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PubMed2002

Standardization of denaturing gradient gel electrophoresis for mutant screening of influenza A (H3N2) virus samples.

Because of the extensive genetic variability of the influenza viruses, new virus mutants arise worldwide. In the human population, some strains may become potentially epidemic after evading the immune response of the host. At present, molecular methods have made it possible to identify these variants. However, if a large number of samples need to be analyzed the identification of randomly mutated nucleotides cannot be achieved by sequencing analysis or restriction fragment length polymorphism (RFLP). In order to improve this process, a denaturing gradient gel electrophoresis (DGGE) protocol capable of discriminating between reference strains representative of different influenza seasons, some mutant strains, and five clinical isolates was standardized Ribonudeic acid (RNA) was isolated and submitted to a one-step RT-PCR that amplified the region codifying for the globular domain of the Haemagglutinin (HA) molecule. The amplicons were analyzed by electrophoresis in 6% polyacrylamide gel at 60 degreeC/150 V for 8 h, using a 31--41% urea--formamide gradient. This method was able to distinguish between closely related nucleotide sequences, confirming its suitability as screening methodology for the analysis of influenza virus epidemiology, by allowing a faster and more extensive evaluation of a large number of the variant strains detected in a specific region of the world.

Amino Acid Sequence↗
PubMed2000

A new procedure to differentiate citrus tristeza virus isolates by hybridisation with digoxigenin-labelled cDNA probes.

A non-isotopic hybridisation procedure was developed to differentiate isolates of citrus tristeza virus (CTV) using digoxigenin (DIG)-labelled cDNA probes and different kinds of target RNA. Hybridisation of DIG-probes with purified double-stranded RNA (dsRNA) or concentrated total RNA extracts spotted on nylon membranes allowed detection of CTV nucleic acid equivalent to as little as 0.1-1 mg infected tissue, when the reaction was developed with a chemiluminiscent substrate. This sensitivity was similar to or slightly better than that obtained by hybridisation with a 32P-labelled probe. CTV was also detectable by hybridisation of DIG-probes with tissue prints from freshly cut young citrus shoots. Hybridisation of tissue prints with DIG-probes under stringent conditions (60 degrees C and 50% formamide) could differentiate CTV isolates in citrus, whether grown in the greenhouse or in the field. This rapid and sensitive procedure can easily be applied to many samples, even under field conditions, and opens the way to monitoring spatio-temporal movement of specific CTV strains (or groups of strains) in epidemiological studies.

Antibodies, Monoclonal↗
PubMed1998

Roles of conserved residues in the arginase family.

Arginases and related enzymes metabolize arginine or similar nitrogen-containing compounds to urea or formamide. In the present report a sequence alignment of 31 members of this family was generated. The alignment, together with the crystal structure of rat liver arginase, allowed the assignment of possible functional or structural roles to 32 conserved residues and conservative substitutions. Two of these residues were previously identified as functionally essential by analysis of inherited defects in the type I arginase gene. Nearly half of the conserved residues are either glycines or prolines located at critical bends in the protein structure. Most metal-coordinating residues, including one histidine and four aspartic acid residues, are strictly conserved. Two additional histidines involved in metal-binding and catalysis are conserved in all arginases and in almost all other family members. Two positions with invariant similarities may serve as indirect metal ligands. Evolutionary relationships within this family were also suggested. Vertebrate type I and II arginases appear to have developed independently from an early gene duplication event. A ureohydrolase sequence from Caenorhabditis elegans is more closely related to other arginases than previously appreciated, while unclassified enzymes from Methanococcus jannaschii and Methanothermus fervidus appear more similar to arginase-related enzymes. In addition, enzymes from Arabidopsis thaliana and Synechocystis, previously identified as arginases, more closely resemble arginase-related enzymes than currently known arginases.

Amino Acid Sequence↗
PubMed2003

Enzymatic synthesis of trehalose esters having lipophilicity.

To improve trehalose lipophilicity, trehalose was regioselectively esterified with vinyl fatty acid esters in dimethyl formamide by protease from Bacillus subtilis to give 6-O-lauroyltrehalose, 6-O-myristoyltrehalose, 6-O-palmitoyltrehalose, 6-O-stearoyltrehalose, 6-O-oleoyltrehalose and 6-O-linoleoyltrehalose. The influence of structural variation by changing fatty acid substitute was examined by measurement of the surface tension and biodegradability.

