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PubMed1999

DNA stretching and compression: large-scale simulations of double helical structures.

Computer-simulated elongation and compression of A - and B -DNA structures beyond the range of thermal fluctuations provide new insights into high energy "activated" forms of DNA implicated in biochemical processes, such as recombination and transcription. All-atom potential energy studies of regular poly(dG).poly(dC) and poly(dA).poly(dT) double helices, stretched from compressed states of 2.0 A per base-pair step to highly extended forms of 7.0 A per residue, uncover four different hyperfamilies of right-handed structures that differ in mutual base-pair orientation and sugar-phosphate backbone conformation. The optimized structures embrace all currently known right-handed forms of double-helical DNA identified in single crystals as well as non-canonical forms, such as the original "Watson-Crick" duplex with trans conformations about the P-O5' and C5'-C4' backbone bonds. The lowest energy minima correspond to canonical A and B -form duplexes. The calculations further reveal a number of unusual helical conformations that are energetically disfavored under equilibrium conditions but become favored when DNA is highly stretched or compressed. The variation of potential energy versus stretching provides a detailed picture of dramatic conformational changes that accompany the transitions between various families of double-helical forms. In particular, the interchanges between extended canonical and non-canonical states are reminiscent of the cooperative transitions identified by direct stretching experiments. The large-scale, concerted changes in base-pair inclination, brought about by changes in backbone and glycosyl torsion angles, could easily give rise to the observed sharp increase in force required to stretch single DNA molecules more than 1.6-1.65 times their canonical extension. Our extended duplexes also help to tie together a number of previously known structural features of the RecA-DNA complex and offer a self-consistent stereochemical model for the single-stranded/duplex DNA recognition brought in register by recombination proteins. The compression of model duplexes, by contrast, yields non-canonical structures resembling the deformed steps in crystal complexes of DNA with the TATA-box binding protein (TBP). The crystalline TBP-bound DNA steps follow the calculated compression-elongation pattern of an unusual "vertical" duplex with base planes highly inclined with respect to the helical axis, exposed into the minor groove, and accordingly accessible for recognition.Significantly, the double helix can be stretched by a factor of two and compressed roughly in half before its computed internal energy rises sharply. The energy profiles show that DNA extension-compression is related not only to the variation of base-pair Rise but also to concerted changes of Twist, Roll, and Slide. We suggest that the high energy "activated" forms calculated here are critical for DNA processing, e.g. nucleo-protein recognition, DNA/RNA synthesis, and strand exchange.

Computer Simulation↗
PubMed1999

Theoretical analysis of the inter-ligand overhauser effect: a new approach for mapping structural relationships of macromolecular ligands.

A theoretical framework has been developed for the evaluation of inter-ligand Overhauser effects (ILOE), predicted when pairs of ligands are observed in the presence of a macromolecular receptor which can form a ternary complex such that some of the protons on the two ligands are in close proximity with each other (generally less than approximately 5 A). Simulations for a pair of ligands with three spins each have been performed for a variety of geometric and rate parameters. Analogous to previously described calculations of TRNOE behavior, theoretical behavior of each of the nine cross peaks, A(ij), in a NOESY experiment involving ligands which can exist in the free, binary, or ternary complex states can be calculated. However, for exchange which is sufficiently rapid on the relaxation and chemical shift time scales, use of a collapsed matrix, C, corresponding to sums of sets of nine elements, will often be appropriate and generally simplifies the analysis. In order to generate inter-ligand Overhauser effects, it is optimal for the fraction of receptor involved in the ternary complex to be reasonably large; i.e., concentrations of both ligands should be near saturation. Based on a model assuming random binding order of the ligands, the dependence of ILOE resonance intensities on kinetic rate constants roughly parallels the dependence of transferred NOE (TRNOE) intensities. For diffusion controlled binding, i.e., k(on) approximately 10(8) M(-1) s(-1), the method is best suited for equilibrium dissociation constants in the micromolar-millimolar range (k(off) approximately 10(2)-10(5) s(-1)). Toward the slower dissociation rate constant end of this range, TRNOE and ILOE effects are still predicted, but the initial build-up curves become markedly nonlinear. For a kinetic binding scheme which assumes ordered binding of the ligands, the inherent asymmetry of the ligand binding process leads to more complex kinetics and alters the dependence of the ILOE on the kinetic parameters. In this case, the binding of the second ligand effectively reduces the exchange rate of the first ligand, reducing the transfer of NOE and ILOE information. The reduction in TRNOE and ILOE information which is prediced for the ordered ligand binding model is overcome at larger dissociation rate constants for either ligand 1 or ligand 2. In addition to the structural information available from ILOE data, the strong dependence of TRNOE and ILOE curves on ordered ligand binding suggests that such measurements could be useful for the characterization of ligand binding kinetics.

