• Sengupta

      Articles written in Journal of Biosciences

    • Developmental changes of the glycolytic enzymes in the human fetal heart

      Jayati Das Gupta Trishna Sengupta Chhabi Dutta Kathakali De S De D Sengupta

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      The ontogeny of hexokinase, phosphofructokinase, phosphoglucoisornerase, aldolase, pyruvate kinase and lactate dehydrogenase activities which are associated with glycolysis, an important energy yielding process, has been studied in human fetal heart for periods ranging from 13 weeks to above 33 weeks of gestation. Hexokinase, phosphoglucoisomerase and pyruvate kinase activities show similar developmental profiles exhibiting maximum activity at 25–28 weeks ofgestation. Phosphofructokinase activity, on the other hand, shows a minimum at this period and exhibits a peak value at early stages (13–16 weeks of gestation). Though considerable activity for aldolase is observed at an early period, it declines thereafter, but again increases in the later period. The probable role and correlations of these glycolytic enzymes with energy demand and general functional development in human fetal heart in ontogeny are evaluated.

    • Ontogeny of human fetal catalase superoxide dismutase and lipid peroxidation: A comparative study

      Kathakali De(Addya) Diptis Sengupta

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      A comparative study on the activity profile of catalase and superoxide dismutase, the two scavenging enzymes, as well as the developmental profile of lipid peroxidation in the human fetal brain, liver and kidney have been done for gestation periods ranging from 12 weeks to 28 weeks and beyond. The activity of the scavenging enzymes increase gradually inall the tissues with the advancement of pregnancy. Brain is an exception in case of catalase where the activity remains more or less same throughout the developmental period except in the case of fetuses, 28 weeks and above where significant decrease in the catalase activity is observed. A high level of lipid peroxidation is observed during early stages of development which declines thereafter.

    • Multisubstrate specifics amylase from mushroomTermitomyces clypeatus

      Anil K Ghosh Subhabrata SenGupta

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      An amylase was purified from the culture filtrate ofTermitomyces clypeatus by ammonium sulphate precipitation, DEAE-Sephadex chromatography and gel filtration on Bio-Gel P-200 column. The electrophoretically homogeneous preparation also exhibited hydrolytic activity (in a decreasing order) on amylose, xylan, amylopectin, glycogen, arabinogalactan and arabinoxylan. The enzyme had characteristically endo-hydrolytic activity on all the substrates tested and no xylose, glucose, arabinose or glucuronic acid could be detected even after prolonged enzymatic digestion of the polysaccharides. Interestingly the enzyme had similar pH optima (5.5), temperature optima (55°C), pH stability (pH 3–10) and thermal denaturation kinetics when acted on both starch and xylan (larch wood) .Km values were found to be 2.63 mg/ml for amylase and 6.25 mg/ml for xylanase activity. Hill’s plot also indicated that the enzyme contained a single active site for both activities. Hg2+ was found to be most potent inhibitor. Ca2+, a common activator for amylase activity, appeared to be an inhibitor for this enzyme. Thus it appeared that the enzyme had multisubstrate specificity acting as α-amylase on starch and also acting as xylanase on side chain oligosaccharides of xylan containing α-linked sugars.

    • Ontogeny of the enzymes related to γ-glutamyl cycle in the human fetal system

      Kathakali De (Addya) Chhabi Dutta Diptis Sengupta

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      Measurements have been made of the enzymes associated with γ-glutamyl cycleviz, γ-glutamyl transpeptidase, γ-glutamyl cysteine synthetase, and 5-oxoprolinase in human fetal brain, liver and kidney over 12–36 weeks of gestation. γ-Glutamyl transpeptidase activity increases gradually with age. γ-Glutamyl cysteine synthetase and 5-oxoprolinase show biphasic pattern of development in human fetal brain. The data presented in this communication may indicate a relationship between γ-glutamyl cycle and amino acid transport.

