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S Kumar

Publications and source records attributed to S Kumar.

At least 487 records · Page 27Linked to original sources
PubMed2001

Site-specific regulation of oestrogen receptor-alpha and -beta by oestradiol in human adipose tissue.

AIM: To examine the expression of oestrogen receptors alpha and beta (ERalpha and ERbeta) and their regulation by 17beta-oestradiol (E2) in stromal cells and adipocytes from human subcutaneous (s.c.) and omental (o.m.) adipose tissue. METHODS: Subcutaneous and o.m. abdominal adipose tissues were obtained from 10 women (mean age 63.5 +/- 4.8 years; mean weight 75.6 +/- 6.7 kg) undergoing elective or cosmetic surgery. Immunohistochemistry and RT-PCR analysis were used to detect the presence of ERalpha and ERbeta. The regulation of ERalpha and ERbeta by E(2) (10(-7) M to 10(-9) M) was examined using Western immunoblotting analysis in both s.c. and o.m. stromal cells and mature adipocytes cultured in serum-free, phenol red-free medium. RESULTS: Immunostaining of s.c. and o.m. adipose tissue showed that the ER subtypes were localized predominantly within the nucleus. Western analysis demonstrated that E2 treatments differentially altered ERalpha and ERbeta expression in s.c. and o.m. adipocytes. In s.c. and o.m. stromal cells, E(2) (10(-8) M) produced a significant up regulation relative to control of 66 kDa ERalpha (s.c.:1.87 +/- 0.22; o.m.:1.97 +/- 0.17; p < 0.05) and 60 kDa ERbeta (s.c.:1.66 +/- 0.3; o.m.: 1.68 +/- 0.16; p < 0.05). In s.c. adipocytes, however, ERalpha expression significantly decreased with E(2) 10(-8) M relative to control while ERbeta expression increased (ERalpha 0.58 +/- 0.06, ERbeta: 1.47 +/- 0.11; p < 0.05). In o.m. adipocytes, the inhibition of ERalpha with E(2) was not observed (ERalpha 1.86 +/- 0.36, ERbeta:1.03 +/- 0.15, p < 0.05) CONCLUSIONS: ERalpha and ERbeta are expressed but differentially regulated by E(2) in s.c. and o.m. adipocytes and stromal cells. The upregulation of ERbeta by E(2) suggests that E(2) maintains the expression of these receptors. The feed-back inhibition of ERalpha expression by E(2) in s.c. but not o.m. adipocytes observed in vitro is consistent with the data from ERalpha knock out mice where s.c. fat is increased. Selective ER modulators may have different effects in different adipose sites.

Adipocytes↗
PubMed2001

Identification and initial characterization of 5000 expressed sequenced tags (ESTs) each from adult human normal and osteoarthritic cartilage cDNA libraries.

OBJECTIVE: To prepare, sequence and analyse adult human cartilage cDNA libraries to study the gene expression pattern between normal and osteoarthritic cartilage. METHODS: Poly A(+)RNA from adult human normal and osteoarthritic articular cartilage was isolated and used to prepare cDNA libraries. Approximately 5000 ESTs from each library were sequenced and analysed using bioinformatic tools. The expression of select genes was confirmed by Northern blot and in situ hybridization analysis. RESULTS: Multiple gene families including several classical cartilage matrix protein encoding genes were identified. Approximately 28-40% of the genes sequenced from these libraries were novel, while half of the genes encoded known proteins and 4-6% of the genes encoded novel homologs of known proteins. Several known genes, whose expression has not been reported previously in cartilage, were also identified. We have confirmed the cartilage expression of three known (CTGF, CTGF-L and clusterin) and two novel homologs of known genes (PCPE-2 and Gal-Nac transferase) by Northern blot and in situ hybridization analysis. CONCLUSION: This is the first report of the preparation and sequencing of cDNA libraries from adult human normal and osteoarthritic articular cartilage. Further analysis of genes identified from these libraries may provide molecular targets for diagnosis and/or treatment of osteoarthritis (OA).

Adult↗
PubMed2001

Clusterin expression in adult human normal and osteoarthritic articular cartilage.

