Publications by authors named "Sourav Bhowmick"

34 Publications

Hollow cuboidal MnCoO coupled with nickel phosphate: a promising oxygen evolution reaction electrocatalyst.

Chem Commun (Camb) 2021 Aug;57(65):8027-8030

Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.

The growth of hierarchical morphologies of complex metal oxides directly on the substrate is a challenging task. Herein we report a unique hollow-cuboidal MnCo2O4 (h-MCO) morphology that offers insights into the efficient charge-transfer and surface kinetics for the oxygen evolution reaction. h-MCO coupled nickel phosphate under alkaline conditions outperforms the benchmark RuO2.
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http://dx.doi.org/10.1039/d1cc02383gDOI Listing
August 2021

Phosphorus nitride nano-dots as a versatile and metal-free support for efficient photoelectrochemical water oxidation.

Chem Commun (Camb) 2021 Jun;57(50):6157-6160

Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.

Phosphorus nitride dots (PNDs) are employed as a metal-free and versatile support over a range of metal oxide-based photoanodes for efficient photoelectrochemical (PEC) water oxidation. PNDs have the ability to form various heterojunctions by virtue of their favorable band positions for enhanced charge separation leading to improved photocurrent densities.
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http://dx.doi.org/10.1039/d1cc01030aDOI Listing
June 2021

Self-Assembly of a [1 + 1] Ionic Hexagonal Macrocycle and Its Antiproliferative Activity.

Front Chem 2018 3;6:87. Epub 2018 Apr 3.

Department of Chemistry, Indian Institute of Technology Patna, Bihta, India.

A unique irregular hexagon was self-assembled using an organic donor clip (bearing terminal pyridyl units) and a complementary organometallic acceptor clip. The resulting metallamacrocycle was characterized by multinuclear NMR, mass spectrometry, and elemental analyses. Molecular modeling confirmed hexagonal shaped cavity for this metallamacrocycle which is a unique example of a discrete hexagonal framework self-assembled from only two building blocks. Cytotoxicity of the Pt-based acceptor tecton and the self-assembled Pt-based macrocycle was evaluated using three cancer cell lines and results were compared with cisplatin. Results confirmed a positive effect of the metallamacrocycle formation on cell growth inhibition.
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http://dx.doi.org/10.3389/fchem.2018.00087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5891631PMC
April 2018

TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks.

Bioinformatics 2018 Jan;34(2):314-316

School of Computer Science and Engineering, Nanyang Technological University, Singapore.

Summary: Cancer hallmarks, a concept that seeks to explain the complexity of cancer initiation and development, provide a new perspective of studying cancer signaling which could lead to a greater understanding of this complex disease. However, to the best of our knowledge, there is currently a lack of tools that support such hallmark-based study of the cancer signaling network, thereby impeding the gain of knowledge in this area. We present TROVE, an user-friendly software that facilitates hallmark annotation, visualization and analysis in cancer signaling networks. In particular, TROVE facilitates hallmark analysis specific to particular cancer types.

Availability And Implementation: Available under the Eclipse Public License from: https://sites.google.com/site/cosbyntu/softwares/trove and https://github.com/trove2017/Trove.
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http://dx.doi.org/10.1093/bioinformatics/btx600DOI Listing
January 2018

First-line antituberculosis drug, pyrazinamide, its pharmaceutically relevant cocrystals and a salt.

Acta Crystallogr B Struct Sci Cryst Eng Mater 2017 Oct 29;73(Pt 5):1007-1016. Epub 2017 Sep 29.

Department of Chemistry, Gauhati University, Guwahati, Assam 781014, India.

A few pyrazinamide (Pyz) cocrystals involving hydroxybenzoic/cinnamic acid derivatives [2,4-dihydroxybenzoic acid (24DHBA); 2,6-dihydroxybenzoic acid (26DHBA); 3,5-dihydroxybenzoic acid (35DHBA) and nutraceutical molecule ferulic acid (FRA)] and the first example of a molecular salt with p-toluenesulfonic acid (pTSA) have been prepared and characterized using various solid-state techniques. A high-temperature cocrystal polymorph of Pyz·FRA has been characterized from the endothermic peaks observed using differential scanning calorimetry. The presence of substituent groups carrying hydrogen bond donors or acceptors and their influence on supramolecular synthon formation has been investigated using a Cambridge Structural Database search. Equilibrium solubility of all the binary complexes of Pyz follows the order of their coformer solubility, i.e. Pyz·pTSA > Pyz·35DHBA > Pyz > Pyz·26DHBA > Pyz·24DHBA > Pyz·FRA. A twofold enhancement in solubility of Pyz·pTSA molecular salt compared with the parent drug suggests a potential drug formulation for the treatment of tuberculosis.
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http://dx.doi.org/10.1107/S2052520617011477DOI Listing
October 2017

Coordination-Driven Self-Assembly of Ionic Irregular Hexagonal Metallamacrocycles via an Organometallic Clip and Their Cytotoxicity Potency.

