Foliar Extrafloral Nectar of Humboldtia brunonis (Fabaceae), a Paleotropic Ant‐plant,is Richer than Phloem Sap and More Attractive than Honeydew

The ant‐plant Humboldtia brunonis secretes extrafloral nectar (EFN) despite the lack of antiherbivore protection from most ants. EFN was richer in composition than phloem sap and honeydew from untended Hemiptera on the plant, suggesting that EFN could potentially distract ants from honeydew, since ants rarely tended Hemiptera on this plant.     

Vibrational spectroscopy of L-valyl-glycyl-glycine,a parallel-chain β-structure

Bands in the ir and Raman spectra of L -valyl-glycyl-glycine (VGG) and VGG-ND have been assigned on the basis of a normal mode analysis of the known parallel-chain β-structure of this tripeptide. Amide I, II, III, and V mode shifts are obtained by the interactions of dipole derivatives in symmetry coordinates, referred to as dipole derivative coupling. These derivatives, obtained from ab initio studies, are also used to calculate ir intensities of amide I, II, and V modes. The agreement between predicted and observed frequencies and intensities is very good, providing confidence in the application of our force fields to the calculation of the vibrational modes of the general parallel-chain β-sheet structure (following paper).     

Vibrational analysis of peptides,polypeptides, and proteins. VI. Assignment of β-turn modes in insulin and other proteins

The normal modes have been calculated for structures having the dihedral angles of the four β-turns of insulin. Frequencies are predicted in the amide I region near 1652 and 1680 cm^?1. The former overlaps the α-helix band at 1658 cm^?1 in the Raman spectrum, while the latter accounts for the hitherto unassignable band at 1681 cm^?1. Calculated amide III frequencies extend above 1300 cm^?1, providing a compelling assignment of the 1303-cm^?1 band in insulin and similar bands in other globular proteins.     

Normal mode spectrum of the parallel-chain β-sheet

Normal mode calculations have been carried out for parallel-chain β-sheet structures. These include the parallel-chain pleated sheet of poly(L -alanine) and the parallel-chain rippled sheet of polyglycine. Dipole derivative coupling has been included for amide I and II modes, and the effects of parallel-sheet and antiparallel-sheet arrangements of varying separation have been examined for the poly(L -alanine) case. Some amide and nonamide modes are distinctly different from their antiparallel-chain counterparts, thus providing a basis for distinguishing between such structures from their ir and Raman spectra. As in our previous studies, these results emphasize the need for both kinds of spectral data in order to draw definitive conclusions about conformation.     

Low-Temperature conformation of Mg2+-Poly(U) in D2O as revealed by IR and Raman Spectroscopy and by normal-mode analysis treatment

Infrared and Raman spectra of the Mg²⁺ salt of poly(U) in D₂O were recorded in the 1600-1800 cm^?1 region and between 1 and 20C. The ir spectra showed a melting curve similar to the uv melting curves with a temperature of transition of about 6.5°C. This spectral change is assumed to be associated with the formation of the secondary structure of Mg²⁺-poly(U) in D₂O at this temperature. Three double-helical and two triple-helical structures were used as inputs to compute the normal modes of vibration. A double-helical structure was found to give the best agreement with the observations. Knowledge of the C=0 eigenvectors, and of the expression for transition probability from quantum mechanics, was used to explain the so far unanswered question of H. T. Miles [(1964) Proc. Natl. Acad. Sci. USA 51, 1104–1109; (1980) Biomolecular Structure, Conformation, Function and Evolution, Pergamon, Oxford, pp. 251–264] as to why there is an increase in the ir vibrational wave number of a carbonyl band when that group is H-bonded to another polynucleotide chain in a helix. Such considerations also explain why a predicted band at about 1648 cm^?1 is not to be seen in the ir spectra but is present in the Raman spectra. The model incorporating the C?O transition dipole-dipole coupling interaction is able to explain also the observed higher intensity of the higher wave-number ir band. The experimental results demonstrate that the complete picture of vibrational dynamics of Mg²⁺-poly(U) in D₂O is obtained only by looking simultaneously at ir and Raman spectra and not at only one of them. Weak ir bands were found to be as useful as the strong ones in understanding structure and vibrational dynamics. On the bases of our ir and Raman spectra, of the normal-mode analyses, and of the literature data, it is concluded that Mg²⁺-poly(U) in D₂O is present in a double-helical structure at temperatures below the temperature of transition, whereby the uracil residues are paired according to arrangement (a) (see Fig. 1). This structure is rodlike and arises by refolding of one poly(U) chain. The computations show that no normal mode is associated with a single C?O group vibration; all C?O group vibrations are heavily mixed motions of various C?O groups.     

Taxonomic description and draft genome of <Emphasis Type="Italic">Pseudomonas sediminis</Emphasis> sp. nov., isolated from the rhizospheric sediment of <Emphasis Type="Italic">Phragmites karka</Emphasis>

The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11^T, isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11^T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11^T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246^T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045^T (99.29%), Pseudomonas toyotomiensis JCM 15604^T (99.15%), Pseudomonas chengduensis DSM 26382^T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016^T (99.08%), and Pseudomonas alcaliphila JCM 10630^T (99.01%). Experimental DNA-DNA relatedness between strain PI11^T and P. indoloxydans JCM 14246^T was 49.4%. The draft genome of strain PI11^T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11^T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C_18:1ω6c/ω7c, C_16:1ω6c/ω7c, and C_16:0. The DNA G + C content of strain PI11^T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11^T was delineated from other closely related type strains. It is proposed that strain PI11^T represents represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11^T (= KCTC 42576^T = DSMZ 100245^T).     

Cytological localization of the maternal effect gene, tuh-1, in Drosophila melanogaster

Summary The sex-linked gene, tuh-1, produces a maternal effect that is associated with the tumorous head abnormality in Drosophila melanogaster. With the aid of various known deletions, tuh-1 has been localized to band 20A1-2 on the salivary chromosome map of the X.Work supported by grant GM 18664-01 from the National Institute of Health, U.S. Public Health Service     

Vibrational analysis of peptides,polypeptides, and proteins. V. Normal vibrations of β-turns

The normal modes have been calculated for β-turns of types I, II, III, I′, II′, and III′. The complete set of frequencies is given for the first three structures; only the amide I, II, and III modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide II modes. The results show that in the amide I region, β-turn frequencies can overlap with those of the α-helix and β-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide III modes of β-turns are predicted at significantly higher frequencies than those of α-helix and β-sheet structures, and this region therefore provides the best possibility of identifying β-turn structures. Amide V frequencies of β-turns may also be distinctive for such structures.