Biomedical subjects

Sudip Chattopadhyay

Publications and source records attributed to Sudip Chattopadhyay.

7 recordsLinked to original sources

PubMed2005

A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth.

The crosstalk of light signaling pathways with other signaling cascades has just started to be revealed. Here, we report the identification and functional characterization of a Z-box binding factor (ZBF1) in light signaling pathways. Arabidopsis thaliana ZBF1 encodes AtMYC2/JIN1, a basic helix-loop-helix transcription factor, which has recently been shown to be involved in abscisic acid (ABA), jasmonic acid (JA), and jasmonate-ethylene signaling pathways. We demonstrate that AtMYC2 interacts with the Z- and G-box light-responsive elements of minimal light-regulated promoters. AtMYC2 is expressed in various light-grown seedlings, including in red, far red, and blue light. Genetic analyses suggest that AtMYC2 acts as a negative regulator of blue light-mediated photomorphogenic growth and blue and far-red-light-regulated gene expression; however, it functions as a positive regulator of lateral root formation. Our results further demonstrate that atmyc2 mutants have compromised sensitivity to ABA- and JA-mediated responses. Taken together, these results demonstrate that AtMYC2 is a common transcription factor of light, ABA, and JA signaling pathways in Arabidopsis.

Abscisic Acid↗

PubMed2005

Regulation of TOP2 by various abiotic stresses including cold and salinity in pea and transgenic tobacco plants.

Although abiotic stress affects plant growth and development, demonstration of its direct effect on regulation of the components of the DNA replication machinery is largely unknown. In this work, we demonstrate that the expression of TOP2 (encoding topoisomerase II) is up-regulated by various abiotic stresses including salinity and low temperature, and phytohormones such as ABA (abscisic acid) and SA (salicylic acid). Transgenic studies with different deletion versions of the TOP2 promoter in tobacco define several promoter determinants responsible for specific abiotic stress responsiveness. Taken together, these results demonstrate a direct involvement of stress in the transcriptional regulation of TOP2.

Abscisic Acid↗

PubMed2005

Comparison of low-order multireference many-body perturbation theories.

Tests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.

Journal Article↗

PubMed2004

A state-specific approach to multireference coupled electron-pair approximation like methods: development and applications.

The traditional multireference (MR) coupled-cluster (CC) methods based on the effective Hamiltonian are often beset by the problem of intruder states, and are not suitable for studying potential energy surface (PES) involving real or avoided curve crossing. State-specific MR-based approaches obviate this limitation. The state-specific MRCC (SS-MRCC) method developed some years ago can handle quasidegeneracy of varying degrees over a wide range of PES, including regions of real or avoided curve-crossing. Motivated by its success, we have suggested and explored in this paper a suite of physically motivated coupled electron-pair approximations (SS-MRCEPA) like methods, which are designed to capture the essential strength of the parent SS-MRCC method without significant sacrificing its accuracy. These SS-MRCEPA theories, like their CC counterparts, are based on complete active space, treat all the reference functions on the same footing and provide a description of potentially uniform precision of PES of states with varying MR character. The combining coefficients of the reference functions are self-consistently determined along with the cluster amplitudes themselves. The newly developed SS-MRCEPA methods are size-extensive, and are also size-consistent with localized orbitals. Among the various versions, there are two which are invariant with respect to the restricted rotations among doubly occupied and active orbitals separately. Similarity of performance of this latter and the noninvariant versions at the crossing points of the degenerate orbitals imply that the all the methods presented are rather robust with respect to the rotations among degenerate orbitals. Illustrative numerical applications are presented for PES of the ground state of a number of difficult test cases such as the model H4, H(8) problems, the insertion of Be into H(2), and Li(2), where intruders exist and for a state of a molecule such as CH(2), with pronounced MR character. Results obtained with SS-MRCEPA methods are found to be comparable in accuracy to the parent SS-MRCC and FCI/large scale CI results throughout the PES, which indicates the efficacy of our SS-MRCEPA methods over a wide range of geometries, despite their neglect of a host of complicated nonlinear terms, even when the traditional MR-based methods based on effective Hamiltonians fail due to intruders.

Journal Article↗

PubMed2003

Light-mediated regulation defines a minimal promoter region of TOP2.

Light signaling has been demonstrated to be an important factor for plant growth and development; however, its role in the regulation of DNA replication and cell cycle has just started to be unraveled. In this work, we have demonstrated that the TOP2 promoter of Pisum sativum (pea) is activated by a broad spectrum of light including far-red light (FR), red light (RL) and blue light (BL). Deletion analyses of the TOP2 promoter in transformed plants, Arabidopsis thaliana and Nicotiana tobaccum (tobacco), define a minimal promoter region that is induced by RL, FR and BL, and is essential and sufficient for light-mediated activation. The minimal promoter of TOP2 follows the phytochrome- mediated low-fluence response similar to complex light regulated promoters. DNA-protein interaction studies reveal the presence of a DNA binding activity specific to a 106 bp region of the minimal promoter that is crucial for light-mediated activation. These results altogether indicate a direct involvement of light signaling in the regulation of expression of TOP2, one of the components of the DNA replication/cell cycle machinery.

Arabidopsis↗

PubMed2003

Identification of Arabidopsis rat mutants.

Limited knowledge currently exists regarding the roles of plant genes and proteins in the Agrobacterium tumefaciens-mediated transformation process. To understand the host contribution to transformation, we carried out root-based transformation assays to identify Arabidopsis mutants that are resistant to Agrobacterium transformation (rat mutants). To date, we have identified 126 rat mutants by screening libraries of T-DNA insertion mutants and by using various "reverse genetic" approaches. These mutants disrupt expression of genes of numerous categories, including chromatin structural and remodeling genes, and genes encoding proteins implicated in nuclear targeting, cell wall structure and metabolism, cytoskeleton structure and function, and signal transduction. Here, we present an update on the identification and characterization of these rat mutants.

Agrobacterium tumefaciens↗

PubMed2002

Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis.

The Z-box is one of the light-responsive elements (LREs) found in the promoters of light inducible genes. We have studied the light responsive characteristics of Z-box containing synthetic as well as native promoters. We show that promoters with Z-box as a single LRE or paired with another LRE can respond to a broad spectrum of light. The response is primarily mediated by phyA, phyB and CRY1 photoreceptors at their respective wavelengths of light. We have demonstrated that CAB1 and Z-GATA containing promoters are down-regulated in hy5 mutants in the light. On the other hand, a promoter with Z-box alone is down-regulated in hy5 mutants both in dark and in light conditions, suggesting involvement of a similar regulatory system in the regulation of the promoter in two distinct developmental pathways: skotomorphogenesis and photomorphogenesis. Furthermore, similar to the CAB1 promoter, a Z-GATA containing promoter is derepressed in cop1 mutants in the dark. DNA-protein interaction studies reveal the presence of a DNA-binding activity that is specific to Z-box. These results provide insights into the regulation of the Z-box LRE mediated by various light signaling components.

Arabidopsis↗