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Sahoo S.,Raidighi College | Das S.,Uluberia College
Current Bioinformatics | Year: 2014

Synonymous codon usage has long been known as a factor that affects the average expression level of proteins in microorganisms. A systematic approach to study the role of codon usage bias underlying gene expression has been described. Facts and ideas presented in this short review are to derive biological information from genome sequences by means of various statistical analyses and appropriate design of algorithms. Using codon usage bias as a numerical estimator of gene expression, a comparative analysis of predicted highly expressed (PHE) genes was performed in bacteria, cyanobacteria, archaea, lower eukaryotes and higher eukaryotes. Here, it is suggested that both codon usage and as well as base compositions at three codon sites regulate the individual gene expression. Any correlation between gene length and expression level, however, remains unexplained. Relationship between gene expression levels and synonymous codon usage provides an important line of evidence for translational selection and suggests some general mechanism underlying protein evolution. © 2014 Bentham Science Publishers.


Das S.,Uluberia College | Roymondal U.,Raidighi College | Chottopadhyay B.,Jadavpur University | Sahoo S.,Raidighi College
Gene | Year: 2012

The expression of functional proteins plays a crucial role in modern biotechnology. The free-living cynobacterium Synechocystis PCC 6803 is an interesting model organism to study oxygenic photosynthesis as well as other metabolic processes. Here we analyze a gene expression profiling methodology, RCBS (the scores of relative codon usage bias) to elucidate expression patterns of genes in the Synechocystis genome. To assess the predictive performance of the methodology, we propose a simple algorithm to calculate the threshold score to identify the highly expressed genes in a genome. Analysis of differential expression of the genes of this genome reveals that most of the genes in photosynthesis and respiration belong to the highly expressed category. The other genes with the higher predicted expression level include ribosomal proteins, translation processing factors and many hypothetical proteins. Only 9.5% genes are identified as highly expressed genes and we observe that highly expressed genes in Synechocystis genome often have strong compositional bias in terms of codon usage. An important application concerns the automatic detection of a set of impact codons and genes that are highly expressed tend to use this narrow set of preferred codons and display high codon bias .We further observe a strong correlation between RCBS and protein length indicating natural selection in favor of shorter genes to be expressed at higher level. The better correlations of RCBS with 2D electrophoresis and microarray data for heat shock proteins compared to the expression measure based on codon usage difference, E(g) and codon adaptive index, CAI indicate that the genomic expression profile available in our method can be applied in a meaningful way to study the mRNA expression patterns, which are by themselves necessary for the quantitative description of the biological states. © 2012 Elsevier B.V.


Sarkar S.K.,Jadavpur University | Sarkar S.K.,Uluberia College | Jana M.S.,Jadavpur University | Mondal T.K.,Jadavpur University | Sinha C.,Jadavpur University
Applied Organometallic Chemistry | Year: 2014

Alcohols are oxidized by N-methylmorpholine-N-oxide (NMO), Bu tOOH and H2O2 to the corresponding aldehydes or ketones in the presence of catalyst, [RuH(CO)(PPh3) 2(SRaaiNR)]PF6 (2) and [RuCl(CO)(PPh3)(S κRaaiNR)]PF6 (3) (SRaaiNR (1) = 1-alkyl-2-{(o- thioalkyl)phenylazo}imidazole, a bidentate N(imidazolyl) (N), N(azo) (N) chelator and SκRaaiNR is a tridentate N(imidazolyl) (N), N(azo) (N), Sκ-R is tridentate chelator; R and R are Me and Et). The single-crystal X-ray structures of [RuH(CO)(PPh3) 2(SMeaaiNMe)]PF6 (2a) (SMeaaiNMe = 1-methyl-2-{(o- thioethyl)phenylazo}imidazole) and [RuH(CO)(PPh3) 2(SEtaaiNEt)]PF6 (2b) (SEtaaiNEt = 1-ethyl-2-{(o- thioethyl)phenylazo}imidazole) show bidentate N,N chelation, while in [RuCl(CO)(PPh3)(SκEtaaiNEt)]PF6 (3b) the ligand SκEtaaiNEt serves as tridentate N,N,S chelator. The cyclic voltammogram shows RuIII/RuII (~1.1 V) and Ru IV/RuIII (~1.7 V) couples of the complexes 2 while Ru III/RuII (1.26 V) couple is observed only in 3 along with azo reductions in the potential window +2.0 to -2.0 V. DFT computation has been used to explain the spectra and redox properties of the complexes. In the oxidation reaction NMO acts as best oxidant and [RuCl(CO)(PPh 3)(SκRaaiNR)](PF6) (3) is the best catalyst. The formation of high-valent RuIV=O species as a catalytic intermediate is proposed for the oxidation process. Copyright © 2014 John Wiley & Sons, Ltd.


Ghosh B.,Jadavpur University | Paul S.N.,Jadavpur University | Das C.,Uluberia College | Paul I.,Jadavpur University | Banerjee S.,Vidyasagar College Day
Brazilian Journal of Physics | Year: 2013

The pseudopotential technique is applied to a multicomponent plasma consisting of nonthermal electrons and warm positive and negative ions with drift motion with a view to studying ion-acoustic double layers. Conditions for the existence of such layers are obtained, two critical concentrations of negative ions being identified which control the formation and nature of the ion-acoustic double layers. The effects of nonthermal electrons, negative-ion concentration, and negative-ion temperature on the double layer formation and structure are also investigated. The nonthermal electrons and the negative ions are shown to contribute significantly to the excitation and structure of the double layers. The importance of the results in the context of magnetospheric and auroral plasmas is discussed. © 2013 Sociedade Brasileira de Física.


