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R Sen

Publications and source records attributed to R Sen.

At least 55 records · Page 3Linked to original sources
PubMed1994

Intrinsic fluorescence of E. coli RNA polymerase as a probe for its conformational changes during transcription initiation.

A simple fluorimetric assay based on internal fluorescence of tryptophan residues of E. Coli RNA polymerase has been developed to ascertain the number of steps during conversion of closed complex of the polymerase-promoter (trp promoter cloned in plasmid pDR720) to open complex. Our results from measurement on relative ratio of fluorescence at 340 nm (lambda ex = 295 nm) for free and promoter-bound RNA polymerase as a function of temperature, within the range 4 degrees C to 37 degrees C, indicate following equilibria for the above conversion: R+P<-->RPc<-->RPi1<-->RPi2<-->RPo. Apart from detection of one more intermediate in terms of conformational states of the bound RNA polymerase, second feature of our studies is the examination of conformational state of the polymerase using accessibility of fluorophor, tryptophan residues, to a neutral quencher, acrylamide, as the probe. We observe that in terms of accessibility of tryptophan residues in protein, intermediate complex, RPi2, is conformationally most perturbed in comparison to free polymerase. Implications of these results are discussed and compared with the available reports from footprinting and gel retardation assays of RNA polymerase-promoter interactions.

Cloning, Molecular↗
PubMed1994

Cyclosporin A sensitivity of the NF-kappa B site of the IL2R alpha promoter in untransformed murine T cells.

We have investigated the characteristics of IL2R alpha gene induction in untransformed murine T cells. Induction of IL2R alpha mRNA by TCR/CD3 ligands in a murine T cell clone and in short-term splenic T cell cultures was inhibited by protein synthesis inhibitors and by CsA. This result was contrary to previous observations in JURKAT T leukemia cells and human peripheral blood T cells, suggesting a difference in the mechanisms of IL2R alpha gene induction in these different cell types. The CsA sensitivity of IL2R alpha mRNA induction represented a direct effect on the TCR/CD3 response, and was not due to CsA-sensitive release of the lymphokines IL2 or tumour necrosis factor alpha (TNF alpha) and consequent lymphokine-mediated induction of IL2R alpha mRNA. The NF-kappa B site of the IL2R alpha promoter was essential for gene induction through the TCR/CD3 complex, and the induction of reporter plasmids containing multimers of this site was significantly inhibited by CsA. Northern blotting analysis indicated that while the p65 subunit of NF-kappa B was constitutively expressed and not appreciably induced upon T cell activation, mRNA for the p105 precursor of p50 NF-kappa B was induced in response to TCR/CD3 stimulation and this induction was sensitive to CsA. Electrophoretic mobility shift assays and antiserum against the p50 subunit of NF-kappa B indicated that p50 was a component of the inducible nuclear complex that bound to the IL2R alpha kappa B site. Appearance of the kB-binding proteins was insensitive to CsA at early times after activation (approximately 15 min), but was partially sensitive to CsA at later times. Based on these results, we propose that the NF-kappa B site of the IL2R alpha promoter mediates at least part of the CsA sensitivity of IL2R alpha gene induction in untransformed T cells, possibly because de novo synthesis of p105 NF-kappa B is required for sustained IL2R alpha expression.

Animals↗
PubMed1994

Cyclosporin-A sensitive induction of NF-AT in murine B cells.

Primary B cells are induced to proliferate by cross-linking surface immunoglobulin or by its pharmacological equivalent, phorbol ester and calcium ionophore. However, nuclear responses that have been studied in activated B cells are typically inducible with phorbol esters alone. We show that a factor, indistinguishable from the nuclear factor of activated T cells (NF-AT), is induced in B cells in response to anti-immunoglobulin signals or the combined action of phorbol ester and ionomycin, but not in response to either reagent alone. The signals necessary for NF-AT induction in B cells, therefore, closely parallel those required to induce B cell proliferation. Transfection analysis shows that B cell NF-AT is a transcriptional activator. Furthermore, NF-AT induction in splenic cells is suppressed by cyclosporin A, suggesting a mechanism by which immunosuppressive agents act on the B cell compartment. We propose that NF-AT should be considered more generally as a nuclear factor of activated lymphoid cells.

