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PubMed2004

Viral DNA synthesis-dependent titration of a cellular repressor activates transcription of the human adenovirus type 2 IVa2 gene.

Synthesis of progeny DNA genomes in cells infected by human subgroup C adenoviruses leads to several changes in viral gene expression. These changes include transcription from previously silent, late promoters, such as the IV(a2) promoter, and a large increase in the efficiency of major-late (ML) transcription. Some of these changes appear to take place sequentially, because the product of the IV(a2) gene has been implicated in stimulation of ML transcription. Our previous biochemical studies suggested that IV(a2) transcription is regulated by viral DNA synthesis-dependent relief of transcriptional repression by a cellular protein that we termed IV(a2)-RF. To test the relevance of such a repressor-titration mechanism during the viral infectious cycle, we introduced into the endogenous IV(a2) promoter two mutations that impair in vitro-binding of IV(a2)-RF, but introduce no change (Rep7) or one conservative amino acid substitution (Rep6) into the overlapping coding sequence for the viral DNA polymerase. The results of run-on transcription assays indicated that both mutations induced earlier-than-normal and more efficient IV(a2) transcription. Both mutations were also observed to result in modest increases in the efficiency of viral DNA synthesis. However, measurement of the concentration of IV(a2) transcripts as a function of IV(a2) template concentration demonstrated that the Rep mutations increased by up to 60-fold the efficiency with which IV(a2) templates were used during the initial period of the late phase of infection, as predicted by the repressor titration hypothesis. These mutations also increased the efficiency of ML transcription in infected cells.

Adenoviruses, Human↗
PubMed2001

Titration of chaos with added noise.

Deterministic chaos has been implicated in numerous natural and man-made complex phenomena ranging from quantum to astronomical scales and in disciplines as diverse as meteorology, physiology, ecology, and economics. However, the lack of a definitive test of chaos vs. random noise in experimental time series has led to considerable controversy in many fields. Here we propose a numerical titration procedure as a simple "litmus test" for highly sensitive, specific, and robust detection of chaos in short noisy data without the need for intensive surrogate data testing. We show that the controlled addition of white or colored noise to a signal with a preexisting noise floor results in a titration index that: (i) faithfully tracks the onset of deterministic chaos in all standard bifurcation routes to chaos; and (ii) gives a relative measure of chaos intensity. Such reliable detection and quantification of chaos under severe conditions of relatively low signal-to-noise ratio is of great interest, as it may open potential practical ways of identifying, forecasting, and controlling complex behaviors in a wide variety of physical, biomedical, and socioeconomic systems.

Algorithms↗
PubMed1980

Net proton-hydroxyl permeability of large unilamellar liposomes measured by an acid-base titration technique.

The net proton-hydroxyl permeability of large unilamellar liposomes has been measured by an acid-base pulse titration technique and has been determined to be several orders of magnitude greater than that measured for other monovalent ions. This permeability is relatively insensitive to variations in lipid composition. Proton permeability and hydroxyl permeability vary with pH 6 to 8, and this variation can occur in the absence of alterations in surface charge density resulting from titrations of acidic and basic groups on the lipids. In order to account for the exceptionally high proton-hydroxyl permeability with respect to other monovalent ions, we propose that protons or hydroxyls or both interact with clusters of hydrogen-bonded water molecules in the lipid bilayer, such that they are transferred across the bilayer by rearrangement of hydrogen bonds in a manner similar to their transport in water and ice.

Acid-Base Equilibrium↗
PubMed1983

Cyclic AMP-dependent constitutive expression of gal operon: use of repressor titration to isolate operator mutations.

When the gal operator region is present in a multicopy plasmid it binds to all ("titrates") the gal repressor and "induces" the chromosomal gal operon. To make operator mutations (Oa) with reduced affinity toward the repressor, plasmid DNA was irradiated with UV light and mutant derivatives were isolated that were unable to release the chromosomal gal genes from repression. Then with such an Oa plasmid operator revertants were isolated that had reacquired the ability to release repression. Both sets of mutations have been localized by DNA sequence analysis. When the Oa mutations were transferred from the plasmid to the chromosome by recombination these mutant operators were found to make gal expression constitutive (independent of repressor) but still dependent on cAMP, whereas the previously reported gal operator mutants (Oc) are constitutive both in the presence and in the absence of cAMP. The titration method of isolating mutants enables the isolation of strains with operator mutations that also affect normal promoter activity, and it provides an easy way to isolate revertants of operator mutations.

