Distributions of measurement errors for single-axis magnetic field meters during measurements near appliances

Comparisons are made between the average magnetic flux density as it would be measured with a single-axis coil probe and the flux density at the center of the probe, assuming that the probe is oriented to measure the maximum field at that point. Probability distributions of the differences between the two quantities are calculated assuming a dipole magnetic field and are found to be asymmetric. The distributions are used to estimate the uncertainty for maximum magnetic field measurements at distances that are large compared with the dimensions of the field source. Bioelectromagnetics 18:273–276, 1997. © 1997 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Identification and characterization of an ecdysiotropic peptide from brain extracts of the gypsy moth,Lymantria dispar

A peptide (Lymantria TE) was isolated from brains of the gypsy moth, Lymantria dispar, which stimulates synthesis of ecdysteroid in the testes of larval and pupal insects. This ecdysiotropic peptide was purified and its structure determined to be NH₂-IIe-Ser-Asp-Phe-Asp-Glu-Tyr-Glu-Pro-Leu-Asn-Asp-Ala-Asp-Asn-Asn-Glu-Val-Leu-Asp-Phe-OH using protein sequence analysis and electrospray mass spectrometry. The peptide was biphasic in activity, with maximal activity in the pupal testes at 10⁻¹³ M and 10⁻⁹ M, with a minimum at 10⁻¹⁰ M, and with maxima at 10⁻¹⁵ M and 10⁻¹⁰ M and minimum at 10⁻¹³ M for larval testes. Arch. Insect Biochem. Physiol. 34:175–189, 1997. © 1997 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

Background

By using a standard Support Vector Machine (SVM) with a Sequential Minimal Optimization (SMO) method of training, Naïve Bayes and other machine learning algorithms we are able to distinguish between two classes of protein sequences: those folding to highly-designable conformations, or those folding to poorly- or non-designable conformations.

Results

First, we generate all possible compact lattice conformations for the specified shape (a hexagon or a triangle) on the 2D triangular lattice. Then we generate all possible binary hydrophobic/polar (H/P) sequences and by using a specified energy function, thread them through all of these compact conformations. If for a given sequence the lowest energy is obtained for a particular lattice conformation we assume that this sequence folds to that conformation. Highly-designable conformations have many H/P sequences folding to them, while poorly-designable conformations have few or no H/P sequences. We classify sequences as folding to either highly – or poorly-designable conformations. We have randomly selected subsets of the sequences belonging to highly-designable and poorly-designable conformations and used them to train several different standard machine learning algorithms.

Conclusion

By using these machine learning algorithms with ten-fold cross-validation we are able to classify the two classes of sequences with high accuracy – in some cases exceeding 95%.

     

Developmental regulation of yolk protein gene expression in Anastrepha suspensa

A partial cDNA clone for the 48,000 dalton yolk polypeptide gene from Anastrepha suspensa was isolated from a cDNA expression library using a yolk polypeptide antibody probe and hybridization to the Drosophila melanogaster yolk protein 1 gene. The sequenced DNA has greatest homology to the yolk protein genes from Ceratitis capitata, D. Melanogaster, and Calliphora erythrocephala and, similar to these genes, shares amino acid sequence domains with those from lipases. RNA hybridization studies indicated that the yolk protein gene expression is completely female-specific and limited to the ovaries, without apparent regulation by 20-hydroxyecdysone or juvenile hormone. This is in contrast to an earlier study which suggested, based on immunological probes, that a very low level of yolk protein synthesis occurred in fat body and was not sex-specific. Arch. Insect Biochem. Physiol. 36:25–35, 1997.Published 1997 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

KDR inhibitor with the intramolecular non-bonded interaction: conformation-activity relationships of novel indole-3-carboxamide derivatives

We previously reported that compound 1, having a similar conformation to PTK787 (2) by forming a pseudo ring structure with an intramolecular non-bonded S-O interaction, exhibited a potent inhibitory activity against VEGFR2 tyrosine kinase (KDR).¹ Applying the ideas of pseudo ring formations, we have designed three types of novel indole carboxamide derivatives 5-7 with an intramolecular hydrogen bonding or non-bonded S-O interaction. We describe the design and synthesis of 5-7, and also discuss the relationships of their KDR inhibitory activity and conformations that were stabilized by their intramolecular non-bonded interactions.     

