detailed understanding of the structure and assembly of a vibriophage is potentially useful in developing phage therapy against cholera as well as for fabricating artificial nanocontainers. Therefore, the aim of the present study was to determine the three-dimensional organization of vibriophage M4 at sub-nanometer resolution by electron microscopy and single-particle analysis techniques to facilitate its use as a therapeutic agent. We found that M4 has a large capsid with T = 13 icosahedral symmetry and a long contractile tail. This double-stranded DNA phage also contains a head-to-tail connector protein complex that joins the capsid to the tail and a prominent baseplate at the end of the tail. This study also provides information regarding the proteome of this phage, which is proteins similar to that of other Myoviridae phages, and most of the encoded proteins are structural proteins that form the exquisite architecture of this bacteriophage.

Preliminary Characterization of El Tor Vibriophage M4.

AIMS: The aim of the present study is the preliminary characterization of an El Tor vibriophage M4 (ATCC 51352-B4). METHODS: We studied the growth characteristics and sustainability of this phage under various stresses like temperature, pH, and UV. The phage morphology and phage genome were also examined using electron microscopy. RESULTS: Sustainability studies showed that the phage is more stable in acidic conditions, which is very uncommon among vibriophages. Studies also showed that M4 is a thermostable phage and it is inactivated by temperatures above 60°C but, like other phages, UV has a high inactivating effect on it. Morphological and genomic studies by electron microscopy showed that this phage has a long contractile tail and a big head. The genome is linear and about 120 kb in length. The genome also has a high packaging density as the value of Vm (the volume occupied per Da of biological macromolecule) is low for this phage. The phage-bacterial interaction was studied by negative staining as well as ultrathin sectioning methods. CONCLUSIONS: M4 belongs to the Myoviridae family and it is generally thermostable. It is prone to destruction by alkali and UV. It also has a large DNA which is densely packed inside of a big capsid.

The ß-prism lectin domain of Vibrio cholerae hemolysin promotes self-assembly of the ß-pore-forming toxin by a carbohydrate-independent mechanism.

Vibrio cholerae cytolysin/hemolysin (VCC) is an amphipathic 65-kDa ß-pore-forming toxin with a C-terminal ß-prism lectin domain. Because deletion or point mutation of the lectin domain seriously compromises hemolytic activity, it is thought that carbohydrate-dependent interactions play a critical role in membrane targeting of VCC. To delineate the contributions of the cytolysin and lectin domains in pore formation, we used wild-type VCC, 50-kDa VCC (VCC(50)) without the lectin domain, and mutant VCC(D617A) with no carbohydrate-binding activity. VCC and its two variants with no carbohydrate-binding activity moved to the erythrocyte stroma with apparent association constants on the order of 10(7) M(-1). However, loss of the lectin domain severely reduced the efficiency of self-association of the VCC monomer with the ß-barrel heptamer in the synthetic lipid bilayer from ∼83 to 27%. Notably, inactivation of the carbohydrate-binding activity by the D617A mutation marginally reduced oligomerization to ∼77%. Oligomerization of VCC(50) was temperature-insensitive; by contrast, VCC self-assembly increased with increasing temperature, suggesting that the process is driven by entropy and opposed by enthalpy. Asialofetuin, the ß1-galactosyl-terminated glycoprotein inhibitor of VCC-induced hemolysis, promoted oligomerization of 65-kDa VCC to a species that resembled the membrane-inserted heptamer in stoichiometry and morphology but had reduced global amphipathicity. In conclusion, we propose (i) that the ß-prism lectin domain facilitated toxin assembly by producing entropy during relocation in the heptamer and (ii) that glycoconjugates inhibited VCC by promoting its assembly to a water-soluble, less amphipathic oligomer variant with reduced ability to penetrate the bilayer.

An inducible and secreted eukaryote-like serine/threonine kinase of Salmonella enterica serovar Typhi promotes intracellular survival and pathogenesis.

