Comparative studies of AOT and NaDEHP by fluorescence technique and z-potential (ζ) measurements

The aggregation behaviors of two surfactants with the same hydrophobic tail, sodium bis(2-ethylhexyl)sulfosuccinate (AOT) and sodium bis(2-ethylhexyl)phosphate (NaDEHP), have been investigated by the fluorescence technique and z-potential (ζ) measurements. Five fine peaks of the pyrene molecule fluorescence spectroscopy appear in the surfactant solution, and the micropolarity at which pyrene locates is monitored from the intensity ratio of the first (I1) and the third peak (I3). A wide peak around 475 nm, the emission spectra of the excimer of pyrene molecules, is observed in the NaDEHP solution, while this is not found for the AOT system. The value of I1/I3 decreases in a more limited concentration range for the AOT system than for NaDEHP, indicating that small aggregates can be more easily formed by NaDEHP molecules. The z-potential results for the aggregates formed by the two surfactants show that the interaction between AOT and PVP is stronger than that between NaDEHP and PVP.

Deep level transient spectroscopy studies of Er and Pr implanted GaN films

Deep level transient spectroscopy measurements were used to characterize the electrical properties of metal organic chemical vapor deposition grown undoped, Er-implanted and Pr-implanted GaN films. Only one deep level located at 0.270 eV below the conduction band was found in the as-grown GaN films. But four defect levels located at 0.300 eV, 0.188 eV, 0.600 eV and 0.410 eV below the conduction band were found in the Er-implanted GaN films after annealing at 900 degrees C for 30 min, and four defect levels located at 0.280 eV, 0.190 eV, 0.610 eV and 0.390 eV below the conduction band were found in the Pr-implanted GaN films after annealing at 1050 degrees C for 30min. The origins of the deep defect levels are discussed. After annealing at 900 degrees C for 30min in a nitrogen flow, Er-related 1538nm luminescence peaks could be observed for the Er-implanted GaN sample. The energy-transfer and luminescence mechanism of the Er-implanted GaN film are described.

Electron diffraction and photoemission studies of clean and water-covered Si(5,5,12) and Si(112) surfaces

The structure of silicon surfaces in the orientation range (113)-(5,5,12)-(337)-(112) has been investigated using high resolution LEED and photoemission both on a spherical and on flat samples. We find that Si(5,5,12) [5.3 degrees from (113) and 0.7 degrees from (937)] is the only stable orientation between (113) and (111) and confirm the result of Baski et al. [Science 269, 1556 (1995)] that it has a 2 x 1 superstructure with a very large unit cell of 7.68 x 53.5 Angstrom(2). Adsorption measurements of water on Si(5,5,12) yield a mobile precursor kinetics with two kinds of regions saturating at 0.25 and 0.15 ML which are related to adsorption on different sites. Using these results, a modified structure model is proposed. Surfaces between (113) and (5,5,12) separate into facets of these two orientations; between (5,5,12) and (112), they separate into (5,5,12) and (111) facets. (337) facets in this range may be considered as defective (5,5,12) facets.

Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin

Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.

XPS and XRD studies of fresh and sulfided Mo2N

Mo surface species of molybdenum nitride and their changes under sulfiding conditions were investigated by XRD and XPS. Mo2N was synthesized by temperature-programmed reaction of MoO3, with NH3. The decomposition of the Mo3d spectra gave a Mo3d doubler which corresponded to Modelta+ (2 less than or equal to delta < 4), Mo4+ and Mo5+ Or Mo6+ species. The BE of the Mo species of passivated Mo2N shifted to higher energy level compared with the freshly prepared Mo2N due to the oxidation of Mo nitride during passivation. When Mo2N was contacted for 4 h with a 15% H2S-H-2 mixture at 400 degrees C, the XRD spectra did not reveal any new phase, which indicates a high stability of Mo2N against sulfidation, but XPS data showed the presence of sulfur, including S-0 and S2- species, and a decrease of the N/Mo atomic ratio revealed some changes in surface composition. More than one monolayer of Mo2N was transformed to sulfide. It is probable that the oxygen incorporated during passivation reacted with sulfur and formed a thin layer of molybdenum sulfide on the Mo2N surface. (C) 1998 Elsevier Science B.V. All rights reserved.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Advances in phylogenetic studies of Nematoda

Nematoda is a metazoan group with extremely high diversity only next to Insecta. Caenorhabditis elegans is now a favorable experimental model animal in modern developmental biology, genetics and genomics; studies. However, the phylogeny of Nematoda and the phylogenetic position of the phylum within animal kingdom have long been in debate. Recent molecular phylogenetic studies gave great challenges to the traditional nematode classification. The new phylogenies not only placed the Nematoda in the Ecdysozoan and divided the phylum into five clades, but also provided new insights into animal molecular identification and phylogenetic biodiversity studies. The present paper reviews major progress and remaining problems in the current molecular phylogenetic studies of Nematoda, and prospects the developmental tendencies of this field.

Specific Adsorption of Trace Amounts of Calcium and Strontium by Hydrous Oxides of Iron and Aluminum1

Freshly prepared Fe and Al hydrous oxide gels and the amorphous product of heating gibbsite selectively adsorbed traces of Ca and Sr from solutions containing a large excess (∼1M) of NaNO3. The fraction of the added Ca (Sr) adsorbed depended principally on the suspension pH, the amount of solid present, and to a lesser extent on the NaNO3 concentration. Significant Ca and Sr adsorption occurred on the Fe and Al gels, and heated gibbsite, at pH values below the points of zero charge (8.1, 9.4, and 8.3±0.1, respectively), indicating specific adsorption. The pH (± 0.10) at which 50% of the Ca was adsorbed (pH50) occurred at pH 7.15 for the Fe gel (0.093M Fe), 8.35 for the Al gel (0.093M Al), and 6.70 for the heated gibbsite (0.181M Al); for Sr, the pH50 values were 7.10, 9.00, and 6.45, respectively. For the Fe gel and heated gibbsite, an empirical model based on the law of mass action described the pH dependence of adsorption reasonably well and suggested that for each Ca or Sr fraction adsorbed, approximately one proton was released. Failure of the Al gel to fit this model may have resulted from its rapid aging.