Inorg Chem 2018 Apr 25;57(7):3615-3625. Epub 2017 Aug 25.

Department of Chemistry , Indian Institute of Technology Patna , Bihta 801103 , Bihar , India.

Two new irregular hexagons (6 and 7) were synthesized from a pyrazine motif containing an organometallic acceptor clip [bearing platinum(II) centers] and different neutral donor ligands (4,4'-bipyridine or pyrazine) using a coordination-driven self-assembly protocol. The two-dimensional supramolecules were characterized by multinuclear NMR, mass spectrometry, and elemental analyses. Additionally, one of the macrocycles (6) was characterized by single-crystal X-ray analyses. Macrocycles are unique examples of [2 + 2] self-assembled ensembles that are hexagonal but irregular in shape. These hexagon frameworks require the assembly of only four tectons/subunits. The cytotoxicity of platinum(II)-based macrocycles was studied using various cell lines such as A549 (human lung carcinoma), KB (human oral cancer), MCF7 (human breast cancer), and HaCaT (human skin keratinocyte) cell lines, and the results were compared with those of cisplatin. The smaller macrocycle (7) exhibited a higher cytotoxic effect against all cell types, and its sensitivity was found to be comparable with that of cisplatin for A549 and MCF7 cells. Cell cycle analysis and live propidium iodide staining suggest that the macrocycles 6 and 7 induced a loss of membrane integrity that ultimately might lead to necrotic cell death.
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http://dx.doi.org/10.1021/acs.inorgchem.7b01561DOI Listing
April 2018

Coupling conditions for globally stable and robust synchrony of chaotic systems.

Phys Rev E 2017 Jun 9;95(6-1):062204. Epub 2017 Jun 9.

Center for Complex System Research Kolkata, Kolkata 700094, India.

We propose a set of general coupling conditions to select a coupling profile (a set of coupling matrices) from the linear flow matrix of dynamical systems for realizing global stability of complete synchronization (CS) in identical systems and robustness to parameter perturbation. The coupling matrices define the coupling links between any two oscillators in a network that consists of a conventional diffusive coupling link (self-coupling link) as well as a cross-coupling link. The addition of a selective cross-coupling link in particular plays constructive roles that ensure the global stability of synchrony and furthermore enables robustness of synchrony against small to nonsmall parameter perturbation. We elaborate the general conditions for the selection of coupling profiles for two coupled systems, three- and four-node network motifs analytically as well as numerically using benchmark models, the Lorenz system, the Hindmarsh-Rose neuron model, the Shimizu-Morioka laser model, the Rössler system, and a Sprott system. The role of the cross-coupling link is, particularly, exemplified with an example of a larger network, where it saves the network from a breakdown of synchrony against large parameter perturbation in any node. The perturbed node in the network transits from CS to generalized synchronization (GS) when all the other nodes remain in CS. The GS is manifested by an amplified response of the perturbed node in a coherent state.
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http://dx.doi.org/10.1103/PhysRevE.95.062204DOI Listing
June 2017

Synergistic target combination prediction from curated signaling networks: Machine learning meets systems biology and pharmacology.

Methods 2017 10 25;129:60-80. Epub 2017 May 25.

DUKE-NUS Medical School, Singapore. Electronic address:

Given a signaling network, the target combination prediction problem aims to predict efficacious and safe target combinations for combination therapy. State-of-the-art in silico methods use Monte Carlo simulated annealing (mcsa) to modify a candidate solution stochastically, and use the Metropolis criterion to accept or reject the proposed modifications. However, such stochastic modifications ignore the impact of the choice of targets and their activities on the combination's therapeutic effect and off-target effects, which directly affect the solution quality. In this paper, we present mascot, a method that addresses this limitation by leveraging two additional heuristic criteria to minimize off-target effects and achieve synergy for candidate modification. Specifically, off-target effects measure the unintended response of a signaling network to the target combination and is often associated with toxicity. Synergy occurs when a pair of targets exerts effects that are greater than the sum of their individual effects, and is generally a beneficial strategy for maximizing effect while minimizing toxicity. mascot leverages on a machine learning-based target prioritization method which prioritizes potential targets in a given disease-associated network to select more effective targets (better therapeutic effect and/or lower off-target effects); and on Loewe additivity theory from pharmacology which assesses the non-additive effects in a combination drug treatment to select synergistic target activities. Our experimental study on two disease-related signaling networks demonstrates the superiority of mascot in comparison to existing approaches.
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http://dx.doi.org/10.1016/j.ymeth.2017.05.015DOI Listing
October 2017

Self-assembly of DNA-porphyrin hybrid molecules for the creation of antimicrobial nanonetwork.

J Photochem Photobiol B 2017 Jul 11;172:28-35. Epub 2017 May 11.

