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S Kumar

Publications and source records attributed to S Kumar.

At least 379 records · Page 21Linked to original sources
PubMed2001

Understanding human disease mutations through the use of interspecific genetic variation.

Data on replacement mutations in genes of disease patients exist in a variety of online resources. In addition, genome sequencing projects and individual gene sequencing efforts have led to the identification of disease gene homologs in diverse metazoan species. The availability of these two types of information provides unique opportunities to investigate factors that are important in the development of genetically based disease by contrasting long and short-term molecular evolutionary patterns. Therefore, we conducted an analysis of disease-associated human genetic variation for seven disease genes: the cystic fibrosis transmembrane conductance regulator, glucose-6-phosphate dehydrogenase, the neural cell adhesion molecule L1, phenylalanine hydroxylase, paired box 6, the X-linked retinoschisis gene and TSC2/tuberin. Our analyses indicate that disease mutations show definite patterns when examined from an evolutionary perspective. Human replacement mutations resulting in disease are overabundant at amino acid positions most conserved throughout the long-term history of metazoans. In contrast, human polymorphic replacement mutations and silent mutations are randomly distributed across sites with respect to the level of conservation of amino acid sites within genes. Furthermore, disease-causing amino acid changes are of types usually not observed among species. Using Grantham's chemical difference matrix, we find that amino acid changes observed in disease patients are far more radical than the variation found among species and in non-diseased humans. Overall, our results demonstrate the usefulness of evolutionary analyses for understanding patterns of human disease mutations and underscore the biomedical significance of sequence data currently being generated from various model organism genome sequencing projects.

Amino Acids↗
PubMed2001

Observation of B --> J/psi K(1)(1270).

We report the first observation of the exclusive decay process B-->J/psi K(1)(1270) using a sample of 11.2M BB macro meson pairs collected in the Belle detector at the KEKB asymmetric energy e(+)e(-) collider. We measure branching fractions of B[B(0)-->J/psi K(0)(1)(1270)] = (1.30+/-0.34+/-0.32) x 10(-3) and B[B(+)-->J/psi K(+)(1)(1270)] = (1.80+/-0.34+/-0.39) x 10(-3), where the first error is statistical and the second is systematic. These modes constitute approximately 15% of the total number of B-->J/psi X decays. No evidence is seen for B-->J/psi K(1)(1400) and we set an upper limit for this branching fraction.

Journal Article↗
PubMed2001

Dynactin-membrane interaction is regulated by the C-terminal domains of p150(Glued).

Dynactin has been proposed to link the microtubule-associated motor cytoplasmic dynein with membranous cargo; however, the mechanism by which dynactin-membrane interaction is regulated is unknown. Here we show that dynein and dynactin exist in discrete cytosolic and membrane-bound states in the filamentous fungus Neurospora crassa. Results from in vitro membrane-binding studies show that dynein and dynactin-membrane interaction is co-dependent. p150(Glued) of dynactin has been shown to interact with dynein intermediate chain and dynactin Arp1 filament; however, it is not known to play a direct role in membrane binding. In this report we describe our analysis of 43 p150(Glued) mutants, and we show that C-terminal deletions which remove the terminal coiled-coil (CC2) and basic domain (BD) result in constitutive dynactin-membrane binding. In vitro addition of recombinant p150(Glued) CC2+BD protein blocks dynactin-membrane binding. We propose that the C-terminal domains of p150(Glued) regulate dynactin-membrane binding through a steric mechanism that controls accessibility of the Arp1 filament of dynactin to membranous cargo.

Alleles↗
PubMed2001

Increased incidence of Staphylococcus aureus bacteremia in hospitalized patients with acquired immunodeficiency syndrome.