Enzymes↗
PubMed1985

High-affinity, sodium-gradient-dependent transport of choline into vesiculated presynaptic plasma membrane fragments from the electric organ of Torpedo marmorata and reconstitution of the solubilized transporter into liposomes.

Vesiculated fragments of presynaptic plasma membranes have been isolated from the purely cholinergic electromotor nerve terminals of Torpedo marmorata. Synaptosomes, generated from the terminals by homogenization, were separated on a discontinuous Ficoll gradient and then lysed by osmotic shock at 2 degrees C, pH 8.5 in the presence of 0.1 mM MgCl2. These conditions for lysis were optimal for choline transport. Electron micrographs of lysed synaptosomes showed vesiculated membranes with diameters smaller than those of synaptosomes; occasionally, synaptic vesicles were observed attached to them. Intact mitochondria or synaptosomes and basal laminae were not present. High-affinity (KT = 1.7 microM) uptake of choline into these vesiculated membrane fragments showed: an absolute dependence on the Na+ gradient (outside greater than inside), a transient Na+-gradient-dependent accumulation of choline over the equilibrium concentration (over-shoot), electrogenicity and rheogenicity, since the uptake was further stimulated in the presence of a Na+ gradient by valinomycin, dependence on the presence of external Cl-, and partial dependence on a Cl- gradient (outside greater than inside), high-affinity (Ki = 25 nM) inhibition by hemicholinium-3 and temperature sensitivity. The plasma membranes were further purified by centrifugal density gradient fractionation on a 4-12% Ficoll gradient. Several enzymes and polypeptides copurified with the specific binding sites for choline present in the membranes. The fraction with the most binding sites was one denser than 12% Ficoll. This was also the fraction richest in acetylcholinesterase, 5'-nucleotidase and polypeptides of relative molecular mass, Mr (X 10(-3)) of greater than 200, 140, 68 (doublet), 57, 54 and 28. Acetylcholinesterase was positively identified as a Mr 68 000 component by immune blot. By contrast the ouabain-sensitive ATPase showed a negative correlation with choline binding sites. When the solubilized proteins of the vesiculated membranes were transferred to liposomes, they conferred on the latter the capacity to take up choline in a manner closely resembling its transport in natural membranes but with an initial (one minute) rate of uptake approximately 10-times greater per mg of protein. Several proteins were selectively transferred to the liposomes including ones of Mr (X 10(-3)) 34, 42, 47, 54, 60, 68, 92, 160 and greater than 200. The polypeptides of Mr (X 10(-3)) 140, 57 and 28 were lost in the transfer.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2005

Approaches to improving the biocompatibility of porous perfluoropolyethers for ophthalmic applications.

