Got Sulfate? Luring Axons This Way and That

Glycosaminoglycans are sulfated in complex and changing patterns that affect neural development. These sugars mediate interactions between macromolecules, and their biological contributions are of high interest. In this issue of Chemistry & Biology, Shipp and Hsieh-Wilson describe microarrays to probe these complex modifications.     

Multielement Analysis of Whole Blood Using a Capacitively Coupled Microwave Plasma Atomic Emission Spectrometer

A capacitively coupled microwave plasma atomic emission spectrometer (CMP-AES) has been evaluated as a means for the direct analysis of several of the primary and trace elements in whole blood. A tungsten filament spiral electrode was used with the CMP, and whole blood samples were deposited on the electrode and subsequently dried, ashed, and atomized. The emission was measured with a spectrometer and a charge-coupled-device detector. A sample size of only 2 μl was required and the time for each sample run was under 4 min. This method has a wide dynamic range, allowing the determination of both the primary elements in blood and elements present in trace quantities. Potassium, sodium, lithium, magnesium, manganese, and zinc were studied. Good linearity was observed and the concentration levels obtained for these elements were consistent with literature values. The primary advantages of this method are that no sample pretreatment or dilution is required, the instrument cost is low, and the method is capable of simultaneous multielement analysis on small, discrete samples.     

Microstructural model for prediction of stress–strain curves of amorphous and semicrystalline elastomers

A fundamental microstructural model was developed to calculate the stress–strain curves of rubbery amorphous polymers and of semicrystalline polymers with a rubbery amorphous phase by numerical simulations. The rubbery amorphous phase was treated by using a version of the theory of rubber elasticity with finite extensibility. Physical entanglements and chemical crosslinks were both allowed. Slippage was implemented by a Monte Carlo algorithm controlled by kinetic parameters such as the activation energy and activation volume for slippage. The crystalline phase was treated in a very idealized manner, including a crude representation of tie chains but not taking the internal structure of the crystallites into account. A two-dimensional embodiment of the model was implemented into software. For amorphous polymers, while lacking truly quantitative accuracy, the model showed sufficiently good agreement with the experimental trends to be used as a qualitative or semiquantitative predictive tool, and it is currently being used in this manner. The more complex semicrystalline version was less accurate and will need to be improved in future work. Most of the limitations of the semicrystalline version could be ascribed unambiguously to specific simplifications made in the software implementation to reduce the amount of computer time required for the calculations. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2715–2739, 1997     

Imidization and interdiffusion of poly(amic ethyl ester) precursors of PMDA/3,4′-ODA

Para-, meta-, and mixed isomeric poly(amic ethyl ester) precursors of the polyimide based on pyromellitic dianhydride (PMDA) and 3,4′-oxydianiline (3,4′-ODA) were synthesized. The intrinsic viscosity of each of the isomers was measured in an NMP solution and found to be less than corresponding isomers derived from PMDA and 4,4′-oxydianiline (4,4′-ODA) precursors with comparable molecular weight. The imidization and solvent retention were measured as a function of imidization temperatures, T_i using forward recoil spectrometry (FRES). For samples cast from a single solvent, either N-methyl pyrrolidone (NMP) or dimethyl sulfoxide (DMSO), no difference was observed in the temperature-dependent imidization behavior between the isomers. In all cases the imide fraction f increased as T_i increased, and reached a value of unity, i.e., full conversion at 400°C. At the same T_i, samples cast from DMSO showed a slightly higher f than samples cast from NMP. FRES and time of flight FRES (TOF-FRES) were used to measure the interdiffusion distance, w, of deuterium-labeled tracers into nondeuterated base layers of the polyimide of PMDA/3,4′-ODA treated at various T_i. The primary determinant of w for all isomers was T_i, and the particular isomer used as either the base or the tracer molecule did not seem to affect w. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 2247–2258, 1998     

