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Biomedical subjects

K Choudhury

Publications and source records attributed to K Choudhury.

At least 19 recordsLinked to original sources
PubMed2006

Fine mapping of a susceptibility locus for bipolar and genetically related unipolar affective disorders, to a region containing the C21ORF29 and TRPM2 genes on chromosome 21q22.3.

Linkage analyses of bipolar families have confirmed that there is a susceptibility locus near the telomere on chromosome 21q. To fine map this locus we carried out tests of allelic association using 30 genetic markers near the telomere at 21q22.3 in 600 bipolar research subjects and 450 ancestrally matched supernormal control subjects. We found significant allelic association with the microsatellite markers D21S171 (P=0.016) and two closely linked single-nucleotide polymorphisms, rs1556314 (P=0.008) and rs1785467 (P=0.025). A test of association with a three locus haplotype across the susceptibility region was significant with a permutation test of P=0.011. A two SNP haplotype was also significantly associated with bipolar disorder (P=0.01). Only two brain expressed genes, TRPM2 and C21ORF29 (TSPEAR), are present in the associated region. TRPM2 encodes a calcium channel receptor and TSPEAR encodes a peptide with repeats associated with epilepsy in the mouse. DNA from subjects who had inherited the associated marker alleles was sequenced. A base pair change (rs1556314) in exon 11 of TRPM2, which caused a change from an aspartic acid to a glutamic acid at peptide position 543 was found. This SNP showed the strongest association with bipolar disorder (P=0.008). Deletion of exon 11 of TRPM2 is known to cause dysregulation of cellular calcium homeostasis in response to oxidative stress. A second nonconservative change from arginine to cysteine at position 755 in TRPM2 (ss48297761) was also detected. A third nonconservative change from histidine to glutamic acid was found in exon 8 of TSPEAR. These changes need further investigation to establish any aetiological role in bipolar disorder.

Amino Acid Substitution↗
PubMed2001

Volatile ketone formation in bacteria: release of 3-oxopentanoate by soil pseudomonads during growth on heptanoate.

During enrichments to search for soil bacteria that form the volatile ketones, acetone and butanone, we isolated pure cultures of Pseudomonas aureofaciens, P. fluorescens, and P. putida that excrete the beta-keto-acid, 3-oxopentanoate (3-OPA), when grown on heptanoic acid as carbon source. Analysis of 3-OPA used enzymatic decarboxylation by acetoacetate decarboxylase to yield butanone, which was detected by headspace gas chromatography. The formation of 3-OPA was strongly dependent on heptanoic acid concentration, the level of oxygen, and the state of growth, and was not seen with even-chain or other odd-chain fatty acids. Uptake of 3-OPA during stationary phase of growth is probably related to polyhydroxyalkanoate (PHA) formation in these isolates. A model for formation and release of 3-OPA is proposed.

Acetone↗
PubMed2001

Clinical profile and outcome in Bacillus endophthalmitis.

OBJECTIVE: To study the clinical presentation, microscopic and organismal culture correlation of vitreous, and species-specific outcome in Bacillus endophthalmitis DESIGN: Retrospective noncomparative case series. INTERVENTION: Thirty-one culture proven Bacillus endophthalmitis patients between January 1991 and February 1998 underwent vitrectomy and intravitreal antibiotic injection. Lensectomy was combined when considered essential, and on a few occasions intravitreal dexamethasone was added. The patients also received topical and systemic antibiotics. The undiluted vitreous biopsy was the source for microbiologic evaluation (microscopy and culture sensitivity). MAIN OUTCOME MEASURES: The duration of symptoms, the presenting visual acuity, and influence of intravitreal dexamethasone with intravitreal antibiotics were examined for any statistical correlation with the final visual acuity. RESULTS: Trauma was the major cause of infection. Vitreous biopsy microscopy demonstrated gram-positive bacillus in 28 of 31 cases, and polymicrobial infection was seen in 12 instances. All Bacillus species were sensitive to gentamicin, followed by vancomycin and ciprofloxacin. Clinical treatment within 7 days of symptoms, use of intravitreal vancomycin, and absence of polymicrobial infection were associated with better visual outcome. CONCLUSIONS: With appropriate treatment that essentially consists of vitrectomy and intravitreal antibiotics, patients with Bacillus endophthalmitis are likely to benefit in many instances. Gram-positive bacilli detected on vitreous microscopy should be empirically treated as Bacillus species unless otherwise proved.

Adolescent↗
PubMed1998

Regulation of the glial glutamate transporter GLT-1 by glutamate and delta-opioid receptor stimulation.