Eukaryote-like serine/threonine kinases (eSTKs) constitute an important family of bacterial virulence factors. Genome analysis had predicted putative eSTKs in Salmonella enterica serovar Typhi, although their functional characterization and the elucidation of their role in pathogenesis are still awaited. We show here that the primary sequence and secondary structure of the t4519 locus of Salmonella Typhi Ty2 have all the signatures of eukaryotic superfamily kinases. t4519 encodes a ∼39-kDa protein (T4519), which shows serine/threonine kinase activities in vitro. Recombinant T4519 (rT4519) is autophosphorylated and phosphorylates the universal substrate myelin basic protein. Infection of macrophages results in decreased viability of the mutant (Ty2Δt4519) strain, which is reversed by gene complementation. Moreover, reactive oxygen species produced by the macrophages signal to the bacteria to induce T4519, which is translocated to the host cell cytoplasm. That T4519 may target a host substrate(s) is further supported by the activation of host cellular signaling pathways and the induction of cytokines/chemokines. Finally, the role of T4519 in the pathogenesis of Salmonella Typhi is underscored by the significantly decreased mortality of mice infected with the Ty2Δt4519 strain and the fact that the competitive index of this strain for causing systemic infection is 0.25% that of the wild-type strain. This study characterizes the first eSTK of Salmonella Typhi and demonstrates its role in promoting phagosomal survival of the bacteria within macrophages, which is a key determinant of pathogenesis. This, to the best of our knowledge, is the first study to describe the essential role of eSTKs in the in vivo pathogenesis of Salmonella spp.

Computational studies to explore inhibitors against the cyclin-dependent kinase 12/13 enzyme: an insilco pharmacophore modeling, molecular docking and dynamics approach.

Cancer is enlisted among the deadliest disease all over the world. The cyclin-dependent kinases 12 and 13 have been identified as cell cycle regulators. They conduct transcription and co-transcriptional processes by phosphorylating the C-terminal of RNA polymerase-II. Inhibition of CDK12 and 13 selectively presents a novel strategy to treat triple-negative breast cancer, but dual inhibitors are still lacking. Here, we report the screening of the natural product compound class against the dual CDK12/13 enzyme by employing various in silico methods. Complexes of CDK12 enzymes are used to form common feature pharmacophore models, whereas we perform receptor-based pharmacophore modelling on CDK13 enzyme owing to the availability of a single PDB. On conducting screening over the representative pharmacophores, the common drug-like screened natural products were shortlisted for conducting molecular docking studies. After molecular docking calculations, the candidates that showed crucial interaction with CDK12 and CDK13 enzymes were shortlisted for simulation studies. Five common docked candidates were selected for molecular dynamics simulations and free energy calculations. Based on the cut-off criteria of free energy calculations, one common hit was selected as the dual CDK12/13 inhibitor. The outcome concluded that the hit with ID CNP0386383 possesses drug-like properties, displays crucial interaction in the binding pocket, and shows stable dynamic behaviour and higher binding energy than the experimentally reported inhibitor of both CDK12 and CDK13 enzymes.Communicated by Ramaswamy H. Sarma.

Identifying natural product inhibitors against CDK9 enzyme via combined multicomplex-based pharmacophore modeling, interaction studies and molecular dynamics simulations.

In the current work, multicomplex-based pharmacophore modeling was performed on the CDK9 enzyme. The generated models possess five, four, and six features, which were subjected to the validation process. Among them, six feature models were selected as representative models to conduct the virtual screening process. The screened drug-like candidates were chosen to perform molecular docking to study their interaction patterns within the binding cavity of the CDK9 protein. Based on the docking score and presence of crucial interactions, out of 780 filtered candidates, only 205 were docked. These docked candidates were further accessed via HYDE assessment. Based on ligand efficiency and Hyde score, only nine candidates passed the criteria. The stability of these nine complexes, along with the reference, was studied by molecular dynamics simulations. Out of nine, only seven displayed stable behaviour during the simulations, and their stability was further assessed by molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA)-based free binding energy calculations and per residue contribution. From the present contribution, we obtained seven unique scaffolds that can be utilized as the starting lead for the development of CDK9 anticancer compounds.

Identification of natural products against enoyl-acyl-carrier-protein reductase in malaria via combined pharmacophore modeling, molecular docking and simulations studies.

