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PubMed1987

Waste disposal tangled by liability and conflicting regulations.

In this issue HMM examines the problem of trash disposal. What are hospitals doing with their wastes? In many areas landfills are either running out of space or increasingly unwilling to accept hospital wastes. The next HMM Price Exclusive will survey the prices materials managers are paying for wound closures. Read the next HMM Price Exclusive and see what kinds of contracts and deals materials managers are getting for these important supplies.

Centers for Disease Control and Prevention, U.S.↗
PubMed1997

Prediction of Mitochondrial Targeting Signals Using Hidden Markov Model.

The mitochondrial targeting signal (MTS) is the presequence that directs nascent proteins bearing it to mitochondria. We have developed a hidden Markov model (HMM) that represents various known sequence characteristics of MTSs, such as the length variation, amino acid composition, amphiphilicity, and consensus pattern around the cleavage site. The topology and parameters of this model are automatically determined by the iterative duplication method, in which a small fully-connected HMM is gradually expanded by state splitting. The model can be used to predict the existence of MTSs for given amino acid sequences. Its prediction accuracy was estimated to be 86.9% using the cross validation test. Furthermore, a higher correlation was observed between the HMM score and the in vitro ATPase activity of MSF, which can be regarded as an experimental measure of signal strength, for various synthetic peptides than was observed with other methods.

Journal Article↗
PubMed2002

Methods for prediction of peptide binding to MHC molecules: a comparative study.

BACKGROUND: A variety of methods for prediction of peptide binding to major histocompatibility complex (MHC) have been proposed. These methods are based on binding motifs, binding matrices, hidden Markov models (HMM), or artificial neural networks (ANN). There has been little prior work on the comparative analysis of these methods. MATERIALS AND METHODS: We performed a comparison of the performance of six methods applied to the prediction of two human MHC class I molecules, including binding matrices and motifs, ANNs, and HMMs. RESULTS: The selection of the optimal prediction method depends on the amount of available data (the number of peptides of known binding affinity to the MHC molecule of interest), the biases in the data set and the intended purpose of the prediction (screening of a single protein versus mass screening). When little or no peptide data are available, binding motifs are the most useful alternative to random guessing or use of a complete overlapping set of peptides for selection of candidate binders. As the number of known peptide binders increases, binding matrices and HMM become more useful predictors. ANN and HMM are the predictive methods of choice for MHC alleles with more than 100 known binding peptides. CONCLUSION: The ability of bioinformatic methods to reliably predict MHC binding peptides, and thereby potential T-cell epitopes, has major implications for clinical immunology, particularly in the area of vaccine design.

Amino Acid Motifs↗
PubMed1975

Effect of F-actin upon the binding of ADP to myosin and its fragments.

The effect of F-actin upon the binding of ADP to rabbit skeletal muscle myosin, heavy meromyosin, and subfragment 1 was studied by equilibrium dialysis, ultracentrifuge transport, and light scattering techniques. Both myosin and H-meromyosin (HMM) bind a maximum of approximately 1.6 mol of ADP/mol of protein, while S-1 binds approximately 0.9 mol of ADP/mol of protein. The affinity for ADP of all three preparations was similar at a given ionic strength (approximately 10(6) M-1 at 0.05 M KCl) and decreased with increasing ionic strength. Under conditions similar to those used for the measurement of ADP binding, the binding sites of myosin, HMM, and subfragment 1 (S-1) are saturated with actin at molar ratios of 2, 2, and 1 mol of actin monomer/mol of protein, respectively, as determined by light scattering, ultracentrifuge transport, and in the case of myosin by ATPase measurements. F-actin was found to inhibit ADP binding, but even at an actin concentration at least twice that required for saturation of myosin, HMM, or S-1, significant ADP binding remained. This ADP binding was inhibited by 10(-4) M pyrophosphate. The observations are consistent with the formation of an actomyosin-ADP complex in which actin and ADP are bound to myosin at distinct but interacting sites.

