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S Gopal

Publications and source records attributed to S Gopal.

At least 19 recordsLinked to original sources
PubMed2001

A functional update of the Escherichia coli K-12 genome.

BACKGROUND: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. RESULTS: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. CONCLUSIONS: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.

Bacterial Proteins↗
PubMed2001

Development and validation of a sensitive analytical method for the simultaneous determination of buprenorphine and norbuprenorphine in human plasma.

A sensitive, specific, and robust capillary gas chromatography-mass spectrometry method has been developed and validated for simultaneous determination of buprenorphine and its active metabolite, norbuprenorphine, in human plasma. Sample preparation involved a clean-up procedure using a Bond Elut Certify cartridge followed by derivatization with pentafluoropropionic anhydride. Separation was carried out on a HP-1 fused silica capillary column using helium as the carrier gas. Selected ion monitoring was used in the electron impact mode. Excellent linearity was found between 0.10 and 20.0 ng/ml with a limit of quantitation of 0.05 and 0.10 ng/ml for buprenorphine and norbuprenorphine, respectively. Interday and intraday assay precisions (%CV) and accuracies were within 15.0% for buprenorphine and norbuprenorphine, respectively. Recoveries were quantitative and concentration-independent. This method will be applied to pharmacokinetic/pharmacodynamic/bioequivalence studies of buprenorphine in humans.

Analgesics, Opioid↗
PubMed2001

Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.

The approach to annotating a genome critically affects the number and accuracy of genes identified in the genome sequence. Genome annotation based on stringent gene identification is prone to underestimate the complement of genes encoded in a genome. In contrast, over-prediction of putative genes followed by exhaustive computational sequence, motif and structural homology search will find rarely expressed, possibly unique, new genes at the risk of including non-functional genes. We developed a two-stage approach that combines the merits of stringent genome annotation with the benefits of over-prediction. First we identify plausible genes regardless of matches with EST, cDNA or protein sequences from the organism (stage 1). In the second stage, proteins predicted from the plausible genes are compared at the protein level with EST, cDNA and protein sequences, and protein structures from other organisms (stage 2). Remote but biologically meaningful protein sequence or structure homologies provide supporting evidence for genuine genes. The method, applied to the Drosophila melanogaster genome, validated 1,042 novel candidate genes after filtering 19,410 plausible genes, of which 12,124 matched the original 13,601 annotated genes. This annotation strategy is applicable to genomes of all organisms, including human.

Animals↗
PubMed2001

Self-reported photophobic symptoms in migraineurs and controls are reliable and predict diagnostic category accurately.

OBJECTIVES: To assess the reliability of self-reported photophobia across different patient populations and to examine how visual stress thresholds and photophobic symptoms may be predictive of diagnosis. BACKGROUND: Relatively little is known about interictal photophobia in migraine. In particular, the variability of photophobia across different patient groups has not previously been studied, and a pathophysiological hypothesis to account for the symptoms is not agreed upon. METHODS AND RESULTS: Study 1 compared 99 self-selected Dutch patients and 101 headache-free controls using survey methods. Patients both with and without aura were significantly more likely to report symptoms, such as the wearing of sunglasses in normal daylight, consistent with interictal photophobia. Study 2 replicated these findings in a series of consecutive referrals to a headache clinic in the United States. Study 3 used a specially designed laboratory test to examine the threshold for visual stress in those patients who had participated in study 2. Visual stress thresholds were significantly lower in patients than in controls. A discriminant function analysis of data from both studies 2 and 3 showed that diagnostic category (migraine; control) could be predicted from photophobic symptoms and visual stress thresholds at a level significantly better than chance. CONCLUSIONS: We suggest that interictal photophobia is common in migraine and similar across different patient populations. One pathophysiological hypothesis is that interictal photophobia is associated with cortical hypersensitivity to stimulation. The predictive validity of interictal photophobic symptoms suggests that clinical diagnosis may be aided by questioning the patient about light sensitivity in the period between attacks.

Humans↗
PubMed2000

Mutagenesis of organophosphorus hydrolase to enhance hydrolysis of the nerve agent VX.

