Covalent assembly-disassembly of poly(ether imine) dendritic macromolecular monomers and megamers

Poly(ether imine) dendritic macromolecules were undertaken to study the reversible dendrimer monomer-megamer assembly-disassembly in aqueous solutions. Synthesis of thiol functionalized poly(ether imine) (PETIM) dendrimers and their covalent aggregation behavior in the aqueous solution of ethanol/water (2:1) is demonstrated. The dendritic megamers were characterized using microscopic techniques. Kinetics of the aggregation behavior was followed using turbidity measurements, light-scattering and atomic force microscopic techniques. Inherent luminescence behavior of PETIM dendrimer monomers was retained in the dendrimer megamers also, which allowed visualization of the megamers through confocal microscopy. Extent of thiol functionalities that remained after the megamer assembly was estimated through Ellman's assay. Subsequent to megamer assembly, disassembly of megamers to dendrimer monomers was conducted, using dithiothreitol reagent. Water-insoluble sudan I dye was encapsulated in dendrimer megamer and subsequent release profile was assessed during the disassembly in aqueous solutions. The studies were conducted using first, second and third generations, representing 4, 8 and 16 sulfhydryl groups at their peripheries of dendrimers, respectively. (C) 2014 Elsevier Ltd. All rights reserved.

Cytotoxicity of TiO2 nanoparticles towards freshwater sediment microorganisms at low exposure concentrations

There is a persistent need to assess the effects of TiO2 nanoparticles on the aquatic ecosystem owing to their increasing usage in consumer products and risk of environmental release. The current study is focused on TiO2 nanoparticle-induced acute toxicity at sub-ppm level (<= 1 ppm) on the three different freshwater sediment bacterial isolates and their consortium under two different irradiation (visible light and dark) conditions. The consortium of the bacterial isolates was found to be less affected by the exposure to the nanoparticles compared to the individual cells. The oxidative stress contributed considerably towards the cytotoxicity under both light and dark conditions. A statistically significant increase in membrane permeability was noted under the dark conditions as compared to the light conditions. The optical and fluorescence microscopic images showed aggregation and chain formation of the bacterial cells, when exposed to the nanoparticles. The electron microscopic (SEM, TEM) observations suggested considerable damage of cells and bio-uptake of nanoparticles. The exopolysaccrides (EPS) production and biofilm formation were noted to increase in the presence of the nanoparticles, and expression of the key genes involved in biofilm formation was studied by RT-PCR. (C) 2014 Elsevier Inc. All rights reserved.

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

Rich data bearing on the structural and evolutionary principles of protein protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial `driver' mutations in oncogenesis. They also provide the foundation toward the design of protein protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. (C) 2014 Elsevier Ltd. All rights reserved.

Agglomeration front dynamics: Drying in sessile nano-particle laden droplets

The drying of sessile, nano-silica laden water droplet is studied under ambient conditions, in the absence of any convection. The drying process can be divided into two distinct regimes. During regime 1, the outer edge of the droplet remains pinned and particles agglomerate at the droplet periphery similar to the traditional coffee ring. However in regime 2, with further evaporation, both the liquid contact line and the agglomeration front starts moving radially inwards from the initial contact edge. The contact between the liquid and the agglomerate is maintained throughout regime 2 and the vaporisation driven liquid edge recession essentially drives the inward growth of the particle deposition. Fast kinetics of particle aggregation results in rapid growth of this agglomeration front as seen from the experiments. A theoretical formulation involving a simplistic model of the agglomeration front growth based on particle mass balance has been proposed. (C) 2014 Elsevier Ltd. All rights reserved,

Multispectral Bayesian reconstruction technique for real-time two color fluorescence microscopy

We have developed a real-time imaging method for two-color wide-field fluorescence microscopy using a combined approach that integrates multi-spectral imaging and Bayesian image reconstruction technique. To enable simultaneous observation of two dyes (primary and secondary), we exploit their spectral properties that allow parallel recording in both the channels. The key advantage of this technique is the use of a single wavelength of light to excite both the primary dye and the secondary dye. The primary and secondary dyes respectively give rise to fluorescence and bleed-through signal, which after normalization were merged to obtain two-color 3D images. To realize real-time imaging, we employed maximum likelihood (ML) and maximum a posteriori (MAP) techniques on a high-performance computing platform (GPU). The results show two-fold improvement in contrast while the signal-to-background ratio (SBR) is improved by a factor of 4. We report a speed boost of 52 and 350 for 2D and 3D images respectively. Using this system, we have studied the real-time protein aggregation in yeast cells and HeLa cells that exhibits dot-like protein distribution. The proposed technique has the ability to temporally resolve rapidly occurring biological events.