The excitatory effect of presynaptically released glutamate is tightly regulated and terminated by high affinity sodium-dependent glutamate transporters. The regulation of the glial glutamate transporter GLT-1 is potentially important in synaptic modulation. Using astroglial cultures prepared from the rat cerebral cortex, we found that the delta-opioid receptor agonist [D-pen2,D-pen5]-enkephalin decreases and glutamate increases the expression of the GLT-1 transporter mRNA. Corresponding changes in the uptake kinetics were found after incubation for 48 h with the respective agonists when glial glutamate uptake was measured in primary astroglial cultures. The data suggest that long-term receptor activation induces alterations in glial glutamate uptake properties.

ATP-Binding Cassette Transporters↗
PubMed1995

Effect of the His175-->Glu mutation on the heme pocket architecture of cytochrome c peroxidase.

Resonance Raman (RR) and electronic absorption spectra of the ferric and ferrous forms of the His175Glu mutant of cytochrome c peroxidase are reported. At 296 K, the FeIII form is five-coordinate high spin and the resonance Reman spectra are very similar to those obtained for the wild type enzyme, even though in the mutant the Fe atom is bound to an oxygen atom of the Glu residue. The only difference is that the bands due to the out-of-plane modes are very weak, indicating a less distorted heme plane compared to CCP. The absorption spectrum is similar to that of CCP, as far as the Soret and alpha, beta bands are concerned, but the charge-transfer band due to the a2u(pi)-->eg(d pi) transition is 8 nm blue-shifted relative to that of the wild type enzyme, indicating that a more negative ligand is bound to the heme iron. As the temperature is lowered, the five-coordinate heme converts to a six-coordinate high-spin form. The conversion is readily reversible. A temperature effect on the protein structure is proposed that permits the Fe atom to approach the heme plane and to bind the distal water molecule. The results are discussed in terms of the X-ray structure, which shows a different disposition of the distal water molecules in the Glu175 mutant. The RR spectra also show that the heme is more contracted and distorted at 19 K than at room temperature.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Role of the proximal ligand in peroxidase catalysis. Crystallographic, kinetic, and spectral studies of cytochrome c peroxidase proximal ligand mutants.

The role of the proximal histidine ligand in peroxidase function was studied by replacing the His side chain in cytochrome c peroxidase with Gln, Glu, or Cys. In addition, a double mutant was prepared where His-175 is converted to Gln and the site of free radical formation in Compound I, Trp-191 (Sivaraja, M., Goodin, D.B., Smith, M., and Hoffman, B. M. (1989) Science 245, 738-740), is converted to Phe. With the exception of the His-175-->Cys mutant, the proximal ligand mutants retain high levels of enzyme activity. Stopped flow studies show that replacing the His ligand with Gln has only a modest effect on the rate of Compound I formation demonstrating that the precise nature of the proximal ligand is not important in achieving a high rate of peroxide O-O bond cleavage. The double mutant, His-175-->Gln/Trp-191-->Phe, also forms Compound I rapidly but the initial product formed is very likely a long-lived porphyrin pi cation radical that slowly converts to a species more closely resembling the heme oxyferryl center of wild type Compound I. The relevance of these studies to the cytochrome c peroxidase-cytochrome c electron transfer system are discussed.

Crystallography, X-Ray↗
PubMed1993

Isolation and characterization of nonhistone proteins associated with DNase-II hypersensitive sites of Sarcoma-180 chromatin.

Limited digestion (2 min) of Sarcoma-180 nuclei by DNase-II released two nonhistone proteins from the hypersensitive sites of chromatin. The apparent molecular weights of these two proteins were 34 and 21 kDa. These proteins showed a moderate but specific inhibition in in vitro cell free transcription assay with native chromatin as template as opposed to no effect on native DNA transcription.

Animals↗
PubMed1992

Conversion of the proximal histidine ligand to glutamine restores activity to an inactive mutant of cytochrome c peroxidase.

Using site-directed mutagenesis, a double mutant in yeast cytochrome c peroxidase (CCP) has been constructed where the proximal ligand, His175, has been converted to glutamine and the neighboring Trp191 has been converted to phenylalanine. The refined 2.4-A crystal structure of the double mutant shows that the Gln175 side chain is within coordination distance of the heme iron atom and that Phe191 occupies the same position as Trp191 in the native enzyme with very little rearrangement outside the immediate vicinity of the mutations. Consistent with earlier work, we find that the single mutant, His175-->Gln, is fully active under steady state assay conditions and that as reported earlier (Mauro et al., 1988), the Trp191-->Phe mutant exhibits only < 0.05% activity. However, the double mutant, His175-->Gln/Phe191-->Phe, exhibits 20% wild type activity. Since it is known that the Trp191-->Phe mutant is inactive because it can no longer transfer electrons from ferrocytochrome c, changing the nature of the proximal ligand is able to restore this activity. These results raise interesting questions regarding the mechanism of interprotein electron transfer reactions.