Base Sequence↗
PubMed1985

Transposase titration in Drosophila melanogaster: a model of cytotype in the P-M system of hybrid dysgenesis.

In the P-M system of hybrid dysgenesis of Drosophila melanogaster, some M strains possess chromosomal P elements. The chromosomes from one of these pseudo-M strains reduced the instability of a P element-insertion mutation of the singed bristle locus. We suggest that this reduction is an indication of competition for a transposase that binds to the P elements on the chromosomes from the pseudo-M strain as well as to the P elements at the singed locus; the pseudo-M strain's P elements might therefore be said to titrate the transposase, reducing its availability to interact with the P elements at the singed locus. We hypothesize that a similar mechanism regulates the movement of P elements in the P strains of D. melanogaster, although in this case we propose that the titrating elements are extrachromosomal and that they are generated by the action of the transposase itself.

Animals↗
PubMed2001

Isothermal titration calorimetry reveals a zinc ion as an atomic switch in the diadenosine polyphosphates.

Diadenosine polyphosphates (diadenosine 5',5'''-P(1),P(n)-polyphosphate (Ap(n)A)) are 5'-5'''-phosphate-bridged dinucleosides that have been proposed to act as signaling molecules in a variety of biological systems. Isothermal titration calorimetry was used to measure the affinities of a variety of metal cations for ATP, diadenosine 5',5'''-P(1),P(3)-triphosphate (Ap(3)A), diadenosine 5',5'''-P(1),P(4)-tetraphosphate (Ap(4)A), and diadenosine 5',5'''-P(1),P(5)-pentaphosphate (Ap(5)A). The binding of Mg(2+), Ca(2+), and Mn(2+) to ATP is shown to take place with the beta,gamma-phosphates (primary site) and be endothermic in character. The binding of Ni(2+), Cd(2+), and Zn(2+) to ATP is found to take place at both the primary site and at a secondary site identified as N-7 of the adenine ring. Binding to this second site is exothermic in character. Generally, the binding of metal cations to diadenosine polyphosphates involves a similar primary site to ATP. No exothermic binding events are identified. Critically, the binding of Zn(2+) to diadenosine polyphosphates proves to be exceptional. This appears to involve a very high affinity association involving the N-7 atoms of both adenine rings in each Ap(n)A, as well as the more usual endothermic association with the phosphate chain. The high affinity association is also endothermic in character. A combination of NMR and CD evidence is provided in support of the calorimetry data demonstrating chemical shift changes and base stacking disruptions entirely consistent with N-7 bridging interactions. N-7 bridging interactions are entirely reversible, as demonstrated by EDTA titration. Considering the effects of Zn(2+) on a wide variety of dinucleoside polyphosphate-metabolizing enzymes, we examine the possibility of Zn(2+) acting as an atomic switch to control the biological function of the diadenosine polyphosphates.

Adenosine Triphosphate↗
PubMed2003

Truncated estrogen receptor product-1 stimulates estrogen receptor alpha transcriptional activity by titration of repressor proteins.