Bacillus subtilis↗
PubMed2000

Controlled biodistribution of galactosylated liposomes and incorporated probucol in hepatocyte-selective drug targeting.

Two types of galactosylated liposomes containing cholesten-5-yloxy-N-(4-((1-imino-2-beta-D-thiogalactosyle thyl)amino)b utyl)formamide (Gal-C4-Chol) as a homing device were prepared to study the biodistribution of liposomal carriers and the incorporated drug. Distearoylphosphatidylcholine (DSPC)/cholesterol (Chol)/Gal-C4-Chol (60:35:5) (Gal DSPC), DSPC/Chol (60:40) (DSPC), egg yolk phosphatidylcholine (eggPC)/Chol/Gal-C4-Chol (60:35:5) (Gal eggPC), and eggPC/Chol (60:40) (eggPC) liposomes labeled with [(3)H]cholesteryl hexadecyl ether (CHE) were tested and [(14)C]probucol, with a partition coefficient between octanol and water (PC(oct)) of 10(10.8), was selected as a model drug with lipophilicity suitable for liposomal incorporation. After intravenous injection of the combination of [(14)C]probucol and [(3)H]liposomes, the liver uptake of [(3)H]CHE was the highest in Gal DSPC liposomes, followed by Gal egg PC liposomes, egg PC liposomes, and DSPC liposomes in that order. [(14)C]Probucol incorporated in Gal DSPC liposomes exhibited lower liver uptake than [(3)H]CHE, suggesting that substantial release from liposomes had taken place. In contrast, [(14)C]probucol incorporated in Gal eggPC liposomes was more stably incorporated under in vivo conditions. Co-administration with galactosylated bovine serum albumin significantly inhibited the liver uptake of [(14)C]probucol in both types of galactosylated liposomes, suggesting that the hepatic uptake of liposomes should be mediated by asialoglycoprotein receptors being [(14)C]probucol incorporated in them.

Animals↗
PubMed2002

Inhibition of liver metastasis by targeting of immunomodulators using mannosylated liposome carriers.

Mannosylated liposomes were prepared by incorporating cholesten-5-yloxy-N-(4-((1-imino-2-beta-D-thiomannosylethyl)amino)butyl)formamide (Man-C4-Chol) into small unilamellar liposomes consisting of cholesterol and distearoyl phosphatidylcholine (DSPC). The biodistribution of liposomes labeled with [3H]cholesteryl hexadecyl ether was examined in mice. The rate and extent of the hepatic uptake of those [3H]liposomes increased proportionally on increasing the mixing ratio of Man-C4-Chol. Their hepatic uptake was reduced by increasing the administered dose due to the limited number of mannose receptors. The liver uptake of [3H]Man-liposomes was preferentially mediated by liver non-parenchymal cells (NPC) and significantly inhibited by co-injection with an excess of Man-BSA, indicating the involvement of a mannose receptor-mediated mechanism in the hepatic uptake of Man-liposomes. Muramyl dipeptide (MDP), an immunomodulator, was also incorporated into the liposomes and its inhibitory effect in an experimental liver metastasis model was examined. In contrast to free MDP treatment, which showed little effect on the inhibition of metastasis, liposomal MDP significantly reduced the number of metastatic colonies in the liver. Active targeting of MDP to liver NPC by Man-liposomes resulted in more effective inhibition than delivery of MDP by liposomes without mannose. Treatment with MDP/Man-liposomes further increased the survival of the tumor-bearing mice. These results suggest that Man-liposomes are effective carriers for targeted delivery of bioactive compounds to liver NPC.

Adjuvants, Immunologic↗
PubMed2001

Aldose reductase (AC)(n) microsatellite polymorphism and diabetic microvascular complications in Caucasian Type 1 diabetes mellitus.