Side-chain entropy and packing in proteins.

What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is a side-chain “freezing” or ordering, i.e., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements (m) have different frequencies, and the frequencies have different dependencies on compactness. mm contacts contribute significantly only at high densities, suggesting that main-chain hydrogen bonding in proteins may be promoted by compactness. The distributions of mm, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces.     

A 2H-NMR study of the A-DNA conformation in films of oriented Na-DNA: evidence of a disordered B-DNA contribution

Solid-state ²H-nmr spectra have been obtained from folded films of oriented Li- and Na-DNA molecules with the purine bases selectively deuterium labeled at the 8 position. From line shape simulations, we find that the Na-DNA sample at 75% relative humidity (rh) contains both A-DNA and surprisingly large amounts of B-DNA

1 Here, B-DNA refers to “B-DNA family” (i.e. B- or C-DNA).

(57%). For the A-DNA component the average base tilt is 23°, and the total distribution width of tilt angles and helix axis orientations is ～ 4° (standard deviation). In the B-DNA component the base tilt is ～ 0° and the total distribution width is ～ 20°. In contrast, films of Li-DNA only exhibit the B-form line shape, consistent with a base tilt of ～ 0° and a total distribution width of base tilt angles and helix axis orientations of 9°. The nmr results that demonstrate the presence of large amounts of B-DNA in the Na-DNA sample contrast with the x-ray diffraction measurements that indicated mainly A-form. The nmr spectra are used to monitor the B-DNA content in the Na-films and to evaluate procedures for increasing the A-DNA fraction.     

Variations on a theme by Debye and Waller: From simple crystals to proteins

Debye and Waller showed how to adjust scattering intensities in diffraction experiments for harmonic motions of atoms about an average, static reference configuration. However, many motions, particularly in biological molecules as compared to simple crystals, are far from harmonic. We show how, using a variety of simple anharmonic, multiconformational models, it is possible to construct a variety of Generalized Debye-Waller Factors, and understand their meaning. A central result for these cases is that, in principle, intensity factors cannot be obtained from true total mean square displacements of the atoms. We make the distinction between the intensity factors for unimodal quasiharmonic motions and those for the anharmonic, multimodal (valley hopping) motions. Only the former affect the conventional B factors. Proteins 29:153–160, 1997. Published 1997 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Enumerating Designing Sequences in the HP Model

The hydrophobic/polar HP model on the square lattice has been widely used toinvestigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the number of contacts, the upper limit on the chain length N has been 18–20 because of the rapid exponential growth of thenumbers of conformations and sequences. We show how a few optimizations push this limit by about 5 units. Based on these calculations, we study the statistical distribution of hydrophobicity along designing sequences. We find that the average number of hydrophobic and polar clumps along the chains is larger for designing sequences than for random ones, which is in agreement with earlier findings for N 18 and with results for real enzymes. We also show that this deviation from randomness disappears if the calculations are restricted to maximally compact structures.     

Sense organs on the antennal flagellum of mayflies (Ephemeroptera)

A few very small sensory pegs with the characteristics of chemoreceptors are present in both males and females on the antennal flagellum of the mayflies, Stenacron interpunctatum (Say)

1 Stenacron interpunctatum (Say) is Stenonema interpunctatum (Say) of earlier literature.

and Cloeon sp. They are situated near the proximal end of the flagellum on its ventro-lateral surface and have escaped the attention of earlier investigators.     