Department of Chemistry, Indian Institute of Technology Patna, Patna 801103, Bihar, India. Electronic address:

DNA derived well-controlled arrangement of porphyrins has emerged as promising hybrid nanostructures. Exceptional biocompatibility and DNA-directed surface addressability coupled with rich symmetry features of the porphyrin have made these hybrid nanostructures attractive candidates for potential biomedical and biotechnological applications. However, the noteworthy photophysical properties of porphyrin and related molecules when present in DNA based nanostructures are yet to be explored fully and should be a matter of intense research that may unearth a plethora of interesting applications of these nanostructures. Herein, we demonstrate the construction of novel self-assembled DNA-porphyrin hybrid nanonetworks that utilize the porphyrin core for antibacterial applications. Porphyrin derivative with four pendant NH groups was synthesized and conjugated with the 5'-PO of ss-DNA by solution phase phosphoramidation coupling reaction. The conjugation was followed by DNA hybridization mediated self-assembly to form DNA-porphyrin hybrid nanonetwork. The enhanced antimicrobial property of the nanonetwork was envisioned following light irradiation at relevant wavelength. In line with this, comparative antimicrobial activities against gram-negative (Escherichia coli BL-21) and gram-positive bacteria (Staphylococcus aureus) have been studied. Interestingly, DNA-porphyrin nanonetwork afforded highly efficient and coherent photoinduced reactive oxygen species (ROS) generation to display antimicrobial activity against Staphylococcus aureus. The escalated and coherent ROS generation from the nanonetworks was attributed to the ordered placement of the porphyrins that inhibits self-quenching. Our work points out to a good alternative for antibiotic free strategies for preservation of biological materials and other applications.
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http://dx.doi.org/10.1016/j.jphotobiol.2017.05.010DOI Listing
July 2017

Design of a flexible organometallic tecton: host-guest chemistry with picric acid and self-assembly of platinum macrocycles.

Dalton Trans 2017 Feb;46(6):1986-1995

Department of Chemistry, Indian Institute of Technology Patna, Patna 801103, Bihar, India.

The synthesis and characterization of a new pyrazine-based "flexible" and ditopic platinum(ii) organometallic molecule (3) is being reported. Flexibility in this molecule is due to the presence of ether functional groups that bridge the rigid core and periphery. Due to the presence of square planar Pt(ii) centers at the two ends, the molecule's potential to act as an acceptor building block in the construction of metallamacrocycles was tested. Upon reaction of 3 with various dicarboxylates in a 1 : 1 stoichiometric ratio, [2 + 2] self-assembled neutral metallacycles (M1-M3) were obtained in high yields. M1-M3 were characterized using multinuclear NMR, high resolution mass spectrometry and elemental analyses. The shape and dimensions of these supramolecular structures were also confirmed by optimizing the geometry using the density functional theory (DFT) approach. Computational studies suggest that M1-M3 are nanoscalar macrocyles. Furthermore, using isothermal titration calorimetry (ITC), it was shown that 3 can bind with picric acid (PA) to yield a 3·(PA) host-guest complex. The magnitude of the binding constant indicates that 3 has significant affinity for PA.
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http://dx.doi.org/10.1039/c6dt03498eDOI Listing
February 2017

Hierarchical coassembly of DNA-triptycene hybrid molecular building blocks and zinc protoporphyrin IX.

Beilstein J Nanotechnol 2016 12;7:697-707. Epub 2016 May 12.

Department of Chemistry, IIT Patna, Bihata 801118, India.

Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)-DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA-organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5'-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA-TPA molecular building blocks as well as a model guest molecule within the DNA-TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD) and atomic force microscopy (AFM) have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA-TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA-DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA-TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT) applications as well as photocatalytic reactions.
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http://dx.doi.org/10.3762/bjnano.7.62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4901925PMC
June 2016

Pyrazine motif containing hexagonal macrocycles: synthesis, characterization, and host-guest chemistry with nitro aromatics.

Inorg Chem 2015 Sep 11;54(18):8994-9001. Epub 2015 Sep 11.

Department of Chemistry, Indian Institute of Technology Patna , Patna 800 013, Bihar, India.

The synthesis and characterization of cationic two-dimensional metallamacrocycles having a hexagonal shape and cavity are described. Both macrocycles utilize a pyrazine motif containing an organometallic acceptor tecton with platinum(II) centers along with different donor ligands. While one macrocycle is a relatively larger [6 + 6], the other is a relatively smaller [2 + 2] polygon. A unique feature of the smaller ensemble is that it is an irregular polygon in which all six edges are not of equal length. Molecular modeling of these macrocycles confirmed the presence of hexagonal cavities. The ability of these π-electron rich macrocycles to act as potential hosts for relatively electron deficient nitroaromatics (DNT = 2,4-dinitrotoluene and PA = picric acid) has been studied using isothermal titration calorimetry (ITC) as a tool. Molecular dynamics simulation studies were subsequently performed to gain critical insight into the binding interactions between the nitroaromatic guest molecules (PA/DNT) and the ionic macrocycles reported herein.
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http://dx.doi.org/10.1021/acs.inorgchem.5b01156DOI Listing
September 2015

TENET: topological feature-based target characterization in signalling networks.

