High-Spin Ferric Ions in <i>Saccharomyces cerevisiae</i> Vacuoles Are Reduced to the Ferrous State during Adenine-Precursor Detoxification

Park, Jinkyu,McCormick, Sean P.,Cockrell, Allison L.,Chakrabarti, Mrinmoy,Lindahl, Paul A. American Chemical Society 2014 Biochemistry Vol.53 No.24

<P/><P>The majority of Fe in Fe-replete yeast cells is located in vacuoles. These acidic organelles store Fe for use under Fe-deficient conditions and they sequester it from other parts of the cell to avoid Fe-associated toxicity. Vacuolar Fe is predominantly in the form of one or more magnetically isolated nonheme high-spin (NHHS) Fe<SUP>III</SUP> complexes with polyphosphate-related ligands. Some Fe<SUP>III</SUP> oxyhydroxide nanoparticles may also be present in these organelles, perhaps in equilibrium with the NHHS Fe<SUP>III</SUP>. Little is known regarding the chemical properties of vacuolar Fe. When grown on adenine-deficient medium (A↓), ADE2Δ strains of yeast such as W303 produce a toxic intermediate in the adenine biosynthetic pathway. This intermediate is conjugated with glutathione and shuttled into the vacuole for detoxification. The iron content of A↓ W303 cells was determined by Mössbauer and EPR spectroscopies. As they transitioned from exponential growth to stationary state, A↓ cells (supplemented with 40 μM Fe<SUP>III</SUP> citrate) accumulated two major NHHS Fe<SUP>II</SUP> species as the vacuolar NHHS Fe<SUP>III</SUP> species declined. This is evidence that vacuoles in A↓ cells are more reducing than those in adenine-sufficient cells. A↓ cells suffered less oxidative stress despite the abundance of NHHS Fe<SUP>II</SUP> complexes; such species typically promote Fenton chemistry. Most Fe in cells grown for 5 days with extra yeast-nitrogen-base, amino acids and bases in minimal medium was HS Fe<SUP>III</SUP> with insignificant amounts of nanoparticles. The vacuoles of these cells might be more acidic than normal and can accommodate high concentrations of HS Fe<SUP>III</SUP> species. Glucose levels and rapamycin (affecting the TOR system) affected cellular Fe content. This study illustrates the sensitivity of cellular Fe to changes in metabolism, redox state and pH. Such effects broaden our understanding of how Fe and overall cellular metabolism are integrated.</P>

A REVIEW ON THE MATHEMATICAL ASPECTS OF FLUID FLOW PROBLEMS IN AN INFINITE CHANNEL WITH ARBITRARY BOTTOM TOPOGRAPHY

Chakrabarti, A.,Martha, S.C. The Korean Society for Computational and Applied M 2011 Journal of applied mathematics & informatics Vol.29 No.5

A special system of partial differential equations (PDEs) occur in a natural way while studying a class of irrotational inviscid fluid flow problems involving infinite channels. Certain aspects of solutions of such PDEs are analyzed in the context of flow problems involving multiple layers of fluids of different constant densities in a channel associated with arbitrary bottom topography. The whole analysis is divided into two parts-part A and part B. In part A the linearized theory is employed along with the standard Fourier analysis to understand such flow problems and physical quantities of interest are derived analytically. In part B, the same set of problems handled in part A are examined in the light of a weakly non-linear theory involving perturbation in terms of a small parameter and it is shown that the original problems can be cast into KdV type of nonlinear PDEs involving the bottom topography occurring in one of the coefficients of these equations. Special cases of bottom topography are worked out in detail and expressions for quantities of physical importance are derived.

A REVIEW ON THE MATHEMATICAL ASPECTS OF FLUID FLOW PROBLEMS IN AN INFINITE CHANNEL WITH ARBITRARY BOTTOM TOPOGRAPHY

A. Chakrabarti,S. C. Martha 한국전산응용수학회 2011 Journal of applied mathematics & informatics Vol.29 No.5

A special system of partial differential equations (PDEs) occur in a natural way while studying a class of irrotational inviscid fluid flow problems involving infinite channels. Certain aspects of solutions of such PDEs are analyzed in the context of flow problems involving multiple layers of fluids of different constant densities in a channel associated with arbitrary bottom topography. The whole analysis is divided into two parts-part A and part B. In part A the linearized theory is employed along with the standard Fourier analysis to understand such flow problems and physical quantities of interest are derived analytically. In part B, the same set of problems handled in part A are examined in the light of a weakly nonlinear theory involving perturbation in terms of a small parameter and it is shown that the original problems can be cast into KdV type of nonlinear PDEs involving the bottom topography occurring in one of the coefficients of these equations. Special cases of bottom topography are worked out in detail and expressions for quantities of physical importance are derived.