Set intersection representations for almost all graphs

Two variations of set intersection representation are investigated and upper and lower bounds on the minimum number of labels with which a graph may be represented are found that hold for almost all graphs. Specifically, if θ_k(G) is defined to be the minimum number of labels with which G may be represented using the rule that two vertices are adjacent if and only if they share at least k labels, there exist positive constants c_k and c′_k such that almost every graph G on n vertices satisfies Changing the representation only slightly by defining θ;_odd (G) to be the minimum number of labels with which G can be represented using the rule that two vertices are adjacent if and only if they share an odd number of labels results in quite different behavior. Namely, almost every graph G satisfies Furthermore, the upper bound on θ_odd(G) holds for every graph. © 1996 John Wiley & Sons, Inc.     

Structural Factors and Mechanisms Underlying the Improved Photodynamic Cell Killing with Silicon Phthalocyanine Photosensitizers Directed to Lysosomes Versus Mitochondria

The phthalocyanine photosensitizer Pc 4 has been shown to bind preferentially to mitochondrial and endoplasmic reticulum membranes. Upon photoirradiation of Pc 4-loaded cells, membrane components, especially Bcl-2, are photodamaged and apoptosis, as indicated by activation of caspase-3 and cleavage of poly(ADP-ribose) polymerase, is triggered. A series of analogs of Pc 4 were synthesized, and the results demonstrate that Pcs with the aminopropylsiloxy ligand of Pc 4 or a similar one on one side of the Pc ring and a second large axial ligand on the other side of the ring have unexpected properties, including enhanced cell uptake, greater monomerization resulting in greater intracellular fluorescence and three-fold higher affinity constants for liposomes. The hydroxyl-bearing axial ligands tend to reduce aggregation of the Pc and direct it to lysosomes, resulting in four to six times more killing of cells, as defined by loss of clonogenicity, than with Pc 4. Whereas Pc 4-PDT photodamages Bcl-2 and Bcl-xL, Pc 181-PDT causes much less photodamage to Bcl-2 over the same dose–response range relative to cell killing, with earlier cleavage of Bid and slower caspase-3-dependent apoptosis. Therefore, within this series of photosensitizers, these hydroxyl-bearing axial ligands are less aggregated than is Pc 4, tend to localize to lysosomes and are more effective in overall cell killing than is Pc 4, but induce apoptosis more slowly and by a modified pathway.     

Effect of the matrix on DNA electrophoretic mobility

DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.     

Conformation of the Group II intron branch site in solution

Group II introns are multidomain ribozymes that catalyze their own removal from pre-mRNA. The nucleophile for the first cleavage step is the 2'OH of a specific adenosine within domain 6 (D6), called the branch site. Mechanistic parallels and limited secondary structural similarity with the eukaryotic spliceosome lead many to speculate that the two systems have a common ancestry. We have elucidated structural features of the branch site region and the importance of the internal loop to branch site conformation within D6 of the ai5gamma Group II intron by NMR and fluorescence spectroscopy. Fluorescence experiments in which 2-aminopurine was substituted for the branch site adenosine suggest that the branch site base is exposed to solvent and that this position is enhanced by Mg2+ or Ca2+. Upfield NMR chemical shifts of imino protons of the two uridine residues flanking the branch site adenosine, and an n --> n + 2 NOE between them, suggest a stacked intrahelical conformation of the two uridines. In contrast, results of NMR and 2-aminopurine fluorescence spectra of a mutated D6 from which the internal loop had been deleted suggest a less exposed position of the branch site adenosine, which is likely to form a G-A base pair with the opposing 3'G. These findings describe a model in which the branch site adenosine of D6 is in an extrahelical position, surrounded by two intrahelical bases. The internal loop and divalent metal ions facilitate this motif.     

A mixed-valent ruthenium-oxo oxalato cluster Na7[Ru4(mu3-O)4(C2O4)6] with potent anti-HIV activities

A structurally characterized mixed-valent tetranuclear ruthenium-oxo oxalato cluster exhibits anti-viral activities toward R5- and X4-tropic HIV-1, and possesses cytoprotective activity toward HIV-1 infected cells.