OBJECTIVE: To characterize the expression pattern of clusterin in adult human normal and osteoarthritic cartilage. METHODS: Clusterin mRNA expression in adult human normal and osteoarthritic cartilage was investigated by analysis of cDNA libraries, TaqMan quantitative RT-PCR, microarray and in situ hybridization. RESULTS: Sequence analysis of ESTs from adult human normal and osteoarthritic cartilage cDNA libraries demonstrated that the abundance of clusterin in these libraries was equivalent to genes which have been more commonly associated with cartilage. To examine tissue distribution, TaqMan Quantitative PCR analysis was performed using RNA from a panel of individual normal tissues. Clusterin was expressed at significant levels in cartilage, brain, liver, and pancreas. The expression of clusterin mRNA was up-regulated in early osteoarthritic vs normal cartilage when analysed by microarray analysis. Using in situ hybridization, chondrocytes of normal cartilage expressed moderate levels of clusterin. Upper mid-zone chondrocytes in cartilage with early stages of osteoarthritic disease expressed high levels of clusterin mRNA. In advanced osteoarthritic cartilage, the overall expression of clusterin was reduced. CONCLUSION: The induction of clusterin has been associated with a variety of disease states where it appears to provide a cytoprotective effect. The increased expression of clusterin mRNA in the early stages of osteoarthritis (OA) may reflect an attempt by the chondrocytes to protect and repair the tissue. In contrast, the decrease in clusterin mRNA in the advanced osteoarthritic cartilage accompanies the final degenerative stages of the disease. An understanding of the expression of clusterin in osteoarthritis may allow consideration of this protein as a marker for cartilage changes in this chronic degenerative condition.

Adult↗
PubMed2001

New naphthoquinones from Arnebia hispidissima roots.

Besides shikonin and arnebifuranone, two new shikonin esters isolated from the roots of Arnebia hispidissima have been characterized as butylshikonin and 2'-methyl-hexa-1',3'-dienoylshikonin by physicochemical methods. Arnebifuranone is the first report from this species.

Food Coloring Agents↗
PubMed2001

Dysembryoplastic neuroepithelial tumors: report of 10 cases from a center where epilepsy surgery is not done.

Dysembryoplastic neuroepithelial tumor (DNT) is a recently recognized tumor entity with distinctive clinicopathological features and an excellent long-term prognosis. We report 10 cases of DNT out of neurosurgical specimens sent for histopathological examination since 1994. Epilepsy surgery is not done at our center, and all the cases were sent with a clinical diagnosis of glioma. On histopathological examination, all the 10 cases contained the specific glioneuronal element. In 6 cases, glial nodules were noted in addition. This study therefore reports 4 cases of simple DNT and 6 cases of complex DNT. There was no nuclear atypia or mitosis in any of the cases. Proliferative index by PCNA varied from negative to <1%. It is very important to recognize this entity, as surgery cures the patient, and radiotherapy or chemotherapy is not required.

Adolescent↗
PubMed2001

Improvement in bioavailability of tricalcium phosphate to Cymbopogon martinii var. motia by rhizobacteria, AMF and Azospirillum inoculation.

The interactive effects of phosphate solubilizing bacteria, N2 fixing bacteria and arbuscular mycorrhizal fungi (AMF) were studied in a low phosphate alkaline soil amended with tricalcium insoluble source of inorganic phosphate on the growth of an aromatic grass palmarosa (Cymbopogon martinii). The microbial inocula consisted of the AM fungus Glomus aggregatum, phosphate solubilizing rhizobacteria Bacillus polymyxa and N2 fixing bacteria Azospirillum brasilense. These rhizobacteria behaved as "mycorrhiza helper" and enhanced root colonization by G. aggregatum in presence of tricalcium phosphate at the rate of 200 mg kg(-1) soil (P1 level). Dual inoculation of G. aggregatum and B. polymyxa yielded 21.5 g plant dry weight (biomass), while it was 21.7 g in B. polymyxa and A. brasilense inoculated plants as compared to 14.9 g of control at the same level. Phosphate content was maximum (0.167%) in the combined treatment of G. aggregatum, B. polymyxa and A. brasilense at P1 level, however acid phosphatase activity was recorded to be 4.75 pmol mg(-1) min(-1) in G. aggregatum, B. polymyxa and A. brasilense treatment at P0 level. This study indicates that all microbes inoculated together help in the uptake of tricalcium phosphate which is otherwise not used by the plants and their addition at 200 mg kg(-1) of soil gave higher productivity to palmarosa plants.

