AG-rich Region Research Articles

Critical evaluation and thermodynamic modeling of the Ag-X (X=Mn, Y, Sr) binary systems

A complete literature review, critical evaluation and thermodynamic assessment of the Ag-X (X = Mn, Y, Sr) binary systems have been conducted. The Modified Quasi-chemical Model in the Pair Approximation (MQMPA) was applied to describe the Gibbs energy of the liquid phase. The Gibbs energy of all intermetallic compounds and terminal solid solutions was described by the Compound Energy Formalism (CEF). The critical literature assessment and thermodynamic modeling of the Ag–Mn binary system were carried out for the first time. The Differential Scanning Calorimetry (DSC) measurement was carried out to resolve the discrepancy of liquidus in Ag-rich region of the Ag–Sr binary system. Thermodynamic re-optimization of the Ag–Sr binary system was performed based on reported literature data and our new measured results using DSC technique. Thermodynamic re-optimization of the Ag–Y binary system was also carried out with considering the ordered bcc_B2 crystal structure of the AgY compound. All reliable experimental data are well reproduced within the experimental limits. A self-consistent thermodynamic database of the Ag-X (X = Mn, Y, Sr) binary systems was constructed for the development of new biomaterials.

Mutational Analysis of sRNA-mRNA Base Pairing by Electrophoretic Mobility Shift Assay.

Small regulatory RNAs (sRNAs) in bacteria often act by base pairing to mRNAs. Direct interactions between an sRNA and its target mRNA can be investigated by electrophoretic mobility shift assay. In this assay, regions engaged in base pairing are analyzed by introducing mutations in one of the RNAs that prevent sRNA-mRNA complex formation, followed by the introduction of complementary mutations in its partner RNA that restore base pairing. Here, we describe the design of a mutational strategy used to analyze the base pairing between two CU-rich regions of the sRNA Rli22 and the AG-rich Shine-Dalgarno region of the mRNA oppA in Listeria monocytogenes. The protocol can be employed for mutational studies of base pairing between any sRNA and its mRNA target(s).

Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization.

Since the proposition of introns-early hypothesis, although many studies have shown that most eukaryotic ancestors possessed intron-rich genomes, evidence of intron existence in genomes of ancestral bacteria has still been absent. While not a single intron has been found in all protein-coding genes of current bacteria, analyses on bacterial genes horizontally transferred into eukaryotes at ancient time may provide evidence of intron existence in bacterial ancestors. In this study, a bacterial gene encoding capsule biosynthesis protein CapI was found in the genome of sea anemone, Nematostella vectensis. This horizontally transferred gene contains a phase 1 intron of 40 base pairs. The nucleotides of this intron have high sequence identity with those encoding amino acids in current bacterial CapI gene, indicating that the intron and the amino acid-coding nucleotides are originated from the same ancestor sequence. Moreover, 5′-splice site of this intron is located in a GT-poor region associated with a closely following AG-rich region, suggesting that deletion mutation at 5′-splice site has been employed to remove this intron and the intron-like amino acid-coding nucleotides in current bacterial CapI gene are derived from exonization. These data suggest that bacterial CapI gene contained intron(s) at ancient time. This is the first report providing the result of sequence analysis to suggest possible existence of spliceosomal introns in ancestral bacterial genes. The methodology employed in this study may be used to identify more such evidence that would aid in settlement of the dispute between introns-early and introns-late theories.

Composition Dependence of the Phase Stability in Au-Cd-Ag Martensitic Alloy

Au52.5-x-Cd47.5-Agx noble metal alloy undergoes martensitic transformation and shows complex Ag dependence on transformation temperature. As Ag composition ratio increases, β- and α- coexistence phase appears. The behavior of this Ag-rich region was studied. Atoms of the β-phase arrange disorderly (A2) in this region. The transformation temperature T0 rises drastically and the magnitude of orthorhombic distortion becomes larger in comparison with that of adjoined β- single phase. This result suggests a correlation between the orthorhombic distortion and T0. Excessively high packing fraction of the α-phase, atomic disorder in the β-phase and small volume ratio of martensite / β-phase makes the β-phase unstable and stimulates transformation.