A case-control study to investigate whether the aldose reductase (AC)(n) dinucleotide polymorphism (termed 5'-ALR2 polymorphism) is useful as a genetic marker for risk of microvascular complications among Caucasians Type 1 diabetic patients in Australia is reported. This marker was amplified from patient genomic DNA and then fractionated in 5% formamide-urea gels. A total of nine alleles was observed with Z, Z-2 and Z+2 being the major alleles. The distribution of alleles was comparable in diabetic subjects with diabetes and microvascular complications, diabetes without complications and normal non-diabetic control subjects. Similarly, when the distribution of alleles was examined in the patients subcategorized according to the presence of diabetic nephropathy or diabetic neuropathy, no significant association was observed. While the size of the study makes it impossible to exclude a weak linkage, it is concluded that the 5'-ALR2 polymorphism is not useful as a genetic marker for susceptibility to diabetic microvascular complications in Caucasian Type 1 diabetic patients.

Aldehyde Reductase↗
PubMed1981

The use of 2-dimensional CNBr peptide maps for the analysis of crosslinked peptides in bone collagen.

CNBr peptides from insoluble bovine cortical bone collagen were analyzed using a 2-D mapping technique. The major type 1 collagen CNBr peptides were detected by fluorography after general-labelling with 3H-NaBH4 in dimethyl-formamide. These maps were similar to those visualized by coomassie blue staining and demonstrated a proportional decrease of alpha 1CB6. New groups of peptides, different from those normally present in soluble type I collagen were detected. Some of these peptides were slightly larger and more acidic than alpha 1CB6 and were highly labelled when the demineralized bone was specifically labelled for the presence of aldehydes and crosslinks with 3H-NaBH4 in a phosphate buffer, pH 7.4. Based on the size and charge characteristics of these specifically labelled peptides, they were tentatively identified as crosslinking peptides containing different combinations of alpha 1CB6, alpha 1CB0,1 and alpha 1CB5. The specificity of the labelling method using 3H-NaBH4 in phosphate buffer was demonstrated by the detection of other known crosslinked peptides and by the virtual absence of label in alpha 1CB7, CB8, and CB3. We feel that this simple methodological approach developed in these experiments will prove to be very useful in the analysis of collagen crosslinks present in insoluble collagens derived from normal tissues of various ages as well as from pathological states.

Animals↗
PubMed1985

Interactions of plasma proteins with group A, B, C and G streptococci.

Streptococci of serological groups A, B, C and G displayed different binding activities for plasma proteins. Most of the streptococci studied, except those of group B, bound immunoglobulin G. All streptococci reacted with fibrinogen and, except those of group B, with fibronectin. The majority of streptococci, but none of group B, had an affinity for alpha 2-macroglobulin. Albumin was bound by all cultures of group G and a few of group C. Haptoglobulin interacted with only 1 group A culture. None of the streptococci bound transferrin. The specificity of binding sites for 125I-labelled plasma proteins was revealed in a series of inhibition experiments with the unlabelled proteins. The binding sites on streptococci of group G showed different sensitivities to trypsin and pepsin. Reactivities for immunoglobulin G, however, remained unaffected after treatments of the streptococci with trypsin. Exposure to heat (30 min, 80 degrees C) partially inactivated binding activities for the plasma proteins. Sodium dodecyl-sulphate and acetylimidazole strongly reduced binding of albumin and to a lesser extent that of alpha 2-macroglobulin. They had no or little effect on the interaction with the other plasma proteins. Dioxane decreased almost all binding activities. Ethanol partially diminished the binding of immunoglobulin G, fibrinogen, fibronectin and alpha 2-macroglobulin. Treatments of group G streptococci with guanidine, urea, formamide or methanol-HC1 did not affect their plasma protein binding activities.

Animals↗
PubMed1987

Comparison of two newly developed forms of an enzyme-linked immunosorbent assay for the detection of staphylococcal toxic shock syndrome toxin-1 (TSST-1).

Two modifications of an enzyme-linked immunosorbent assay (ELISA) were applied to the quantitative determination of TSST-1 in culture supernatants of S. aureus strains. In both techniques, biotinylated antibodies (anti-TSST-1), obtained by means of either glutaraldehyde or N,N-dimethyl formamide were used. IgG and biotin were conjugated in various ratios and the different conjugates thus obtained were examined for their reactivity in the ELISA tests. The application of the glutaraldehyde-method resulted in more active, sensitive and stable conjugates. Furthermore, acceptable TSST-1 standard curves under fixed conditions were only obtained when the appropriate ratio of biotin to IgG had been determined before the biotinylated antibodies were employed.

