Resolving the discrepancies among nucleic acid conformational analyses

Growing interest in understanding the relationship between the global folding of nucleic acids and the sequence-dependent structure of individual base-pair steps has stimulated the development of new mathematical methods to define the geometry of the constituent base-pairs. Several approaches, designed to meet guidelines set by the nucleic acid community, permit rigorous comparative analyses of different three-dimensional structures, as well as allow for reconstruction of chain molecules at the base-pair level. The different computer programs, however, yield inconsistent descriptions of chain conformation. Here we report our own implementation of seven algorithms used to determine base-pair and dimer step parameters. Aside from reproducing the results of individual programs, we uncover the reasons why the different algorithms come to conflicting structural interpretations. The choice of mathematics has only a limited effect on the computed parameters, even in highly deformed duplexes. The results are much more sensitive to the choice of reference frame. The disparate schemes yield very similar conformational descriptions if the calculations are based on a common reference frame. The current positioning of reference frames at the inner and outer edges of complementary bases exaggerates the rise at distorted dimer steps, and points to the need for a carefully defined conformational standard.

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as flexible "hinges" fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.

Structure and conformation of helical nucleic acids: analysis program (SCHNAaP)

We present a new versatile program, SCHNAaP, for the analysis of double-helical nucleic acid structures. The program uses mathematically rigorous and fully reversible procedures for calculating the structural parameters: the Cambridge University Engineering Department Helix computation Scheme (CEHS) is used to determine the local helical parameters and an analogous procedure is used to determine the global helical parameters. These parameters form a complete set that conforms to the "Cambridge Accord" on definitions and nomenclature of nucleic acid structure parameters. In addition to the two standard Watson-Crick base-pairs, the program handles mismatched base-pairs and chemically modified bases. An analysis of the sugar-phosphate backbone conformation is included. Standardized base-stacking diagrams of each dinucleotide step with reference to the mid-step triad are generated. Structures are classified as one of the four polymorphic families, A/B, Z, W or R, although W- and R-DNA (two types of hypothetical structure) have yet to be observed experimentally.

Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP)

We present a program, SCHNArP, for rebuilding double-helical nucleic acid structures from a set of helical parameters. The parameter sets are based on mathematically reversible schemes that allow direct comparison of data from experimental X-ray crystal structures analyzed using the analysis program, SCHNAaP (see accompanying paper), and structures built using the rebuilding program, SCHNArP. The program uses either local CEHS helical parameters or global helical parameters. A number of standard parameter sets from the literature are included that allow comparison of oligomer and polymer structures generated using different models for sequence-dependent DNA bending. Exact atomic models are provided for the bases. Schematic models that trace the path of the backbone and use rectangular blocks for the bases can be generated.

Construction of double-helical DNA structures based on dinucleotide building blocks

We present a new method for building full 3-D structures of DNA sequences. A database of the conformational properties of dinucleotide steps has been compiled using X-ray crystal structures of oligonucleotides. The protocol uses these dinucleotides as building blocks to generate three dimensional structures of any required sequence in any required conformation.

DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures

Experimental data on the conformational properties of dinucleotides taken from high-resolution X-ray crystal structures of oligonucleotides have been compared with theoretical energy calculations on the base-stacking interactions. The conformational properties of the dinucleotides determined by calculation agree well with the experimental data, which shows that the method used for computing the stacking interactions is reliable. In addition, the calculations provide insight into the origins of the major trends that are observed in the experimental data. The values of the step parameters roll, tilt and rise, are determined entirely by the van der Waals interactions, and this reflects the strong requirement that the bases remain stacked in close contact. Slide, shift and twist do not affect the vertical separation of the bases and are therefore less tightly constrained. Electrostatic interactions play an important role in determining the values of shift and slide, but the base-stacking interaction energy is essentially independent of the value of twist. Thus the experimental value of twist is most likely fixed by the constraints of the backbone, which are missing in these calculations.