Bioinformatics 2015 Oct 16;31(20):3306-14. Epub 2015 Jun 16.

Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Motivation: Target characterization for a biochemical network is a heuristic evaluation process that produces a characterization model that may aid in predicting the suitability of each molecule for drug targeting. These approaches are typically used in drug research to identify novel potential targets using insights from known targets. Traditional approaches that characterize targets based on their molecular characteristics and biological function require extensive experimental study of each protein and are infeasible for evaluating larger networks with poorly understood proteins. Moreover, they fail to exploit network connectivity information which is now available from systems biology methods. Adopting a network-based approach by characterizing targets using network features provides greater insights that complement these traditional techniques. To this end, we present Tenet (Target charactErization using NEtwork Topology), a network-based approach that characterizes known targets in signalling networks using topological features.

Results: Tenet first computes a set of topological features and then leverages a support vector machine-based approach to identify predictive topological features that characterizes known targets. A characterization model is generated and it specifies which topological features are important for discriminating the targets and how these features should be combined to quantify the likelihood of a node being a target. We empirically study the performance of Tenet from a wide variety of aspects, using several signalling networks from BioModels with real-world curated outcomes. Results demonstrate its effectiveness and superiority in comparison to state-of-the-art approaches.

Availability And Implementation: Our software is available freely for non-commercial purposes from: https://sites.google.com/site/cosbyntu/softwares/tenet

Contact: [email protected] or [email protected]

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btv360DOI Listing
October 2015

Non-symbiotic N2-fixation and phosphate-solubility in Gangetic alluvial soil as influenced by pre-emergence herbicide residues.

Chemosphere 2015 Sep 15;135:202-7. Epub 2015 May 15.

Department of Agricultural Chemistry and Soil Science, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal 741252, India.

An experiment has been conducted under laboratory conditions to investigate the effect of two pre-emergence herbicides viz., thiobencarb (at 1.5 and 4.5 kg a.i. ha(-1)) and pretilachlor (at 0.5 and 1.5 kg a.i. ha(-1)), on the changes of growth and activities of aerobic non-symbiotic N2-fixing bacteria and phosphate-solubilizing microorganisms in relation to availability of mineral nitrogen and soluble phosphorus in the Gangetic alluvial soil (Typic Haplustept) of West Bengal, India. Application of herbicides, in general, significantly increased growth and activities of microorganisms, resulting in greater release of available nitrogen and soluble phosphorus in soil; and the stimulation was more pronounced when the herbicides were applied at their lower concentrations (recommended field application rates), more so with thiobencarb, as compared to pretilachlor. As compared to untreated control, application of thiobencarb at lower concentration increased the proliferation of aerobic non-symbiotic N2-fixing bacteria, phosphate-solubilizing microorganisms and non-symbiotic N2-fixing capacity of soil to the extent of 54.0, 44.6 and 31.7%, respectively; and accumulated the highest amount of available nitrogen (37.8%) and phosphorus (54.5%) in soil, while pretilachlor at field application rate highly induced (37.2%) phosphate-solubilizing capacity of soil. At higher concentration, pretilachlor was superior to thiobencarb in augmenting the growth and activities of phosphate-solubilizers. The results of the present study also indicated that gradual increase in concentration of the herbicides over their recommended field application rates was not much conducive for growth and activities of microorganisms, and subsequent release of nutrients in soil.
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http://dx.doi.org/10.1016/j.chemosphere.2015.04.039DOI Listing
September 2015

Pyrazine-based organometallic complex: synthesis, characterization, and supramolecular chemistry.

Inorg Chem 2015 Mar 26;54(6):2543-50. Epub 2015 Feb 26.

Department of Chemistry, Indian Institute of Technology Patna , Patna 800 013, Bihar, India.

The design, synthesis, and characterization of a new pyrazine-based ditopic platinum(II) organometallic complex are reported. The molecular structure of the organoplatinum pyrazine dipod was determined by single-crystal X-ray crystallography. The potential utility of this organometallic ditopic acceptor as a building block in the construction of neutral metallasupramolecular macrocycles containing the pyrazine motif was explored. Pyrazine motifs containing supramolecules were characterized by multinuclear NMR (including (1)H DOSY), mass spectrometry, and elemental analysis. The geometry of each supramolecular framework was optimized by employing the PM6 semiempirical molecular orbital method to predict its shape and size. The ability of the pyrazine-based organoplatinum complex to act as a host for nitroaromatic guest (2,4-dinitrotoluene and PA) molecules was explored by isothermal titration calorimetry (ITC). The binding stoichiometry and thermodynamic parameters of these host-guest complexation reactions were evaluated using ITC. Theoretical calculations were performed to obtain insight into the binding pattern between the organometallic host and nitroaromatic guests. The preferable binding propensity of the binding sites of complex 1 for both nitroaromatics (PA and 2,4-dinitrotoluene) determined by molecular simulation studies corroborates well with the experimental results as obtained by ITC experiments.
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http://dx.doi.org/10.1021/ic502581xDOI Listing
March 2015

Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity.