Interaction of surface water waves with small bottom undulation on a sea-bed

S. C. Martha,S. N. Bora,A. Chakrabarti 한국전산응용수학회 2009 Journal of applied mathematics & informatics Vol.27 No.5

The problem of interaction of surface water waves by small undulation at the bottom of a laterally unbounded sea is treated on the basis of linear water wave theory for both normal and oblique incidences. Perturbation analysis is employed to obtain the first order corrections to the reflection and transmission coefficients in terms of integrals involving the shape function c(x) representing the bottom undulation. Fourier transform method and residue theorem are applied to obtain these coefficients. As an example, a patch of sinusoidal ripples is considered in both the cases as the shape function. The principal conclusion is that the reflection coefficient is oscillatory in the ratio of twice the surfacewave number to the wave number of the ripples. In particular, there is a Bragg resonance between the surface waves and the ripples, which is associated with high reflection of incident wave energy. The theoretical observations are validated computationally The problem of interaction of surface water waves by small undulation at the bottom of a laterally unbounded sea is treated on the basis of linear water wave theory for both normal and oblique incidences. Perturbation analysis is employed to obtain the first order corrections to the reflection and transmission coefficients in terms of integrals involving the shape function c(x) representing the bottom undulation. Fourier transform method and residue theorem are applied to obtain these coefficients. As an example, a patch of sinusoidal ripples is considered in both the cases as the shape function. The principal conclusion is that the reflection coefficient is oscillatory in the ratio of twice the surfacewave number to the wave number of the ripples. In particular, there is a Bragg resonance between the surface waves and the ripples, which is associated with high reflection of incident wave energy. The theoretical observations are validated computationally

Hygrothermal analysis of laminated composites using C⁰ FE model based on higher order zigzag theory

S.K. Singh,A.Chakrabarti 국제구조공학회 2017 Steel and Composite Structures, An International J Vol.23 No.1

A C⁰ FE model developed based on an efficient higher order zigzag theory is used for hygrothermal analysis of laminated composite plates. The C⁰ FE model satisfies the inter-laminar shear stress continuity at the interfaces and zero transverse shear stress conditions at plate top and bottom. In this model the first derivatives of transverse displacement have been treated as independent variables to circumvent the problem of C¹ continuity associated with the above plate theory. In the present theory the above mentioned C⁰ continuity of the present element is compensated in the stiffness matrix formulation by using penalty parameter approach. In order to avoid stress oscillations observed in the displacement based finite element, the stress field derived from temperature/moisture fields (initial strains) must be consistent with total strain field. Special steps are introduced by field consistent approach (e.g., sampling at gauss points) to compensate this problem. A nine noded C⁰ continuous isoparametric element is used in the proposed FE model. Comparison of present numerical results with other existing solutions shows that the proposed FE model is efficient, accurate and free of locking.

A proposed organic Schottky barrier photodetector for application in the visible region

A.D.D. Dwivedi,Arun Kumar Singh,Rajiv Prakash,P. Chakrabarti 한국물리학회 2010 Current Applied Physics Vol.10 No.3

The fabrication and characterization of an organic photodetector (OPD) in the form of ITO coated glass/polycarbazole (PCz)/Al Schottky contact is reported. The device has been fabricated in our laboratory for the first time using the polymer synthesized by us. The device has been subsequently characterized in respect of electrical and optical properties in order to explore its potential for possible use as a detector in the visible region at 650 nm. It is observed that the detector exhibits a reasonably high value of peak detectivity (~6 × 106 cm Hz1/2W-1) near zero bias voltage at V = 0.2 V.

Structure and relaxor behavior of BaBi4Ti4−xZrxO15 ceramics

A. Chakrabarti,J. Bera 한국물리학회 2010 Current Applied Physics Vol.10 No.2

BaBi4Ti4-xZrxO15 with x = 0.1, 0.2, 0.3 and 0.5, has been synthesized via modified solid state reaction route. X-ray diffraction studies confirmed the formation of single phase Zr4+ substituted BaBi4Ti4O15 up to x = 0.2. ZrO2 and Bi2O3 based impurity phases were found at x = 0.3 and 0.5 substitutions. However,Rietveld refinement showed the increase in lattice parameters of BaBi4Ti4O15 up to x = 0.5 substitutions. A broad dielectric peak associated with frequency dependence dielectric maximum temperature was observed at low substitutions. Relaxor behavior was suppressed at x = 0.5 substitution. A broadening and shifting of permittivity-temperature peak was found for the substitution. The high temperature slopes of dielectric peaks were analyzed by quadratic law for relaxors. The degree of relaxation and phase transformation diffusiveness were investigated at different substitutions.