Animals↗
PubMed1999

Rapid HLA class I DNA typing using microtiter plate-reverse hybridization assay (MRHA) by simple thermoregulation: high-resolution subtyping of the HLA-A2 and -B40 antigen groups.

We have established a precise, rapid, simple and economical subtyping method for alleles encoding the HLA-A2 and -B40 antigens using microtiter plate-reverse hybridization assay (MRHA), which is based on the general principle of HLA oligotyping by reverse dot blot hybridization. Amino-modified sequence-specific oligonucleotide (SSO) probes were immobilized covalently onto a carboxylate-modified microtiter plate. In order to perform high-resolution subtyping of the HLA-A2 and -B40 antigen groups, the alpha1 and alpha2 domain regions were amplified using a pair of group-specific primers composed of an unlabeled sense primer and a biotinylated antisense primer. PCR-amplified products were hybridized with SSO probes in hybridization buffer containing formamide for 1 hour at 37 degrees C. After washing with 2 X SSC at room temperature, the bound PCR products were detected by alkaline phosphatase-conjugated streptavidine followed by color development. All of 8 HLA-B40 suballeles, all of 2 HLA-B47 suballeles (B40 group-specific primers used in this study allowed also B47 amplification) and 17 out of 21 HLA-A2 suballeles were discriminated. The remaining four HLA-A2 suballeles were determined by analysis after exon 4 amplification. HLA-DNA typing by this method was easily and exactly performed regardless of sample number. The greatest advantages of this technique are strong positive signals obtained, reproducibility and the ease of thermoregulation for hybridization and washing as compared to previously reported microtiter plate hybridization methods.

DNA Probes↗
PubMed1997

Complex organics in laboratory simulations of interstellar/cometary ices.

We present the photochemical and thermal evolution of both non-polar and polar ices representative of interstellar and pre-cometary grains. Ultraviolet photolysis of the non-polar ices comprised of O2, N2, and CO produces CO2, N2O, O3, CO3, HCO, H2CO, and possibly NO and NO2. When polar ice analogs (comprised of H2O, CH3OH, CO, and NH3) are exposed to UV radiation, simple molecules are formed including: H2, H2CO, CO2, CO, CH4, and HCO (the formyl radical). Warming produces moderately complex species such as CH3CH2OH (ethanol), HC(=O)NH2 (formamide), CH3C(=O)NH2 (acetamide), R-CN and/or R-NC (nitriles and/or isonitriles). Several of these are already known to be in the interstellar medium, and their presence indicates the importance of grain processing. Infrared spectroscopy, 1H and 13C nuclear magnetic resonance (NMR) spectroscopy, and gas chromatography-mass spectrometry demonstrate that after warming to room temperature what remains is an organic residue composed primarily of hexamethylenetetramine (HMT, C6H12N4) and other complex organics including the amides above and polyoxymethylene (POM) and its derivatives. The formation of these organic species from simple starting mixtures under conditions germane to astrochemistry may have important implications for the organic chemistry of interstellar ice grains, comets and the origins of life.

Astronomical Phenomena↗
PubMed2002

Examination of a vehicle for use with water soluble materials in the murine local lymph node assay.