Acid Phosphatase↗
PubMed2001

Protein folding: binding of conformationally fluctuating building blocks via population selection.

Here we review different aspects of the protein folding literature. We present a broad range of observations, showing them to be consistent with a general hierarchical protein folding model. In such a model, local relatively stable, conformationally fluctuating building blocks bind through population selection, to yield the native state. The model includes several components: (1) the fluctuating building blocks that constitute local minima along the polypeptide chain, which even if unstable still possess higher population times than all alternate conformations; (2) the landscape around the bottom of the funnels; (3) the consideration that protein folding involves intramolecular recognition; (4) similar landscapes are observed for folding and for binding, and that (5) the landscape is dynamic, changing with the conditions. The model considers protein folding to be guided by native interactions. The reviewed literature includes the effects of changing the conditions, intermediates and kinetic traps, mutations, similar topologies, fragment complementation experiments, fragments and pathways, focusing on one specific well-studied example, that of the dihydrofolate reductase, chaperones, and chaperonines, in vivo vs. in vitro folding, still using the dihydrofolate example, amyloid formation, and molecular "disorder". These are consistent with the view that binding and folding are similar events, with the differences stemming from different stabilities and hence population times.

Models, Molecular↗
PubMed2001

Analytical models for time resolved fluorescence spectroscopy in tissues.

Laser induced fluorescence is a rapidly growing technique for diagnostics and imaging in scattering material, most notably in in vivo biomedical testing. Most previous applications have relied on the measurements of the steady-state emission spectrum, with subsequent analysis of the spectrum for relative concentrations of potential fluorophores. Only recently a few investigators have explored the use of the fluorescence lifetimes as a diagnostic tool by taking advantage of the perturbation of the lifetime by multiple scattering of the excitation and emission light in the tissue. We have developed a model to study the fluorescence signal generated by fluorophores distributed in a scattering medium. This model is based on two coupled time-dependent photon migration phenomena: the transport of the pulsed source laser light and the transport of the induced fluorescent light excited by the source. The coupling of these two is through the source for the induced fluorescence where the strength of the local fluorescence emission depends on the absorption of the laser intensity at that location. Whereas previous research focused mainly on the fluorescence properties of various dyes, compounds and materials, transport phenomena have only recently been addressed by researchers. We have presented general analytical and numerical solutions for finite, infinite, cylindrical and spherical geometries.

Algorithms↗
PubMed2001

Null mutants of the neurospora actin-related protein 1 pointed-end complex show distinct phenotypes.

Dynactin is a multisubunit complex that regulates the activities of cytoplasmic dynein, a microtubule-associated motor. Actin-related protein 1 (Arp1) is the most abundant subunit of dynactin, and it forms a short filament to which additional subunits associate. An Arp1 filament pointed-end--binding subcomplex has been identified that consists of p62, p25, p27, and Arp11 subunits. The functional roles of these subunits have not been determined. Recently, we reported the cloning of an apparent homologue of mammalian Arp11 from the filamentous fungus Neurospora crassa. Here, we report that N. crassa ro-2 and ro-12 genes encode the respective p62 and p25 subunits of the pointed-end complex. Characterization of Delta ro-2, Delta ro-7, and Delta ro-12 mutants reveals that each has a distinct phenotype. All three mutants have reduced in vivo vesicle trafficking and have defects in vacuole distribution. We showed previously that in vivo dynactin function is required for high-level dynein ATPase activity, and we find that all three mutants have low dynein ATPase activity. Surprisingly, Delta ro-12 differs from Delta ro-2 and Delta ro-7 and other previously characterized dynein/dynactin mutants in that it has normal nuclear distribution. Each of the mutants shows a distinct dynein/dynactin localization pattern. All three mutants also show stronger dynein/dynactin-membrane interaction relative to wild type, suggesting that the Arp1 pointed-end complex may regulate interaction of dynactin with membranous cargoes.

