Search PubMed⌕ Search

Biomedical subjects

S Sarkar

Publications and source records attributed to S Sarkar.

At least 127 records · Page 7Linked to original sources

A hybrid technique for spectroscopic imaging with reduced truncation artifact.

Traditionally, Fourier spectroscopic imaging is associated with a small k-space coverage which leads to truncation artifacts such as "bleeding" and ringing in the resultant image. Because substantial truncation artifacts mainly arise from regions having intense signals, such as the subcutaneous lipid in the head, effective reduction of truncation artifacts can be achieved by obtaining an extended k-space coverage for these regions. In this paper, a hybrid technique which employs phase-encoded spectroscopic imaging (SI) to cover the central portion of the k-space and echo-planar spectroscopic imaging (EPSI) to measure the peripheral portion of the k-space is developed. EPSI, despite its inherently low SNR characteristics, provides a sufficient SNR for outer high-spatial frequency components of the aforementioned high signal regions and supplies an extended k-space coverage of these regions for the reduction of truncation artifacts. The data processing includes steps designed to remove inconsistency between the two types of data and a previously described technique for selectively retaining only outer k-space information for the high signal regions during the reconstruction. Experimental studies, in both phantoms and normal volunteers, demonstrate that the hybrid technique provides significant reduction in truncation artifacts.

Artifacts↗

Cortical activation during oesophageal stimulation: a neuromagnetic study.

We investigated the neuromagnetic responses to mechanical stimulation of the oesophagus. In six healthy right-handed volunteers (mean age 31.6 years) the proximal and distal oesophagus were stimulated by electronically controlled pump-inflation of a silicone balloon once every 4.5-5.5 sec (dwell time 145 msec). The balloon volume was adjusted to induce different sensation levels (i) just above threshold of perception, (ii) strong sensation and (iii) painful sensation. Evoked magnetic brain responses were recorded time-locked to stimulus onset with a Neuromag-122TM whole-head neuromagnetometer and modelled as equivalent current diploe (ECD) sources. ECDs were superimposed on individual magnetic resonance imaging (MRI) scans. Magnetic brain responses following distal oesophageal stimulation were adequately explained by a time-varying 2-4 dipole model with unilateral or bilateral sources in second somatosensory cortex and later sources in the frontal cortex. With increasing stimulus intensities, latencies of the sources decreased and amplitudes increased. Proximal oesophageal stimulation led to activation of source areas spatially similar to those of distal oesophageal stimulation but with shorter response latencies. Both painful and nonpainful mechanical stimulation of the oesophagus activate the second somatosensory cortex (SII). Evidence for topographic organization of oesophageal afferents in SII is poor.

Adult↗

Signatures of chaos in the entanglement of two coupled quantum kicked tops.

We investigate the rate at which two initially decoupled quantum kicked tops become entangled upon the introduction of an interaction between them. We find that the entanglement eventually increases linearly in time. Moreover, we find that the rate of this linear increase is itself a linear function of the sum of the positive Lyapunov exponents when averaged over initial points drawn from the classical distributions corresponding to the initial quantum product state. The entanglement measure that is used allows us to identify entanglement with sensitive dependence on initial conditions.

Journal Article↗

Specificity determinants of proteolytic processing of Aspergillus PacC transcription factor are remote from the processing site, and processing occurs in yeast if pH signalling is bypassed.

The Aspergillus nidulans transcription factor PacC, which mediates pH regulation, is proteolytically processed to a functional form in response to ambient alkaline pH. The full-length PacC form is unstable in the presence of an operational pH signal transduction pathway, due to processing to the relatively stable short functional form. We have characterized and used an extensive collection of pacC mutations, including a novel class of "neutrality-mimicking" pacC mutations having aspects of both acidity- and alkalinity-mimicking phenotypes, to investigate a number of important features of PacC processing. Analysis of mutant proteins lacking the major translation initiation residue or truncated at various distances from the C terminus showed that PacC processing does not remove N-terminal residues, indicated that processing yields slightly heterogeneous products, and delimited the most upstream processing site to residues approximately 252 to 254. Faithful processing of three mutant proteins having deletions of a region including the predicted processing site(s) and of a fourth having 55 frameshifted residues following residue 238 indicated that specificity determinants reside at sequences or structural features located upstream of residue 235. Thus, the PacC protease cuts a peptide bond(s) remote from these determinants, possibly thereby resembling type I endonucleases. Downstream of the cleavage site, residues 407 to 678 are not essential for processing, but truncation at or before residue 333 largely prevents it. Ambient pH apparently regulates the accessibility of PacC to proteolytic processing. Alkalinity-mimicking mutations L259R, L266F, and L340S favor the protease-accessible conformation, whereas a protein with residues 465 to 540 deleted retains a protease-inaccessible conformation, leading to acidity mimicry. Finally, not only does processing constitute a crucial form of modulation for PacC, but there is evidence for its conservation during fungal evolution. Transgenic expression of a truncated PacC protein, which was processed in a pH-independent manner, showed that appropriate processing can occur in Saccharomyces cerevisiae.