    • Glycogen metabolism in human fetal testes

      K Misra Datta J Dasgupta T Sengupta S De Sengupta

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      The ontogeny of glycogen synthetase, glycogen Phosphorylase and α-D-glucosidase, enzymes which are associated with glycogen metabolism and glycogen level has been studied in human fetal testes of gestational age ranging from 14–32 weeks. Glycogen synthetase activity reaches the peak value at 17–20 weeks of gestation, thereafter it decreases. α-D-Glucosidase activity increases with the advancement of pregnancy up to 28 weeks of gestation decreasing thereafter very rapidly. Phosphorylase activity remains more or less constant throughout gestation. The maximum increase in glycogen content at early stages of gestation (17–20 weeks) and gradual reduction with the advancement of pregnancy are correlated with histochemical observation by the periodic acid-Schiff technique.

    • Coupling of proteins to liposomes and their role in understanding delayed type of hypersensitivity in human and mice

      U Sengupta Sudhir Sinha V Chaturvedi R B Narayanan Sreevatsa C M Gupta

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      Liposome-coupled lepromin was found to elicit a 3-week skin reaction in leprosy patients similar to that elicited by wholeMycobacterium leprae. The present study suggests that the presentation of antigens in a specific orientation is necessary for evoking delayed type hypersensitivity response in humans.

    • Methyl directed DNA mismatch repair inVibrio cholerae

      Rupa Bandyopadhyay Aditya Sengupta Tapan K Bera Kishor K Bhakat Chitra Dutta Jyotirmoy Das

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      Mismatches in DNA occur either due to replication error or during recombination between homologous but non-identical DNA sequences or due to chemical modification of bases. The mismatch in DNA, if not repaired, result in high spontaneous mutation frequency. The repair has to be in the newly synthesized strand of the DNA molecule, otherwise the error will be fixed permanently. Three distinct mechanisms have been proposed for the repair of mismatches in DNA in prokaryotic cells and gene functions involved in these repair processes have been identified. The methyl-directed DNA mismatch repair has been examined inVibrio cholerae, a highly pathogenic gram negative bacterium and the causative agent of the diarrhoeal disease cholera. The DNA adenine methyltransferase encoding gene (dam) of this organism which is involved in strand discrimination during the repair process has been cloned and the complete nucleotide sequence has been determined.Vibrio cholerae dam gene codes for a 21.5 kDa protein and can substitute for theEscherichia coli enzyme. Overproduction ofVibrio cholerae Dam protein is neither hypermutable nor lethal both in Escherichia coli andVibrio cholerae. WhileEscherichia coli dam mutants are sensitive to 2-aminopurine,Vibrio cholerae 2-aminopurine sensitive mutants have been isolated with intact GATC methylation activity. The mutator genesmutS andmutL involved in the recognition of mismatch have been cloned, nucleotide sequence determined and their products characterized. Mutants ofmutS andmutL ofVibrio cholerae have been isolated and show high rate of spontaneous mutation frequency. ThemutU gene ofVibrio cholerae, the product of which is a DNA helicase II, codes for a 70 kDa protein. The deduced amino acid sequence of themutU gene hs all the consensus helicase motifs. The DNA cytosine methyltransferase encoding gene (dam) ofVibrio cholerae has also been cloned. Thedcm gene codes for a 53 kDa protein. This gene product might be involved in very short patch (VSP) repair of DNA mismatches. The vsr gene which is directly involved in VSP repair process codes for a 23 kDa protein. Using these information, the status of DNA mismatch repair inVibrio cholerae will be discussed.

    • Efforts in diagnosing early leprosy using serological techniques

      Om Parkash M K Beuria B K Girdhar K Katoch U Sengupta

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      Skin scrapings obtained from the lesions of leprosy patients of all types showed 96 % positivity to the serum antibody competition test using monoclonal antibody (ML04)to 35 kDa antigen ofMycobacterium leprae. Further, in vitro culture of full thickness skin biopsies from lepromatous patients were noted to release IgG antibodies toM. leprae with a peak antibody response at 48 h. The significance of this local antibody response toM. leprae in skin has been discussed for its possible use in diagnosing early leprosy.