3′-UTR variations and G6PD deficiency

The combination of two silent mutations, c.1311C>T in exon 11 and IVS11 T93C (glucose-6-phosphate dehydrogenase (G6PD) 1311T/93C), with unknown mechanism, have been reported in G6PD-deficient individuals in Asian populations including Malaysian aboriginal group, Negrito. Here, we report the screening of G6PD gene in 103 Negrito volunteers using denaturing high-performance liquid chromatography (dHPLC) and direct sequencing. A total of 48 individuals (46.6%) were G6PD deficient, 83.3% of these carried G6PD 1311T/93C with enzyme activity ranging from 1.8 to 4.8 U gHb(-1). Three novel single-nucleotide polymorphisms (SNPs), rs112950723, rs111485003 and rs1050757, were found in the G6PD 3'-untranslated region (UTR). Strong association was observed between haplotype 1311T/93C and rs1050757G, which is located inside the 35 bp AG-rich region. In silico analysis revealed that the transition of A to G at position rs1050757 makes significant changes in the G6PD mRNA secondary structure. Moreover, putative micro (mi)RNA target sites were identified in 3'-UTR of G6PD gene, two of these in the region encompassing rs1050757. It could be speculated that rs1050757 have a potential functional effect on the downregulation of mRNA and consequently G6PD deficiency either by affecting mRNA stability and translation or mirRNA regulation process. This is the first report of biochemical association of an SNP in 3'-UTR of G6PD gene and the possible role of mRNA secondary structure.

Structural and energetic asymmetry in liquid Ag–Al alloys

The thermodynamic and microscopic structure of Ag–Al liquid alloy at 1273 K has been studied by using regular associated solution model. This model has been utilised to determine the complex concentration in a regular associated solution of Ag and Al. We have then used the complex concentration to calculate the free energy of mixing, enthalpy of mixing, entropy of mixing, activity and concentration fluctuations in long wavelength limit S CC(0) and the Warren–Cowley short-range parameter α 1. The analysis suggests that heterocoordination leading to the formation of complex Ag3Al is likely to exist in the liquid but is of a weakly interacting nature. The theoretical analysis reveals that the pairwise interaction energies between the species depend considerably on temperature and the alloy is more ordered towards Ag-rich region. The alloy behaves like a segregating system in Al-rich region.

Concentration dependence of the structure and thermodynamic properties of silver–antimony alloys

The regular associated solution model has been used to estimate the concentration of Ag 3Sb type clusters in AgSb liquid alloys at 1250 K. The equilibrium constant for the dissociation of clusters and pairwire interaction energies between unassociated atoms and clusters have been evaluated using the concentrations of clusters. These enable estimation of thermodynamic and microscopic properties of the alloys at any desired concentration. The analysis suggests that the alloy is more ordered in Ag-rich region. The alloy behaves like a segregating system in Sb-rich end.

Molecular evolution of toxin genes in Elapidae snakes

The venom of the sea krait, Laticauda semifasciata, consists primarily of two toxic proteins, phospholipase A(2) (PLA(2)) and a three-finger-structure toxin. We have cloned both toxic protein genes, including the upstream region. PLA(2) genes contain three types of inserted sequences: an AG-rich region, a chicken repeat 1-like long interspersed nucleotide element sequence and an intron II 3' side repeat sequence. The molecular divergence of L. semifasciata PLA(2) genes was defined on the basis of the inserted sequences and their sequence homology. The length of intron I in the three-finger-structure toxin genes differs from species to species. The alignment analysis of intron I of the three-finger-structure toxin genes revealed that the intron I sequence of the ancestral gene comprised ten genetic regions. A hypothetical evolutionary process for the three-finger-structure toxin genes has also been developed.

Analysis of sequence patterns surrounding the translation initiation sites on Cyanobacterium genome using the hidden Markov model.