The truncated estrogen receptor product-1 (TERP-1, or TERP) is a pituitary-specific isoform of estrogen receptor alpha (ERalpha), and its expression is regulated by estrogen. TERP modulates the transcriptional activity of ERalpha but has no independent effect on transcription of estrogen-response element-containing promoters. At low concentrations, TERP stimulates ERalpha transcriptional activity in transient transfection assays. At TERP concentrations equal to or greater than full-length ERalpha, TERP forms dimers with ERalpha and reduces both ligand-dependent and -independent transcription. A dimerization mutant of TERP, TERP L509R, stimulated ERalpha transcription at all concentrations. We hypothesized that TERP stimulates ERalpha transcriptional activity by titrating suppressors of ERalpha activity. We found that repressor of estrogen receptor activity (REA), originally isolated from human breast cancer cells, is present in mouse pituitary gonadotrope cell lines. Levels of REA vary slightly throughout the rat reproductive cycle, but TERP mRNA and protein vary much more dramatically. In transfection experiments, REA suppressed ERalpha transcriptional activity, and TERP L509R was able to alleviate transcriptional suppression by REA. In glutathione S-transferase pull-down assays, TERP bound to REA more efficiently than did ERalpha at equivalent concentrations, suggesting that REA will preferentially bind to TERP. Our findings suggest that the stimulation of pituitary ERalpha activity by low concentrations of TERP can occur by titration of corepressors such as REA.

Animals↗
PubMed2003

Unfolding of rabbit muscle creatine kinase induced by acid. A study using electrospray ionization mass spectrometry, isothermal titration calorimetry, and fluorescence spectroscopy.

Electrospray ionization mass spectrometry, isothermal titration calorimetry (ITC), fluorescence spectroscopy, and glutaraldehyde cross-linking SDS-PAGE have been used to study the unfolding of rabbit muscle creatine kinase (MM-CK) induced by acid. The mass spectrometric experiments show that MM-CK is unfolded gradually when titrated with acid. MM-CK is a dimer (the native state) at pH 7.0 and becomes an equilibrium mixture of the dimer and a partially folded monomer (the intermediate) between pH 6.7 and 5.0. The dimeric protein becomes an equilibrium mixture of the intermediate and an unfolded monomer (the unfolded state) between pH 5.0 and 3.0 and is almost fully unfolded at pH 3.0 reached. The results from a "phase diagram" method of fluorescence show that the conformational transition between the native state and the intermediate of MM-CK occurs in the pH range of 7.0-5.2, and the transition between the intermediate and the unfolded state of the protein occurs between pH 5.2 and 3.0. The intrinsic molar enthalpy changes for formation of the unfolded state of MM-CK induced by acid at 15.0, 25.0, 30.0, and 37.0 degrees C have been determined by ITC. A large positive molar heat capacity change of the unfolding, 8.78 kcal mol-1 K-1, at all temperatures examined indicates that hydrophobic interaction is the dominant driving force stabilizing the native structure of MM-CK. Combining the results from these four methods, we conclude that the acid-induced unfolding of MM-CK follows a "three-state" model and that the intermediate state of the protein is a partially folded monomer.

Acetates↗
PubMed2005

The multidrug efflux regulator TtgV recognizes a wide range of structurally different effectors in solution and complexed with target DNA: evidence from isothermal titration calorimetry.

TtgV modulates the expression of the ttgGHI operon, which encodes an efflux pump that extrudes a wide variety of chemicals including mono- and binuclear aromatic hydrocarbons, aliphatic alcohols, and antibiotics of dissimilar chemical structure. Using a 'lacZ fusion to the ttgG promoter, we show that the most efficient in vivo inducers were 1-naphthol, 2,3-dihydroxynaphthalene, 4-nitrotoluene, benzonitrile, and indole. The thermodynamic parameters for the binding of different effector molecules to purified TtgV were determined by isothermal titration calorimetry. For the majority of effectors, the interaction was enthalpy-driven and counterbalance by unfavorable entropy changes. The TtgV-effector dissociation constants were found to vary between 2 and 890 mum. There was a relationship between TtgV affinity for the different effectors and their potential to induce gene expression in vivo, indicating that the effector binding constant is a major determinant for efficient efflux pump gene expression. Equilibrium dialysis and isothermal titration calorimetry studies indicated that a TtgV dimer binds one effector molecule. No evidence for the simultaneous binding of multiple effectors to TtgV was obtained. The binding of TtgV to a 63-bp DNA fragment containing its cognate operator was tight and entropy-driven (K(D) = 2.4 +/- 0.35 nm, DeltaH = 5.5 +/- 0.04 kcal/mol). The TtgV-DNA complex was shown to bind 1-napthol with an affinity comparable with the free soluble TtgV protein, K(D) = 4.8 +/- 0.19 and 3.0 +/- 0.15 mum, respectively. The biological relevance of this finding is discussed.