Naturally occurring analogs of Lymantria testis ecdysiotropin,a gonadotropin isolated from brains of Lymantria dispar pupae1

Lymantria testis ecdysiotropin (LTE) was isolated from the most prominent peptide peak corresponding to an active fraction obtained by high pressure liquid chromatographic (HPLC) separation of a homogenate of 13,000 Lymantria dispar pupal brains. In this work we examined the other active fractions from this separation as well as a second HPLC separation of an additional 2,300 pupal brains. Bioassay of the ecdysteroidogenic effects of each peak on L. dispar testes allowed detection of 20 peptide peaks with testis ecdysiotropic activity in addition to LTE. Of these, ten peptides were purified and sequenced. All of them were comparable to LTE in molecular weight. The amino acid sequences of five of the peptides were similar enough to LTE to be considered to be members of an LTE family. However, the other five peptides had no significant homology with LTE or with each other. A BLAST database search indicated LTE family homology with portions of inhibitory peptides such as those inhibiting cytolysis. In contrast, non-LTE ecdysiotropic peptides, in which undetermined residues designated X were assumed to be cysteine, were strikingly homologous to portions of vertebrate and invertebrate zinc finger peptides and to vertebrate and invertebrate virus proteins. Arch. Insect Biochem. Physiol. 36:37–50, 1997.Published 1997 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Syntheses and conformational studies of poly- ,N-alkyl L-asparagines

Several β,N-alkyl L -asparagines were prepared from the phthalyl and benzyloxycarbonyl derivatives. High-molecular-weight poly-β,N-benzyl L -asparagine and poly-β,N-(1)-phenethyl L -asparagine were prepared from the corresponding N-carboxyanhy-drides. From the results obtained by a study of the infrared absorption spectra and the optical rotatory dispersion, poly-β-N-benzyl L -asparagine was found to be a random coil structure in dichloroacetic acid and the optical rotatory dispersion curves gradually changed into the left-handed α-helix structure when chloroform was added to the solution. The coil-to-helix transition was observed in the vicinity of 20% dichloroacetic acid in a dichloroacetic acid-chloroform mixture. Poly-β,N-(d), (l), and (d + l, 1:1)

1 (d + l, 1:1): mixed polymer containing the same weighed poly-β,N-(d) and (l)-(1)-phenethyl L -asparagines.

-(1)-phenethyl L -asparagines showed a nearly constant specific rotation in the dichloroacetic acidchloroform solvent system. Poly-β,N-(dl)-(1)-phenethyl L -asparagine caused a gradual folding of the helix at dichloroacetic acid content of less than 20%.     

Activity-dependent regulation of N-cadherin in DRG neurons: Differential regulation of N-cadherin,NCAM, and L1 by distinct patterns of action potentials

Cell adhesion molecule (CAM) expression is highly regulated during nervous system development to control cell migration, neurite outgrowth, fasciculation, and synaptogenesis. Using electrical stimulation of mouse dorsal root ganglion (DRG) neurons in cell culture, this work shows that N-cadherin expression is regulated by neuronal firing, and that expression of different CAMs is regulated by distinct patterns of neural impulses. N-cadherin was down-regulated by 0.1 or 1 Hz stimulation, but NCAM mRNA and protein levels were not altered by stimulation. L1 was down-regulated by 0.1 Hz stimulation, but not by 0.3 Hz, 1 Hz, or pulsed stimulation. N-cadherin expression was lowered with faster kinetics than L1 (1 vs. 5 days), and L1 mRNA returned to higher levels after terminating the stimulus. The RSLE splice variant of L1 was not regulated by action potential stimulation, and activity-dependent influences on L1 expression were blocked by target-derived influences. The results are consistent with changes in firing pattern accompanying DRG development and suggest that functional activity can influence distinct developmental processes by regulating the relative abundance of different CAMs. © 1997 John Wiley & Sons, Inc. J Neurobiol 33: 735–748, 1997

1 This is a US Government work and, as such, is in the public domain in the United States of America.

     