GHG footprint of major cities in India

Concentration of greenhouse gases (GHG) in the atmosphere has been increasing rapidly during the last century due to ever increasing anthropogenic activities resulting in significant increases in the temperature of the Earth causing global warming. Major sources of GHG are forests (due to human induced land cover changes leading to deforestation), power generation (burning of fossil fuels), transportation (burning fossil fuel), agriculture (livestock, farming, rice cultivation and burning of crop residues), water bodies (wetlands), industry and urban activities (building, construction, transport, solid and liquid waste). Aggregation of GHG (CO2 and non-CO2 gases), in terms of Carbon dioxide equivalent (CO(2)e), indicate the GHG footprint. GHG footprint is thus a measure of the impact of human activities on the environment in terms of the amount of greenhouse gases produced. This study focuses on accounting of the amount of three important greenhouses gases namely carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) and thereby developing GHG footprint of the major cities in India. National GHG inventories have been used for quantification of sector-wise greenhouse gas emissions. Country specific emission factors are used where all the emission factors are available. Default emission factors from IPCC guidelines are used when there are no country specific emission factors. Emission of each greenhouse gas is estimated by multiplying fuel consumption by the corresponding emission factor. The current study estimates GHG footprint or GHG emissions (in terms of CO2 equivalent) for Indian major cities and explores the linkages with the population and GDP. GHG footprint (Aggregation of Carbon dioxide equivalent emissions of GHG's) of Delhi, Greater Mumbai, Kolkata, Chennai, Greater Bangalore, Hyderabad and Ahmedabad are found to be 38,633.2 Gg, 22,783.08 Gg, 14,812.10 Gg, 22,090.55 Gg, 19,796.5 Gg, 13,734.59 Gg and 91,24.45 Gg CO2 eq., respectively. The major contributors sectors are transportation sector (contributing 32%, 17.4%, 13.3%, 19.5%, 43.5%, 56.86% and 25%), domestic sector (contributing 30.26%, 37.2%, 42.78%, 39%, 21.6%, 17.05% and 27.9%) and industrial sector (contributing 7.9%, 7.9%, 17.66%, 20.25%, 1231%, 11.38% and 22.41%) of the total emissions in Delhi, Greater Mumbai, Kolkata, Chennai, Greater Bangalore, Hyderabad and Ahmedabad, respectively. Chennai emits 4.79 t of CO2 equivalent emissions per capita, the highest among all the cities followed by Kolkata which emits 3.29 t of CO2 equivalent emissions per capita. Also Chennai emits the highest CO2 equivalent emissions per GDP (2.55 t CO2 eq./Lakh Rs.) followed by Greater Bangalore which emits 2.18 t CO2 eq./Lakh Rs. (C) 2015 Elsevier Ltd. All rights reserved.

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.

Characterization of rice small heat shock proteins targeted to different cellular organelles

Small heat shock proteins (sHSPs) are a family of ATP-independent molecular chaperones which prevent cellular protein aggregation by binding to misfolded proteins. sHSPs form large oligomers that undergo drastic rearrangement/dissociation in order to execute their chaperone activity in protecting substrates from stress. Substrate-binding sites on sHSPs have been predominantly mapped on their intrinsically disordered N-terminal arms. This region is highly variable in sequence and length across species, and has been implicated in both oligomer formation and in mediating chaperone activity. Here, we present our results on the functional and structural characterization of five sHSPs in rice, each differing in their subcellular localisation, viz., cytoplasm, nucleus, chloroplast, mitochondria and peroxisome. We performed activity assays and dynamic light scattering studies to highlight differences in the chaperone activity and quaternary assembly of sHSPs targeted to various organelles. By cloning constructs that differ in the length and sequence of the tag in the N-terminal region, we have probed the sensitivity of sHSP oligomer assembly and chaperone activity to the length and amino acid composition of the N-terminus. In particular, we have shown that the incorporation of an N-terminal tag has significant consequences on sHSP quaternary structure.

