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Biomedical subjects

A Novikov

Publications and source records attributed to A Novikov.

8 recordsLinked to original sources
PubMed2006

Efficient dynamic Monte Carlo algorithm for time-dependent catalytic surface chemistry.

Several numerical algorithms for dynamic Monte Carlo simulations of surface chemistry have been proposed in the past. The variable step size method (VSSM) is commonly used for systems where the rate coefficients are constant in time, owing to its good efficiency. If rate coefficients vary in time, the first reaction method (FRM) has been shown to be more efficient. However, the cost of this algorithm to execute a reaction step depends on the considered lattice size, which can make this method inefficient for systems involving surface phenomena on different scales. Here we propose a general and efficient algorithm, the fast first reaction method (fFRM), which has the advantages of being applicable to systems with constant and time-varying rate coefficients, and of having a computational cost per reaction step that is independent of the lattice size. An additional feature of fFRM is that it is rejection-free, which means that once a reaction class is selected, a reaction of that type will be executed. A rejection-free variant of VSSM, called rVSSM, is also presented, which leads to an approximately 15% speedup compared with the VSSM algorithm for the considered example.

Journal Article↗
PubMed2004

Solid phase peptide synthesis on epoxy-bearing methacrylate monoliths.

Monoliths based on a copolymer of glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) can be used directly as sorbents for affinity chromatography after solid phase peptide synthesis. The quality of the synthesized products, the amount of grown peptides on a support and the reproducibility of the process must be considered. A determination of the quantity of the introducing beta-Ala (and, consequently, the total amount of synthesized peptide) was carried out. Three peptides complementary to recombinant tissue plasminogen activator (t-PA) have been synthesized using Fmoc-chemistry on GMA-EDMA disks. The peptidyl ligands were analysed by amino acid analysis, ES-MS and HPLC methods. The affinity binding parameters were obtained from frontal elution data. The results were compared with those established for GMA-EDMA affinity sorbents formed by the immobilization of the same but separately synthesized and purified ligands. The immobilization on GMA-EDMA disks was realized using a one-step reaction between the amino groups of the synthetic ligand and the original epoxy groups of monolithic material. The affinity constants found for two kinds of sorbent did not vary significantly. Finally, the directly obtained affinity sorbents were tested for t-PA separation from a cellular supernatant.

Chromatography, Affinity↗
PubMed2004

Orthogonal time-of-flight secondary ion mass spectrometric analysis of peptides using large gold clusters as primary ions.

Secondary ion mass spectrometry (SIMS) for biomolecular analysis is greatly enhanced by the instrumental combination of orthogonal extraction time-of-flight mass spectrometry with massive gold cluster primary ion bombardment. Precursor peptide molecular ion yield enhancements of 1000, and signal-to-noise improvements of up to 20, were measured by comparing SIMS spectra obtained using Au(+) and massive Au(400) (4+) cluster primary ion bombardment of neat films of the neuropeptide fragment dynorphin 1-7. Remarkably low damage cross-sections were also measured from dynorphin 1-7 and gramicidin S during prolonged bombardment with 40 keV Au(400) (4+). For gramicidin S, the molecular ion yield increases slightly as a function of Au(400) (4+) beam fluence up to at least 2 x 10(13) Au(400) (4+)/cm(2). This is in marked contrast to the rapid decrease observed when bombarding with ions such as Au(5) (+) and Au(9) (+). When gramicidin S is impinged with Au(5) (+), the molecular ion yield decreases by a factor of 10 after a fluence of only 8 x 10(12) ions/cm(2). Comparison of these damage cross-sections implies that minimal surface damage occurs during prolonged Au(400) (4+) bombardment. Several practical analytical implications are drawn from these observations.

Dynorphins↗
PubMed2001

Mild and moderate asthma is associated with airway goblet cell hyperplasia and abnormalities in mucin gene expression.