Refinement of human lysozyme at 1.5 Å resolution analysis of non-bonded and hydrogen-bond interactions

The structure of human lysozyme has been crystallographically refined at 1.5 Å resolution by difference map and restrained least-squares procedures to an R factor of 0.187. A comprehensive analysis of the non-bonded and hydrogen-bonded contacts in the lysozyme molecule, which were not restrained, revealed by the refinement has been carried out. The non-bonded CC contacts begin at ~3.45 Å, and the shorter contacts are dominated, as expected, by interactions between trigonal and tetrahedral carbon atoms. The CO contact distances have a “foot” at 3.05 Å. The CN distance plot shows a significant peak at 3.25 Å, which results from close contact between peptide NHs and carbonyl carbons involved in N_iC′_{i ? 2} interactions in α-helices and reverse turns. The distances involving sulphur atoms discriminate SC trigonal interactions at 3.4 to 3.6 Å from SC tetrahedral interactions at 3.7 Å. All these types of non-bonded interactions show minimum distances close to standard van der Waals' separations.Analysis of hydrogen-bond distances has been carried out by using standard geometry to place hydrogen atoms and measuring the XHO distances. On this basis, there are 130 intramolecular hydrogens: 111 NHO bonds, of which 69 are between main-chain atoms, 13 between side-chain atoms and 29 between mainchain and side-chain atoms. If a cluster of four well-defined internal water molecules is included in the protein structure, there is a total of 19 OHO hydrogen bonds. The mean NO, NHO distances and HN?O angles are 2.96 ± 0.17 Å, 2.05 ± 0.18 Å and 18.5 ± 9.6 °, and the mean OO, OHO distances and HÔO angles are 2.83 ± 0.19 Å, 1.98 ± 0.26 Å and 23.8 ± 13.4 °. The distances agree well with standard values, although the hydrogen bonds are consistently more non-linear than in equivalent small molecules. An analysis of the hydrogen-bond angles at the receptor atom indicates that the α-helix, β-sheet and reverse turn have characteristic angular values. A detailed analysis of the regularity of the α-helices and reverse turns shows small but consistent differences between the α-helices in lysozyme and the current standard model, which may now need revision. Of the 21 reverse turns that include a hydrogen bond, the conformations of 19 agree very closely with four of the five standard types. We conclude that the restrained least-squares method of refinement has been validated by these analyses.     

The distribution of PBAN (pheromone biosynthesis activating neuropeptide)-like immunoreactivity in the nervous system of the gypsy moth,Lymantria dispar

The production of sex pheromone in many moths is regulated by the neuropeptide PBAN (pheromone biosynthesis-activating neuropeptide). Studies in a number of species have shown that pheromone production can be linked to a hemolymph factor and that continuity in the ventral chain of ganglia is not required. However, it has recently been shown that production of pheromone in the gypsy moth, Lymantria dispar, is largely prevented in females with a transected ventral nerve cord (VNC). To begin to understand the cellular basis for this dependence on the VNC, we sought to determine the distribution of PBAN in the central nervous system and its neurohemal sites, including those associated with the VNC. Using an antiserum to L. dispar-PBAN in immunocytochemical methods, we have mapped the distribution of PBAN-like immunoreactivity (PLI). PLI is found in three clusters of ventral midline somata in the subesophageal ganglion (SEG), in three clusters of midline cells in each segmental ganglion, and in bilateral pairs of cells located posterolaterally in each abdominal ganglion. The SEG cells comprise both interneurons, with endings in the neuropil of each segmental ganglion, as well as neurosecretory cells, with endings in the retrocerebral complex and in an unusual neurohemal structure near the anterior aspect of the SEG. The latter structure, which we have named the corpus ventralis, receives axons from the two anterior clusters of cells in the SEG. In the abdominal ganglia, the posterolateral clusters of cells have immunoretroreactive axons exiting the ganglia via the ventral nerves. Endings of these axons reach the perivisceral organ in the next posterior ganglion and pass anteriorly into the median nerve, forming additional varicose endings. We did not detect PLI in the terminal nerve. Thus, our findings raise the possibility that the requirement for an intact VNC in pheromone production reflects a role for descending regulation of neurosecretory cells in the segmental ganglia. Arch. Insect Biochem. Physiol. 34:391–408, 1997. Published 1997 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Conformational characteristics of polyglutamic acid esters: Persistence of orientational correlation along the side chain flanking the α-helical backbone