Animals↗
PubMed1994

Comparative evaluation of commonly used catheters through histopathological changes induced in bladder urothelium.

There is growing concern about the toxic potential of chemicals coating various catheter materials, especially due to lack of international standards for toxicity testing. The present study evaluates the toxicity potential in terms of pathological changes induced by the catheters commonly used in practice, i.e. latex-, silicone- and Teflon-coated catheters. Teflon-coated catheters appear to be superior to others in the present study.

Biopsy↗
PubMed1994

Clinico-haematological profile in acute and chronic Plasmodium falciparum malaria in children.

The clinicohaematological findings of acute state (Group A, 30 patients) and chronic state (Group B, 34 patients) of falciparum malaria in paediatric patients are compared. The children with chronic falciparum malaria were apyrexic and presented with features of moderate to severe anaemia with hepato-splenomegaly. Greater severity of anaemia and haemolysis, higher incidence and severity of neutropenia, atypical lymphocytosis, monocytosis and thrombocytopenia were observed in patients with chronic falciparum malaria as compared to patients with acute falciparum malaria despite lesser degree of parasitaemia in the former as compared to the latter. While mechanical destruction of parasitised RBC's, ineffective and dysplastic erythropoiesis either due to unmasking of border line dierty folic acid deficiency or otherwise, transient hypoplasia of bone marrow, impaired utilization of iron and immune destruction of RBCs with hypersplenism may be the mechanisms for anaemia, transient hypoplasia of bone marrow and hypersplenism may be the factors responsible for thrombocytopenia and neutropenia.

Acute Disease↗
PubMed1993

Switch recombination breakpoints occur at nonrandom positions in the S gamma tandem repeat.

Ig switch (S) recombination is clearly focused on S regions. It is possible that S-specific DNA binding proteins facilitate the alignment of these regions before recombination. The S gamma 3-specific DNA binding proteins, SNAP and SNIP/NF-kappa B, interact with two discrete regions of the S gamma 3 tandem repeat, the A and B sites. Recombination breakpoints in the S gamma 3 region were found to significantly correlate with the binding sites of the S gamma 3 binding proteins. We now report the conservation of the SNIP and SNAP binding sites in S gamma 2b and S gamma 1 DNA. SNIP/NF-kappa B interacts with its cognate sites in S gamma 2b and S gamma 1 DNA as determined by mobility shift assays, competition binding studies, and supershift analysis using an antiserum specific for the p50 component. SNAP binds specifically to S gamma 2b and S gamma 1 as measured by mobility shift assays and competition binding studies. SNAP is composed of two closely traveling mobilities that do not separate on partial purification. SNIP and SNAP are expressed in nuclear extracts derived from murine splenic B cell cultures stimulated with mitogen or mitogen and IL-4. No new DNA binding proteins specific for S gamma 1 tandem repeats are detectable in nuclear extracts from B cells stimulated with mitogen and IL-4. The sites at which recombination occurs in the S gamma 2b and S gamma 1 regions have been analyzed statistically and found to correlate with the SNIP/NF-kappa B and SNAP binding sites. Distinctions have been found regarding the use of DNA substrates within the tandem repeat between primary (mu-->gamma) and successive (gamma-->x) S recombination.

Animals↗
PubMed1993

Interaction of ribonucleotides with T7 RNA polymerase: probable role of GTP in transcription initiation.

Interaction of ribonucleotides (NTP where N = G, A, C or U) with bacteriophage T7 RNA polymerase (T7 RNAP) was studied by fluorescence emission spectroscopy of the enzyme. From the NTP-concentration-dependent quenching of fluorescence of the enzyme, apparent dissociation constants for NTP-T7 RNAP was found to be in following order: UTP>CTP>>ATP>GTP. Acrylamide quenching of tryptophan fluorescence of free and bound enzyme suggests a conformational change, particularly in the case of GTP (and ATP). This is the first report of high affinity binding of the enzyme with purine ribonucleotides in the absence of promoter. These results also suggest that GTP may induce a promoter-specific conformation of the enzyme. The observation could account for specific requirement of GTP in transcription initiation reported earlier (1-4).

Bacteriophage T7↗
PubMed1993

Functional GATA-3 binding sites within murine CD8 alpha upstream regulatory sequences.