Actins↗
PubMed2005

Mutational analysis of 9 different tumour-associated genes in human malignant mesothelioma cell lines.

Seven tumour suppressor genes (Chk1, Chk2, Apaf1, Rb1, p53, p16(INK4a) and p14(ARF)) and two oncogenes (N-ras and BRAF) were screened in nine human malignant melanoma (HMM) cell lines for point mutations or small deletions/insertions by DGGE, TGGE and SCCP analysis. For the first time in human mesothelioma, Chk1 gene mutations were detected in two of the nine investigated HMM cell lines. P53 gene mutations were found in three cell lines and p16(INK4a) mutations in 5. Mutation of the Chk1 gene implies a novel disruption mechanism of the p53 pathway in HMM, without affecting p53 itself. According to our knowledge, this is the first mutation screening of Chk1, Chk2, Apaf1 and Rb1 in human malignant mesothelioma.

Base Sequence↗
PubMed2006

Fuzzy Hidden Markov Models: a new approach in multiple sequence alignment.

This paper proposes a novel method for aligning multiple genomic or proteomic sequences using a fuzzyfied Hidden Markov Model (HMM). HMMs are known to provide compelling performance among multiple sequence alignment (MSA) algorithms, yet their stochastic nature does not help them cope with the existing dependence among the sequence elements. Fuzzy HMMs are a novel type of HMMs based on fuzzy sets and fuzzy integrals which generalizes the classical stochastic HMM, by relaxing its independence assumptions. In this paper, the fuzzy HMM model for MSA is mathematically defined. New fuzzy algorithms are described for building and training fuzzy HMMs, as well as for their use in aligning multiple sequences. Fuzzy HMMs can also increase the model capability of aligning multiple sequences mainly in terms of computation time. Modeling the multiple sequence alignment procedure with fuzzy HMMs can yield a robust and time-effective solution that can be widely used in bioinformatics in various applications, such as protein classification, phylogenetic analysis and gene prediction, among others.

Base Sequence↗
PubMed1991

[Comparison of 2 field methods for urinary assay of chloroquine].

Two methods of urinary chloroquine assay were tested in pregnant women in the town of Banfora (Burkina Faso): the method with bromothymol blue (Bergqvist) and the method with methyl-orange (Haskins and Mount or HMM II). Urinary assay of chloroquine was performed with both methods in 45 women chosen at random whether or not under chemoprophylactic treatment (21 taking a weekly prophylaxis of 300 mg of chloroquine, and 24 controls). The HMM II method proved to be more sensitive (100%) and more specific (91.7%) than the Bergqvist method (80.9% and 83.3% respectively); it was also more reliable with regard to positive (91.3% versus 80.9%) and negative (100% versus 91.3%) predictive values. Moreover, the quantitative appreciation of the levels of chloroquine excretion proved to be superior with the HMM II method. Finally, this method is faster to perform, easier to use and cheaper, making it the method of choice for field assay of chloroquine in urine.

Azo Compounds↗
PubMed1990

Processing of lipoproteins in human monocyte-macrophages.

Subcellular fractionation of human monocyte-macrophages (HMM) yielded a fraction rich in endosomes, lysosomes, and mitochondria. This pellet was further fractionated in a metrizamide gradient and the subcellular organelles were distributed among seven distinct bands. All of the bands contained lysosomal enzymes in similar amounts. However one band, poor in mitochondria, was markedly enriched in cathepsin D and cholesteryl ester hydrolase activities. A number of different ligands (low density lipoproteins (LDL), malondialdehyde-altered LDL, beta-migrating very low density lipoprotein, high density lipoprotein, reductively methylated LDL, mannose-bovine serum albumin, and transferrin) were presented to HMM at a concentration of 20 micrograms/ml at 4 degrees C. Three minutes after warming the cells at 37 degrees C all ligands except two were found predominantly in the cathepsin D- and cholesteryl ester hydrolase-rich fraction. Unlike the other ligands, LDL had distributed to other more dense fractions and reductively methylated LDL was found mainly in less dense fractions. At a lower concentration, 2 micrograms/ml, the distribution of LDL was identical to the other ligands. In vitro incubation of the fractions obtained from the gradient suggested that cathepsin D was largely responsible for the hydrolysis of the lipoproteins. We conclude that studies of LDL metabolism in HMM must take into account the different processing of this ligand at commonly used concentrations.