BMC Syst Biol 2015 21;9 Suppl 1:S4. Epub 2015 Jan 21.

The ongoing cancer research has shown that malignant tumour cells have highly disrupted signalling transduction pathways. In cancer cells, signalling pathways are altered to satisfy the demands of continuous proliferation and survival. The changes in signalling pathways supporting uncontrolled cell growth, termed as rewiring, can lead to dysregulation of cell fates e.g. apoptosis. Hence comparative analysis of normal and oncogenic signal transduction pathways may provide insights into mechanisms of cancer drug-resistance and facilitate the discovery of novel and effective anti-cancer therapies. Here we propose a hybrid modelling approach based on ordinary differential equation (ODE) and machine learning to map network rewiring in the apoptotic pathways that may be responsible for the increase of drug sensitivity of tumour cells in triple-negative breast cancer. Our method employs Genetic Algorithm to search for the most likely network topologies by iteratively generating simulated protein phosphorylation data using ODEs and the rewired network and then fitting the simulated data with real data of cancer signalling and cell fate. Most of our predictions are consistent with experimental evidence from literature. Combining the strengths of knowledge-driven and data-driven approaches, our hybrid model can help uncover molecular mechanisms of cancer cell fate at systems level.
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http://dx.doi.org/10.1186/1752-0509-9-S1-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331679PMC
November 2015

Binding and interaction of di- and tri-substituted organometallic triptycene palladium complexes with DNA.

J Biol Inorg Chem 2014 Oct 27;19(7):1221-32. Epub 2014 Jul 27.

Department of Chemistry, Indian Institute of Technology Patna, Patliputra Colony, Patna, 800013, Bihar, India.

Two triptycene-based ligands with pendant bromophenyl units have been prepared. These triptycene derivatives have been used as synthons for the synthesis of di and tri nuclear palladium complexes. The organic molecules and their corresponding organometallic complexes have been fully characterized using nuclear magnetic resonance (NMR), infrared (IR) spectroscopy and mass spectrometry. The mode of binding and effect of the complexes on pUC19 plasmid, calf thymus DNA and oligomer duplex DNA have been investigated by a host of analytical methods. The complexes brought about unwinding of supercoiled plasmid and the unwinding angle was found to be related to the binding affinity of the complexes with DNA, where both these parameters were guided by the structure of the complexes. Concentration-dependent inhibition of endonuclease activity of SspI and BamHI by the complexes indicates preference for G/C sequence for binding to DNA. However, neither the complexes did not introduce any cleavage at abasic site in oligomer duplex DNA, nor they created linear form of the plasmid upon co-incubation with the DNA samples. The interactions of the complexes with DNA were found to be strongly guided by the structure of the complexes, where intercalation as well as groove binding was observed, without inflicting any damage to the DNA. The mode of interaction of the complexes with DNA was further confirmed by isothermal calorimetry.
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http://dx.doi.org/10.1007/s00775-014-1180-zDOI Listing
October 2014

Triptycene based organometallic complexes: a new class of acceptor synthons for supramolecular ensembles.

Dalton Trans 2014 Sep;43(35):13270-7

Department of Chemistry, Indian Institute of Technology Patna, Patna 800 013, Bihar, India.

Preparation and characterization of two new triptycene based polytopic Pt(II) organometallic complexes are being reported. These complexes have three trans-bromobis(trialkylphosphine)platinum(II) units directly attached to the central triptycene unit. These organoplatinum complexes were converted to the corresponding nitrate salts for subsequent use in self-assembly reactions. Characterization of these organometallic triptycene complexes by multinuclear NMR, FTIR, mass spectrometry and elemental analyses is described. The molecular structure of one of the organoplatinum triptycene tripods was determined by single-crystal X-ray crystallography. The potential utility of these organometallic tritopic acceptors as building blocks in the construction of metallasupramolecular cages containing the triptycene motif is explored. Additionally, for the first time, 3,3'-bipyridine has been used as a flexible donor tecton for self-assembly of discrete and finite metallacages using triptycene based tritopic organometallic acceptor units. Triptycene motif containing supramolecules were characterized by multinuclear NMR (including (1)H DOSY), mass spectrometry and elemental analyses. Geometry of each supramolecular framework was optimized by employing the PM6 semiempirical molecular orbital method to predict its shape and size.
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http://dx.doi.org/10.1039/c4dt01298dDOI Listing
September 2014

DiffNet: automatic differential functional summarization of dE-MAP networks.