Plasmodium falciparum is counted as one of the deadly species causing malaria. In that respect, enoyl acyl carrier protein reductase is recognized as one of the attractive druggable targets for the identification of antimalarials. Thus, from the structural proteome of ENR, common feature pharmacophores were constructed. To identify the representative models, all the hypotheses were subjected to validation methods, like, test set, enrichment factor, and Güner-Henry method, and the selected representative hypotheses were used to screen out the drug-like natural products. Further, the screened candidates were advanced to molecular docking calculations. Based on the docking score criteria and presence of essential interaction with Tyr277, seven candidates were shortlisted to conduct the HYDE and QSAR assessment. Further, the stability of these complexes was evaluated by employing molecular dynamics simulations, molecular mechanics-generalized born surface area approach-based free binding energy calculations with the residue-wise contribution of PfENR to the total binding free energy of the complex. On comparing the root mean square deviation, and fluctuation plots of the docked candidates with the reference, all the candidates displayed stable behavior, and the same outcome was depicted from the secondary structure element. However, from the free energy calculations, and residue-wise contribution conducted after dynamics, it was observed that out of seven, only five candidates sustain the binding with Tyr277 and cofactor of PfENR. Therefore, in the current work, the hybrid study of screening and stability lead to the identification of five structurally diverse candidates that can be employed for the design of novel antimalarials.Communicated by Ramaswamy H. Sarma.

Antibacterial activities of polyethylene glycol, tween 80 and sodium dodecyl sulphate coated silver nanoparticles in normal and multi-drug resistant bacteria.

Antibacterial activity of silver nanoparticles coated with different functionalizing agents i.e., polyethylene glycol, tween 80 and sodium dodecyl sulphate were evaluated on both normal and multi-drug resistant strains of bacteria. Under the same reaction conditions, these functionalizing agents were added separately to coat silver nanoparticles. Among these, polyethylene glycol coated nanoparticles were most effective in killing all the bacterial strains which includes Escherichia coli DH5a, Bacillus subtilis, Micrococcus luteus, Staphylococcus aureus and multi-drug resistant clinical isolates of Shigella spp. (flexneri, boydii, sohnea) and Vibrio cholerae. The minimum inhibitory concentration of polyethylene glycol coated silver nanoparticles was also less compared to the other two sets of nanoparticles. Consistence with that polyethylene glycol coated nanoparticles produced more intracellular reactive oxygen species in bacteria. Moreover, when human cell lines MCF7 and Chang Liver were incubated in presence of these nanoparticles for 18 h with same concentrations as used for bacteria, no toxicity was observed. But significant increase in cell killing was observed with longer incubation time. Thus our present investigation implicates the potential therapeutic use of silver nanoparticles as antibacterial agent particularly the polyethylene glycol coated one.

Antioxidant and metabolic impairment result in DNA damage in arsenic-exposed individuals with severe dermatological manifestations in Eastern India.

Arsenic is an environmental toxicant, free-radical generator, carcinogenic agent, and aging promoter. Recently, blood samples were analyzed from individuals (control- male 12, female 13; arsenic-exposed- male 16, female 14; and exposed to ≥100 µg/L As, ≥10 y) with dermatological symptoms in few affected villages in Eastern India to unravel their hematopoietic, metabolic, and antioxidant profiles. White blood cells recovered from buffy coat were used for DNA fragmentation test. Present observation suggests that significant number of individuals developed pigmentation and palmoplantar hyperkeratosis with black-brownish patch on their body and many of those developed carcinomas. Hematopoietic data show a significant increase in eosinophil and decrease in monocyte count in either sex. Though insignificant, an increase in neutrophil in female and lymphocyte count in male arsenic-exposed individuals are supported by the earlier report on sex dimorphic immune sensitization. Significant increase in serum alanine transaminase in both sexes and bilirubin only in male suggests the eventuality of hepatic disintegration. Arsenic exposure significantly decreased serum amylase in female. A significant decrease in antioxidant components like catalase, soluble thiol, and recently recognized uric acid worsened the situation by generating free radicals as observed in significant rise in malondialdehyde level, which finally increased DNA fragmentation and arsenic-associated mutagenesis and carcinogenesis. This could attribute to lowering in immune competence and related necrotic and/or apoptotic manifestations.

Structure of vibriophage D10 tail sheath revealed by electron microscopy and computational image processing.