Staphylococcus aureus is a common cause of bacterial infections in patients infected with human immunodeficiency virus (HIV). We studied 53 male patients who had 57 episodes of S. aureus bacteremia (SAB). The incidence of SAB per 1000 hospitalized patients was 13.2 among HIV-positive male patients and 0.8 among HIV-negative male patients, yielding a 16.5-fold increase in the odds ratio for SAB among HIV-positive male patients. Almost all episodes of SAB were community acquired. Long-term indwelling catheters were the most common predisposing factor. Prior antibiotic use was more frequently associated with SAB in HIV-positive patients than in HIV-negative patients. A trend was seen among HIV-positive patients toward more numerous infections with beta-lactam antibiotic-resistant (i.e., methicillin-resistant) S. aureus, but such patients had similar outcomes, even though they often did not receive vancomycin during the initial 48 hours of treatment. A better understanding of the epidemiology and clinical manifestations of SAB in HIV-positive patients will offer important opportunities for prevention of this frequent complication.

AIDS-Related Opportunistic Infections↗
PubMed2001

Multicomponent remote sensing of vehicle exhaust by dispersive absorption spectroscopy. 2. Direct on-road ammonia measurements.

Remote sensing was employed for the first time to measure NH3 levels in the exhaust of on-road light duty motor vehicles. The sensor also measured the concentration of CO2, CO, hydrocarbons, and NO, among other pollutants, in the emitted exhaust. Field measurements were conducted at a Los Angeles freeway on-ramp; vehicles traveled at cruise speeds between 20 and 25 m s(-1) (45-55 mi h(-1)). Mean fleet NH3 levels of 44.7 +/- 4.1 ppm were observed. These emissions exhibited a highly skewed distribution: 50.1% of the emitted NH3 was contributed by 10% of the sampled fleet. The pollutant distribution among high NH3 emitters is analyzed to identify the conditions that lead to three-way catalyst malfunction and, hence, NH3 formation. In contradiction with previous reports, we found that high NH3 emissions could not be attributed to vehicles running under rich air-fuel conditions. We estimate a mean fleet NH3 mass emission rate of 667 +/- 57 mg L(-1) (Er = 94 +/- 8 mg km(-1)). These findings could have significant implications on air quality in the South Coast Air Basin (SoCAB) of California, since they support the hypothesis that emissions from motor vehicles constitute a dominant regional source of NH3, between 20 and 27% of total daily emissions. As NH3 is the predominant atmospheric base, tropospheric levels play a key role in the buffering capacity of the atmosphere and, hence, the formation of fine aerosol. Our results could explain the ubiquitous distribution of ammonium fine particles observed during fall stagnation conditions in the SoCAB.

Air Pollutants↗
PubMed2001

A genomic timescale for the origin of eukaryotes.

BACKGROUND: Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes. RESULTS: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (approximately 4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events. CONCLUSIONS: We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.

Animals↗
PubMed2001

Hypertensive end-organ damage and premature mortality are p38 mitogen-activated protein kinase-dependent in a rat model of cardiac hypertrophy and dysfunction.

BACKGROUND: Numerous pathological mediators of cardiac hypertrophy (eg, neurohormones, cytokines, and stretch) have been shown to activate p38 MAPK. The purpose of the present study was to examine p38 MAPK activation and the effects of its long-term inhibition in a model of hypertensive cardiac hypertrophy/dysfunction and end-organ damage. METHODS AND RESULTS: In spontaneously hypertensive stroke-prone (SP) rats receiving a high-salt/high-fat diet (SFD), myocardial p38 MAPK was activated persistently during the development of cardiac hypertrophy and inactivated during decompensation. Long-term oral treatment of SFD-SP rats with a selective p38 MAPK inhibitor (SB239063) significantly enhanced survival over an 18-week period compared with the untreated group (100% versus 50%). Periodic echocardiographic analysis revealed a significant reduction in LV hypertrophy and dysfunction in the SB239063-treatment groups. Little or no difference in blood pressure was noted in the treatment or vehicle groups. Basal and stimulated (lipopolysaccharide) plasma tumor necrosis factor-alpha concentrations were reduced in the SB239063-treatment groups. In vitro vasoreactivity studies demonstrated a significant preservation of endothelium-dependent relaxation in animals treated with the p38 MAPK inhibitor without effects on contraction or NO-mediated vasorelaxation. Proteinuria and the incidence of stroke (53% versus 7%) were also reduced significantly in the SB239063-treated groups. CONCLUSIONS: These results demonstrate a crucial role for p38 MAPK in hypertensive cardiac hypertrophy and end-organ damage. Interrupting its function with a specific p38 MAPK inhibitor halts clinical deterioration.