    • Induction of blindness by formoguanamine hydrochloride in adult male roseringed parakeets (Psittacula krameri)

      Anamika Sengupta Yoshihiko Obara Tapan K Banerji Saumen K Maitra

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      Formoguanamine (2,4-diamino-s-triazine) was known to be an effective chemical agent in inducing blindness in poultry chicks, but not in adult birds. The present study was undertaken to demonstrate the influences, if any, of this chemical on the visual performance and retinal histology in an adult sub-tropical wild bird, the roseringed parakeet (Psittacula krameri). Formoguanamine (FG) hydrochloride was subcutaneously injected into adult parakeets at a dosage of 25 mg (dissolved in 0.75 ml physiological saline)/100 g body weight/day, for two consecutive days while the control birds were injected only with a placebo. The effects were studied after 10, 20 and 30 days of the last treatment of FG. Within 24 h of the treatment of FG, about 90% of the total birds exhibited lack of visual responses to any light stimulus and even absence of pupillary light reactions. The remaining birds became totally blind on the day following the last injection of FG and remained so till the end of investigation. At the microscopic level, conspicuous degenerative changes were noted in the outer pigmented epithelium and the photoreceptive layer of rods and cones in the retinas of FG treated birds. A significant reduction in the thickness of the outer nuclear layer was also found in the retinas of FG treated parakeets, compared to that in the control birds. However, the inner cell layers of the retina in the control and FG administered parakeets were almost identical. It deserves special mention that the effects of FG, noted after 30 days of last treatment, were not very different from those noted just after 10 days of treatment. Collectively, the results of the present investigation demonstrate that FG can be used as a potent pharmacological agent for inducing irreversible blindness through selective damage in retinal tissue even in the adult wild bird, thereby making FG treatment an alternative euthanasic device to a cumbersome, stressful, surgical method of enucleation of the ocular system for laboratory studies.

    • Human Y-chromosome: a hall of mirrors

      B J Rao Kundan Sengupta

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    • Bilaterally symmetric Fourier approximations of the skull outlines of temnospondyl amphibians and their bearing on shape comparison

      Dhurjati P Sengupta Debapriya Sengupta Parthasarathi Ghosh

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      Present work illustrates a scheme of quantitative description of the shape of the skull outlines of temnospondyl amphibians using bilaterally symmetric closed Fourier curves. Some special points have been identified on the Fourier fits of the skull outlines, which are the local maxima, or minima of the distances from the centroid of the points at the skull outline. These points denotes break in curvature of the outline and their positions can be compared to differentiate the skull shapes. The ratios of arc-lengths of the posterior and lateral outline of 58 temnospondyl skulls have been plotted to generate a triaguarity series of the skulls. This series grades different families, some of their genera and species as well as some individuals according to their posterior and lateral skull length ratios. This model while comparing different taxa, takes into account the entire arc-length of the outline of the temnospondyl skulls, and does not depend on few geometric or biological points used by earlier workers for comparing skull shapes.

    • Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties

      Dipankar Sengupta Deeptak Verma Pradeep K Naik

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      Delvardine and its structural derivatives are important non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs). In this work, 15 delvardine analogues were studied. A free energy-of-binding (FEB) expression was developed in the form of an optimized linear combination of van der Waal (vdW), electrostatic, solvation and solvent-accessible surface area (SASA) energy terms. The solvation energy terms estimated by generalized born/surface area (GB/SA) play an important role in predicting the binding affinity of delvardine analogues. Out of 15 derivatives, substitution of CH3 with H at the Y and R positions, as well as substitution of SO2CH3 with only CH2 at the Z position in S2, S8 and S12 analogues, were found to be the most potent (glide score = –7.60, –8.06 and –7.44; pIC50 = 7.28, 7.37 and 7.64) in comparison with the template delvardine (which is used currently as the drug candidate). All the three analogues also passed the absorption, distribution, metabolism and excretion (ADME) screening and Lipinski’s rule of 5, and have the potential to be used for second-generation drug development. The work demonstrates that dock molecular mechanics-generalized born/surface area (MM–GB/SA–ADME) is a promising approach to predict the binding activity of ligands to the receptor and further screen for a successful candidate drug in a computer-aided rational drug design.