The murine local lymph node assay (LLNA) is a validated method for identifying skin sensitization hazard. Vehicle choice can influence the sensitization potential of haptens in both the LLNA and in humans, therefore selection of an appropriate vehicle is important. Suggested vehicles for the LLNA include organic solvents and organic-aqueous mixtures. However, due to its high surface tension and poor wetting qualities, water is not recommended and therefore testing aqueous soluble materials can be problematic. The aims of this investigation were to identify a water-based vehicle that possesses better skin wetting properties than water alone, and to assess its performance relative to other solvents in the LLNA using aqueous soluble haptens. The selected wetting agent was the surfactant Pluronic(R) L92 (L92). Concentrations of L92 of up to 50% did not induce positive responses in the LLNA. 1% aqueous L92 was chosen for further examination. Dose-response analyses were performed with dinitrobenzene sulfonic acid (DNBS) and formaldehyde formulated either in water, 1% L92, dimethyl sulfoxide (DMSO) or dimethyl formamide (DMF). Potassium dichromate (PDC) and nickel sulfate were tested in 1% L92, DMSO or DMF. The highest concentration of potassium dichromate was retested in each vehicle and in water to assess the effect of the wetting agent. Estimates of the relative sensitizing potency in each vehicle were determined by calculation of EC3 values (the estimated concentration required to induce a threshold positive response). While DNBS and formaldehyde produced positive responses in all four vehicles, their relative potency varied among the vehicles. The rank ordering of potencies for both materials was, from highest to lowest, DMF > or = DMSO > 1% L92 > water. Compared with water, use of 1% L92 resulted in >2-fold increase in potency for DNBS and >3-fold increase for formaldehyde. PDC was positive in DMF, DMSO and 1% L92. The potency ranking was DMF > or = DMSO > 1% L92. Re-evaluation of 0.5% PDC confirmed that formulations of both DMSO and DMF induced strong proliferative responses, whereas somewhat less proliferation was recorded with the 1% L92 vehicle. PDC in water was without activity. The performance of 1% L92 as a vehicle for nickel sulfate was assessed relative to DMSO and DMF. In DMSO, nickel sulfate produced a stimulation index (SI) >3 at only the highest level. Testing in DMF induced low levels of proliferation, but failed to produce a SI of 3 at any concentration tested. When formulated in 1% L92, nickel sulfate caused a SI of 3 when tested at 2.5%. Based on the results of these experiments, for identification of sensitization hazard of aqueous soluble materials using the LLNA, DMF and DMSO are the preferred vehicles. However, if a test material is not soluble in DMF or DMSO, or if higher test concentrations can be achieved in an aqueous vehicle, then 1% L92 may provide a better alternative to water alone in terms of improved assay performance.

Allergens↗
PubMed1979

Preferential incorporation of an exogenous cytokinin, N6-benzyladenine, into 18S and 25S ribosomal RNA of tobacco cells in suspension culture.

Cytokinin-requiring tobacco cells were incubated for 10 h in the presence of a labeled cytokinin. N6-benzyl-[2-3H]Ade, and of [8-14C]Ado. After alkaline hydrolysis of total RNA and fractionation of the resulting nucleotides, 80 per cent of the 3H radioactivity of RNA were recovered as the N6-benzyl-Ado nucleotide, covalently inserted into polynucleotidic chains. The N6-benzyl-Ado nucleotide was not significantly labled by 14C: at most one part of this nucleotide per 10 000 may result from a transfer of the benzyl moiety to adenyl residues in preformed RNA. Thus, the covalent insertion of N6-benzyl-Ade into RNA involves the intact N6-substituted base. Total RNA was fractionated either by sucrose density gradient centrifugation or by polyacrylamide gel electrophoresis. All identified RNA species were shown to contain N6-benzyl-Ade. The insertion frequency, measured as the molecular proportion of N6-benzyl-Ade to the total base content, was 3 to 4 times larger in 25S and 18S rRNA than in 5S and 4S RNA. The amount of N6-benzyl-Ade inserted into cytoplasmic ribosomal RNA accounted for about 90 per cent of the amount incorporated into total RNA. Electrophoresis of denatured RNA in the presence of formamide provided additional evidence that N6-benzyl-Ade was indeed incorporated into RNA molecules.

Adenine↗
PubMed1979

Characterization of simian virus 40 transcriptional intermediates in infected CV1 cell nuclei.

Simian Virus (SV40) transcriptional intermediates (T.I.) were isolated from infected cell nuclei incubated in vitro in the presence of the four ribonucleoside triphosphates. The nascent mRNA strands in the viral DNA-RNA hybrid molecules were hydrogen bonded to their template by 200-250 nucleotides on the average, as judged from the extent of their RNase resistance and the aspect of T.I. under electron microscope after treatment with 50 per cent formamide. The RNA polymerase involved (RNA polymerase II) synthesized up to full length transcripts at a rate of approximately 150 nucleotides/min. at 25 degrees C. Each SV40 infected cell was found to contain about 200 active T.I. molecules at the peak of late transcription. The DNA in the T.I. molecules was exclusively form I DNA only in cell infected with the tsA30 mutant of SV40 that had been transferred to non-permissive temperature in order to arrest DNA replication, but both form I DNA and molecules behaving as replicative intermediates (R.I.) in wild type infected cells.