Animals↗
PubMed2001

Structured disorder and conformational selection.

Traditionally, molecular disorder has been viewed as local or global instability. Molecules or regions displaying disorder have been considered inherently unstructured. The term has been routinely applied to cases for which no atomic coordinates can be derived from crystallized molecules. Yet, even when it appears that the molecules are disordered, prevailing conformations exist, with population times higher than those of all alternate conformations. Disordered molecules are the outcome of rugged energy landscapes away from the native state around the bottom of the funnel. Ruggedness has a biological function, creating a distribution of structured conformers that bind via conformational selection, driving association and multimolecular complex formation, whether chain-linked in folding or unlinked in binding. We classify disordered molecules into two types. The first type possesses a hydrophobic core. Here, even if the native conformation is unstable, it still has a large enough population time, enabling its experimental detection. In the second type, no such hydrophobic core exists. Hence, the native conformations of molecules belonging to this category have shorter population times, hindering their experimental detection. Although there is a continuum of distribution of hydrophobic cores in proteins, an empirical, statistically based hydrophobicity function may be used as a guideline for distinguishing the two disordered molecule types. Furthermore, the two types relate to steps in the protein folding reaction. With respect to protein design, this leads us to propose that engineering-optimized specific electrostatic interactions to avoid electrostatic repulsion would reduce the type I disordered state, driving the molten globule (MG) --> native (N) state. In contrast, for overcoming the type II disordered state, in addition to specific interactions, a stronger hydrophobic core is also indicated, leading to the denatured --> MG --> N state.

Enzyme Stability↗
PubMed2001

Incomplete taxon sampling is not a problem for phylogenetic inference.

A major issue in all data collection for molecular phylogenetics is taxon sampling, which refers to the use of data from only a small representative set of species for inferring higher-level evolutionary history. Insufficient taxon sampling is often cited as a significant source of error in phylogenetic studies, and consequently, acquisition of large data sets is advocated. To test this assertion, we have conducted computer simulation studies by using natural collections of evolutionary parameters--rates of evolution, species sampling, and gene lengths--determined from data available in genomic databases. A comparison of the true tree with trees constructed by using taxa subsamples and trees constructed by using all taxa shows that the amount of phylogenetic error per internal branch is similar; a result that holds true for the neighbor-joining, minimum evolution, maximum parsimony, and maximum likelihood methods. Furthermore, our results show that even though trees inferred by using progressively larger taxa subsamples of a real data set become increasingly similar to trees inferred by using the full sample, all inferred trees are equidistant from the true tree in terms of phylogenetic error per internal branch. Our results suggest that longer sequences, rather than extensive sampling, will better improve the accuracy of phylogenetic inference.

Amino Acids↗
PubMed2001

Observation of Cabibbo suppressed B --> D(*)K- decays at Belle.

We report observations of the Cabibbo suppressed decays B-->D((*))K- using a 10.4 fb(-1) data sample accumulated at the Upsilon(4S) resonance with the Belle detector at the KEKB e(+)e(-) storage ring. We find that the ratios of Cabibbo suppressed to Cabibbo favored branching fractions are B(B--->D0K-)/B(B--->D0pi(-)) = 0.079+/-0.009+/-0.006, B(B(0)-->D+K-)/B(B(0)-->D+pi(-)) = 0.068+/-0.015+/-0.007, B(B--->D(*0)K-)/B(B--->D(*0)pi(-)) = 0.078+/-0.019+/-0.009, and B(B(0)-->D(*+)K-)/B(B(0)-->D(*+)pi(-)) = 0.074+/-0.015+/-0.006. These are the first observations of the B-->D+K-, D(*0)K-, and D(*+)K- decay processes.

Journal Article↗
PubMed2001

Simultaneous fetal cell identification and diagnosis by epsilon-globin chain immunophenotyping and chromosomal fluorescence in situ hybridization.