Organophosphorus hydrolase (OPH) is capable of hydrolyzing a wide variety of organophosphorus pesticides and chemical warfare agents. However, the hydrolytic activity of OPH against the warfare agent VX is less than 0.1% relative to its activity against parathion and paraoxon. Based on the crystal structure of OPH and the similarities it shares with acetylcholinesterase, eight OPH mutants were constructed with the goal of increasing OPH activity toward VX. The activities of crude extracts from these mutants were measured using VX, demeton-S methyl, diisopropylfluoro-phosphate, ethyl parathion, paraoxon, and EPN as substrates. One mutant (L136Y) displayed a 33% increase in the relative VX hydrolysis rate compared to wild type enzyme. The other seven mutations resulted in 55-76% decreases in the relative rates of VX hydrolysis. There was no apparent relationship between the hydrolysis rates of VX and the rates of the other organophosphorus compounds tested.

Acetylcholinesterase↗
PubMed2000

Essential role for p38alpha mitogen-activated protein kinase in placental angiogenesis.

The p38 family of mitogen-activated protein kinases (MAPKs) mediates signaling in response to environmental stresses and inflammatory cytokines, but the requirements for the p38 MAPK pathway in normal mammalian development have not been elucidated. Here, we show that targeted disruption of the p38alpha MAPK gene results in homozygous embryonic lethality because of severe defects in placental development. Although chorioallantoic placentation is initiated appropriately in p38alpha null homozygotes, placental defects are manifest at 10.5 days postcoitum as nearly complete loss of the labyrinth layer and significant reduction of the spongiotrophoblast. In particular, p38alpha mutant placentas display lack of vascularization of the labyrinth layer as well as increased rates of apoptosis, consistent with a defect in placental angiogenesis. Furthermore, p38alpha mutants display abnormal angiogenesis in the embryo proper as well as in the visceral yolk sac. Thus, our results indicate a requirement for p38alpha MAPK in diploid trophoblast development and placental vascularization and suggest a more general role for p38 MAPK signaling in embryonic angiogenesis.

Animals↗
PubMed2000

Electronic Spectrum of the Antimony Monoxide Radical.

The 0-1 band (4271.3 Å) of the B(2)Sigma(+)-X(2)(2)Pi(3/2) transition, the 0-6 band (4275 Å) of the H(2)Pi(3/2)-X(2)(2)Pi(3/2) transition, the 0-0 band (3776.2 Å) of the B(2)Sigma(+)-X(1)(2)Pi(1/2) transition, and the 2-0 (3251.3 Å) as well as the 3-0 (3194.2 Å) bands of the C(2)Sigma(-)-X(1)(2)Pi(1/2) transition of SbO have been photographed at high resolution using the single isotope of antimony (121)Sb. An unambiguous analysis of the rotational structure of all these bands has been carried out for the first time. The magnitude and sign of the Lambda doubling constant p(0) of the X(1)(2)Pi(1/2) state have been determined and as a result of that, the symmetry of the C state has been uniquely identified as C(2)Sigma(-). Accurate rotational constants of all the states involved have been determined by a global linear least-squares fit. Copyright 2000 Academic Press.

Journal Article↗
PubMed2000

Bilateral breast MALT lymphoma: a case report and review of the literature.

Breast lymphoma is a rare disease. Both primary and secondary breast involvement have been reported. Most primary breast lymphomas are high-grade malignant neoplasms, mainly large cell and Burkitt type. Low-grade lymphomas of the breast, particularly mucosa-associated lymphoid tissue (MALT) lymphomas, have been exceedingly rare. In this report we present a patient with bilateral breast involvement by MALT lymphoma. Our patient developed localized MALT lymphoma in both breasts in a sequential fashion. She was treated with bilateral lumpectomy, followed by radiation therapy to both breasts. The patient is alive and well more than 1 year after therapy with no recurrence. We believe this is the first such case described in detail in the literature.

Aged↗
PubMed2000

Fix and flap: the radical orthopaedic and plastic treatment of severe open fractures of the tibia.