Amino Acid Sequence↗

Dominant genetic alterations in immortalization: role for 20q gain.

Gain of 20q has been observed in many cancer types, including bladder cancers. However, the biological significance of low-copy-number 20q gain in human cancer pathogenesis has not yet been defined. We reported that immortalization of human uroepithelial cells (HUC) transformed with human papillomavirus 16 (HPV 16) E7 is associated with single-copy 20q gain (P = 2 x 10(-7)). We also observed 20q13.2 amplification in some cell lines, but only after 20 passages. Thus, we hypothesized that low-copy gain of 20q gene(s) contributes in a dominant way to bypassing HUC senescence. To test this hypothesis, we fused precrisis E7-transformed HUCs (pcE7s) with three independent immortal E7-HUCs that acquired a single-copy 20q gain at immortalization. In one of these lines, a single-copy gain of 20q and a 10p12.1-pter loss were the only cytogenetic alterations. Immortal cell hybrids were obtained with all three crosses. Southern analysis for unique HPV16 insertion sites, as well as fluorescence in situ hybridization (FISH) with whole chromosome 20 painting probes (WCP20) for marker chromosomes in the immortal clones, confirmed the hybrid and independent nature of representative immortal clones. In contrast, when we used the same protocol, no immortal somatic cell hybrids were obtained when HPV16 E6 immortal HUC (E6-HUC) that showed 3p and 9p losses, but no 20q gain, were fused with precrisis E6-transformed HUC (pcE6s). This latter observation is consistent with many results demonstrating that recessive changes are required for cell immortalization. Therefore, the new results reported herein for the first time demonstrate that dominant changes can contribute to bypassing senescence, and that such genes may be located on 20q. Genes Chromosomes Cancer 26:304-311, 1999.

Cell Transformation, Neoplastic↗

Osteoblastoma of dorsal spine: a case report.

A case of benign osteoblastoma affecting posterior element of spine with pain and paraplegia in a female is being presented with brief review of literature. Early diagnosis and surgical excision remains the mainstay of treatment.

Adolescent↗

Changes in the arch length following premature loss of deciduous molars.

When the normal physiological process of deciduous tooth exfoliation and eruption of its successor is disrupted, a series of changes are observed in the dental arches. The aim of the study was to evaluate the amount of changes in arch length after the premature loss of deciduous molars. The sample consisted of 82 children, 53 without premature loss and 29 with premature loss of either deciduous first or second molar or both, unilaterally. A reduction in arch length was observed both in the maxilla and mandible at the molar region and an increase in arch length at the canine region in the mandible. Reduction in arch length was due to mesial migration of the molar and the increase in arch length was due to the distal migration of canine. It was seen that arch length reduction was more in maxilla as compared to the mandible and that distal drifting of canine was observed only in the mandible.

Child↗

"Talon cusp-heredity origin"--a case report.

Talon cusp is a very unusual anomalous structure of tooth. The etiology is still unknown. It may be due to mal-interaction between ecto and mesoderm of epithelial bulgings present on premaxillary region at the time of complex odontogenesis. Genetics may have some role in the formation of Talon cusp. Talon cusp may cause clinical complications.

Adult↗

Tyrosine phosphorylation and translocation of LAT in platelets.

Platelet aggregation is accompanied by the tyrosine phosphorylation of several proteins including syk. However, some of these proteins are not identified. Recent studies showed that LAT is a syk substrate and is tyrosine phosphorylated during T cell stimulation. In this study, we demonstrated that LAT is present in platelets and is tyrosine phosphorylated in response to ADP- and thrombin-stimulated aggregation. Moreover, LAT, like syk and beta3, translocates to the cytoskeleton during the late stage of thrombin-stimulated irreversible aggregation and not during ADP-stimulated reversible aggregation.