Porous perfluoropolyether (PFPE) membranes for ophthalmic applications were prepared with a zwitterion monomer, 3-[[2-(methacryloxy) ethyl](N,N-dimethyl)ammonio]-propane-1-sulphonate, copolymerized in weight ratios of 0-10%. The polymer samples were assessed for a range of physical properties, including equilibrium water content, bovine serum albumin permeability, transparency, refractive index and the ability to support corneal epithelial cell and tissue attachment, growth and migration. In vitro assessment of the polymers using bovine corneal epithelial cells and tissue showed that a zwitterion incorporation level of between 0% and 6% in the PFPE membranes supported the migration of an intact sheet of epithelial tissue without compromising epithelial cell attachment and growth, with 4-6% being the optimal level for these properties. Binding patterns of the cell adhesion glycoprotein fibronectin were also found to reflect the cell and tissue response. Effective nutrient permeability, refractive index and optical transparency were also maintained by the porous PFPE polymers containing this concentration of zwitterionic monomer. The presence of amounts of zwitterion greater than 6% was inhibitory to both tissue migration and cell growth and was associated with increased optical haze. These results demonstrated that it is possible to achieve the potential for increased biocompatibility in zwitterion-containing PFPE polymers without compromising existing beneficial characteristics.

Animals↗
PubMed2001

Microcalorimetric studies of the interaction mechanisms between proteins and Q-sepharose at pH near the isoelectric point (pI) effects of NaCl concentration, pH value, and temperature.

This study examined the interaction mechanisms of beta-lactoglobulins A and B (Lg A, Lg B) with an anion exchanger, Q-Sepharose at pH near the isoelectric point at which the proteins are expected to be electrically neutralized under various NaCl concentrations and temperatures by the equilibrium binding analysis and the adsorption enthalpy directly measured by isothermal titration calorimetry. The data evaluated from isotherms fitted by the Langmuirean model reveal that the addition of NaCl considerably reduced the binding affinities and capacities of both the proteins with Q-Sepharose at pH 5.2, indicating that electrostatic forces are dominant during the adsorption. However, the hydrophobic interaction seems to be involved in adsorption as well at a higher NaCl concentration, and the adsorption enthalpies confirm this suggestion. In addition, the effects of temperature on the equilibrium binding behaviors for Lg A or Lg B with Q-Sepharose were found to be salt concentration-dependent, probably due to their different binding mechanisms at 0.03 M and 0.3 M NaCl. Where, at 0.3 M NaCl, the hydrophobic interaction plays a more pronounced role. This implication was again supported by the adsorption enthalpies. The presented data provide further insight to the interaction mechanisms between proteins and ion exchangers, facilitating the optimization of protein separations.

Calorimetry↗
PubMed1998

Biomedical imaging using hyperpolarized noble gas MRI: pulse sequence considerations.

Hyperpolarized noble gas MRI is a new technique for imaging of gas spaces and tissues that have been hitherto difficult to image, making it a promising diagnostic tool. The unique properties of hyperpolarized species, particularly the non-renewability of the large non-equilibrium spin polarization, raises questions about the feasibility of hyperpolarized noble gas MRI methods. In this paper, the critical issue of T1 relaxation is discussed and it is shown that a substantial amount of polarization should reach the targets of interest for imaging. We analyse various pulse sequence designs, and point out that total scan times can be decreased so that they are comparable or shorter than tissue T1 values. Pulse sequences can be optimized to effectively utilize the non-renewable hyperpolarization, to enhance the SNR, and to eliminate image artifacts. Hyperpolarized noble gas MRI is concluded to be quite feasible.

Echo-Planar Imaging↗
PubMed1993

Interactions of bacteriophage T7 DNA primase/helicase protein with single-stranded and double-stranded DNAs.