Isolating fetal erythroblasts from maternal blood offers a promising noninvasive alternative for prenatal diagnosis. The current immunoenzymatic methods of identifying fetal cells from background maternal cells postenrichment by labeling gamma-globin are problematic. They are nonspecific because maternal cells may produce gamma-globin, give poor hybridization efficiencies with chromosomal fluorescence in situ hybridization (FISH), and do not permit simultaneous visualization of the fetal cell identifier and the FISH signal. We describe a novel technique that allows simultaneous visualization of fetal erythroblast morphology, chromosomal FISH, and epsilon-globin labeled with AMCA (7-amino-4-methylcoumarin-3-acetic acid). AMCA was chosen as the fluorescent label to circumvent the problem of heme autofluorescence because the mean difference in relative fluorescence intensity between fetal erythroblasts stained positive for antiglobin antibody and autofluorescence of unstained cells was greater with AMCA (mean 43.2; 95% confidence interval [CI], 34.6-51.9; SD = 14.0) as the reporting label compared with fluorescein isothiocyanate (mean 24.2; 95% CI, 16.4-31.9; SD = 12.4) or phycoerythrin (mean 9.8; 95% CI, 4.8-14.8; SD = 8.0). Median FISH hybridization efficiency was 97%, comparable to the 98% (n = 5 paired samples) using Carnoy fixative. One epsilon-positive fetal erythroblast was identified among 10(5) maternal nucleated cells in 6 paired mixture experiments of fetal erythroblasts in maternal blood (P <.001). Male epsilon-positive fetal erythroblasts were clearly distinguishable from adult female epsilon-negative erythroblasts, with no false positives (n = 1000). The frequency of fetal erythroblasts expressing epsilon-globin declines linearly from 7 to 14 weeks' gestation (y = -15.8 x + 230.8; R(2) = 0.8; P <.001). We describe a rapid and accurate method to detect simultaneously fetal erythroblast morphology, intracytoplasmic epsilon-globin, and nuclear FISH. (Blood. 2001;98:554-557)

Adult↗
PubMed2001

Facile, regioselective [4 + 2] cycloaddition involving 1-aryl-4-phenyl-1-azadienes and allenic esters: an efficient route to novel substituted 1-aryl-4-phenyl-1,4-dihydropyridines.

[reaction: see text]1-Aryl-4-phenyl-1-azadienes undergo facile, regioselective [4 + 2] cycloaddition to the C2,C3 pi-bond of allenic esters in refluxing benzene, and the formed adducts undergo a 1,3-H shift to afford novel 2-alkyl-1-aryl-3-ethoxycarbonyl-4-phenyl-1,4-dihydropyridines (78-97%). However, when the reaction is carried at room temperature, besides the [4 + 2] addition, the [2 + 2] mode of addition involving C=N of azadiene and C3,C4 pi-bond of allenic esters also intervenes. The resulting N-aryl-2-ethoxy-carbonyl-methylidene-4-styrylazetidines (17-28%) undergo reorganization on silica gel to afford 2-cyclohexen-1-ones.

Journal Article↗
PubMed2001

The presence of a widened vestibular aqueduct and progressive sensorineural hearing loss in the branchio-oto-renal syndrome. A family study.

OBJECTIVE: A new large family with the BOR syndrome is reported with special reference to the presence of a widened vestibular aqueduct and a progressive sensorineural component in the mixed hearing loss. A review of the BOR literature of 184 patients is given. SETTING: University Hospitals. RESULTS: A BOR family with 17 affected members was studied. Fourteen of those 17 were still alive and 12 of those cooperated in this clinical study. Detailed radiological studies showed in three out of 12 affected family members a widened vestibular aqueduct and progressive sensorineural hearing loss. This raises the question whether there is a true correlation or whether those are coincidental. CONCLUSION: In our family with the Branchio-Oto-Renal syndrome, a widened vestibular aqueduct and progressive hearing loss is found in a few affected family members. Imaging of the temporal bones and long-term audiometric follow-up could help to reveal whether the widened vestibular aqueduct is the cause for the progressive hearing loss.

Adolescent↗