Adaptor Proteins, Signal Transducing↗

Requirement of GM2 ganglioside activator for phospholipase D activation.

Sequence analysis of a heat-stable protein necessary for the activation of ADP ribosylation factor-dependent phospholipase D (PLD) reveals that this protein has a structure highly homologous to the previously known GM2 ganglioside activator whose deficiency results in the AB-variant of GM2 gangliosidosis. The heat-stable activator protein indeed has the capacity to enhance enzymatic conversion of GM2 to GM3 ganglioside that is catalyzed by beta-hexosaminidase A. Inversely, GM2 ganglioside activator purified separately from tissues as described earlier [Conzelmann, E. & Sandhoff, K. (1987) Methods Enzymol. 138, 792-815] stimulates ADP ribosylation factor-dependent PLD in a dose-dependent manner. At higher concentrations of ammonium sulfate, the PLD activator protein apparently substitutes for protein kinase C and phosphatidylinositol 4,5-bisphosphate, both of which are known as effective stimulators of the PLD reaction. The mechanism of action of the heat-stable PLD activator protein remains unknown.

Amino Acid Sequence↗

A recombinant monocysteine mutant (Ser to Cys-155) of fast skeletal troponin T: identification by cross-linking of a domain involved in a physiologically relevant interaction with troponins C and I.

Troponin T (TnT), a subunit of the heterotrimeric troponin (Tn) complex, is essential for the Ca2+ regulation of vertebrate striated muscle contraction both in vivo and in vitro. With the exception of bovine cardiac TnT, all known vertebrate TnT isoforms lack a thiol group, a property which makes the wild-type proteins unsuitable as cross-linking substrate. We generated a mutant human fast skeletal TnT in which Ser155 was changed to Cys (TnT-Cys155). Mutation of this residue in TnT as well as in vitro expression in Escherichia coli and purification of the recombinant mutant protein did not affect its biological properties in terms of in vitro binding to troponin I (TnI), troponin C (TnC), actin-tropomyosin (actin-Tm), and actomyosin ATPase activity. TnT-Cys155 was labeled with 4-maleimidobenzophenone (BP-TnT155) and photo-cross-linked to TnI, TnC, Tm, and all of the thin filament proteins. BP-TnT155 did not cross-link to Tm and showed weak Ca2+/Mg2+-independent cross-linking with TnI in the binary complex and in the presence of all thin filament protein components. BP-TnT155 showed Ca2+/Mg2+-dependent cross-linking with TnC in the binary and ternary complexes and Ca2+-favored cross-linking with TnI in the ternary complex. Thus, residue 155 of TnT is within 10 A (the length of cross-linker) of TnC in the presence or absence of Ca2+ and comes within 10 A of both TnI and TnC in the presence of Ca2+. TnT residue 155 is in close proximity to or may even partly encompass the Tm binding site. These results suggest that TnT, in association with TnI, may participate in the "information transfer" mediated by the Ca2+ binding signal from TnC to Tm and the region around TnT residue 155 probably acts as a linker between troponin and actin-Tm in this signal transmission process. Our results also suggest that TnT contains at least one Ca2+/Mg2+-dependent TnC binding region located between its Tm and TnI binding regions. A recombinant truncated fragment of TnI, TnI96-181, containing amino acid residues 96-181 and labeled with BP at Cys-133, failed to cross-link with TnT, indicating that the region around Cys-133 of TnI is not involved in binary interaction with TnT.

Animals↗

Strain differences in cytochrome P4501A1 gene expression caused by 2,3,7,8-tetrachlorodibenzo-p-dioxin in the rat liver: role of the aryl hydrocarbon receptor and its nuclear translocator.