Cathepsin D↗
PubMed1979

[Study of the Mg2+-ATPase reaction of myosin using the NMR-31P method. Detection of adenylate kinase activity in a purified myosin subfragment I].

Isolated myosin heads (HMM-S1) were concentrated by ultrafiltration in an "Amicon" cell to a concentration of 120 mg/ml. Incubation of HMM-S1 with ATP in the presence of Mg2+ produced an AMP peak in the spectrum of NMR-31P whose size was increasing linearly with the reaction time. It was demonstrated that after heating of the sample the appearance of AMP in the incubation mixture was due to the presence of a small amount of adenylate kinase (or myokinase) in the purified preparation of HMM-S1.

Adenosine Triphosphatases↗
PubMedDate not supplied

Compared cytotoxicity effects of five anticancer drugs on human (HBL) and mouse (B16) melanoma cells in vitro.

In order to assess the potential interest of replacing the murine cell lines by human cell lines for in vitro cytotoxic assays, the sensitivity and the selectivity of the murine B16 and the human HBL melanomas to five chemotherapeutic drugs were investigated in vitro. The cytotoxicities of Melphalan, Daunorubicin (DNR), Hexamethylmelamine (HMM), Hydroxymethylpentamethylmelamine (HMPMM), and Dihydroxymethyltetramethylmelamine (DHTMM), 2 HMM derivatives, were measured in the two cell lines using two different techniques: reduction of a tetrazolium derivative (MTT) and tritiated thymidine uptake into DNA. The cytotoxicity at inhibitory concentration 50 (IC50) was determined after one hour as well as after 2 days exposure of cell after one hour as well as after 2 days exposure of cells to each drug. The results indicate that the HBL human melanoma was generally more sensitive to Melphalan and DHTMM than the B16 murine melanoma cells as far as the IC50 was concerned. In contrast, no difference of sensitivity was found to DNR and DHTMM. HMM was found to be inactive in both cell lines. The analysis of variance on IC50 values showed that the sensitivity of murine and human melanoma cell lines to drugs was statistically different. Despite the identical selectivity of the two cell lines, two promising observations can be made as far as the comparison of the two cell lines is concerned: 1) the higher sensitivity of HBL human cell line to Melphalan in the in vitro assays and 2) the slightly lower sensitivity of HBL to DNR, a drug without clinical activity against human melanoma.

Analysis of Variance↗
PubMed1989

[The effect of phosphorylation of myosin light chains on the structural state of tropomyosin in thin filaments, decorated with heavy meromyosin].

The structural state of tropomyosin (TM) modified by 5-(iodoacetamidoethyl)-aminonaphthalene-1-sulfonate (1.5-IAEDANS) upon F-actin decoration with myosin subfragment 1 (S1) and heavy meromyosin (HMM) in glycerinated myosin- and troponin-free muscle fibers was studied. HMM preparations contained native phosphorylated myosin light chains, while S1 preparations did not. The changes in the polarized fluorescence of 1.5-IAEDANS-TM during the F-actin interaction with S1 were independent of light chains phosphorylation and Ca2+ concentration, but were dependent on these factors during the F-actin interaction with HMM. The binding of myosin heads to F-actin is supposed to initiate conformational changes in TM which are accompanied by changes in the flexibility and molecular arrangement of TM. In the presence of light chains, the structural changes in TM depend on light chains phosphorylation and Ca2+ concentration. The conformational changes in TM seem to be responsible for the mechanisms of coupling of the myosin and tropomyosin modulation system during the actin-myosin interaction in skeletal muscles.