We performed a retrospective review of the case notes of 84 consecutive patients who had suffered a severe (Gustilo IIIb or IIIc) open fracture of the tibia after blunt trauma between 1990 and 1998. All had been treated by a radical protocol which included early soft-tissue cover with a muscle flap by a combined orthopaedic and plastic surgery service. Our ideal management is a radical debridement of the wound outside the zone of injury, skeletal stabilisation and early soft-tissue cover with a vascularised muscle flap. All patients were followed clinically and radiologically to union or for one year. After exclusion of four patients (one unrelated death and three patients lost to follow-up), we reviewed 80 patients with 84 fractures. There were 67 men and 13 women with a mean age of 37 years (3 to 89). Five injuries were grade IIIc and 79 grade IIIb; 12 were site 41, 43 were site 42 and 29 were site 43. Debridement and stabilisation of the fracture were invariably performed immediately. In 33 cases the soft-tissue reconstruction was also completed in a single stage, while in a further 30 it was achieved within 72 hours. In the remaining 21 there was a delay beyond 72 hours, often for critical reasons unrelated to the limb injury. All grade-IIIc injuries underwent immediate vascular reconstruction, with an immediate cover by a flap in two. All were salvaged. There were four amputations, one early, one mid-term and two late, giving a final rate of limb salvage of 95%. Overall, nine pedicled and 75 free muscle flaps were used; the rate of flap failure was 3.5%. Stabilisation of the fracture was achieved with 19 external and 65 internal fixation devices (nails or plates). Three patients had significant segmental defects and required bone-transport procedures to achieve bony union. Of the rest, 51 fractures (66%) progressed to primary bony union while 26 (34%) required a bone-stimulating procedure to achieve this outcome. Overall, there was a rate of superficial infection of the skin graft of 6%, of deep infection at the site of the fracture of 9.5%, and of serious pin-track infection of 37% in the external fixator group. At final review all patients were walking freely on united fractures with no evidence of infection. The treatment of these very severe injuries by an aggressive combined orthopaedic and plastic surgical approach provides good results; immediate internal fixation and healthy soft-tissue cover with a muscle flap is safe. Indeed, delay in cover (>72 hours) was associated with most of the problems. External fixation was associated with practical difficulties for the plastic surgeons, a number of chronic pin-track infections and our only cases of malunion. We prefer to use internal fixation. We recommend primary referral to a specialist centre whenever possible. If local factors prevent this we suggest that after discussion with the relevant centre, initial debridement and bridging external fixation, followed by transfer, is the safest procedure.

Adolescent↗
PubMed1999

ATP-Dependent colchicine transport by human erythrocyte glutathione conjugate transporter.

We have recently demonstrated mutually inhibitory ATP-dependent transport of dinitrophenyl-S-glutathione (DNP-SG) and doxorubicin by DNP-SG ATPase purified from human erythrocyte membranes (S. Awasthi et al., 1998a,b). Our previous studies indicate a broad substrate specificity for this transport mechanism, including some P-glycoprotein substrates. Present studies were carried out to determine whether colchicine (COL), a classical P-glycoprotein substrate, could be transported by purified human erythrocyte DNP-SG ATPase reconstituted in artificial liposomes. We also investigated whether leukotriene C4 (LTC4), an endogenous proinflammatory glutathione-conjugate derived from arachidonic acid, would inhibit colchicine transport. Uptake of COL was compared in proteoliposomes reconstituted with the purified DNP-SG ATPase as well as control liposomes in the presence or absence of ATP. Increased colchicine uptake was observed upon addition of ATP to proteoliposomes, but not control liposomes. Uptake was linear with respect to the amount of vesicle protein used. Sensitivity to osmolarity was consistent with intravesicular COL accumulation. The ATP-dependent colchicine uptake was sensitive to temperature in a manner consistent with a protein-mediated transport process with activation energy of 7.3 kcal/mol. Time-dependent COL uptake by proteoliposomes in the presence of ATP was consistent with a single compartment model with an apparent rate constant of 0.21 +/- 0.02 min-1. Kinetic studies indicated a saturable behavior with respect to ATP (Km 2.3 +/- 0.7 mM) and colchicine (Km 4.3 +/- 0.2 microM). LTC4 was found to be a competitive inhibitor of COL transport (Kis 16.4 microM). Since DNP-SG ATPase is present in many tissues, it may play an important role in determining colchicine accumulation in cells. Increased LTC4 would tend to increase cellular COL accumulation.

Adenosine Triphosphatases↗
PubMed1998

Effect of target gene CpG content on spontaneous mutation in299 transgenic mice.