The side chain conformations of α-helical poly(L -glutamic acid) esters $ \rlap{--}[NHCH(CH_2 CH_2 COOR)CO\rlap{--}]_x $, carrying a homologous series of ester residues such as R = ? (CH₂)_n? with n = 1–3, have been studied in the lyotropic liquid crystalline state (chloroform 20 v/v%) by the deuterium nmr method. In order to study the surface chirality of the molecule, the phenyl groups situated at the terminal of the side chain have been deuterated. From the observed deuterium quadrupolar splittings, the average inclination θ_p of the para-axis of the phenyl group with respect to the α-helical backbone was elucidated. A distinct odd–even oscillation in the quantity such as 〈 cos² θ_p〉 was observed with the number of methylene units n. A rotational isomeric state analysis has indicated that the observed orientational correlation arises from the interdependence of the neighboring bond rotation along the side chain. Preference of the “extended” conformations is also enhanced by the mutual conformational exclusion of neighboring side chains.     

Dual labeling of the cytoskeleton and DNA strand breaks in porcine embryos produced in vivo and in vitro

In vitro-produced embryos exhibit decreased cell numbers, small inner cell masses and reduced pregnancy rates after transfer. Evaluation of intracellular components of in vitro-produced or -manipulated embryos will lead to improved methodology for embryo production. Whole mount techniques were developed to utilize terminal deoxynucleotidyl-transferase 3′ nick end labeling (TUNEL) to detect broken DNA. Subsequent labeling of either tubulin or actin filaments provides further evidence of cytological damage. Porcine embryos produced in vitro or in vivo were evaluated throughout the cleavage and preimplantation stages of development. Early cleavage stages up to the 8-cell stage never contained TUNEL-labeled nuclei. However, TUNEL labeling of in vitro-produced morula revealed some blastomeres with broken DNA. Nearly all in vitro-produced blastocysts displayed some TUNEL positive cells, whereas in vivo-collected embryos at a similar stage displayed few, if any, TUNEL-labeled nuclei. The ratio of TUNEL-labeled DNA to total DNA area of in vitro-derived blastocysts was significantly greater than their in vivo counterparts (P < 0.05). Microtubule and microfilament labeling identified blastomeres of unequal size and shape that were losing cellular integrity. These data suggest that the combination of these labeling techniques may be useful in evaluating cellular damage in embryos produced under in vitro conditions. Mol. Reprod. Dev. 51:59–65, 1998. Published 1998 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Base-catalyzed racemization of 3-O-acyloxazepam

Enantiomers of 3-O-acyloxazepam (oxazepam 3-acetate; OXA) underwent base-catalyzed hydrolysis and racemization. Kinetics of reaction products formed from an OXA enantiomer in buffered and unbuffered alkaline solutions were analyzed by chiral stationary phase high-performance liquid chromatography. Racemization occurred with varying rates in aqueous solutions with pH ranging from 7.5 to 14. Racemization mechanism was studied by the dependence of rates of hydrolysis and racemization on temperature and pH. Mass spectral analysis of racemization products derived from an OXA enantiomer in a deuterated solvent indicated that racemization was accompanied by a proton exchange with the solvent. The results indicated that a base-catalyzed keto-enol tautomerism between the C2-carbonyl group and the C3 carbon was responsible for the observed racemization. © 1994 Wiley-Liss, Inc.

1 This article is a US Goverment work and, as such, is in the public domain in the United States of America.