Methods 2014 Oct 5;69(3):247-56. Epub 2014 Jul 5.

Biological Engineering Department, Massachusetts Institute of Technology, MA, USA; Singapore-MIT Alliance, Nanyang Technological University, Singapore.

The study of genetic interaction networks that respond to changing conditions is an emerging research problem. Recently, Bandyopadhyay et al. (2010) proposed a technique to construct a differential network (dE-MAPnetwork) from two static gene interaction networks in order to map the interaction differences between them under environment or condition change (e.g., DNA-damaging agent). This differential network is then manually analyzed to conclude that DNA repair is differentially effected by the condition change. Unfortunately, manual construction of differential functional summary from a dE-MAP network that summarizes all pertinent functional responses is time-consuming, laborious and error-prone, impeding large-scale analysis on it. To this end, we propose DiffNet, a novel data-driven algorithm that leverages Gene Ontology (go) annotations to automatically summarize a dE-MAP network to obtain a high-level map of functional responses due to condition change. We tested DiffNet on the dynamic interaction networks following MMS treatment and demonstrated the superiority of our approach in generating differential functional summaries compared to state-of-the-art graph clustering methods. We studied the effects of parameters in DiffNet in controlling the quality of the summary. We also performed a case study that illustrates its utility.
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http://dx.doi.org/10.1016/j.ymeth.2014.06.012DOI Listing
October 2014

Effect of thiobencarb and pretilachlor on microorganisms in relation to mineralization of C and N in the Gangetic alluvial soil of West Bengal.

Environ Monit Assess 2014 Oct 5;186(10):6849-56. Epub 2014 Jul 5.

Department of Agricultural Chemistry and Soil Science, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, West Bengal, India.

An experiment was conducted under laboratory conditions to investigate the effect of two pre-emergence herbicides, viz., thiobencarb (at 1.5 and 4.5 kg active ingredient (a.i.) ha(-1)) and pretilachlor (at 0.5 and 1.5 kg a.i. ha(-1)), on the growth and multiplication of some microorganisms (bacteria, actinomycetes and fungi) in relation to transformations and availability of C and N in the Gangetic alluvial soil (Typic Haplustept) of West Bengal, India. Application of both the herbicides, in general, significantly increased microbial biomass, resulting in greater retention, mineralization and availability of oxidizable organic C and N in soil, and the stimulations were more pronounced when the herbicides were applied at their lower concentrations (recommended field application rates), more so with thiobencarb, as compared to pretilachlor. Compared to untreated control soil, the application of thiobencarb at lower concentration increased the proliferation of total bacteria, actinomycetes and fungi by 57.3, 36.6 and 55.2%, respectively, and released the highest amount (40.2%) of soluble NO₃(-) in soil, while pretilachlor at field application rate induced the growth and multiplication of bacteria and fungi by 58.3 and 17.6%, respectively. Irrespective of the concentrations, the stimulations were at par for both the herbicides towards the retention of oxidizable organic C, total N and exchangeable NH₄(+) in soil.
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http://dx.doi.org/10.1007/s10661-014-3893-4DOI Listing
October 2014

Synthesis, characterization and DNA interaction studies of new triptycene derivatives.

Beilstein J Org Chem 2014 5;10:1290-8. Epub 2014 Jun 5.

Department of Chemistry, Indian Institute of Technology Patna, Patna 800 013, Bihar, India.

A facile and efficient synthesis of a new series of triptycene-based tripods is being reported. Using 2,6,14- or 2,7,14-triaminotriptycenes as synthons, the corresponding triazidotriptycenes were prepared in high yield. Additionally, we report the transformation of 2,6,14- or 2,7,14-triaminotriptycenes to the corresponding ethynyl-substituted triptycenes via their tribromo derivatives. Subsequently, derivatization of ethynyl-substituted triptycenes was studied to yield the respective propiolic acid and ethynylphosphine derivatives. Characterization of the newly functionalized triptycene derivatives and their regioisomers were carried out using FTIR and multinuclear NMR spectroscopy, mass spectrometry, and elemental analyses techniques. The study of the interaction of these trisubstituted triptycenes with various forms of DNA revealed interesting dependency on the functional groups of the triptycene core to initiate damage or conformational changes in DNA.
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http://dx.doi.org/10.3762/bjoc.10.130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077457PMC
July 2014

DualAligner: a dual alignment-based strategy to align protein interaction networks.

Bioinformatics 2014 Sep 28;30(18):2619-26. Epub 2014 May 28.

Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Motivation: Given the growth of large-scale protein-protein interaction (PPI) networks obtained across multiple species and conditions, network alignment is now an important research problem. Network alignment performs comparative analysis across multiple PPI networks to understand their connections and relationships. However, PPI data in high-throughput experiments still suffer from significant false-positive and false-negatives rates. Consequently, high-confidence network alignment across entire PPI networks is not possible. At best, local network alignment attempts to alleviate this problem by completely ignoring low-confidence mappings; global network alignment, on the other hand, pairs all proteins regardless. To this end, we propose an alternative strategy: instead of full alignment across the entire network or completely ignoring low-confidence regions, we aim to perform highly specific protein-to-protein alignments where data confidence is high, and fall back on broader functional region-to-region alignment where detailed protein-protein alignment cannot be ascertained. The basic idea is to provide an alignment of multiple granularities to allow biological predictions at varying specificity.

Results: DualAligner performs dual network alignment, in which both region-to-region alignment, where whole subgraph of one network is aligned to subgraph of another, and protein-to-protein alignment, where individual proteins in networks are aligned to one another, are performed to achieve higher accuracy network alignments. Dual network alignment is achieved in DualAligner via background information provided by a combination of Gene Ontology annotation information and protein interaction network data. We tested DualAligner on the global networks from IntAct and demonstrated the superiority of our approach compared with state-of-the-art network alignment methods. We studied the effects of parameters in DualAligner in controlling the quality of the alignment. We also performed a case study that illustrates the utility of our approach.

Availability And Implementation: http://www.cais.ntu.edu.sg/∼assourav/DualAligner/.
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http://dx.doi.org/10.1093/bioinformatics/btu358DOI Listing
September 2014

Diverse routes of transition from amplitude to oscillation death in coupled oscillators under additional repulsive links.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Mar 5;89(3):032901. Epub 2014 Mar 5.

CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India.

We report the existence of diverse routes of transition from amplitude death to oscillation death in three different diffusively coupled systems, which are perturbed by a symmetry breaking repulsive coupling link. For limit-cycle systems the transition is through a pitchfork bifurcation, as has been noted before, but in chaotic systems it can be through a saddle-node or a transcritical bifurcation depending on the nature of the underlying dynamics of the individual systems. The diversity of the routes and their dependence on the complex dynamics of the coupled systems not only broadens our understanding of this important phenomenon but can lead to potentially new practical applications.
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http://dx.doi.org/10.1103/PhysRevE.89.032901DOI Listing
March 2014

How to induce multiple delays in coupled chaotic oscillators?

Chaos 2013 Dec;23(4):043115

CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India.

Lag synchronization is a basic phenomenon in mismatched coupled systems, delay coupled systems, and time-delayed systems. It is characterized by a lag configuration that identifies a unique time shift between all pairs of similar state variables of the coupled systems. In this report, an attempt is made how to induce multiple lag configurations in coupled systems when different pairs of state variables attain different time shift. A design of coupling is presented to realize this multiple lag synchronization. Numerical illustration is given using examples of the Rössler system and the slow-fast Hindmarsh-Rose neuron model. The multiple lag scenario is physically realized in an electronic circuit of two Sprott systems.
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http://dx.doi.org/10.1063/1.4828515DOI Listing
December 2013

Plasmin triggers a switch-like decrease in thrombospondin-dependent activation of TGF-β1.

Biophys J 2012 Sep;103(5):1060-8

Singapore-MIT Alliance, Computational Systems Biology Programme, Singapore.

Transforming growth factor-β1 (TGF-β1) is a potent regulator of extracellular matrix production, wound healing, differentiation, and immune response, and is implicated in the progression of fibrotic diseases and cancer. Extracellular activation of TGF-β1 from its latent form provides spatiotemporal control over TGF-β1 signaling, but the current understanding of TGF-β1 activation does not emphasize cross talk between activators. Plasmin (PLS) and thrombospondin-1 (TSP1) have been studied individually as activators of TGF-β1, and in this work we used a systems-level approach with mathematical modeling and in vitro experiments to study the interplay between PLS and TSP1 in TGF-β1 activation. Simulations and steady-state analysis predicted a switch-like bistable transition between two levels of active TGF-β1, with an inverse correlation between PLS and TSP1. In particular, the model predicted that increasing PLS breaks a TSP1-TGF-β1 positive feedback loop and causes an unexpected net decrease in TGF-β1 activation. To test these predictions in vitro, we treated rat hepatocytes and hepatic stellate cells with PLS, which caused proteolytic cleavage of TSP1 and decreased activation of TGF-β1. The TGF-β1 activation levels showed a cooperative dose response, and a test of hysteresis in the cocultured cells validated that TGF-β1 activation is bistable. We conclude that switch-like behavior arises from natural competition between two distinct modes of TGF-β1 activation: a TSP1-mediated mode of high activation and a PLS-mediated mode of low activation. This switch suggests an explanation for the unexpected effects of the plasminogen activation system on TGF-β1 in fibrotic diseases in vivo, as well as novel prognostic and therapeutic approaches for diseases with TGF-β dysregulation.
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http://dx.doi.org/10.1016/j.bpj.2012.06.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433618PMC
September 2012

FACETS: multi-faceted functional decomposition of protein interaction networks.