Bacterial Proteins↗
PubMed1985

Specificity of the binding of bacteriophage M13 encoded gene-5 protein to DNA and RNA studied by means of fluorescence titrations.

The fluorescence quenching of the bacteriophage M13 encoded gene-5 protein was used to study its binding characteristics to different polynucleotides. Experiments were performed at different salt concentrations and in some instances at different temperatures. The affinity of the protein depends on the base and sugar composition of the polynucleotides involved and may differ appreciably, i.e. by orders of magnitude. The salt dependence of binding is within experimental accuracy equal for all single stranded polynucleotides. A method is presented to estimate values of the cooperativity constant from salt titration curves. These values are systematically higher than those obtained from titration experiments in which protein is added to a polynucleotide solution. A comparison is made between the binding constants of the gene-5 protein and the gene-32 protein encoded by the T4 phage. Possible implications of the binding characteristics of the gene-5 protein for an understanding of its role in vivo are discussed.

Base Sequence↗
PubMed1993

Abolition of intrinsically bent DNA structure components in AT clusters by netropsin interaction; titration viscometric investigations.

It is argued that the enhancement of the apparent DNA contour length by the specifically binding non-intercalating drug netropsin (Nt) (Reinert et al., NAR 9, 2335, 1981) at very low Nt/DNA-phosphate ratios essentially is the result of an abolition of periodically arranged intrinsic helix bends in A.T rich tracts of base pairs. In the preceding paper the existence of pronounced DNA tertiary structure components has been postulated for (two species of) natural eukaryotic DNA. The resulting model suggests local apparent solenoid-related DNA tertiary structure components at high sodium ion concentration cs, partly/totally molten out at 45/60 C. With decreasing cs the tertiary structure components have been found to be gradually reduced, at least below cs = 0.010 M, as titration viscometrically revealed by a gradual rise of the apparent DNA contour length (Reinert et al., JBSD 9, 537, 1991). Hence, we performed titration viscometric analyses about Nt interaction with calf thymus DNA (ctDNA) at cs = 0.075 M, 0.010 M and 0.004 M Na+. The concomitant DNA conformational changes are quantitatively described in terms of the relative changes of both DNA persistence length and hydrodynamically operative apparent DNA contour length for the three first resolved interaction modes below a Nt/DNA-P ratio of 0.03. These experiments, together with previous respective analyses at cs = 0.20 M Na+ and different temperatures (l.c.), suggest that those DNA sites binding Nt most strongly predominantly are responsible for the formation of solenoid-related DNA tertiary structure components. Most probably these are A tract-containing sequences. As the essential factor for their apparent elongation effect at low Na+ concentrations, a gradual alteration of the number of base pairs per helix turn seems to occur below cs = 0.010 M Na+ and, concomitantly, a change in phasing between intrinsic helix bends and helix screw.

Adenine↗
PubMed1996

Deformyldistamycin-DNA interaction; DNA conformational changes as revealed by titration rotational viscometry.

The conformational changes of a natural DNA species on binding of deformyl-distamycin (dDst) have been analysed, at 22 degrees C and 7.6 degrees C, in terms of changes of apparent persistence length (a) and of apparent contour length (L), by means of titration rotational viscometry with both high and low molar mass calf thymus (ct) DNA molecules. Next to ligand binding mediated alterations in DNA stiffness, changes of a are the result of helix bending and also of unbending of intrinsic helix bends. A test for the latter are viscosity measurements at different temperatures. Changes of L, on binding of non-intercalating ligands, are interpreted as the result of changes in the intrinsic solenoidal structure components of the natural eukaryotic DNA. Such tertiary-structure components do exist if base sequence dependent helix bends of (nucleosomal) DNA are phased with the helix screw [Drew & Travers, JMB 186, 773 (1985); Reinert et al., JBSD 9, 537 (1991)]. Hence, the measured very small changes of L at ligand/DNA-P ratios r < 0.02 are mainly understood as a partial abolition of intrinsic tertiary structure components and the following negative ones as a respective reinforcement of such structures by dDst binding to AT rich binding sites. Several r-intervals with different slope of the viscosity changes could be resolved at r < 0.05. The resolution of more than four modes of dDst interaction with ctDNA at very low r values is comparable to DNA interaction of Nt and several other ligands but not of distamycin. Advanced titration rotational DNA-viscometry is again able to resolve subtle quantitative details of ligand mediated DNA conformational changes of high stereochemical relevance.