Adenosine Triphosphatases↗
PubMed2001

MEGA2: molecular evolutionary genetics analysis software.

UNLABELLED: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. AVAILABILITY: http://www.megasoftware.net. CONTACT: s.kumar@asu.edu

DNA↗
PubMed2001

Tumorigenicity of racemic and optically pure bay region diol epoxides and other derivatives of the nitrogen heterocycle dibenz[a,h]acridine on mouse skin.

CD-1 female mice were initiated with a single topical application of 500 nmol dibenz[a,h]acridine (DB[a,h]Acr), its racemic trans-1,2-, 3,4-, 8,9- and 10,11-dihydrodiols, racemic DB[a,h]Acr 3,4-diol 1,2-epoxide-1 and -2 or racemic DB[a,h]Acr 10,11-diol 8,9-epoxide-1 and -2, where the benzylic hydroxyl group is either cis (isomer 1) or trans (isomer 2) to the epoxide oxygen. The mice were subsequently treated twice weekly with 12-O-tetradecanoylphorbol 13-acetate for 25 weeks. High tumorigenicity was observed only for DB[a,h]Acr, its 10,11-dihydrodiol and DB[a,h]Acr 10,11-diol 8,9-epoxide-2 (3.3, 1.2 and 1.6 tumors/mouse, respectively). The tumor-initiating activity of a 50 nmol dose of DB[a,h]Acr and the optically active (+)- and (-)-enantiomers of DB[a,h]Acr 10,11-dihydrodiol and of the optically active DB[a,h]Acr 10,11-diol 8,9-epoxide-1 and -2 were also studied. Only DB[a,h]Acr, (-)-DB[a,h]Acr (10R,11R)-dihydrodiol and the bay region (+)-(8R,9S,10S,11R)-diol epoxide-2 were highly active (1.6, 1.7 and 2.4 tumors/mouse, respectively). These results are consistent with previous studies which showed that the corresponding bay region RSSR diol epoxides of benzo[a]pyrene, benz[a]anthracene, chrysene and benzo[c]phenanthrene as well as the aza-polycyclic dibenz[c,h]acridine are the most tumorigenic isomers.

Acridines↗
PubMed2001

Determination of the number of conserved chromosomal segments between species.

Genomic divergence between species can be quantified in terms of the number of chromosomal rearrangements that have occurred in the respective genomes following their divergence from a common ancestor. These rearrangements disrupt the structural similarity between genomes, with each rearrangement producing additional, albeit shorter, conserved segments. Here we propose a simple statistical approach on the basis of the distribution of the number of markers in contiguous sets of autosomal markers (CSAMs) to estimate the number of conserved segments. CSAM identification requires information on the relative locations of orthologous markers in one genome and only the chromosome number on which each marker resides in the other genome. We propose a simple mathematical model that can account for the effect of the nonuniformity of the breakpoints and markers on the observed distribution of the number of markers in different conserved segments. Computer simulations show that the number of CSAMs increases linearly with the number of chromosomal rearrangements under a variety of conditions. Using the CSAM approach, the estimate of the number of conserved segments between human and mouse genomes is 529 +/- 84, with a mean conserved segment length of 2.8 cM. This length is <40% of that currently accepted for human and mouse genomes. This means that the mouse and human genomes have diverged at a rate of approximately 1.15 rearrangements per million years. By contrast, mouse and rat are diverging at a rate of only approximately 0.74 rearrangements per million years.

Animals↗
PubMed2001

Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences.

A common assumption in comparative sequence analysis is that the sequences have evolved with the same pattern of nucleotide substitution (homogeneity of the evolutionary process). Violation of this assumption is known to adversely impact the accuracy of phylogenetic inference and tests of evolutionary hypotheses. Here we propose a disparity index, ID, which measures the observed difference in evolutionary patterns for a pair of sequences. On the basis of this index, we have developed a Monte Carlo procedure to test the homogeneity of the observed patterns. This test does not require a priori knowledge of the pattern of substitutions, extent of rate heterogeneity among sites, or the evolutionary relationship among sequences. Computer simulations show that the ID-test is more powerful than the commonly used chi2-test under a variety of biologically realistic models of sequence evolution. An application of this test in an analysis of 3789 pairs of orthologous human and mouse protein-coding genes reveals that the observed evolutionary patterns in neutral sites are not homogeneous in 41% of the genes, apparently due to shifts in G + C content. Thus, the proposed test can be used as a diagnostic tool to identify genes and lineages that have evolved with substantially different evolutionary processes as reflected in the observed patterns of change. Identification of such genes and lineages is an important early step in comparative genomics and molecular phylogenetic studies to discover evolutionary processes that have shaped organismal genomes.