Vitellogenin Induction and Histo-metabolic Changes Following Exposure of Cyprinus carpio to Methyl Paraben

Barse, A.V.,Chakrabarti, T.,Ghosh, T.K.,Pal, A.K.,Kumar, Neeraj,Raman, R.P.,Jadhao, S.B. Asian Australasian Association of Animal Productio 2010 Animal Bioscience Vol.23 No.12

Methyl paraben (MP), which is used as a preservative in pharmaceutical and cosmetic (shampoo) products, foods and beverages, enters into the aquatic environment and can pose a potential fish health hazard. In this experiment, effects of MP were evaluated in adult male common carp (Cyprinus carpio) by exposing them to fractions (1/$143^{rd}$ to 1/29th) of the $LC_{50}$ dose with every change of water for 28 days. Vitellogenin induction, metabolic enzymes, somatic indices and bioaccumulation were studied at weekly intervals. The $96^{th}$ h $LC_{50}$ of MP in fingerlings was 120 mg/L. Compared to the control, except for increases (p<0.01) in alkaline phosphatase (EC 3.1.3.1), alanine aminotransferase (EC 2.6.1.2) and liver size, there were decreases (p<0.01) in activity of acid phosphatase (EC 3.1.3.2), aspartate aminotransferase (EC 2.6.1.1), and testiculosomatic index following exposure to any dose of MP. Vitellogenin induction was significantly higher (p<0.01) in exposed than unexposed (control) fish. The bioaccumulation of MP in testis, liver, brain, gills and muscle tissues of fish increased significantly (p<0.01) with increase of dose from 0.84 ppm to 1.68 ppm. Dose and duration of exposure (p<0.01) indicated that an exposure period of 1 to 2 weeks was sufficient to cause changes in the quantifiable parameters studied. Fish exposed to 4.2 ppm MP became lethargic after the $26^{th}$ d. Histologically, degeneration, vacuolization and focal necrotic changes in liver and fibrosis-like changes in testicular tissue were noted.

Finite element analysis of functionally graded sandwich plates under nonlinear sense for aerospace applications

M.N.A. GulshanTaj,Anupam Chakrabarti,R. Malathy,S.R.R. Senthil Kumar 국제구조공학회 2021 Structural Engineering and Mechanics, An Int'l Jou Vol.80 No.3

Owing to the increase in demand for composite materials for different applications in aircraft structures, the nonlinear response of functionally graded ceramic-metal sandwich plates under mechanical loading is studied in the present research work. Geometric nonlinearity (GNL) is considered by Green-strain components and further assumes the form of von Kármán strains. It is ascertained that the effective mechanical properties vary through the thickness direction as a function of volume fraction of ceramic and metal constituents and obeys power law equation. Higher order displacement model proposed by Reddy is incorporated in the study to arrive for 2D isoparametric finite element C0 formulation. A nine node Lagrangian element is accomplished to model the assumed plate geometry. Different thickness schemes are proposed to model the sandwich plate with graded layer as core/ face sheets. Although the model can handle thickness scheme of any kind, results are exposed for four types of symmetric sandwich plates. Comparison statement between isotropic and graded plates is drawn in each case by appropriate selection of power law exponent value. The present investigation may be useful for design engineers/researchers to arrive for particular thickness scheme based on the results, while performing large deformation analysis of functionally graded sandwich plates (FGSP).

RNAi-based transgene conferred extreme resistance to the geminivirus causing apical leaf curl disease in potato

Garima Tomar,S. K. Chakrabarti,Nitya Nanda Sharma,A. Jeevalatha,S. Sundaresha,Kanika Vyas,Wamik Azmi 한국식물생명공학회 2018 Plant biotechnology reports Vol.12 No.3

Potato apical leaf curl disease is an emerging geminiviral disease in tropics and subtropics. It was reported for the first time in the year 1999 in northern plains of India but quickly spread to almost all potato growing regions of the country largely due to prevalence of warmer weather during early crop growth, thereby favoring whitefly vector. The problem of apical leaf curl disease in India became more severe due to lack of seed indexing for this virus in conventional seed production scheme. Although it accounts for major yield loss, there is no conventional source of resistance available in potato against Tomato Leaf Curl New Delhi Virus-Potato (ToLCNDV-Potato) that causes this disease in potato. In the present study, we have investigated the potential use of RNAi for obtaining resistance against this DNA virus in potato. The replication-associated protein gene (AC1) of the virus was used to obtain pathogen-derived resistance. The AC1 gene was PCR amplified from field-infected potato leaves, cloned and sequenced (JN393309). It showed 93% sequence similarity with the AC1 gene of Tomato Leaf Curl Virus-New Delhi (TOLCV-NDe; DQ169056) virus. Transgenic plants encoding the AC1 gene in three different orientations, viz. sense, antisense and hairpin loop, were raised. Transgenic lines when challenge inoculated with ToLCNDV-Potato showed different levels of resistance for all three constructs. Transgene integration and copy number in selected transgenic lines were determined by qPCR and further confirmed by Southern blot analysis. Though a reduction in viral titer was observed in transgenic lines encoding either antisense or hairpin loop constructs of AC1 gene, the latter transgenics showed most significant results as shown by reduction in the level of symptom expression in glasshouse screening as well as real-time data of in vivo virus concentration. In fact, we obtained a few totally asymptomatic transgenic lines with hairpin loop strategy.