Animals↗
PubMed1985

A rapid air titration method for determining SO2 concentration in inhalation chambers.

A rapid air titration method for determining SO2 concentration in inhalation chambers has been validated using the pararosaniline-formaldehyde (PRA) method of West and Gaeke. This air-titration (iodate) method is an adaptation of iodometric methods using a starch indicator. Potassium iodate and an excess of potassium iodide are used in the reaction. Sampling is completed in ten minutes or less and concentration is calculated by use of a simple formula. Linear equations were derived over the range of concentrations from 0.5 to 100 ppm SO2 for uncorrected iodate bubbler results, data corrected for tandem bubbler concentrations and data corrected for mean iodate bubbler efficiency. Linear correlation with the PRA method over this range was 0.999 for all three sets of data.

Atmosphere Exposure Chambers↗
PubMedDate not supplied

A capture enzyme-linked immunosorbent assay for virus infectivity titrations as exemplified in an adenovirus system.

An enzyme-linked immunosorbent assay (ELISA), employing a capturing antihexon monoclonal antibody specifically recognizing free hexons, was developed for quantitative infectivity titration of adenovirus in a microscale titration assay. The method is based on the quantitative assessment of the total excess production of the major structural protein late in infection in samples consisting of 10(5) virus-infected HeLa cells maintained as stationary suspension cultures. Results are obtained with a coefficient of variation of 10% within 50 hours after virus infection. The method was designed for monitoring substances interfering with viral replication, e.g., neutralizing antibodies or antiviral drugs. Since it measured the total antigen content associated with cells as well as antigens possibly released into the growth medium the general approach should be applicable to any viral system where a structural protein is synthesized in excess.

Adenoviridae↗
PubMed1956

Studies on the aggregation reactions and basic dye binding of tobacco mosaic virus. I. Variation of pH, particle asymmetry, acid and base titration results, irreversible binding of methylene blue, ultraviolet absorption, and extent of heat denaturation in tobacco mosaic virus solutions with time of standing.

1. Aqueous solutions of tobacco mosaic virus were found to undergo a number of spontaneous changes on standing in the cold. The results of pH measurements, acid and base titrations, intrinsic viscosity determinations, studies on the irreversible binding of methylene blue with the virus, ultraviolet absorption, and the extent of nucleic acid splitting by heat denaturation indicated the occurrence of two successive reactions, the first one causing the release of hydrogen ions and a greater lability of the nucleic acid, and the second one, which involved end-to-end dimerization and which took place after 8 days of standing, requiring hydrogen ions. 2. The first over-all reaction was found to be a mixture of various types of reversible disaggregation and aggregation reactions, the nature of which depended on the pretreatment, the TMV concentration, the time of standing, and the phosphate concentration. For longer times of standing at high protein concentration a sudden drop in ultraviolet absorption is noted after dilution; also the drops in viscosity and pH are largest with a steep rise following, indicating the greatest breakup of end-to-end aggregates with formation of the side-to-side type. For concentrated solutions of TMV in water which have not stood long no drop in ultraviolet absorption is noted on dilution; the decrease in the other quantities is less, indicating that only a less extensive breakdown of end-to-end aggregates occurs. Addition of phosphate to concentrated solutions of TMV causes formation of side-to-side aggregates which break up on dilution. 3. Using the results for the pH increase and the viscosity increase in a given time interval for a given TMV preparation and also the slope of the corresponding titration curve at the pH mean, a value for the number of hydrogen ions taken up per TMV monomer in the formation of the end-to-end dimer was finally calculated. The average result obtained for two preparations was 3300. 4. Methylene blue, in the polymeric form, was demonstrated to cause complete irreversible conversion of TMV monomers to end-to-end dimers. At dye concentrations above 10(-4)M, higher TMV polymers are formed, but these are broken down to dimers on removal of free dye by dialysis. The irreversible binding ratios were shown to be decreased in accordance with the extent of the end-to-end aggregation of the preparation at the time of the experiment, which is in agreement with the concept that the irreversibly bound dye polymers go into the junction formed between two interacting TMV monomers. On the basis that only the monomers initially present in solution can react, maximum binding ratios corresponding to complete conversion of monomers to dimers were calculated from the observed irreversible binding ratios and from the fraction of dimers initially present which was obtained from viscosity data. The average result for three preparations in different states of aggregation was calculated to be 6565 for tetrameric binding or 3230 for dimeric binding, which agrees closely with the result obtained for the uptake of hydrogen ions per TMV monomer in the spontaneous dimerization.