Animals↗
PubMed1989

[Cytochemical localization of actin filaments in endothelial cells of rabbit trabecular meshwork].

Localization of actin filaments in the endothelial cells of rabbit trabecular meshwork was studied by the nitrobenzoxadiazole-phallacidin (NBD-ph) staining method for fluorescence microscopy and modified heavy meromyosin (HMM) decoration method for electron microscopy. Endothelial cells stained with NBD-ph exhibited intense fluorescence which was apparently associated with the basal plasma membrane area. By the modified HMM decoration method, labeled actin filaments were readily detected in the prefixed endothelial cells, because of the distinctive arrowhead-like appearance, observed beneath the basal plasma membrane facing the trabecular collagen sheet. The actin filaments were arranged with dual directionality within the bundle. In contrast, intermediate (10nm) filaments in the deeper region of endothelial cells were always unlabeled with HMM. The function of the actin filament bundles in endothelial cells may be to maintain the cell shape and provide contractility of the trabecular meshwork resulting in an alteration of the outflow resistance of aqueous humor drainage.

Actins↗
PubMed1985

A conformational transition in gizzard heavy meromyosin involving the head-tail junction, resulting in changes in sedimentation coefficient, ATPase activity, and orientation of heads.

Gizzard heavy meromyosin (HMM) sediments in the ultracentrifuge as a single peak, whose sedimentation coefficient (S20,w) decreases from 9 to 7.5 S upon increasing the NaCl concentration from 0.02 to 0.3 M. This decrease is accompanied by a parallel increase in Mg2+-ATPase activity, suggesting that both changes have a common molecular basis. Phosphorylation decreases S20,w and increases ATPase activity, while ATP increases S20,w. Sedimentation equilibrium studies indicate that HMM undergoes no detectable aggregation at 0.02 or 0.4 M NaCl, remaining monomeric with a molecular weight of 3.4 X 10(5). In contrast, S20,w of subfragment 1 does not change with changes in ionic strength, and its ATPase activity does not decrease at low ionic strengths. Electron micrographs of samples of HMM prepared at low ionic strength show that up to half of the molecules are flexed, i.e. the heads are bent at the neck and project back toward the tail, while the remaining molecules have either one or both of the heads pointing away from the tail. In samples prepared at high ionic strength only about 10% of the molecules are flexed. There is a linear relationship between the fraction of flexed molecules and S20,w, with no significant bending or folding of the tail and no detectable change in the shape of the heads. This correlation suggests that the changes in ATPase activity and S20,w may be a result of the reorientation of the heads.

Acetates↗
PubMed1988

Combined effects of host antitumor immune responses and chemotherapy. Studies with hexamethylmelamine.

The antitumor activity of hexamethylmelamine (HMM) was tested in various mouse tumor models in the presence or absence of host-vs-tumor graft responses. The drug was moderately active against Sarcoma-180 growing in different strains of non-sensitized mice. Strong protection was afforded when recipients were preimmunized with irradiated tumor cells 15 days before tumor challenge followed by HMM treatment. The drug did not show antitumor activity against two radiation-induced lymphomas of congenic mice of B10 background, inoculated into H-2 compatible hosts, or into mice incompatible for subregions of H-2. In this model HMM increased mortality of allogeneic mice presumably through impairment of host-vs-lymphoma graft resistance. In conclusion this study shows that synergistic or antagonistic effects can be obtained by combining chemotherapy with antitumor immune responses.

Altretamine↗
PubMed1985

Investigation of myosin substrate-binding site using phosphorylating analogs of the substrate.