    • Non-coding RNAs in polyglutamine disorders: friend or foe?

      Sonali Sengupta Subramaniam Ganesh

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    • An insight into the sequential, structural and phylogenetic properties of banana 1-aminocyclopropane-1-carboxylate synthase 1 and study of its interaction with pyridoxal-5'-phosphate and aminoethoxyvinylglycine

      Swarup Roy Choudhury Sanjay Kumar Singh Sujit Roy Dibyendu N Sengupta

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      In banana, ethylene production for ripening is accompanied by a dramatic increase in 1-aminocyclopropane-1-carboxylate (ACC) content, transcript level of Musa acuminata ACC synthase 1 (MA-ACS1) and the enzymatic activity of ACC synthase 1 at the onset of the climacteric period. MA-ACS1 catalyses the conversion of 𝑆-adenosyl-L-methionine (SAM) to ACC, the key regulatory step in ethylene biosynthesis. Multiple sequence alignments of 1-aminocyclopropane-1-carboxylate synthase (ACS) amino acid sequences based on database searches have indicated that MA-ACS1 is a highly conserved protein across the plant kingdom. This report describes an in silico analysis to provide the first important insightful information about the sequential, structural and phylogenetic characteristics of MA-ACS1. The three-dimensional structure of MA-ACS1, constructed based on homology modelling, in combination with the available data enabled a comparative mechanistic analysis of MA-ACS1 to explain the catalytic roles of the conserved and non-conserved active site residues. We have further demonstrated that, as in apple and tomato, banana-ACS1 (MA-ACS1) forms a homodimer and a complex with cofactor pyridoxal-5′-phosphate (PLP) and inhibitor aminoethoxyvinylglycine (AVG). We have also predicted that the residues from the PLP-binding pocket, essential for ligand binding, are mostly conserved across the MA-ACS1 structure and the competitive inhibitor AVG binds at a location adjacent to PLP.

    • Clipboard: Controversy over the report on a bacterium that feeds on arsenic

      Dipanwita Sengupta Madhab K Chattopadhyay

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    • Metabolism in bacteria at low temperature: A recent report

      Dipanwita Sengupta Madhab K Chattopadhyay

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      The adaptability of bacteria to extreme cold environments has been demonstrated from time to time by various investigators. Metabolic activity of bacteria at subzero temperatures is also evidenced. Recent studies indicate that bacteria continue both catabolic and anabolic activities at subzero temperatures. Implications of these findings are discussed.

    • Feature selection using feature dissimilarity measure and density-based clustering: Application to biological data

      Debarka Sengupta Indranil Aich Sanghamitra Bandyopadhyay

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      Reduction of dimensionality has emerged as a routine process in modelling complex biological systems. A large number of feature selection techniques have been reported in the literature to improve model performance in terms of accuracy and speed. In the present article an unsupervised feature selection technique is proposed, using maximum information compression index as the dissimilarity measure and the well-known density-based cluster identification technique DBSCAN for identifying the largest natural group of dissimilar features. The algorithm is fast and less sensitive to the user-supplied parameters. Moreover, the method automatically determines the required number of features and identifies them. We used the proposed method for reducing dimensionality of a number of benchmark data sets of varying sizes. Its performance was also extensively compared with some other well-known feature selection methods.

    • Genome 3D-architecture: Its plasticity in relation to function


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      The genome of higher eukaryotes is non-randomly organized in the interphase nucleus. However, notwithstanding theabsence of membrane bound sub-compartments, the nucleus coordinates a number of functions largely by organizingchromatin in a non-random but dynamic manner. The plasticity of chromatin structure and function relies on epigeneticmodifications as well as its association with nuclear landmarks such as the nuclear envelope, nuclear lamina, nuclear porecomplex and nuclear bodies such as the nucleolus among others. In the absence of membrane-bound compartments, cellsand the nucleus, in particular, employ phase-separation, which unmixes phases that constrain biochemical reactions incomplex non-membranous sub-compartments such as the nucleolus or even the heterochromatin. This review attempts toprovide a glimpse into the microcosm of phase-separated nuclear sub-compartments, that regulate nuclear structure–function relationships.