Recapitulation of the pathway for trophoblast giant cell differentiation in vitro: stage-specific expression of members of the prolactin gene family

The trophoblast giant cell lineage is characterized by endoreduplication and expression of members of the PRL gene family. This report describes the functional consequences following in vitro manipulation of a rat trophoblast cell line, termed Rcho-1. Rcho-1 cells can be cultured under conditions that promote proliferation or differentiation. Proliferation is maintained by culturing the cells in the presence of fetal bovine serum under subconfluent conditions. Differentiation is induced by growing the cells to confluence and removing the mitogenic source. Differentiation is characterized by continued synthesis of DNA in the absence of proliferation (endoreduplication) and the sequential expression of members of the PRL gene family. Western and Northern blot analyses demonstrated that placental lactogen-I (PL-I) was first expressed, followed sequentially by PL-II, PRL-like protein-A, and PRL-like protein-C. The ontogeny of expression of members of the PRL gene family by the Rcho-1 cells recapitulated the pattern of in situ expression by trophoblast giant cells of the junctional zone of the chorioallantoic placenta. A notable difference between in vivo trophoblast giant cell differentiation and in vitro Rcho-1 cell differentiation is the termination of PL-I expression in normal trophoblast giant cells developing in vivo and the continued expression of PL-I in differentiated Rcho-1 cell cultures. The Rcho-1 cell line provides a unique in vitro model for investigating the initiation and maintenance of the trophoblast giant cell differentiation pathway.

Spontaneous differentiation of trophoblast cells along the spongiotrophoblast cell pathway: expression of members of the placental prolactin gene family and modulation by retinoic acid

The purpose of this study was to examine part of the trophoblast cell multilineage pathway and its modulation by retinoic acid. A method for studying trophoblast cell differentiation along the spongiotrophoblast cell pathway in vitro was established and characterized. Cells were isolated from junctional zones of Day 13 rat chorioallantoic placentas via mechanical dissection, enzymatic digestion, and enrichment through a Percoll cushion. The cells were cultured up to 8 days and analyzed for their purity, morphology, and ability to express members of the placental prolactin (PRL) family. Cell preparations contained minimal mesenchymal contamination as estimated by immunocytochemical analysis for vimentin. The cells expressed PRL-like protein-A (PLP-A), PLP-B, PLP-C, and placental lactogen-I variant (PL-Iv) indicative of their differentiated spongiotrophoblast cell phenotype. Expression of members of the PRL family increased markedly during culture. Temporally the increase in PLP-A expression preceded the increased expression of PLP-B (0.9 kb), PLP-C, and PL-Iv. These in vitro observations paralleled the behavior of spongiotrophoblast cells developing in situ. Some differences were evident, including the immediate activation of PLP-B (1.2 kb) following enzymatic isolation of the cells. These cells were also susceptible to experimental manipulation. Exposure to retinoic acid influenced the morphology of the cells and the profile of members of the placental PRL family expressed by in vitro differentiated cells. In summary, a culture system has been devised to examine the control of spongiotrophoblast cell differentiation and the regulation of expression of members of the placental PRL gene family. Spongiotrophoblast cells spontaneously differentiate in vitro through discrete developmental phases that are susceptible to modulation by retinoic acid.

[Scanning electron microscopy of adult Trichuris trichiura]

The paper reports the result of the observation on the ultrastructure of the body surface of adult T. trichiura by scanning electron microscopy. Unique features of T. trichiura are described including the presence of labial-shape structures at the periphery of mouth, eight cephalic pores and a pair of amphids around the mouth pore and vesicle-shaped cuticular protuberances on the abdomen of T. trichiura. Cuticular pores were found scattering on the surface of T. trichiura. Detailed descriptions of male copulatory sheath and spicule were presented.

[Scanning electron microscopic observations on the copulatory spicules of the male Necator americanus and Ancylostoma duodenale]

Scanning electron microscopic observations were made on the morphological structures of the two copulatory spicules of the male Necator americanus and Ancylostoma duodenale. In both species, one of the two copulatory spicules was in the shape of a concave groove and the other, in the shape of an oblate tube. Owing to the difference in the concavity of the groove shaped copulatory spicule between the two species as shown by the cross sections, Necator americanus usually appear to have only one copulatory spicule whereas Ancylostoma duodenale usually show two separate copulatory spicules in appearance (Figs 1-10).

Joint transform correlator that uses wavelet transforms

A joint transform correlation system based on wavelet transforms is introduced. The selection of wavelets and the optical wavelet transform of images enables this optical correlator to identify the specific features and distinguish similar characters. Preliminary experimental results are given.