Animals↗
PubMed2001

Study on curcumin-oligonucleotide conjugate as a probable anticancer agent: its hybridisation with telomere target sequence 5'-GGGATTGGGATT-3'.

Curcumin-oligonucleotide conjugate was synthesised by attaching diglycyl conjugate of curcumin to 12-mer complementary telomere sequence 5'-AATCCCAATCCC-3'. An enhanced Tm of 6 degrees C was found, showing high affinity for the target strand. This may be exploited for the suppression of cancer i.e. by blocking the expression of telomere sequence [GGGATT]n repeats.

Antineoplastic Agents↗
PubMed2001

The staircase phenomenon: implications for monitoring of neuromuscular transmission.

BACKGROUND: Repeated indirect stimulation enhances the evoked mechanical response of muscle (the staircase phenomenon). There are few data that document the magnitude of this effect in man. Inexpensive acceleromyographic monitors of neuromuscular function are now available. If these units are to be used as scientific tools or clinical monitors, additional information regarding how to achieve proper baseline stabilization and calibration is needed. METHODS: Anesthesia was induced and maintained with nitrous oxide, propofol, and an opioid. Tracheal intubation or laryngeal mask insertion was accomplished without muscle relaxants. Thirty adult patients classified as American Society of Anesthesiologists physical status I or II were divided into groups of 10. The mechanical response of the thumb to supramaximal ulnar nerve stimulation was recorded continuously with an acceleromyograph. Group 1 had train-of-four stimuli at 15-s intervals for 25 min. Group 2 had single stimuli at 1.0 Hz for 10 min. Group 3 had the same stimuli as group 1 except that a 50-Hz tetanus of 5 seconds' duration immediately preceded instrument calibration. RESULTS: In group 1, average twitch height (T1) increased rapidly to 148+/-19% (mean +/- SD) of control at 15 min and then more slowly to reach 158+/-26% of control at 25 min. The train-of-four fade ratio did not vary with the duration of stimulation. In group 2, T1 increased to 172+/-19% of control after 400 stimuli (6.7 min) and 180+/-22% of control at 10 min In group 3, average T1 did not decrease below 97+/-5% or increase above 105+/-15% of control at any time. CONCLUSIONS: A 5-s, 50-Hz tetanus administered before initial twitch calibration considerably shortens the time required to achieve baseline stability.

Adolescent↗
PubMed2001

Identification of cervical radiculopathies: optimizing the electromyographic screen.

OBJECTIVE: To determine the optimal electromyography screening examination of the upper limb that ensures detection of those cervical radiculopathies, which can be electrodiagnostically confirmed, yet minimizes the number of muscles studied. DESIGN: A prospective multicenter study was conducted from May 1996 to September 1997 at five institutions. Patients who were referred to participating electrodiagnostic laboratories with suspected cervical radiculopathy were recruited. A standard set of muscles were examined by needle electromyography. Patients with electrodiagnostically confirmed cervical radiculopathies, based on electromyography findings, were selected for analysis. Muscle screens were tested against this group to determine whether the screen identified the patients with radiculopathy. RESULTS: There were 101 patients with cervical radiculopathies representing all cervical root levels. When paraspinal muscles were one of the screening muscles, five muscle screens identified 90% to 98% of radiculopathies, six muscle screens identified 94% to 99%, and seven muscle screens identified 96% to 100%. When paraspinal muscles were not part of the screen, eight distal limb muscles recognized 92% to 95% of radiculopathies. CONCLUSION: This study demonstrated that six muscle screens including paraspinal muscles yielded consistently high identification rates. Studying additional muscles led to marginal increases in identification.

Adolescent↗