Secondary structures of mRNAs and splicing of introns in eukaryotes.

After analyzing the secondary structures of 68 exon-intron-exon and the corresponding exon-exon sequence segments, it is found that about 90% of 5' and 3' terminal bases G (splicing sites) of introns are situated in the loops of secondary structures or at the ends of stems near the loops, and most of "G" s in loops are closed to the ends of loops. Approximately 92% of the connecting sites of the adjoining exons also show the similar features. About 82% of the branch point "A" s are situated in loops or at the ends of stems near the loops. Splicing sites and branch points approach each other in space because of the folding.

Secondary structure of yeast genomic downstream region and polyadenylation signals

Polyadenylation of 3 ' -forming in eukaryote concerns three elements located in precursor mRNA downstream region: efficiency element (EE), position element (PE) and the actual site for cleavage and polyadenylation. Several base sequences of EE and PE have

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

The relation between translation speed and protein secondary structure

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/ avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation

It is extremely difficult to explore mRNA folding structure by biological experiments. In this report, we use stochastic sampling and folding simulation to test the existence of the stable secondary structural units of-mRNA, look for the folding units, and explore the probabilistic stabilization of the units. Using this method, We made simulations for all possible local optimum secondary structures of a single strand mRNA within a certain range, and searched for the common parts of the secondary structures. The consensus secondary structure units (CSSUs) extracted from the above method are mainly hairpins, with a few single strands. These CSSUs suggest that the mRNA folding units could be relatively stable and could perform specific biological function. The significance of these observations for the mRNA folding problem in general is also discussed. (c) 2004 Elsevier B.V. All rights reserved.

La 0.7Ca 0.3MnO 3 / Mn 3O 4 composites: Does an insulating secondary phase always enhance the low field magnetoresistance of manganites

Composites of magnetoresistive La 0.7Ca 0.3MnO 3 (LCMO) with insulating Mn 3O 4 are useful as a model system because no foreign cation is introduced in the LCMO phase by interdiffusion during the heat treatment. Here we report the magnetotransport properties as a function of sintering temperature T sinter for a fixed LCMO/Mn 3O 4 ratio. Decreasing T sinter from 1250 °C to 800 °C causes an increase in low field magnetoresistance (LFMR) that correlates with the decrease in crystallite size (CS) of the LCMO phase. When plotting LFMR at (77 K, 0.5 T) versus 1/CS, we find that the data for the LCMO/Mn 3O 4 composites sintered between 800 °C and 1250 °C follow the same trend line as data from the literature for pure LCMO samples with crystallite size >∼25 nm. This differs from the LFMR enhancement observed by many authors in the usual manganite composites, i.e., composites where the insulating phase contains cations other than La, Ca or Mn. This difference suggests that diffusion of foreign cations into the grain boundary region is a necessary ingredient for the enhanced LFMR. © 2012 American Institute of Physics.

Spray drying: An alternative synthesis method for polycationic oxide compounds

Synthesis of polycationic compounds by the spray-drying technique is an interesting alternative in the domain of aqueous precursor synthesis methods. Spray drying yields high quality samples with good reproducibility. The possibility of scaling up for production of large quantities with fast processing time is well established by the commercial availability of powders of various compositions. In this paper, we have discussed the advantages and limitations of this method and demonstrated its interest by synthesizing a few polycationic compounds selected for their attractive properties of thermoelectricity [Bi1.68Ca2Co1.69O 8, La0.95A0.05CoO3 (A=Ca, Sr, Ba)] or magnetoresistance [La0.70A0.30MnO3 (A=Sr, Ba)]. We have confirmed the quality of these samples by reporting their structure, magnetic and transport properties. © 2010 Elsevier Ltd All rights reserved.

LiMn2-xTixO4 spinel-type compounds (x ≤ 1): Structural, electrical and magnetic properties

LiMn2-xTixO4 compounds with 0 ≤ x ≤ 1 were prepared by solid state reaction and Pechini technique. Powder X-ray diffraction showed that all samples crystallize with the spinel crystal structure (S.G. Fd3-m). The cubic unit-cell parameter increases with the Ti content. The influence of the Ti content and cationic distribution on the magnetic properties of the compounds was studied by measuring the temperature and magnetic field dependences of the magnetization: substitution by non-magnetic d0 Ti4+ ions appeared to weaken the magnetic interactions between the manganese ions. The electrical properties of LiMnTiO4 were studied by AC impedance spectroscopy and DC polarisation measurements, which revealed the electronic character of the conduction process. © 2006 Elsevier B.V. All rights reserved.

Low-field magnetoresistance in La0.7Ca0.3MnO 3 manganite compounds prepared by the spray drying technique

Calcium-substituted lanthanum manganite compounds were synthesized by the spray drying technique. This method - whose main advantages are versatility, high reproducibility and scalability - yields small grain materials of high homogeneity and displaying low-field magnetoresistance effects. We report about the physical and chemical characterizations of these samples in order to investigate the potential interest of spray drying for the production of materials for low-field magnetoresistance applications. We have studied the dependence of the low-field magnetoresistance on the temperature and duration of the thermal treatment applied to the pelletized powders. The issue of the shape anisotropy (demagnetisation effects) influence on the magnetoresistance properties has also been dealt with. © 2005 Springer Science + Business Media, Inc.