Isopentenyl-diphosphate isomerase: irreversible inhibition by 3-methyl-3,4-epoxybutyl diphosphate

Isopentenyl-diphosphate:dimethylallyl-diphosphate isomerase (EC 5.3.3.2) catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl diphosphate (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP). Incubation of yeast IPP isomerase with 3-methyl-3,4-epoxybutyl diphosphate (EIPP) resulted in a time-dependent first-order loss of activity characteristic of an active-site-directed irreversible process, where k2 = 0.63 +/- 0.10 min-1 and KI = 0.37 +/- 0.11 microM. A 1:1 covalent E-I complex was formed upon incubation with [1-14C]EIPP. The inhibited enzyme was treated with trypsin to give two radioactive fragments, which were purified by reversed-phase HPLC on a C18 column. The modified amino acid in each fragment was identified as C139 by sequencing the radiolabeled peptides. Incubation of IPP isomerase with [2,4,5-13C3]EIPP gave a 13C-labeled E-I complex. A 1H-13C heteronuclear multiquantum correlation spectrum had strong cross-peaks at 1.2/28 and 2.9/48 ppm, which we assigned to the labeled methyl group and C(4) methylene, respectively, of the inhibitor. In addition, a weak signal at 2.17/42 ppm may be from the C(2) methylene. Comparison of these chemical shifts with those of a synthetic adduct isolated from treatment of EIPP with cysteine indicates C139 attacks C(4) of EIPP to generate a thioether linkage between the enzyme and the inhibitor.

Ring-array processor distribution topology for optical interconnects

The existing linear and rectangular processor distribution topologies for optical interconnects, although promising in many respects, cannot solve problems such as clock skews, the lack of supporting elements for efficient optical implementation, etc. The use of a ring-array processor distribution topology, however, can overcome these problems. Here, a study of the ring-array topology is conducted with an aim of implementing various fast clock rate, high-performance, compact optical networks for digital electronic multiprocessor computers. Practical design issues are addressed. Some proof-of-principle experimental results are included.

Allogeneic bone marrow transplantation for the treatment of leukemia

Eighteen patients with leukemia have received HLA-identical allogeneic bone marrow transplantation (BMT) at our hospital since 1981. Fifteen of these patients have been living without relapse. for prophylaxis of GVHD, MTX was used in 8 patients, and cyclosporine (CSP) together with MTX in 6 patients, 3 received multiple agents at much smaller dosage, including monoclonal antibody. All patients received intravenous placental gamma-globulin, and 16 received garlic extract. Three patients died. One, who neither received MTX, nor CSP died of hyperacute GVHD, one who did not receive garlic extract died of GMV pneumonia, and the third one died of tuberculosis 18 months after BMT.

Diffraction by a 3-D oriented grating and its use in scanning correlation detection

The equation of diffraction directions for a3-D oriented grating is derived. By rotating and tilting the grating it is shown that a square array of filters can be generated. This technique has been used in object plane scanning correlation detection and results of a demonstration experiment are also presented.

Implementation of Boolean logic gates using a microchannel spatial light modulator with liquid-crystal televisions

A programmable optical system that can perform binary Boolean logic operations with a microchannel spatial light modulator (MSLM) is presented. The MSLM is used as an adder, an inverter, a subtractor, or a buffer. We used three liquid-crystal televisions with a computer as input interfacing devices. Through the use of its feedback loop, the system can consecutively execute a series of logic operations. Experimental results are provided.

Role of calcium in electron-acupuncture analgesia and the developments of analgesic tolerance to electro-acupuncture and morphine

Role of brain Ca2+ in electro-acupuncture analgesia and the development of analgesic tolerance to electro-acupuncture and morphine were studied. At the same time, the inhibition by protein synthesis inhibitors of the development of analgesic tolerance to electro-acupuncture was observed. The results showed that like morphine tolerance, the brain Ca2+ and cAMP levels in mice were enhanced with the development of analgesic tolerance to electro-acupuncture. After treatment with protein synthesis inhibitors anisomycin, actinomycin or cycloheximide the development of analgesic tolerance to electro-acupuncture was inhibited, and concurrently, the brain Ca2+ and cAMP levels in the animals greatly reduced. From the changes of brain Ca2+ and cAMP levels, the analgesic effects by electro-acupuncture, morphine and lanthanides seem to be very similar and share a mutual ion basis and the mechanism of action. So does the development of analgesic tolerance to electro-acupuncture and morphine. These findings also suggest that the inhibition induced by the inhibitors of the analgesic tolerance to electro-acupuncture and morphine may be related to synthesis of new peptides or RNA in brain.

Large-capacity real-time spatial-spectral scanning optical correlator

A large-capacity real-time spatial-spectral scanning optical correlator utilizing the concept of a rotating multicolor grating is described. It was experimentally observed that implementation of a closed-circuit TV system gives the correlator a real-world application. The color sensitivity of the correlator is also demonstrated. The experimental results using single and double lasers with two primary colors are presented.