Rat strain variation in hepatic cytochrome P4501A1 (CYP1A1) gene expression caused by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) was investigated along with possible underlying mechanism. TCDD at a single oral dose of 13.5 ng/kg body weight significantly increased hepatic CYP1A1 mRNA expression in DRH, Long-Evans Cinamon (LEC), Long-Evans (LE), and Holtzman (HO) rats, but not in Sprague-Dawley (SD), Wistar-Imamichi (WI), Lewis (LEW), and Fisher-344 (F344) strains. All showed significant induction of CYP1A1 mRNA at a dose of 40 ng/kg, the relative levels decreasing in the order DRH, LEC, HO, LE, F344, WI, LEW, and SD. A more than 35-fold difference in the induction of CYP1A1 RNA was evident between the DRH and SD strains. Based on CYP1A1 induction, classification into two distinctly separate groups was possible, high responders (DRH, LEC, HO, and LE) and low responders (SD, LEW, WI, and F344). The expression levels closely correlated with the steady-state aryl hydrocarbon receptor (AhR) mRNA expression, this being approximately four-fold higher in the high than in the low responder group. Analysis of the aryl hydrocarbon receptor nuclear translocator (ARNT) showed the presence of a wild type as well as an alternately spliced variant in all strains, with a 45-bp deletion whose sequence corresponded to part of 5' end of the basic region of the basic helix-loop-helix domain. Expressed levels of both products were almost equal in all the strains except DRH, LEC and HO, where the wild form predominated. The results suggest that differential expression of both AhR and ARNT are responsible for rat strain-specific differences in TCDD induced CYP1A1 expression.

Amino Acid Sequence↗

Identification and characterization of receptors for riboflavin carrier protein in the chicken oocyte. Role of the phosphopeptide in mediating receptor interaction.

Riboflavin carrier protein (RCP) is a phosphoglycoprotein found in the egg and the serum of laying birds and other animals. We have investigated the binding of chicken RCP (cRCP) to membranes prepared from the whole chicken oocytes. RCP binding had an absolute requirement for calcium, with an affinity (Kd 10(-8) M) high enough to be physiologically relevant. Ligand blotting experiments using labeled RCP and vitellogenin, with proteins solubilized from oocyte membranes, indicated that RCP and vitellogenin bound specifically to three proteins of Mr 380, 260 and 110 kDa. Vitellogenin also bound to proteins of Mr 515 kDa and 97 kDa, similar in size to those identified by receptor associated protein of RAP. Reduced and carboxyamidated RCP inhibited the binding of 125I-labeled RCP to chicken oocyte membranes, but recombinant RCP expressed in E. coli, and dephosphorylated RCP, failed to interact with the receptors, indicating that post-translational modifications were necessary for ligand-receptor interaction. The purified phosphopeptide, prepared from tryptic digests of egg white RCP, was able to inhibit the binding of RCP to the receptor proteins, with an affinity comparable to native RCP indicating that the phosphopeptide sequence present in RCP serves as the focal point for RCP-receptor interactions.

Amino Acid Sequence↗

Identification and mutagenesis of a highly conserved domain in troponin T responsible for troponin I binding: potential role for coiled coil interaction.

Troponin T (TnT), a thin filament myofibrillar protein, is essential for the Ca2+ regulation of striated muscle contraction in vertebrates, both in vivo and in vitro. To understand the role of TnT in this process, its interaction with two other troponin components, troponin I (TnI) and troponin C (TnC) was examined by using the yeast two hybrid system, which is a genetic approach to detect protein-protein interactions. Computer assisted analysis of phylogenetically distant TnT amino acid sequences unveiled a highly conserved protein domain that is characterized by a heptad repeat (HR) motif with a potential for alpha-helical coiled coil formation. A similar, potentially coiled coil forming domain is also conserved in all known TnI sequences. These protein motifs appeared to be the regions where TnI-TnT interaction may take place. Deletions and point mutations in TnT, which disrupted its HR motif, severely reduced or abolished TnI binding, but binding to TnC was not affected, indicating that the TnT-TnI and TnT-TnC binary interactions can be uncoupled. Remarkably, the truncated fragments of TnT and TnI in which the HR motifs were retained showed binary interaction in the yeast two hybrid system. It was also observed that the formation of the TnT-TnI heterodimers is favored over the homodimers TnT-TnT and TnI-TnI. These results indicate that the evolutionarily conserved HR motifs may play a role in TnT-TnI dimerization, presumably through the formation of alpha-helical coiled coils.

Amino Acid Sequence↗

Influence of alkali-treated cornsteep liquor containing medium on protein A production by Staphylococcus aureus.

Staphylococcus aureus cultivated in liquid media containing untreated cornsteep liquor (CSL) and alkali-treated CSL produced similar biomass yields (6.5-6.9 g/L). However, contents of protein A in the biomass was 0.5% and 1.56% for untreated CSL and treated CSL, respectively. Addition of treated CSL at 20 g/L achieved optimal enhancement of protein A production (0.11 g/L). Probable factors associated in treated CSL for the enhanced protein A production are discussed.

Culture Media↗