Protein-DNA interactions of bacteriophage T7 DNA primase/helicase protein 4A' with small synthetic oligodeoxynucleotides were investigated using a 20-base-paired hairpin duplex, and 10-, 30-, and 60-base-long single-stranded DNA. The effect of nucleotide cofactors on DNA binding was examined using membrane binding assays which showed that 4A' binds DNA optimally only in the presence of MgdTMP-PCP, the nonhydrolyzable analog of dTTP. About 20% of single-stranded DNA binding was observed in the presence of MgdTDP, but none was detectable in the absence of nucleotides. Native polyacrylamide gel electrophoresis showed that the DNAs bind predominantly to the hexameric form of 4A'. Larger oligomers of 4A' can bind DNA, but no DNA binding was observed to species smaller than the hexamer. Quantitative equilibrium binding studies at increasing 4A' concentrations and at increasing DNA concentrations showed tight binding of one 10-mer or 30-mer per hexamer. The 4A' hexamer can bind a second strand of DNA, but with a 50-fold weaker affinity than the first strand. The 60-mer showed tight binding to two 4A' hexamers, suggesting that a hexamer may interact with only 30-40 bases of single-stranded DNA. This was corroborated by nuclease protection experiments where the smallest length of DNA protected by 4A' or 4B protein was found to be about 30 bases. Equilibrium binding studies and competitive DNA binding data are consistent with a weaker affinity of 4A' for the duplex DNA. Only 20-25% of duplex DNA binding was observed at increasing 4A' protein in the presence of MgdTMP-PCP. About four duplex DNAs can bind each 4A' hexamer at increasing DNA concentrations, but their weaker binding was evident from their facile dissociation from 4A' in the presence of competing single-stranded DNA.

Bacteriophage T7↗
PubMed2006

Relativistic computational investigation: the geometries and electronic properties of TaSi(n)+ (n = 1-13, 16) clusters.

The equilibrium geometries, stabilities, and electronic properties of the TaSi(n)+ (n = 1-13, 16) clusters are investigated systematically by using the relativistic density functional method with generalized gradient approximation. The small-sized TaSi(n)+ clusters with slight geometrical adjustments basically keep the frameworks that are analogous to the neutrals while the medium-sized charged clusters significantly deform the neutral geometries, which are confirmed by the calculated AIP and VIP values. Furthermore, the optimized geometries of the charged clusters agree with the experimental results of Hiura and co-workers (Hiura, H.; Miyazaki, T.; Kanayama, T. Phys. Rev. Lett. 2001, 86, 1733). The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) gaps of the charged clusters are generally increased as the cluster size goes from n = 1 to 13; and the large HOMO-LUMO gaps of charged clusters resulting from the positive charge indicate that their chemical stabilities are stronger than their neutral counterparts, especially for n = 4, 6, and 7 clusters. Additionally, the contributions of the d orbitals of the Ta atom to the HOMO and LUMO reveal that the chemical activity of the d orbitals of the Ta atom decreases gradually as the number of silicon atoms increases. This interesting finding is in good agreement with the recent experimental results on the reactive activities of the H2O and transition-metal silicon clusters (Koyasu, K.; Akutsu, M.; Mitsui, M.; Nakajima, A. J. Am. Chem. Soc. 2005, 127, 4998). Generally, the positive charge significantly influences the electronic and geometric structures of the charged clusters. Finally, the most stable neutral and charged TaSi16 clusters are found to be fullerene-like structures and the HOMO-LUMO gap in charged form is detectable experimentally.

Journal Article↗
PubMed2006

The emergence of geometric order in proliferating metazoan epithelia.

The predominantly hexagonal cell pattern of simple epithelia was noted in the earliest microscopic analyses of animal tissues, a topology commonly thought to reflect cell sorting into optimally packed honeycomb arrays. Here we use a discrete Markov model validated by time-lapse microscopy and clonal analysis to demonstrate that the distribution of polygonal cell types in epithelia is not a result of cell packing, but rather a direct mathematical consequence of cell proliferation. On the basis of in vivo analysis of mitotic cell junction dynamics in Drosophila imaginal discs, we mathematically predict the convergence of epithelial topology to a fixed equilibrium distribution of cellular polygons. This distribution is empirically confirmed in tissue samples from vertebrate, arthropod and cnidarian organisms, suggesting that a similar proliferation-dependent cell pattern underlies pattern formation and morphogenesis throughout the metazoa.

Animals↗
PubMed2004

Phase transitions in a disordered system in and out of equilibrium.