Genes encoding the accessory molecules CD8 and CD4 are activated early in thymocyte development, generating CD4+8+ double positive intermediates, which give rise to two functionally distinct mature T cell subsets that express either CD4 or CD8. The mechanisms that govern the activation or suppression of the CD8 gene are likely to be central to the T cell development program. To identify the key regulatory factors, we have initiated an analysis of the transcriptional regulation of the murine CD8 alpha gene. We have identified three CD8+ cell-specific DNAase I hypersensitive sites (HSS) located upstream of the murine CD8 alpha gene. In vitro mobility shift analysis of the -4.0-kb HSS region has revealed multiple binding sites for the T cell-restricted transcription factor GATA-3. In vitro translated murine GATA-3 binds specifically to both CD8 GATA sites, and coexpression of this factor in transient transfection assays transactivates a reporter construct containing these sequences. These results provide the first evidence for the role of a T cell-restricted factor in the regulation of either CD8 or CD4 genes.

Animals↗
PubMed1993

Regulation of lymphoid-specific immunoglobulin mu heavy chain gene enhancer by ETS-domain proteins.

The enhancer for the immunoglobulin mu heavy chain gene (IgH) activates a heterologous gene at the pre-B cell stage of B lymphocyte differentiation. A lymphoid-specific element, microB, is necessary for enhancer function in pre-B cells. A microB binding protein is encoded by the PU.1/Spi-1 proto-oncogene. Another sequence element, microA, was identified in the mu enhancer that binds the product of the ets-1 proto-oncogene. The microA motif was required for microB-dependent enhancer activity, which suggests that a minimal B cell-specific enhancer is composed of both the PU.1 and Ets-1 binding sites. Co-expression of both PU.1 and Ets-1 in nonlymphoid cells trans-activated reporter plasmids that contained the minimal mu enhancer. These results implicate two members of the Ets family in the activation of IgH gene expression.

Animals↗
PubMed1993

Abnormal kappa B-binding protein in the cytoplasm of a plasmacytoma cell line that lacks nuclear expression of NF-kappa B.

The transcription factor NF-kappa B appears to play an important role in immunoglobulin gene expression and lymphokine production, and may play a role in primary B cell activation. Constitutive nuclear expression of NF-kappa B has been found in all mature B cell lines with the notable exception of the murine plasmacytoma, S107. We report herein that S107 cells express cytoplasmic kappa B-binding material detected by electrophoretic mobility shift assay that by several criteria represents authentic NF-kappa B. Despite the presence of cytoplasmic NF-kappa B, several stimuli known to induce nuclear translocation of NF-kappa B failed to do so in S107 cells, including: the PKC agonist, PMA; the protein synthesis inhibitor, cycloheximide; and LPS. Transfection of S107 cells with a kappa B-CAT reporter gene construct confirmed the absence of functional activity. Importantly, a global failure of nuclear transcription factor expression was ruled out by the ability of PMA to induce nuclear expression of another trans-acting factor, AP-1. Thus, rather than lacking NF-kappa B altogether, S107 cells manifest disordered regulation of NF-kappa B in which cytoplasmic material is incapable of translocation to the nucleus. While Northern analysis failed to reveal a gross defect in the mRNA coding for the DNA binding subunit of NF-kappa B, UV-photo-cross-linking followed by denaturing gel electrophoresis demonstrated the presence of a cytoplasmic kappa B-binding protein of abnormally elevated molecular size. This finding suggests that the abnormal regulation of NF-kappa B in S107 cells is associated with the appearance of an unusual kappa B-binding molecule.

Animals↗
PubMed1992

Switch recombination breakpoints are strictly correlated with DNA recognition motifs for immunoglobulin S gamma 3 DNA-binding proteins.