    • HflX protein protects Escherichia coli from manganese stress


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      The ribosome-binding GTPase HflX is required for manganese homeostasis in E. coli. While under normal conditionsDhflX cells behave like wild type E. coli with respect to growth pattern and morphology, deletion of hflX makes E. coli cellsextremely sensitive to manganese, characterized by arrested cell growth and filamentation. Here we demonstrate that uponcomplementation by hflX, manganese stress is relieved. In phenotypic studies done in a manganese-rich environment, DhflXcells were highly sensitive to antibiotics that bind the penicillin binding protein 3 (PBP3), suggesting that the manganesestress led to impaired peptidoglycan biosynthesis. An irregular distribution of dark bands of constriction along filaments,delocalization of the dark bands from midcell towards poles and subpoles, lack of septum formation and arrested celldivision were observed in DhflX cells under manganese stress. However, chromosome replication and segregation ofnucleoids were unaffected under these conditions, as observed from confocal microscopy imaging and FACS studies. Weconclude that absence of HflX leads to manganese accumulation in E. coli cells, affecting cell septum formation, probablyby modulating the activity of the cell division protein PBP3 (FtsI), a major component of the divisome apparatus. Wepropose that HflX acts as a gatekeeper, regulating the influx of manganese into the cell.

    • Emerging roles of long non-coding RNAs in cancer


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      Cancer is a physiological condition that has both the endogenous and exogenous influences on its progression. It originatesfrom unusual cell growth, where the cells undergo massive genetic alterations, bypass the signaling machinery andcompromise its genetic cohesion. Literature has well narrated the DNA damage studies including driver mutations thatinterfere with the treatment strategies. However, with evolving medical excellence, recent day studies are trying to unveilthe contribution of RNAs in the progression of tumor malignancies. A number of non-coding RNAs have been identified asan active component in cancer genomics. This article aims to review the role of long non-coding RNAs in the spectra ofcancers and its prognostic value as the biomarkers in molecular targeting with clinical utility and therapeutic beneficence.

    • Recent advances in the spatial organization of the mammalian genome


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      The mammalian genome is complex and presents a dynamic structural organization that reflects function.Organization of the genome inside the mammalian nucleus impacts all nuclear processes including but notlimited to transcription, replication and repair, and in many biological contexts such as early development,differentiation and physiological adaptations. However, there is limited understating of how 3D organization ofthe mammalian genome regulates different nuclear processes. Recent advances in microscopy and a myriad ofgenomics methods—propelled by next-generation sequencing—have advanced our knowledge of genomeorganization to a great extent. In this review, we discuss nuclear compartments in general and recent advancesin the understanding of how mammalian genome is organized in these compartments with an emphasis ondynamics at the nuclear periphery.

    • A novel role of tumor suppressor ZMYND8 in inducing differentiation of breast cancer cells through its dual-histone binding function


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      Accumulating evidences indicate the involvement of epigenetic deregulations in cancer. While some epigeneticregulators with aberrant functions in cancer are targeted for improving therapeutic outcome in patients,reinstating the functions of tumor-suppressor-like epigenetic regulators might further potentiate anti-cancertherapies. Epigenetic reader zinc-finger MYND-type-containing 8 (ZMYND8) has been found to be endowedwith multiple anti-cancer functions like inhibition of tumor cell migration and proliferation. Here, we reportanother novel tumor suppressor role of ZMYND8 as an inducer of differentiation in breast cancer cells, byupregulating differentiation genes. Interestingly, we also demonstrated that ZMYND8 mediates all its antitumorroles through a common dual-histone mark binding to H4K16Ac and H3K36Me2. We validated thesefindings by both biochemical and biophysical analyses. Furthermore, we also confirmed the differentiationinducingpotential of ZMYND8 in vivo, using 4T1 murine breast cancer model in Balb/c mice. Differentiationtherapy holds great promise in cancer therapy, since it is non-toxic and makes the cancer cells therapysensitive.In this scenario, we propose epigenetic reader ZMYND8 as a potential therapeutic candidate fordifferentiation therapy in breast cancer.

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