Ghosh B.,Jadavpur University | Paul S.N.,Swami Vivekananda Institute of Science and Technology | Das C.,Uluberia College | Sinhamahapatra A.,B N Mahavidyalaya | Paul I.,Jadavpur University
Indian Journal of Physics | Year: 2011

To describe the nonlinear interactions of a magneto-hydrodynamic wave with its second harmonic propagating in a planar waveguide filled with cold magnetized plasma, coupled mode equations have been derived. Solution of these equations shows the possibility of energy transfer between the fundamental and the second harmonic. © 2011 IACS.


Sarkar S.K.,Jadavpur University | Sarkar S.K.,Uluberia College | Jana M.S.,Jadavpur University | Mondal T.K.,Jadavpur University | Sinha C.,Jadavpur University
Journal of Organometallic Chemistry | Year: 2012

[Ru(CO) 2Cl 2(α/β-NaiR)] (1, 2) and [Ru(CO) 2I 2(α/β-NaiR)] (3, 4) are synthesized by the reaction of [Ru(CO) 2Cl 2] n or [Ru(CO) 4I 2] with α/β-NaiR (1-alkyl-2-(naphthyl- α/β-azo)imidazole (α-NaiR/β-NaiR, where, R = Me, CH 2CH 3 and CH 2Ph)) and have been characterized by spectroscopic data. The geometry of the representative complexes [Ru(CO) 2Cl 2(β-NaiMe)] (2a) and [Ru(CO) 2I 2(β-NaiEt)] (4b) have been structurally confirmed by X-ray diffraction study. The redox property is examined by electrochemistry. Catalytic activity of these compounds is investigated to the oxidation of PhCH 2OH to PhCHO, 2-butanol (C 4H 9OH) to 2-butanone, 1-phenylethanol (PhC 2H 4OH) to acetophenone, cyclopentanol (C 5H 9OH) to cyclopentanone and cyclohexanol to cyclohexanone by N-methylmorpholine-N-oxide (NMO), H 2O 2 or Bu tOOH in CH 2Cl 2 and NMO shows highest yield. The catalytic efficiency is again dependent on Ru-X (X = Cl or I) bond and higher yield is observed for [Ru(CO) 2Cl 2(α/β- NaiR)] (1, 2). Electronic structure, spectral and redox properties are explained based on DFT and TD-DFT calculations on the representative complexes. © 2012 Elsevier B.V. All rights reserved.


Saha D.,Jadavpur University | Hazra D.K.,Uluberia College | Maity T.,Jadavpur University | Koner S.,Jadavpur University
Inorganic Chemistry | Year: 2016

A series of copper- and alkaline-earth-metal-based multidimensional metal-organic frameworks, {[CuMg(pdc)2(H2O)4]·2H2O}n (1), [CuCa(pdc)2]n (2), [CuSr(pdc)2(H2O)3]n (3), and {[Cuba(pdc)2(H2O)5]·H2O}n (4), where H2Pdc = pyridine-2,5-dicarboxylic acid, were hydrothermally synthesized and characterized. Two different metals act as the active center to catalyze two kinds of reactions, viz., olefin to its epoxide followed by epoxide ring opening to afford the corresponding vicinal diol in a sequential manner. © 2016 American Chemical Society.


PubMed | Jadavpur University and Uluberia College
Type: Journal Article | Journal: Inorganic chemistry | Year: 2016

A series of copper- and alkaline-earth-metal-based multidimensional metal-organic frameworks, {[CuMg(pdc)2(H2O)4]2H2O}n (1), [CuCa(pdc)2]n (2), [CuSr(pdc)2(H2O)3]n (3), and {[CuBa(pdc)2(H2O)5]H2O}n (4), where H2Pdc = pyridine-2,5-dicarboxylic acid, were hydrothermally synthesized and characterized. Two different metals act as the active center to catalyze two kinds of reactions, viz., olefin to its epoxide followed by epoxide ring opening to afford the corresponding vicinal diol in a sequential manner.


Dinda B.,Mahishamuri Ramkrishna Vidyapith | Samanta T.K.,Uluberia College | Bera U.K.,City College
New Mathematics and Natural Computation | Year: 2012

In this paper, we introduce intuitionistic fuzzy derivative, intuitionistic fuzzy Gateaux derivative and intuitionistic fuzzy Fréchet derivative and some of their properties are studied. The relations between intuitionistic fuzzy Gateaux derivative and intuitionistic fuzzy Fréchet derivative are studied. © 2012 World Scientific Publishing Company.


Samanta T.K.,Uluberia College | Mohinta S.,Uluberia College
Cybernetics and Information Technologies | Year: 2013

Using the concept of converse commuting mappings, our target is to prove some common fixed point theorems with respect to a contractive condition under implicit function relations and an integral type contractive condition in fuzzy symmetric spaces.

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