The deletion looping out model of switch (S) recombination predicts that the intervening DNA between switch regions will be excised as a circle. Circular excision products of immunoglobulin switch recombination have been recently isolated from lipopolysaccharide (LPS)-stimulated spleen cells. The recombination breakpoints in these large circles were found to fall within switch regions. Since switch recombination is clearly focused on switch regions, we hypothesized that some DNA-binding protein factor might be involved in specifically recognizing and facilitating the alignment of switch regions before recombination. Two DNA-binding proteins that specifically interact with two discrete regions of the S gamma 3 tandem repeat have been identified in crude and partially purified nuclear extracts derived from LPS- and dextran sulfate (DxS)-activated splenic B cells. The first factor has been found indistinguishable from NF-kappa B by mobility shift assays, methylation interference, competition binding studies, and supershift analysis using an antiserum specific for the p50 component. The second appears to be composed of two closely traveling mobilities that do not separate upon partial purification. This second complex is unique and specific for S gamma 3 by methylation interference assays and competition-binding analysis. The sites at which recombination occurs in the S gamma 3 switch region have been analyzed and found to strictly correlate with the binding sites of the S gamma 3 switch binding proteins.

Amino Acid Sequence↗
PubMed1992

Interaction between antitumor antibiotic chromomycin A3 and Mg2+. I. Evidence for the formation of two types of chromomycin A3-Mg2+ complexes.

Chromomycin A3 (CHRA3) is an antitumor antibiotic which binds to Mg2+. In the present communication, we show, by means of equilibrium spectroscopic studies (such as absorption, fluorescence and circular dichroism), that two types of CHRA3-Mg2+ complexes (of 1:1 and 1.9:1 stoichiometries in terms of CHRA3:Mg2+, respectively) are formed depending on the concentrations of CHRA3 and Mg2+. The rate constant and activation energy for the formation of two complexes are different, thereby reinforcing the proposition that they are different molecular species. This observation is novel and significant in order to understand the anticancer property of the drug. It also provides explanation for earlier observations that site, affinity parameters and mode of interaction of the drug with DNA in the presence of Mg2+ depend on the relative concentration of Mg2+.

Chromomycin A3↗
PubMed1992

Role of magnesium ion in the interaction between chromomycin A3 and DNA: binding of chromomycin A3-Mg2+ complexes with DNA.

Chromomycin A3 is an antitumor antibiotic which blocks macromolecular synthesis via reversible interaction with DNA template only in the presence of divalent metal ions such as Mg2+. The role of Mg2+ in this antibiotic-DNA interaction is not well understood. We approached the problem in two steps via studies on the interaction of (i) chromomycin A3 and Mg2+ and (ii) chromomycin A3-Mg2+ complex(es) and DNA. Spectroscopic techniques such as absorption, fluorescence, and CD were employed for this purpose. The results could be summed up in two parts. Absorption, fluorescence, and CD spectra of the antibiotic change upon addition of Mg2+ due to complex formation between them. Analysis of the quantitative dependence of change in absorbance of chromomycin A3 (at 440 nm) upon input concentration of Mg2+ indicates formation of two types of complexes with different stoichiometries and formation constants. Trends in change of fluorescence and CD spectroscopic features of the antibiotic in the presence of Mg2+ at different concentrations further corroborate this result. The two complexes are referred to as complex I (with 1:1 stoichiometry in terms of chromomycin A3:Mg2+) and complex II (with 2:1 stoichiometry in terms of chromomycin A3:Mg2+), respectively, in future discussions. The interactions of these complexes with calf thymus DNA were examined to check whether they bind differently to the same DNA. Evaluation of binding parameters, intrinsic binding constants, and binding stoichiometry, by means of spectrophotometric and fluorescence titrations, shows that they are different. Distinctive spectroscopic features of complexes I and II, when they are bound to DNA, also support that they bind differently to the above DNA. Measurement of thermodynamic parameters characterizing their interactions with calf thymus DNA shows that complex I-DNA interaction is exothermic, in contrast to complex II-DNA interaction, which is endothermic. This feature implies a difference in the molecular nature of the interactions between the complexes and calf thymus DNA. These observations are novel and significant to understand the antitumor property of the antibiotic. They are also discussed to provide explanations for the earlier reports that in some cases appeared to be contradictory.

Animals↗
PubMed1992

A T cell nuclear factor resembling NF-AT binds to an NF-kappa B site and to the conserved lymphokine promoter sequence "cytokine-1".