Coloring Agents↗
PubMed1982

Titration of transport and modifier sites in the red cell anion transport system.

This work demonstrates the existence of titratable transport and modifier sites in the anion transport system of human red cells. Effects of alkaline extracellular pH on chloride exchange were studied up to pH 13 at 0 degrees C. The studies revealed two sets of reversible titratable groups. One set, having a pK of or approximately 11, appeared to be identical with the inhibitory halide-binding modifier site. Deprotonation of this site stimulated anion transport. The apparent dissociation constants of chloride and iodide at this modifier site were 0.3 and 0.06 M, respectively, and it was confirmed that the organic sulfonate NAP-taurine inhibits anion transport reversibly by a high-affinity interaction with halide-binding modifier sites at the extracellular side of the membrane. Other groups, with apparent pK of or approximately 12 at chloride concentrations above 0.1 M, were named as "transport sites" because transport function depended totally on their protonation. The apparent pK decreased when extracellular halide concentrations was lowered below 0.1 M. It was dependent of the intracellular chloride concentration, and was equally sensitive to extracellular pH of 13, was fully reversible. Hydroxyl ions were not transported to an appreciable extent by the anion exchange system. The pK values of both sets of groups make it likely that they are both arginyl residues, functioning as anion recognition sites similar to the role of functionally essential arginyl residues observed with numerous enzymes.

Biological Transport↗
PubMed1990

New method for titration of virus infectivity by immunostaining.

We have developed a new method for titration of viruses utilizing automated microtiter technology. Compared to existing methods such as plaque assay or hemagglutination titration of influenza virus, the new method offers distinct advantages in terms of time and effort. In addition because multiple replicates can easily be employed accuracy can be increased.

Animals↗
PubMed2006

Effects of a loading dose of morphine before i.v. morphine titration for postoperative pain relief: a randomized, double-blind, placebo-control study.

BACKGROUND: I.V. morphine titration (MT) allows adjustment of the dose needed for pain relief in the post-anaesthesia care unit (PACU). However, MT has limitations such as a delay to achieve pain relief. We thus assessed the effect of a fixed intraoperative loading dose of morphine administered before titration. METHODS: One hundred patients who were undergoing major orthopaedic surgery were included in a double-blind, randomized study comparing a loading dose of morphine (0.15 mg kg(-1)) with placebo administered intraoperatively. MT was then administered in the PACU followed by patient-controlled analgesia (PCA) over 24 h. Data are expressed as mean (sd). RESULTS: The initial VAS [41 (36) vs 52 (35), NS] was not decreased in the morphine group. The VAS was lower in the morphine group in the PACU and PCA periods. The time to achieve effective pain relief was not decreased in the morphine group. The total dose of morphine administered in the PACU (including the loading dose) was significantly increased in the morphine group (+31% in mg kg(-1), P<0.05). Morphine requirements during the PCA period were not different between groups. The incidence of sedation was increased and a severe episode of ventilatory depression occurred in the morphine group. CONCLUSIONS: A loading dose of morphine administered at the end of surgery slightly decreased the VAS but did not reduce the time to pain relief or morphine consumption within the first 24 h. This slight improvement in analgesia was obtained at the expense of morphine-related adverse events.

Adolescent↗