The equilibrium and nonequilibrium disorder-induced phase transitions are compared in the random-field Ising model. We identify in the demagnetized state the correct nonequilibrium hysteretic counterpart of the T=0 ground state, and present evidence of universality. Numerical simulations in d=3 indicate that exponents and scaling functions coincide, while the location of the critical point differs, as corroborated by exact results for the Bethe lattice. These results are of relevance for optimization, and for the generic question of universality in the presence of disorder.

Journal Article↗
PubMed1987

Oxygen transfer in the corneal-contact lens system.

The clinical results of contact lens wearers indicate that materials which theoretically are adequate to prevent corneal hypoxia and edema do not perform optimally under actual wearing conditions. Optimization of the cornea-tear-lens system requires an analysis of the modes of oxygen transport, mass transfer resistances, and characteristic dimensions. The lens properties are a function of polymer composition. Thus, investigations for ideal lens materials may result in limitless test copolymers and graft polymers of siloxane, methylmethacrylate, 2-hydroxyethyl-methacrylate, vinylpyrollidone, vinylacetate, and cellulose acetate butyrate of varying degrees of cross-linking and crystallinity. In an attempt to channel research efforts, this review will state the developments to date and the desirable properties of an optimal cornea-tear-lens system. The logic should encompass a theory and model whereby parameters are identified and varied within satisfactory physiological limitations, and experiments which provide data indicative of the in vivo conditions. The parameters must reflect the inherent transport properties of the corneal-contact lens system. Contact lenses may be categorized as soft, gas-permeable rigid/hydrophobic flexible, or hard. The major differences between these three categories are the properties: equilibrium water content or degree of hydration, tendency for water pervaporation and/or dehydration, surface hydrophobicity, thermal conductivity, oxygen diffusivity and solubility, lens thickness, rest height over corneal tear, flexibility, lens mobility over the cornea, cross-linking, crystallinity, stagnant boundary layer resistances, and manufacturing processes. Aside from complications presented by lens coatings and cleansing solutions, the most common problems experienced by lens wearers include corneal edema, dehydration involving the lens and the cornea, "blurry" vision due to localized corneal anoxia, debris trapped under the lens, and deposits on th surface of the lens. All of the aforementioned phenomena are either explicitly or implicitly associated with transport processes through and around the lens. Convection of tear fluid under a lens during a blink, diffusion of oxygen and water through the lens and the stagnant boundary-layer effect for mass transfer in the tear between blinks, and the overall nonisothermal effects on the transport of oxygen and water between the cornea and ambient conditions are reviewed.

Biocompatible Materials↗
PubMed2004

A new mechanism for metal ion-assisted interchain helix assembly in a naturally occurring peptide mediated by optimally spaced gamma-carboxyglutamic acid residues.

Helix-helix interactions, such as those that occur in coiled-coil domains, four-helix bundles, or membrane-spanning helical bundles, are important to the structural organization and function of numerous proteins. However, tractable peptide models for studying such structural elements have been limited to synthetic analogs of coiled-coil protein domains and de novo designed peptides. The present study provides evidence that conantokin-G (con-G), a gamma-carboxyglutamate (Gla)-rich neuroactive peptide from a venomous marine snail, can self-associate in the presence of certain divalent metal cations. Sedimentation equilibrium analyses of con-G show that Ca2+ binding promotes peptide dimerization, while the addition of the tighter binding divalent cations, Mg2+, Zn2+, and Mn2+, does not result in intermolecular association. The effects of specific residue replacements indicate that an i, i + 4, i + 7, i + 11 arrangement of Gla residues is essential for con-G self-assembly. To determine the relative chain orientation of the dimeric assembly, distributions of Cys-containing con-G variants were examined in thiol-disulfide rearrangement assays and the results were consistent with an antiparallel alignment. Our data suggest that the driving force for con-G dimerization stems from the appropriate balance of interchain and intrachain metal ion coordination by Gla residues in similar locations. These findings suggest a new role for Gla residues and accompanying cation binding in the stabilization of interstrand helix association in a natural product and provide a model for controlled assembly of peptide chains or segments of larger proteins.