Nuclear extracts from a nontransformed murine T lymphocyte clone contained two inducible factors that bound to a nuclear factor kappa B (NF-kappa B) site. One factor was NF-kappa B, and the other was differentiated from NF-kappa B by its mobility in the electrophoretic mobility shift assay and its lack of sensitivity to protein kinase C depletion. Competition and methylation interference assays showed that the binding site for the novel factor was limited to nucleotides in the 3' half of the kappa B site. This part of the kappa B site resembled sequences in the binding site for a second inducible nuclear factor of T cells, NF-AT, as well as a conserved sequence found in several lymphokine genes, termed "cytokine-1" (CK-1). Competition and methylation interference analysis showed that both NF-AT and CK-1 sequences bound a factor similar to the novel kappa B-binding factor and that binding involved a four-nucleotide sequence (TTCC) that the kappa B, CK-1, and NF-AT sites have in common. The complexes that form with each site have characteristics of NF-AT: they are induced upon T cell receptor stimulation, are sensitive to protein synthesis inhibitors and cyclosporin A, and are not sensitive to protein kinase C depletion. Thus, a factor or factors similar to NF-AT can bind to three distinct promoter sequences which occur commonly in several T cell activation genes. These results raise the possibility that related factors binding to kappa B, CK-1, and NF-AT sequences could play a role in the coordinate induction of T cell activation genes. In addition, our results suggest that kappa B and CK-1 sites represent potential cyclosporin-sensitive promoter elements by virtue of their ability to bind an NF-AT-like factor.

Animals↗
PubMed1992

Regulation of immunoglobulin gene transcription.

Analysis of the immunoglobulin gene suggests that their expression is controlled through the combinatorial action of tissue- and stage-specific factors (OTF-2, TF-microB, NF-kappa B), as well as more widely expressed E motif-binding factors such as E47/E12. Two basic issues cloud understanding of how these factors are involved in immunoglobulin gene regulation. First, cloning of these factors shows them to be members of families of proteins, all with similar DNA-binding specificities. OTF-2 is a member of the POU domain family, NF-kappa B is a related protein, and the microE5/kappa E2-binding factors are members of the bHLH family. Second, these binding sites and associated factors are involved in the regulation of many genes, not only the immunoglobulin genes, and in fact not only lymphoid-specific genes. These facts complicate understanding which member of a family is in fact responsible for interaction with, and activation of, a particular binding element in an enhancer/promoter. Recently, more detailed analysis of the interactions between such proteins and their related binding sites suggest that a certain level of specificity may in fact be encoded by the DNA element such that one family member of a protein is preferentially bound, or alternatively that the protein-DNA interactions that occur give subtle alterations in protein conformation that unmask an activation or protein-protein interactive domain. An additional level of regulation is imparted by combinatorial mechanisms such as adjacent DNA-binding elements and factors that may alter activity, as well as "cofactors" that, by forming a complex with the bound factor, affect its activation of a gene in a particular cell type. A third level of specificity may be obtained by factors such as NF-kappa B and the bHLH family due to their ability to create heterogeneous complexes, creating unique complexes in a tissue- or stage-specific manner. The multiple functions transcription factors such as NF-kappa B and OTF-2 play in the transcriptional regulation of multiple genes seems complex in contrast to a one factor, one gene regulation model. However, this type of organization may limit the number of factors lymphocytes would require if each lymphoid-specific gene were activated by a unique factor. Thus what appears to be complexity at the molecular level may reflect an economical organization at the cellular level. Investigation of the key factors controlling these genes suggests an ordered cascade of transcription factors becomes available in the cell during B cell differentiation.(ABSTRACT TRUNCATED AT 400 WORDS)

Base Sequence↗
PubMed1991

Physiologic activation of T cells via the T cell receptor induces NF-kappa B.

The transcription factor NF-kappa B has been implicated in the mitogen-induced expression of several genes that are critical for the immunologic function of T cells such as those encoding IL-2 and the IL-2R alpha chain (IL-2R alpha). We show here that NF-kappa B is induced in T cells activated by Ag, anti-CD3 antibody, or allogeneic stimulation. The induction of NF-kappa B via the TCR was dependent on protein kinase C. IL-2, which also activates IL-2R alpha expression and proliferation in T cells, was not able to induce NF-kappa B. TCR-mediated induction of NF-kappa B suggests a central role for this factor in activated T cells and also provides a mechanism for activation of latent HIV provirus during the normal immune response.

Animals↗