Amino Acid Sequence↗
PubMed1991

Inter-relationships between selenium and thyroid hormone metabolism in the rat and man.

Labelling of rat kidney microsomes in vitro with [125I]-bromoacetyl T4 produced two bands on SDS/PAGE with Mr of 55 kDa and 27.5 kDa representing protein disulphide isomerase and type I iodothyronine deiodinase (ID-I) respectively. The amount of the 55 kDa band was unchanged by selenium (Se) deficiency but the 27.5 kDa protein was markedly decreased in kidney microsomal fraction obtained from Se-deficient rats. Concurrent Se and iodine deficiency produced a significant increase in thyroid weight, plasma thyrotrophin (TSH) and a decrease in thyroidal iodine when compared with either single Se or iodine deficiency. These results suggest that ID-I is a selenoprotein and that Se deficiency can exacerbate the hypothyroidism observed in iodine deficiency. In man, blood glutathione peroxidase and blood Se levels were decreased in hyperthyroidism due to Graves' disease whilst normal levels of these analytes were found in patients treated for Graves' disease. These results suggest that thyroid status can affect Se balance rather than Se deficiency predisposes to Graves' disease.

Animals↗
PubMed1989

Metabolism of small RNAs in cultured human cells.

There are gaps in what is known about the metabolism of some mammalian small RNA species. Our present observations can be summarized as follows. The level of radiolabeled mature U1 RNA doubled between 2 and 24 hr of label chase, while that of all other small RNA species tested did not change. These results are compatible with the possibility that the nucleotide precursor pool for U1 RNA transcription may be partly segregated, or that there may be a second pathway of U1 RNA formation. Precursors of nucleolar U3 RNA were detected whose electrophoretic mobilities are equivalent to those of transcripts approximately 14 and approximately 8 nucleotides longer than the mature species, and which are apparently cytoplasmic. The ladder of U2 RNA precursors showed a gap, suggesting that some of the cleavages during U2 RNA processing are endonucleolytic. We detected an apparent U5 RNA precursor whose electrophoretic mobility is equivalent to that of a species approximately 1 nucleotide longer than mature U5 RNA. There was a predominant band in the middle of the ladder of U4 RNA precursors (apparently approximately 3 nucleotides longer than mature U4 RNA) which suggests that U4 RNA maturation may pause briefly at that intermediate. There are apparently two additional species of mature hY3 RNA, which are less abundant and are about 1 and 2 bases longer than the major hY3 RNA species. An apparent hY3 RNA precursor was detected, which may be approximately 2-3 nucleotides longer than the main mature hY3 RNA species.

Cells, Cultured↗
PubMed1989

Ultraviolet light-induced inhibition of small nuclear RNA synthesis.

Two apparently distinct types of inhibition of the synthesis of U1, U2, U3, U4, and U5 small nuclear RNA, induced by ultraviolet (UV) radiation, have been described before: immediate and delayed. Our present observation can be summarized as follows: a) neither the immediate nor the delayed inhibition appear to be mediated by the formation of cyclobutane pyrimidine dimers, since they were not prevented by photoreactivating light, in ICR 2A frog cells; b) the inhibition of U1 RNA synthesis, monitored in HeLA cells within the first few minutes after irradiation, extrapolated to a substantial suppression at time zero of postirradiation cell incubation, providing further support for the proposal that the immediate inhibition is a reaction separate from the delayed UV light-induced inhibition of U1 RNA synthesis; c) the transition from the pattern of the immediate inhibition to that of the delayed inhibition (disappearance of the UV-resistant fraction of U1 RNA synthesis and increased rate of inhibition) occurred gradually, without an apparent threshold, within the first 2 hr of incubation after irradiation; and d) the incident UV dose that resulted in a 37% level of residual U1 RNA synthesis (D37) during the delayed inhibition was about 7 J/m2, with an apparent UV dose threshold, and was about 60 J/m2 for the immediate inhibition.

Animals↗
PubMed1989

Mechanism of action of alpha-methylene-gamma-lactone derivatives of substituted nucleic acid bases in tumour cells.

Some alpha-methylene-gamma-lactone derivatives of substituted nucleic acid bases, which showed significant antitumour activity against experimental tumours, were tested for their possible mechanism of action. Derivatives 1, 4 and 7 strongly inhibit active transport of uridine through sarcoma-180 ascites tumour cells. Derivatives 1, 7 and 10 strongly inhibit a translation process in these cells, besides apparent inhibition in transcription. It appears that active transport and translation might be the primary steps inhibited by these drugs.