Sequence patterns surrounding the translation initiation sites of Cyanobacterium were precisely analyzed by the hidden Markov model (HMM) based on the actual translation initiation sites. In a previous study, 72 actual protein coding regions and their translation initiation sites on the genome of Synechocystis sp. strain PCC6803 were determined by Sazuka et al. using protein two-dimensional electrophoresis and microsequening. In this work, we extracted the sequence patterns surrounding translation initiation sites as HMM using the computer program YEBIS. The constructed HMM could recognize all but one translation initiation site. The HMM contains an AG-rich region (5.7 bp on average), as the Shine-Dalgarno sequence exclusively contains purines, upstream of the translation initiation site (-9.7 position on average) and a CT rich region (4.2 bp on average) just upstream from the translation initiation site. In addition, we found that the second amino acid (-4.5,6) could be classified into two types, one of which had C as their second codon while another of which has a nucleotide distribution relatively similar to the distribution among amino acids in the 72 proteins. This fact corresponds well to our earlier finding that when the second nucleotide of the second amino acid of a translated protein was C, an initial methionine was processed and that otherwise the methionine was intact with high frequency.

Magnetic and structural properties of liquid Ag-polyvalent systems

An investigation based on the results of the magnetic susceptibility and structural properties for liquid Ag-polyvalent metal alloys has been carried out. Magnetic susceptibilities of liquid Ag-In, -Sn, -Ga, and -Zn systems have been measured over a temperature range from 600 to 1085 °C. The concentration dependences of the electron susceptibility ( χ electron ) for these four alloys show a characteristic behavior in the Ag-rich region. The concentration dependences of d χelectron /dT as a function of the number of electrons per atom have a similar feature, qualitatively. The results of resistivity measurements are also discussed.

The mouse Fau gene: genomic structure, chromosomal localization, and characterization of two retropseudogenes

The Fau gene is the cellular homolog of the fox sequence of the Finkel—Biskis—Reilly murine sarcoma virus (FBR-MuSV). FBR-MuSV acquired the Fau gene by transduction in a transcriptional orientation opposite to that of the genomic Fau gene. The genomic structure of the mouse Fau gene (MMFAU) and its upstream elements have been determined and are similar to those of the human FAU gene. The gene consists of five exons and is located on chromosome 19. The first exon is not translated. The promoter region has no well-defined TATA box but contains the polypyrimidine initiator flanked by regions of high GC content (65%) and shows all of the characteristics of a housekeeping gene. The 5′ end of the mRNA transcript was determined by 5′ RACE analysis and is located, as expected, in the polypyrimidine initiator site. Furthermore, the sequences of two retropseudogenes ( Fau-ps1 and Fau-ps2) are reported. Both pseudogenes are approximately 75% identical to the Fau cDNA, but both are shorter due to a deletion at the 5′ end and do not encode a functional protein. Fau-prs is interrupted by an AG-rich region of about 350 bp within the S30 region of the Fau cDNA. Fau-ps1 was localized on chromosome 1 and Fau-ps2 on chromosome 7.

Human Decorin Gene: Intron-Exon Junctions and Chromosomal Localization

All of the protein-encoding exons and the 3' flanking region of the human decorin gene have been cloned and partially sequenced. The locations of the intron-exon junctions within the coding portion of the gene were identical to those found for the homologous human gene, biglycan. The sizes of the introns in the decorin gene, however, were substantially larger than those of the same introns of the biglycan gene. Portions of introns 1, 2, and 3 as well as exon 1 were not found during our extensive screening process. The 5' end of intron 2 was found to have an AG-rich region followed immediately by a CT-rich region. Furthermore, the 5' end of intron 3 was very rich in thymidine, whereas the 3' end of intron 7 was rich in adenosine. Several cDNA clones constructed from cultured human bone cell mRNA were found to contain a different sequence at the 5' end compared to that previously published for mRNA from a human embryonic fibroblast cell line. We were also unable to find the alternate 3' flanking region of the previously published cDNA sequence. We have mapped the human decorin gene by in situ methods to chromosome 12q21.3.