Energy Sharing for Multiple Sensor Nodes With Finite Buffers

We consider the problem of finding optimal energy sharing policies that maximize the network performance of a system comprising of multiple sensor nodes and a single energy harvesting (EH) source. Sensor nodes periodically sense the random field and generate data, which is stored in the corresponding data queues. The EH source harnesses energy from ambient energy sources and the generated energy is stored in an energy buffer. Sensor nodes receive energy for data transmission from the EH source. The EH source has to efficiently share the stored energy among the nodes to minimize the long-run average delay in data transmission. We formulate the problem of energy sharing between the nodes in the framework of average cost infinite-horizon Markov decision processes (MDPs). We develop efficient energy sharing algorithms, namely Q-learning algorithm with exploration mechanisms based on the epsilon-greedy method as well as upper confidence bound (UCB). We extend these algorithms by incorporating state and action space aggregation to tackle state-action space explosion in the MDP. We also develop a cross entropy based method that incorporates policy parameterization to find near optimal energy sharing policies. Through simulations, we show that our algorithms yield energy sharing policies that outperform the heuristic greedy method.

Oriented nanometric aggregates of partially inverted zinc ferrite: One-step processing and tunable high-frequency magnetic properties

In this work, it is demonstrated that the in situ growth of oriented nanometric aggregates of partially inverted zinc ferrite can potentially pave a way to alter and tune magnetocrystalline anisotropy that, in turn, dictates ferromagnetic resonance frequency (f(FMR)) by inducing strain due to aggregation. Furthermore, the influence of interparticle interaction on magnetic properties of the aggregates is investigated. Mono-dispersed zinc ferrite nanoparticles (<5 nm) with various degrees of aggregation were prepared through decomposition of metal-organic compounds of zinc (II) and iron (III) in an alcoholic solution under controlled microwave irradiation, below 200 degrees C. The nanocrystallites were found to possess high degree of inversion (>0.5). With increasing order of aggregation in the samples, saturation magnetization (at 5 K) is found to decrease from 38 emu/g to 24 emu/g, while coercivity is found to increase gradually by up to 100% (525 Oe to 1040 Oe). Anisotropy-mediated shift of f(FMR) has also been measured and discussed. In essence, the result exhibits an easy way to control the magnetic characteristics of nanocrystalline zinc ferrite, boosted with significant degree of inversion, at GHz frequencies. (C) 2015 AIP Publishing LLC.

Developing acetylcholinesterase-based inhibition assay by modulated synthesis of silver nanoparticles: applications for sensing of organophosphorus pesticides

A novel and highly sensitive sensing strategy for the detection of organophosphorus compounds (OPs) based on the catalytic reaction of acetylcholinesterase (AChE) and acetylcholine (ATCh) during the modulated synthesis of silver nanoparticles (AgNPs) has been developed. The enzymatic hydrolysis of ATCh by AChE yields thiocholine (TCh), which induces the aggregation of AgNPs during synthesis, and the absorption peak at 382 nm corresponding to AgNPs decreases. The enzymatic reaction can be regulated by OPs, which can covalently bind to the active site of AChE and decrease the TCh formation, thereby decreasing the aggregation and significantly enhancing the absorption peak at 382 nm. The proposed system achieved good linearity and limits of detection of 0.078 nM and 2.402 nM for trichlorfon and malathion, respectively, by UV-visible spectroscopy. Further, the sensitivity of the proposed system was demonstrated through the determination of OPs in different spiked real samples. The described work shows the potential application for further development of a colorimetric sensor for other OP pesticide detection during the synthesis of AgNPs using enzyme-based assays.

Mapping Key Residues of ISD11 Critical for NFS1-ISD11 Subcomplex Stability IMPLICATIONS IN THE DEVELOPMENT OF MITOCHONDRIAL DISORDER, COXPD19

Biogenesis of the iron-sulfur (Fe-S) cluster is an indispensable process in living cells. In mammalian mitochondria, the initial step of the Fe-S cluster assembly process is assisted by the NFS1-ISD11 complex, which delivers sulfur to scaffold protein ISCU during Fe-S cluster synthesis. Although ISD11 is an essential protein, its cellular role in Fe-S cluster biogenesis is still not defined. Our study maps the important ISD11 amino acid residues belonging to putative helix 1 (Phe-40), helix 3 (Leu-63, Arg-68, Gln-69, Ile-72, Tyr-76), and C-terminal segment (Leu-81, Glu-84) are critical for in vivo Fe-S cluster biogenesis. Importantly, mutation of these conserved ISD11 residues into alanine leads to its compromised interaction with NFS1, resulting in reduced stability and enhanced aggregation of NFS1 in the mitochondria. Due to altered interaction with ISD11 mutants, the levels of NFS1 and Isu1 were significantly depleted, which affects Fe-S cluster biosynthesis, leading to reduced electron transport chain complex (ETC) activity and mitochondrial respiration. In humans, a clinically relevant ISD11 mutation (R68L) has been associated in the development of a mitochondrial genetic disorder, COXPD19. Our findings highlight that the ISD11 R68A/R68L mutation display reduced affinity to form a stable subcomplex with NFS1, and thereby fails to prevent NFS1 aggregation resulting in impairment of the Fe-S cluster biogenesis. The prime affected machinery is the ETC complex, which showed compromised redox properties, causing diminished mitochondrial respiration. Furthermore, the R68L ISD11 mutant displayed accumulation of mitochondrial iron and reactive oxygen species, leading to mitochondrial dysfunction, which correlates with the phenotype observed in COXPD19 patients.