Vibriophage D10, a member of the Vibrio cholerae O-1El-Tor phage typing scheme, is used to detect the spread of the cholera epidemic and belongs to the Myoviridae family. The outer sheath of the tail of vibriophage is highly contractile in nature. We have used electron microscopy and computational image-processing techniques to determine the structure of this contractile tail sheath. The three-dimensional density map of the tail sheath reveals the presence of ∼35 Å long and ∼25 Å wide protrusions, extending out of the tail structure. The electron micrographs revealed that the tail sheaths of a considerable number of D10 phage particles undergo axial compression up to 51% at almost neutral pH (7.2) and at room temperature (20°). We find that the genome of the phage particles is ejected out when the tail sheath of the phage particles are deliberately made to contract by subjecting them to a surrounding environment of pH 10.5. We infer that the contraction of the tail sheath is responsible for the loss of the phage genome even at neutral pH and room temperature. This may be a plausible reason for the unusual behavior of rapid decline of the phage within a span of 48-72 h of its preparation.

The role of C-terminus carbohydrate-binding domain of Vibrio cholerae haemolysin/cytolysin in the conversion of the pre-pore ß-barrel oligomer to a functional diffusion channel.

BACKGROUND & OBJECTIVES: Vibrio cholerae cytolysin/hemolysin (VCC) is a 65 kDa pore-forming toxin (PFT) secreted by O1 El Tor and non-O1 strains. The purified toxin, which contains two C-terminus carbohydrate-binding domains in addition to the cytolytic domain at the core, causes lysis of a wide spectrum of eukaryotic cells at picomolar concentrations, apoptogenesis of intestinal and immune cells and accumulation of fluid in rabbit ligated ileal loop. Therefore, it may potentially complement the action of cholera toxin (CT) in diarrheagenic strains that do not produce CT. We showed earlier that ß1-galactosyl-terminated glycoconjugates are strong inhibitors of its pore-forming activity, though carbohydrates are not functional receptors of VCC. Here, we investigate how the 15 kDa C-terminus ß-prism lectin domain contributed to pore formation in erthrocytes. METHODS: VCC was isolated from the culture supernatant of late log phase grown bacteria and purified to homogeneity by chromatography. The 50 kDa truncated variant was generated by restricted proteolysis. Liposome was prepared by sonication of a suspension of phospholipids and calceine release assay was done by spectrofluorometric monitoring of the released dye trapped in liposome. Formation of ß-barrel oligomers in erythrocyte stroma was monitored by scanning electron microscopy. RESULTS: Proteolytic truncation of the C-terminus ß-prism lectin domain decreased hemolytic activity of the toxin by ~800-fold without causing a significant change in pore-forming activity toward synthetic lipid vesicles devoid of incorporated glycoproteins/glycolipids. Truncation at the C-terminus did not impair membrane-binding or assembly to the oligomeric pore. INTERPRETATION & CONCLUSIONS: Our data indicated that the C-terminus domain played a critical role in translocation of the pre-pore oligomeric assembly from the cell surface or lipid-water interface to the hydrocarbon core of the membrane bilayer, signaling the formation of functional diffusion channels.

Three-dimensional structure of different functional forms of the Vibrio cholerae hemolysin oligomer: a cryo-electron microscopic study.

Vibrio cholerae hemolysin (HlyA) is a 65-kDa water-soluble pore-forming toxin that causes lysis of eukaryotic cells by destroying selective permeability of the plasma membrane bilayer. The HlyA monomer self-assembles on the target cell surface to the more stable beta-barrel amphipathic heptamer, which inserts into the membrane bilayer to form a diffusion channel. Deletion of the 15-kDa beta-prism lectin domain at the C terminus generates a 50-kDa hemolysin variant (HlyA50) with an approximately 1,000-fold decrease in hemolytic activity. Because functional differences are eventually dictated by structural differences, we determined three-dimensional structures of 65- and 50-kDa HlyA oligomers, using cryo-electron microscopy and single-particle methods. Our study clearly shows that the HlyA oligomer has sevenfold symmetry but that the HlyA50 oligomer is an asymmetric molecule. The HlyA oligomer has bowl-like, arm-like, and ring-like domains. The bowl-like domain is coupled with the ring-like domain, and seven side openings are present just beneath the ring-like domain. Although a central channel is present in both HlyA and HlyA50 oligomers, they differ in pore size as well as in shape of the molecules and channel. These structural differences may be relevant to the striking difference in efficiencies of functional channel formation by the two toxin forms.