Transgenic mutation assays utilizing bacterial target genes display a high frequency of spontaneous mutation at CpG sequences. This is believed to result from the fact that: (1) the prokaryotic genes currently being used as transgenic mutation targets have a high CpG content and (2) these sequences are methylated by mammalian cells to produce 5-methylcytosine (5MC), a known promutagenic base. To study the effect of CpG content on the frequency and type of spontaneous mutation, we have synthesized an analogue of the bacterial lacI target gene (mrkII) that contains a reduced number of CpG sequences. This gene was inserted into a lambda vector and used to construct transgenic mice that undergo vector rescue from genomic DNA upon in vitro packaging. Results on spontaneous mutation frequency and spectrum have been collected and compared to those observed at the lacI gene in Big Blue transgenic mice. Spontaneous mutations at the mrkII gene occurred at a frequency in the mid-10-5 range and were predominantly base pair substitutions, similar to results seen in Big Blue. However, mrkII mutations were distributed toward the carboxyl end of the gene instead of the bias toward the amino terminus seen in lacI. Unexpectedly, 23% of the spontaneous mrkII mutations were GC-->AT transitions at CpG sequences (compared to 32% in lacI), despite the reduction in CpG number from 95 in lacI to only 13 in mrkII. Nine of the CpG bases undergoing transition mutations in mrkII have not been recorded previously as spontaneous sites in Big Blue. Therefore, substantial reduction of the number of CpG sequences in the lacI transgene did not significantly reduce the rate of spontaneous mutation or alter the contribution of CpG-related events. This suggests that other factors are also operating to establish frequency and composition of spontaneous mutations in transgenic targets.

Animals↗
PubMed1998

The Quilty lesion enigma: focal apoptosis/necrosis and lymphocyte subsets in human cardiac allografts.

Quilty lesions, as first described by Billingham in 1981, or 'Quilty Effect' (QE) are distinct endomyocardial mononuclear cell infiltrates that have been observed in human heart transplant recipients, as well as in experimental models of heart transplantation. In the present investigations, the pattern and extent of apoptosis (programmed cell death) and myocyte necrosis, as well as specific lymphocyte subsets in Quilty lesions was assessed. Endomyocardial biopsies obtained from 13 patients at 10-3362 days post-transplant were examined. Apoptosis, as identified by DNA nick end-labeling, was found in myocytes at the periphery of Quilty lesions in 11 of 13 cases (85%), and 'early' stages of myocyte necrosis, as demonstrated by specific staining with alpha light chain myosin monoclonal antibodies (mAb), was observed at the same sites in 10 of 13 cases (77%) of both Quilty type A and type B lesions. Apoptosis was not identified in the lymphocyte infiltrates of any of the lesions examined. Lymphocyte subsets were characterized using mAb for T cell receptor (CD3), for helper/inducer T cells (CD4), for cytotoxic/suppressor T cells (CD8) and for mature B cells (CD20). Immunostaining revealed separate clusters of T lymphocytes with less prevalent B cells within the Quilty lesions. CD4+ cells were found in larger numbers than CD8+ cells in all cases. Non-B, non-T large lymphocytes were occasionally present. Except for the extent of the cellular infiltrate, no major cytochemical lymphocyte distribution differences were found between Quilty type A and B lesions. Myocyte apoptosis and early necrosis at the periphery of Quilty lesions suggest that early myocyte injury occurring in B lesions may represent initial or 'abortive stages' of cardiac allograft rejection. Why these lesions do not progress to overt rejection indeed warrant further detailed studies.

Actin Cytoskeleton↗
PubMed1993

Conjunctival involvement in malignancy-associated acanthosis nigricans.

Acanthosis nigricans classically presents with pigmented skin lesions over the neck, groin and axillae. It may involve the mucosal surfaces, particularly the oral mucosa. Conjunctival involvement is very rare, especially in the variety associated with malignancy. We report a case of acanthosis nigricans associated with squamous cell carcinoma of the bronchus where bilateral papillary conjunctivitis, progressing to hypertrophic papillary conjunctival and lid margin lesions, was the presenting feature. Topical treatment with corticosteroid and artificial tear drops resulted in the partial improvement of the ocular symptoms.

Acanthosis Nigricans↗