Animals↗
PubMed1999

Effects of solvents interacting favorably with hydrophilic segments of the membrane surface of phosphatidylcholine on their gel-phase membranes in water.

We have investigated the effects of two kinds of solvents forming the lamellar liquid-crystalline (L(alpha)) phase in phosphatidylcholine (PC) membranes in neat condition, such as formamide and 1,3-propanediol, on phase behaviors of multilamellar vesicle (MLV) of DPPC (DPPC-MLV). These solvents induced the interdigitated gel (L(beta)I) phase in DPPC-MLV in excess water above their critical concentrations. Solubility measurement indicates that these solvents interact favorably with the hydrophilic segment of the PC membrane but interact unfavorably with the alkyl chains. Based on these results, we propose the mechanism of the induction of the L(beta)I phase by these solvents.

Journal Article↗
PubMed2000

Small angle X-ray scattering studies on local structure of tobacco mosaic virus RNA in solution.

Effects of temperature and ionic strength (S) on the local structure of tobacco mosaic virus RNA in phosphate buffer solution are studied by analyzing the small-angle X-ray scattering (SAXS) curves. The root-mean-square radius of a cross-section of RNA chain was kept at 0.845+/-0.005 nm over a wide range of S from 0.2 to 0.003 at 20 degrees C, whereas it gradually diminished from 0.85 to 0.61 nm when the temperature is raised from 20 to 50 degrees C at S = 0.2. Nevertheless, all of SAXS curves reflecting the backbone structures were equally mimicked by theoretical ones of freely hinged rod (FHR) models, i.e. several straight rods joined with freely hinged joints in the form of a combination of the letter Y, if the constituent rod lengths in the models are adjusted. From these facts, it is suggested that the local structure of the RNA chain in aqueous solution is characterized by an essential feature that unpaired bases in the partially double-stranded helix are constantly far isolated from each other along the helix and the rod-like structure of the helix is preserved over a range of helical contents. Such a characteristic local structure of the chain is entirely collapsed in the formamide solution at 50 degrees C.

Buffers↗
PubMed2000

Biodistribution characteristics of mannosylated, fucosylated, and galactosylated liposomes in mice.

The in vivo disposition behavior and pharmacokinetic characteristics of galactosylated (Gal), mannosylated (Man) and fucosylated (Fuc) liposomes were compared in this study. For the preparation of the glycosylated liposomes, cholesten-5-yloxy-N-(4-((1-imino-2-beta-D-thiogalactosyle thyl)amino)a lkyl)formamide (Gal-C4-Chol) (Kawakami et al., Biochem. Biophys. Res. Commun. 252 (1998) 78-83) and its mannosylated and fucosylated derivatives (Man-C4-Chol and Fuc-C4-Chol, respectively) were synthesized. The glycosylated liposomes are composed of distearoylphosphatidylcholine (DSPC), cholesterol (Chol), and Gal-C4-Chol (or Man-C4-Chol or Fuc-C4-Chol) with the molar ratio of 60:35:5. After intravenous injection in mice, these three types of [(3)H]cholesteryl hexadecyl ether-labeled glycosylated liposomes were rapidly eliminated from the circulating blood and preferentially recovered in the liver. In contrast, DSPC/Chol (60:40) liposomes without glycosylation were retained for a long time in the circulating blood. The uptake ratios by parenchymal cells (PC) and nonparenchymal cells (NPC) (PC/NPC ratios) for 0.5% Gal, Man and Fuc liposomes were found to be 15.1, 0.6 and 0.2, respectively. The effect of predosing glycosylated proteins and liposomes on the hepatic uptake of 0.5% (3)H-labeled Gal, Man, and Fuc liposomes was investigated and the results support the conclusion that Gal, Man, and Fuc liposomes are taken up by the liver via asialoglycoprotein receptors in PC, mannose receptors in NPC, and fucose receptors in NPC, respectively. Interestingly, Gal liposomes were taken up by NPC rather than by PC at a high dose (5%). Together with the finding that 5% Gal liposomes inhibit the hepatic uptake of (3)H-labeled Fuc liposomes, this suggests that Gal-liposomes administered at a high dose will also be taken up by fucose receptors in NPC, that are considered to act as galactose particle receptors.

Animals↗