Cloning, Sequencing and Expression of the Sialidase Gene fromActinomyces viscosusDSM 43798

Chromosomal DNA from Actinomyces viscosus was digested with restriction endonucleases and the fragments ligated with pUC-vectors were used to transform Escherichia coli cells. Clones bearing the required sialidase gene were detected by spraying the colonies with the fluorogenic sialidase substrate MU-Neu5Ac. The identity of the cloned sialidase was confirmed after the 5700-fold enrichment and comparison with the purified enzyme of A. viscosus. Both sialidases were identical with regard to molecular mass, substrate specificity tested with sialyllactoses, and the inhibition of their activity by heterologous antisialidase antibodies. The sequenced insert (EMBL accession number X62276) revealed a mol% G + C of 68.2, typical for A. viscosus. An open reading frame of 2739 bp follows a sequence with dyad symmetry and an AG-rich region, and codes for 913 amino acids representing a molecular mass of 113 kDa. The conserved amino acid sequence [Ser-X-Asp-X-Gly-X-Thr-Trp] typical for bacterial sialidases was found at five positions in the predicted amino acid sequence. The gene of this enzyme is expressed by E. coli, despite the low relatedness of both species.

Drilling holes in silver ionic conductor using the high current density STEM probe

High current density STEM probe can be used to drill holes and to draw wonderful pictures through samples such as metal β-aluminas, feuoride and titaniun oxide etc. Resently, we have also found that the high current density subnanometer probe in the HB-5 and HB-501 STEM rapidly drills small holes in samples of Ag ionic conductor (Agl+XZr2Si2P3−xO12,x between 0 and 3) from which silver filaments can be easily extruded under the irradiation of electron beam. By means of electron diffraction, EDX, MAP pattern,HREM and EELS,we discovered that the filaments are absolute pure, and there are not any element distribution of Zr,Si,P and O on the filaments, except for a little carbon contamenation. Most of the Ag filaments were single crystal, and others were polycrystal with the length of crystal grains over 100nm. It would interrupt the extrusion to remove the electron beam, but if the irradiation restore in several seconds the Ag filament will be continued to extruse slowly, otherwise never again for the root of the filament has crystallized quite well and solidly connected with the sample grain. We suggest that there exist lot of miniature tunnels in the sample for the Ag filaments do not contain any other elements, and the filament must be formed by the collection of some tunnels. Whether the hole-drilling is easily and the dimension of holes are related to the thickness, drill tine and beam current intensity, but they mainly depend on the content of silver in the drilling region. The less the content of Ag, the easier the hole- drilling. We can not drill any hole in the silver filaments and Ag particles on the surface of sample grains. The holes are easily contaminted for the EELS we obtained was almost belong to carbon as the tine passed. A silver filament on the right had been extruded from a sample grain as shown in Fig.1a, and the root of the silver filament was connected with a pear-shaped Ag-rich region. When the electron beam gradually approached near the edge of the pear-shaped region from the edge of the grain, we found that the dimension of holes increased from 10nm to 30 nm. But we could not obtain holes with more than 10 nm in diameter after entering the pearshaped region. As soon as the electron probe entered the centre of the Ag-rich region, the pear-shaped region was broken into two parts and a hole with 26 nm in diameter appeared. Meanwhile, a new Ag filament with 24 nm in diameter was extruded from the left broken part shown in Fig.1b. It was proved by EDX that there was not any content of silver in this hole-drilling region. The Ag filament on the right was still connected with the right broken part, and it was not continued to extrude. The nearer to the root of the Ag filament, the more difficult to drill holes in the right part,e.g., it spent 180 seconds to drill a hole with only 5 nm in diameter where 40 nm to the root of the filament. Holes could not be drilled in such sample grains in which x is not between 0 and 3 and any Ag filaments can not be extruded.

The Ag-Sr (Silver-Strontium) system

The Ag-Sr diagram was investigated by [30Wei] using a thermal analysis technique and by [70Heu] using thermal analysis, microstructural examination, X-ray diffraction, electrical resistivitz and magnetic sensitivity measurements. [30Wei] investigated the entire composition range, whereas [70Heu] studied alloy compositions between 0 and 30 at.% St. In the Ag-rich region there were serious differences between the diagram proposed by [30Wei] and the data of [70Heu]. In addition, later crystal structure determinations by [65Kos] and [84Mer] placed other regions of the diagram of [30Wei] in question.