Bioinformatics 2012 Oct 20;28(20):2624-31. Epub 2012 Aug 20.

School of Computer Engineering, Nanyang Technological University, Singapore.

Motivation: The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein-protein interaction (PPI) network using graph theoretic analysis. Despite the recent progress, systems level analysis of high-throughput PPIs remains a daunting task because of the amount of data they present. In this article, we propose a novel PPI network decomposition algorithm called FACETS in order to make sense of the deluge of interaction data using Gene Ontology (GO) annotations. FACETS finds not just a single functional decomposition of the PPI network, but a multi-faceted atlas of functional decompositions that portray alternative perspectives of the functional landscape of the underlying PPI network. Each facet in the atlas represents a distinct interpretation of how the network can be functionally decomposed and organized. Our algorithm maximizes interpretative value of the atlas by optimizing inter-facet orthogonality and intra-facet cluster modularity.

Results: We tested our algorithm on the global networks from IntAct, and compared it with gold standard datasets from MIPS and KEGG. We demonstrated the performance of FACETS. We also performed a case study that illustrates the utility of our approach.

Supplementary Information: Supplementary data are available at the Bioinformatics online.

Availability: Our software is available freely for non-commercial purposes from: http://www.cais.ntu.edu.sg/~assourav/Facets/
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http://dx.doi.org/10.1093/bioinformatics/bts469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467740PMC
October 2012

Lag synchronization and scaling of chaotic attractor in coupled system.

Chaos 2012 Jun;22(2):023151

Central Instrumentation, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India.

We report a design of delay coupling for lag synchronization in two unidirectionally coupled chaotic oscillators. A delay term is introduced in the definition of the coupling to target any desired lag between the driver and the response. The stability of the lag synchronization is ensured by using the Hurwitz matrix stability. We are able to scale up or down the size of a driver attractor at a response system in presence of a lag. This allows compensating the attenuation of the amplitude of a signal during transmission through a delay line. The delay coupling is illustrated with numerical examples of 3D systems, the Hindmarsh-Rose neuron model, the Rössler system, a Sprott system, and a 4D system. We implemented the coupling in electronic circuit to realize any desired lag synchronization in chaotic oscillators and scaling of attractors.
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http://dx.doi.org/10.1063/1.4731263DOI Listing
June 2012

Experimental evidence of synchronization of time-varying dynamical network.

Chaos 2012 Jun;22(2):023105

Central Instrumentation, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.

We investigate synchronization of time varying networks and stability conditions. We derive interesting relations between the critical coupling constants for synchronization and switching times for time-varying and time average networks. The relations are based on the additive property of Lyapunov exponents and are verified experimentally in electronic circuit.
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http://dx.doi.org/10.1063/1.3701949DOI Listing
June 2012

FUSE: a profit maximization approach for functional summarization of biological networks.

BMC Bioinformatics 2012 Mar 21;13 Suppl 3:S10. Epub 2012 Mar 21.

School of Computer Engineering, Nanyang Technological University, Singapore.

Background: The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator) that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL) principle to maximize information gain of the summary graph while satisfying the level of detail constraint.

Results: We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI.

Conclusion: By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.
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http://dx.doi.org/10.1186/1471-2105-13-S3-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402926PMC
March 2012

Steady states and dynamics of urokinase-mediated plasmin activation in silico and in vitro.

Biophys J 2011 Oct;101(8):1825-34

Singapore-MIT Alliance, National University of Singapore, Singapore.

Plasmin (PLS) and urokinase-type plasminogen activator (UPA) are ubiquitous proteases that regulate the extracellular environment. Although they are secreted in inactive forms, they can activate each other through proteolytic cleavage. This mutual interplay creates the potential for complex dynamics, which we investigated using mathematical modeling and in vitro experiments. We constructed ordinary differential equations to model the conversion of precursor plasminogen into active PLS, and precursor urokinase (scUPA) into active urokinase (tcUPA). Although neither PLS nor UPA exhibits allosteric cooperativity, modeling showed that cooperativity occurred at the system level because of substrate competition. Computational simulations and bifurcation analysis predicted that the system would be bistable over a range of parameters for cooperativity and positive feedback. Cell-free experiments with recombinant proteins tested key predictions of the model. PLS activation in response to scUPA stimulus was found to be cooperative in vitro. Finally, bistability was demonstrated in vitro by the presence of two significantly different steady-state levels of PLS activation for the same levels of stimulus. We conclude that ultrasensitive, bistable activation of UPA-PLS is possible in the presence of substrate competition. An ultrasensitive threshold for activation of PLS and UPA would have ramifications for normal and disease processes, including angiogenesis, metastasis, wound healing, and fibrosis.
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http://dx.doi.org/10.1016/j.bpj.2011.08.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192967PMC
October 2011
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