Affinity modification of HMM has been performed, using mixed anhydrides of AMP, epsilon AMP, ADP or IMP and sterically hindered aromatic carbonic acids. The affinity labelling site of HMM was demonstrated to be highly specific towards the adenosine fragment of the affinity analog. The number of phosphate groups and the hydrophobicity of the aromatic acid substitutents did not influence the mode of the analogs interaction with HMM. The data obtained confirms our previous suggestion that the nucleotide analogs in question modify the substrate binding site which is other than the active site of the enzyme.

Adenine Nucleotides↗
PubMed1986

[Phosphorylation of light chains of myosin from rabbit skeletal muscles affects the type of conformation changes of F-actin induced by heavy meromyosin].

The changes in F-actin conformation in myosin-free single ghost fiber induced by the binding of heavy meromyosin (HMM) with dephosphorylated or phosphorylated light chains-2 (LC2) have been studied by measuring intrinsic tryptophan polarized fluorescence of F-actin. It has been found that at low concentrations of Ca2+ (pCa greater than or equal to 8), the binding of HMM with dephosphorylated LC2 to F-actin in ghost fibres increases, whereas the binding of HMM with phosphorylated LC2 decreases the anisotropy of polarized tryptophan fluorescence. The effect is reversed at high concentrations of Ca2+ (pCa = 5). It has been assumed that this effect of myosin light chains phosphorylation may be due to its influence on the type of myosin head binding to F-actin.

Actins↗
PubMed1978

[Polarized ultraviolet fluorescence microscopic study of the structural changes in muscle fiber contractile proteins. V. The possible nature of the conformational rearrangements in heavy meromyosin in fiber relaxation].

The mode and degree of tryptophanyl orientation relative to muscle fiber axes within hydrophobic and hydrophylic sites of myosin macromolecule in the presence of a fluorescence quencher (acrylamide, NO-3) during rigor and relaxation of glycerinated muscle fibers were studied using the polarized ultraviolet fluorescent microscopy. It was shown that myosin tryptophanyls both in LMM and HMM are oriented with their short axes along the longer axis of muscle fiber. Tryptophanyls in LMM have a more pronounced anisotropy of orientation in comparison with the fluorophore orientation anisotropy in hydrophobic sites of HMM. During the muscle fiber relaxation, conformational changes in HMM take place owing to which a section of polypeptide chain with a hydrophilic fluorophore is probably submerged deep into the macromolecule and becomes unapprochable to the quencher.

Animals↗
PubMed1984

Effects of Ca2+ and Mg2+ on the actin-activated ATP hydrolysis by phosphorylated heavy meromyosin from arterial smooth muscle.

Actin-activated ATP hydrolysis by phosphorylated arterial myosin is Ca2+-dependent at Mg2+ concentrations which allow myosin to bind 2 mol of Ca2+ per mol (S. Chacko and A. Rosenfeld (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 292-296). The possible effects of myosin filament formation and conformational change involving the rod portion of the myosin molecule on actin-myosin interaction and actin-activated ATP hydrolysis was eliminated by utilizing soluble heavy meromyosin (HMM). HMM was prepared from phosphorylated arterial myosin by chymotryptic digestion and purified by gel filtration on Sepharose CL-6B. Actin-activated ATPase activity of the phosphorylated HMM was measured either at constant Mg2+ and variable Ca2+ or at constant Ca2+ and variable Mg2+ concentrations. At constant (0.05 M) ionic strength and pCa 5, the actin-activated ATPase activity increased until the free Mg2+ reached between 0.5-1 mM; this was followed by a decrease in activity to a very low level at 7 mM free Mg2+. Removal of Ca2+ at 1 mM free Mg2+ lowered the actin-activated ATPase activity (40-60% inhibition). These experiments demonstrated that Mg2+ and Ca2+ had a direct effect on actin-activated ATP hydrolysis. This effect was not due to myosin filament formation and was independent of the conformational change involving the rod portion of the myosin molecule.

Actins↗