Infiltration of Matrix-Non-producers Weakens the Salmonella Biofilm and Impairs Its Antimicrobial Tolerance and Pathogenicity

Bacterial biofilms display a collective lifestyle, wherein the cells secrete extracellular polymeric substances (EPS) that helps in adhesion, aggregation, stability, and to protect the bacteria from antimicrobials. We asked whether the BPS could act as a public good for the biofilm and observed that infiltration of cells that do not produce matrix components weakened the biofilm of Salmonella enterica serovar Typhimurium. PS production was costly for the producing cells, as indicated by a significant reduction in the fitness of wild type (WT) cells during competitive planktonic growth relative to the non-producers. Infiltration frequency of non-producers in the biofilm showed a concomitant decrease in overall productivity. It was apparent in the confocal images that the non producing cells benefit from the BPS produced by the Wild Type (WT) to stay in the biofilm. The biofilm containing non-producing cells were more significantly susceptible to sodium hypochlorite and ciprofloxacin treatment than the WT biofilm. Biofilm infiltrated with non-producers delayed the pathogenesis, as tested in a murine model. The cell types were spatially assorted, with non producers being edged out in the biofilm. However, cellulose was found to act as a barrier to keep the non-producers away from the WT microcolony. Our results show that the infiltration of non-cooperating cell types can substantially weaken the biofilm making it vulnerable to antibacterials and delay their pathogenesis. Cellulose, a component of BPS, was shown to play a pivotal role of acting as the main public good, and to edge-out the non-producers away from the cooperating microcolony.

Macroporous three-dimensional graphene oxide foams for dye adsorption and antibacterial applications

Several reports illustrate the wide range applicability of graphene oxide (GO) in water remediation. However, a few layers of graphene oxide tend to aggregate under saline conditions thereby reducing its activity. The effects of aggregation can be minimized by having a random arrangement of GO layers in a three dimensional architecture. The current study emphasizes the potential benefits of highly porous, ultralight graphene oxide foams in environmental applications. These foams were prepared by a facile and cost effective lyophilization technique. The 3D architecture allowed the direct use of these foams in the removal of aqueous pollutants without any pretreatment such as ultrasonication. Due to its macroporous nature, the foams exhibited excellent adsorption abilities towards carcinogenic dyes such as rhodamine B (RB), malachite green (MG) and acriflavine (AF) with respective sorption capacities of 446, 321 and 228 mg g(-1) of foam. These foams were also further investigated for antibacterial activities against E. coli bacteria in aqueous and nutrient growth media. The random arrangement of GO layers in the porous foam architecture allowed it to exhibit excellent antibacterial activity even under physiological conditions by following the classical wrapping-perturbation mechanism. These results demonstrate the vast scope of GO foam in water remediation for both dye removal and antibacterial activity.

Mechano-fluorochromic Pt-II Luminogen and Its Cysteine Recognition

A new triphenylamine-based organometallic Pt-II luminogen (1) and its analogous organic compound (2) are reported. The molecules are decorated with aldehyde functionality to improve their photophysical properties by utilising donor-acceptor interactions. The single crystal X-ray structure analysis of PtII analogue 1 revealed that the neighbouring molecules were loosely organised by weak intermolecular C-H center dot center dot center dot pi interactions. Because of the twisted nature of the triphenylamine backbone the compounds showed aggregation-induced emission enhancement in THF/water mixture. Due to their loose crystal packing, upon application of external stimuli these luminogens exhibited mechano-fluorochromic behaviour. The crystalline forms of the compounds displayed a more superior emission efficiency than the grinded samples. Moreover, the compounds showed crystallization-induced emission enhancement (CIEE) and exhibited chemodosimetric response towards cysteine under physiological condition.