1-Carboxyglutamic Acid↗
PubMed1979

Intracellular pH changes during the cell cycle in Tetrahymena.

The equilibrium distribution of 5,5-dimethyloxazoladine 2,4-dione (DMO) between intra- and extracellular volume was used to estimate intracellular pH (pHi) in Tetrahymena pyiformis. In control experiments, DMO was found to equilibrate rapidly in response to a pH gradient. Under normal growth conditions, pHi was constant over a finite range of external pH, being maintained near pH 7.1 over the external pH range 5.2 to 7.3. This same range of external pH was also optimal for growth. pHi was monitored during the cell cycle of a synchronous population of T. pyriformis GL. The cells were synchronized either by starvation/refeeding or heat shock. Under both conditions, there were two alkaline shifts of approximately 0.4 pH units per cell cycle. These shifts in pH retained a constant remporal relationship to S phase and were not affected by changes in the time, duration, or magnitude of cytokinesis.

Cell Cycle↗
PubMed1997

Dependence of salt concentration on glycosaminoglycan-lysozyme interactions in cartilage.

The cationic protein, lysozyme, has an extracellular distribution in cartilage but its precise role in this tissue has not yet been established. This study describes the dependence of salt concentration on the binding properties of lysozyme isoforms of different cationic charges, isolated from bovine cartilage, to the two major and structurally similar glycosaminoglycans of cartilage, i.e., chondroitin sulfate and hyaluronan. The binding of most cartilage lysozyme isoforms and hen egg-white lysozyme (control) to chondroitin sulfate and hyaluronan linked to agarose supports displayed optimal levels at approximately 20 and 5-10 mM salt, respectively, but decreased at both lower and higher salt concentrations indicating the electrostatic nature of the interactions. However, optimal binding of the most cationic lysozyme isoform to chondroitin sulfate occurred at 60 mM salt, with significant binding remaining at 150 mM. This isoform also showed binding to hyaluronan up to 60 mM salt, while for the other isoforms binding was observed only up to 150 and 40 mM salt for chondroitin sulfate and hyaluronan, respectively. The low salt concentrations at which these interactions occur are likely to exist in cartilage as shown from equilibrium dialysis studies performed using solutions of chondroitin sulfate (up to 10%, a concentration likely to occur in cartilage). From Scatchard analysis, the affinity of binding of all lysozymes to chondroitin sulfate was similar (Kd = 10(-6) M) and slightly lower than their binding to hyaluronan (Kd = 10(-7) M) of similar molecular mass.

Animals↗
PubMed1985

Subcellular localization and properties of lipase activities in human polymorphonuclear leukocytes.

A fluorimetric assay for lipase activity has been optimized for measurement of the enzyme in human neutrophils. Activity was maximal at acid (4.5) and alkaline (9.5) pH, although there was also a neutral peak of activity at pH 6.5. Neutrophils were homogenised in isotonic sucrose and subjected to analytical subcellular fractionation by sucrose density gradient centrifugation. The gradient fractions were assayed for acid, neutral and alkaline lipase activity and for the principal organelle marker enzymes. Neutral lipase showed a unimodal distribution with an equilibrium density of 1.19 g . cm-3, corresponding to the distribution of particulate leucine aminopeptidase. Acid and alkaline lipase activities showed very similar distribution profiles to each other with both soluble components and a broad peak of particulate activity. The broad modal density of 1.19-1.22 g . cm-3 suggests that acid and alkaline lipase activities could be localised to more than one population of cytoplasmic granule. Fractionation experiments with neutrophils homogenised in sucrose medium containing digitonin confirmed the localisation of neutral lipase and leucine aminopeptidase to the same cytoplasmic granule, and suggested that at least part of the acid lipase activity was localised to the specific granule. No lipase activity could be attributed to the alkaline phosphatase-containing granule. Neutrophils were isolated from control subjects, patients with chronic granulocytic leukaemia and women in the third trimester of pregnancy. The specific activity of acid, neutral and alkaline lipase, and leucine aminopeptidase, in contrast to that of alkaline phosphatase, were similar in the three patient groups.