Excessive airway mucus is an important cause of morbidity and mortality in asthma, but the relationship between accumulation of mucus and goblet cell size, number, and function is incompletely understood. To address these questions, stored mucin in the epithelium and goblet cell size and number were measured morphometrically, and mucin gene expression was measured by polymerase chain reaction and immunohistochemistry in endobronchial biopsies from 13 subjects with mild and moderate asthma and from 12 healthy control subjects. Secreted mucin was measured in induced sputum. We found that stored mucin in the airway epithelium was three times higher than normal in the subjects with asthma (p < 0.005). Goblet cell size was similar in both groups, but goblet cell number was significantly higher in the subjects with asthma (93,043 +/- 15,824 versus 41,959 +/- 9,230/mm3, p < 0.05). In mild asthma (FEV1 > or = 80% pred, n = 7), the level of stored mucin was as high as in moderate asthma (FEV1 < 80% pred, n = 6), but the level of secreted mucin was significantly lower (28.4 +/- 6.3 versus 73.5 +/- 47.5 microg/ml, p < 0.05). Secreted mucin was inversely correlated with stored mucin for the whole asthma group (rs = -0.78, p = 0.007). MUC5AC was the predominant mucin gene expressed in healthy subjects and subjects with asthma, and MUC5AC protein was increased in the subjects with asthma. We conclude that even mild asthma is associated with goblet cell hyperplasia and increased stored mucin in the airway epithelium, whereas moderate asthma is associated with increased stored mucin and secreted mucin. These findings suggest that acute degranulation of hyperplastic goblet cells may represent a mechanism for asthma exacerbations in mild and moderate asthma and that chronic degranulation of goblet cells may contribute to chronic airway narrowing in moderate asthma.

Adult↗
PubMed1998

Hepatitis G virus encodes protease activities which can effect processing of the virus putative nonstructural proteins.

The genome of a recently identified virus, hepatitis G virus (HGV), shows considerable homology to hepatitis C virus (HCV). Two HGV proteases similar to nonstructural proteins NS2 and NS3 of HCV were identified, and their cleavage site specificity was investigated. Amino acids essential for the protease activities were determined by mutation analysis. NS4A of HGV was demonstrated to be a cofactor for NS3-mediated proteolysis, with a region critical for activity residing between Leu1561, and Ala1598.

Amino Acid Sequence↗
PubMed1996

Human Rad50 is physically associated with human Mre11: identification of a conserved multiprotein complex implicated in recombinational DNA repair.

In this report, we describe the identification and molecular characterization of a human RAD50 homolog, hRAD50. hRAD50 was included in a collection of cDNAs which were isolated by a direct cDNA selection strategy focused on the chromosomal interval spanning 5q23 to 5q31. Alterations of the 5q23-q31 interval are frequently observed in myelodysplasia and myeloid leukemia. This strategy was thus undertaken to create a detailed genetic map of that region. Saccharomyces cerevisiae RAD50 (ScRAD50) is one of three yeast RAD52 epistasis group members (ScRAD50, ScMRE11, and ScXRS2) in which mutations eliminate meiotic recombination but confer a hyperrecombinational phenotype in mitotic cells. The yeast Rad50, Mre11, and Xrs2 proteins appear to act in a multiprotein complex, consistent with the observation that the corresponding mutants confer essentially identical phenotypes. In this report, we demonstrate that the human Rad50 and Mre11 proteins are stably associated in a protein complex which may include three other proteins. hRAD50 is expressed in all tissues examined, but mRNA levels are significantly higher in the testis. Other human RAD52 epistasis group homologs exhibit this expression pattern, suggesting the involvement of human RAD52 epistasis group proteins in meiotic recombination. Human RAD52 epistasis group proteins are highly conserved and act in protein complexes that are analogous to those of their yeast counterparts. These findings indicate that the function of the RAD52 epistasis group is conserved in human cells.

Amino Acid Sequence↗
PubMedDate not supplied

Matrix implanted laser desorption ionization (MILDI) combined with ion mobility-mass spectrometry for bio-surface analysis.

The implantation of low velocity massive gold cluster ions allows homogeneous incorporation of a metallic matrix into the near-surface region of rat brain tissues. Subsequent analysis by laser desorption ionization mass spectrometry yields spectra exhibiting molecular ion peaks in the mass range up to 35 kDa similar to those observed by matrix-assisted LDI. Matrix-implanted LDI when combined with ion-mobility preseparation promises to be a useful technique for molecular imaging of biotissues with a laser microprobe.

Animals↗