4-Butyrolactone↗
PubMed1989

Effect of anthracycline antibiotics on in vitro transcription of chromatin in a Sarcoma-180 whole cell extract.

A soluble extract capable of transcribing Sarcoma-180 chromatin and DNA in a cell-free transcription system was prepared from Sarcoma-180 mouse ascites tumour cells. Incorporation of [3H]UTP into trichloroacetic acid-precipitable fraction is (i) reduced by 50% on removing DNase I hypersensitive sites of chromatin and (ii) inhibited by DNA binding antitumour anthracyclines, suggesting that this cell-free assay represents true transcription of active genes of Sarcoma-180 chromatin. Preparation of this soluble extract from mouse ascites tumour cells thus presents a very convenient way of studying cell-free transcription of active genes of chromatin and effect of antitumour agents on chromatin transcription.

Animals↗
PubMed1988

Effect of ultraviolet light on the expression of genes for human U1 RNA.

Two types of UV-light-induced inhibitions of the synthesis of small nuclear RNA species U1, U2, U3, U4, and U5 were described previously: an immediate inhibition and a separate, delayed suppression that requires 1-2 hr of postirradiation cell incubation and UV doses that are about tenfold lower. In the present report, U1 RNA transcription in isolated nuclei from HeLa cells, assayed by RNAase T1 protection, reproduced the delayed inhibition. The sizes of the protected RNA fragments suggest that it is the initiation of U1 RNA transcription that is blocked during this inhibition. Transient expression of a marked human U1 RNA gene that contains 425 and 92 nucleotides of the 5' and 3' flanking sequences, respectively, showed delayed, but not immediate inhibition (while the endogenous U1 RNA genes exhibited immediate suppression). This indicates that continuity of the U1 gene flanking sequences beyond those segments and/or chromosomal integration of the U1 gene are not needed for the delayed inhibition, but may be required for the immediate inhibition. Irradiation of a U1 RNA gene, followed by its injection into Xenopus laevis oocyte nuclei, did not reproduce the immediate or delayed inhibitions. This suggests that direct UV radiation damage to DNA in the U1 RNA gene region is not the critical lesion in either the immediate or delayed UV-light-induced inhibitions of U1 RNA synthesis. In addition, the RNAase T1 protection pattern of transcripts synthesized in isolated nuclei from nonirradiated HeLa cells suggests that these cells may produce small amounts of U1 RNA molecules with variant nucleotide sequences in the mature region of the transcript.

Animals↗
PubMed1988

Metabolism of U6 RNA species in nonirradiated and UV-irradiated mammalian cells.

We observed a series of rapidly labeled U6 RNA bands, which were hybrid selected with U6 DNA, in nonirradiated human cells. The electrophoretic mobility of these bands in denaturing gels was lower than that of the known mature U6 RNA species, and was equivalent to transcripts up to approximately 7 nucleotides longer. These multiple U6 RNA species lost their label during a chase without a proportional increase in radioactivity in the known mature U6 RNA, which suggests that a substantial fraction is not processed into the major mature U6 RNA. During a label chase, the multiple U6 RNA bands appeared first in the cytoplasmic fraction and later in nuclei. One of the major rapidly labeled U6 RNA bands had the electrophoretic mobility of an RNA species one nucleotide shorter than the known mature U6 RNA. UV light induced a UV dose-dependent, preferential disappearance of recently synthesized molecules of the U6 RNA species of higher gel electrophoretic mobility, including the known mature U6 RNA. Since this effect was seen in cells pulse-labeled immediately before or after irradiation, it suggests that UV radiation induces the specific degradation of the electrophoretically faster moving species of U6 RNA, which are apparently shorter chains. The effect of UV light was RNA species-specific, was not seen in molecules synthesized long (e.g., 22 hr) before irradiation, and occurred in human and mouse cells.

Animals↗
PubMed1987

Characterization of DNA binding proteins released from sarcoma-180 chromatin during brief digestion with DNase-I.

Brief digestion of sarcoma-180 chromatin (less than or equal to 5%) by pancreatic DNase-I releases six non-histone proteins with Mol. wt. 21.5K, 26K, 72.5K, 77K, 90K and 120K dalton and pI values ranging from 4.7 to 12.4. The protein of Mol. wt. 77K dalton was obtained at high alkaline range of pH = 12.4. The antibodies against these proteins induce dose dependent inhibition in transcription of native chromatin. Results suggest a role of these proteins in positive control of gene transcription in sarcoma-180 cells.

Animals↗