Adult↗
PubMed1984

The esterase D polymorphism as revealed by isoelectric focusing in ultra-thin polyacrylamide gels.

The polymorphism of human red cell esterase D (EsD) was studied using isoelectric focusing (pH 4-6) in ultra-thin polyacrylamide gels. Typing was possible without the EsD isozymes attaining true equilibrium focusing conditions. Using this single method, six phenotypes (EsD 1, 2-1, 2, 5-1, 5-2 and 5) could be recognized in the White population of south-east England. Family studies showed these to be controlled by three co-dominant alleles and the gene frequencies were calculated to be EsD1 0.8856; EsD2 0.0946 and EsD5 0.0198. For successful and reliable EsD typing by this method, the electrophoretic system must be carefully optimized with respect to the duration of electrophoresis and the temperature attained in the gel during the electrophoretic run.

Acrylic Resins↗
PubMed1999

Quantifying aggregation of IgE-FcepsilonRI by multivalent antigen.

Aggregation of cell surface receptors by multivalent ligand can trigger a variety of cellular responses. A well-studied receptor that responds to aggregation is the high affinity receptor for IgE (FcepsilonRI), which is responsible for initiating allergic reactions. To quantify antigen-induced aggregation of IgE-FcepsilonRI complexes, we have developed a method based on multiparameter flow cytometry to monitor both occupancy of surface IgE combining sites and association of antigen with the cell surface. The number of bound IgE combining sites in excess of the number of bound antigens, the number of bridges between receptors, provides a quantitative measure of IgE-FcepsilonRI aggregation. We demonstrate our method by using it to study the equilibrium binding of a haptenated fluorescent protein, 2,4-dinitrophenol-coupled B-phycoerythrin (DNP25-PE), to fluorescein isothiocyanate-labeled anti-DNP IgE on the surface of rat basophilic leukemia cells. The results, which we analyze with the aid of a mathematical model, indicate how IgE-FcepsilonRI aggregation depends on the total concentrations of DNP25-PE and surface IgE. As expected, we find that maximal aggregation occurs at an optimal antigen concentration. We also find that aggregation varies qualitatively with the total concentration of surface IgE as predicted by an earlier theoretical analysis.

2,4-Dinitrophenol↗
PubMed2000

Practical applications of genotypic surveys for forensic STR testing.

Legitimate genotype frequency estimation for multiallelic loci relies on component allele frequencies, as population surveys represent only a fraction of possible DNA profiles. Multilocus genotypes from two ethnic human populations, African American (n=195) and U.S. Caucasian (n=200), were compiled at 13 STR loci that are used worldwide in forensic investigation (D3S1358, vWA, FGA, D16S539, TH01, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820). Sex-specific AmpFlSTR multiplexes provided stringent PCR-based STR typing specifically optimized for multicolor fluorescence detection. Heterozygosity at each STR locus ranged from 0.57 to 0.89 and encompassed from seven (TH01) to twenty-one (D21S11) alleles. Homozygosity tests, tests based on the distinct numbers of observed homozygous and heterozygous classes, log likelihood ratio tests, and exact tests assessed that the degree of divergence from theoretical Hardy-Weinberg proportions for all 13 STRs does not have practical consequence in genotype frequency estimation. Departures from linkage equilibrium, between loci, that imposed significance to forensic calculations were not indicated by observed variance of the number of heterozygous loci or Karlin interclass correlation tests. For forensic casework, reliable multilocus profile estimates may be obtained from the product of component genotype frequencies, each calculated through application of the Hardy-Weinberg equation to population database allele frequency estimates reported here. The average probability that two randomly selected, unrelated individuals possess an identical thirteen-locus DNA profile was one in 1.8x10(15) African Americans and one in 3.8x10(14) U.S. Caucasians.

Black or African American↗