Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location.

Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon SORE-1. We analyzed SORE-1, inserted in exon 1 of the GmphyA2 gene, one of the newest insertions in this family so far identified. Cytosine methylation was detected in this element but was barely present in the adjacent regions. These results were correlated, respectively, with the presence and absence of the production of short interfering RNAs. Cytosine methylation profiles of 74 SORE-1 elements in the Williams 82 reference genome indicated that methylation frequency in the adjacent regions of SORE-1 was profoundly higher in pericentromeric regions than in euchromatic chromosome arms and was only weakly correlated with the length of time after insertion into the genome. Notably, the higher level of methylation in the 5' adjacent regions of SORE-1 coincided with the presence of repetitive elements in pericentromeric regions. Together, these results suggest that epigenetic influence of SORE-1 on the adjacent regions is influenced by its location on the chromosome.

Transcription of soybean retrotransposon SORE-1 is temporally upregulated in developing ovules.

MAIN CONCLUSION: Transcription of soybean retrotransposon SORE-1 was temporally upregulated during ovule development. This transcriptional pattern was under intrinsic control conferred by the long terminal repeat of SORE-1. Transcriptionally active retrotransposons are capable of inducing random disruption of genes, providing a powerful tool for mutagenesis. Activation of retrotransposons in reproductive cells, in particular, can lead to heritable changes. Here, we examined developmental control of transcription of soybean retrotransposon SORE-1. Transgenic Arabidopsis plants that contain ß-glucuronidase (GUS) reporter gene fused with the SORE-1 long terminal repeat (LTR) had GUS staining in the ovule. Quantitative analysis of transcripts in plants with this DNA construct and those with the full-length SORE-1 element indicated a temporal upregulation of SORE-1 transcription during ovule development. A comparable phenomenon was also observed in soybean plants that had a recent insertion of this element in the GmphyA2 gene. These results provide evidence that the temporal upregulation of SORE-1 in the reproductive organ is sufficiently controlled by its LTR and indicate that the intrinsic expression pattern of SORE-1 is consistent with its mutagenic property.

Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions.

Retrotransposons constitute a large portion of plant genomes. The chromosomal distribution of a wide variety of retrotransposons has been analyzed using genome sequencing data in several plants, but the evolutionary profile of transposition has been characterized for a limited number of retrotransposon families. Here, we characterized 96 elements of the SORE-1 family of soybean retrotransposons using genome sequencing data. Insertion time of each SORE-1 element into the genome was estimated on the basis of sequence differences between the 5' and 3' long terminal repeats (LTRs). Combining this estimation with information on the chromosomal location of these elements, we found that the insertion of the existing SORE-1 into gene-rich chromosome arms occurred on average more recently than that into gene-poor pericentromeric regions. In addition, both the number of insertions and the proportion of insertions into chromosome arms profoundly increased after 1 million years ago. Solo LTRs were detected in these regions at a similar frequency, suggesting that elimination of SORE-1 via unequal homologous recombination was unbiased. Taken together, these results suggest the preference of a recent insertion of SORE-1 into chromosome arms comprising euchromatic regions. This notion is contrary to an earlier view deduced from an overall profiling of soybean retrotransposons and suggests that the pattern of chromosomal distribution can be more diverse than previously thought between different families of retrotransposons.

Frequent generation of mutants with coincidental changes in multiple traits via ion-beam irradiation in soybean.

Ion beams are powerful mutagens that can induce novel mutants in plants. We previously established a system for producing a mutant population of soybean via ion-beam irradiation, isolated plants that had chlorophyll deficiency, and maintained their progeny via self-fertilization. Here we report the characterization of the progeny plants in terms of chlorophyll content, flowering time and isoflavone content in seeds. Chlorophyll deficiency in the leaf tissues was linked with reduced levels of isoflavones, the major flavonoid compounds accumulated in soybean seeds, which suggested the involvement of metabolic changes associated with the chlorophyll deficiency. Intriguingly, flowering time was frequently altered in plants that had a reduced level of chlorophyll in the leaf tissues. Plant lines that flowered either earlier or later than the wild-type plants were detected. The observed coincidental changes were presumed to be attributable to the following origins: structural changes of DNA segments leading to the loss of multiple gene functions, or indirect effects of mutations that affect one of these traits, which were manifested as phenotypic changes in the background of the duplicated composition of the soybean genome.

Successful acquisition of a neutralizing monoclonal antibody against a novel neutrophil-activating peptide, mitocryptide-1.

Mitocryptide-1 (MCT-1) is a novel neutrophil-activating peptide derived from mitochondrial cytochrome c oxidase subunit VIII, and its physiological role and involvement in various diseases have not yet been elucidated. Generating neutralizing antibodies against the function of MCT-1 is of particular importance for investigating its physiological and pathophysiological roles, because MCT-1 is a fragmented peptide of its mother protein and hence it is very difficult to manipulate its expression level genetically without affecting expression of the mother protein. Here, we report the successful generation of a neutralizing monoclonal antibody (MAb) against MCT-1. This MAb, designated NM1B1, which specifically bound to the region of positions 9-22 of MCT-1, showed concentration-dependent inhibition of MCT-1-induced migration and ß-hexosaminidase release in neutrophilic/granulocytic differentiated HL-60 cells. Thus, NM1B1, as a neutralizing MAb against MCT-1, could elucidate not just the physiological regulatory mechanisms of MCT-1 but also its pathophysiological involvement in various inflammatory diseases in vivo.

Computational study on the in-plane symmetry of electron wavefunctions in self-assembled InAs/GaAs quantum dots.

We made a computational study of electron wavefunction symmetry in two types of InAs/GaAs self-assembled quantum dot (QD): one is a normal domical and pyramidal Stranski-Krastanow(SK)-type QD but embedded in InGaAs strain-reducing layer, and the other is a columnar-shaped QD fabricated via direct perpendicular stacking of SK-type QDs. Our calculations based on the three-dimensional finite element method suggested that the in-plane symmetry of the electron wavefunction is superior to that of the crystallographic QD structure. The presence of an InGaAs strain-reducing layer helps to improve the symmetry of SK-type QD. The higher the indium composition of the strain-reducing layer, the greater the improvement. The improvement is greater with domical QD than with pyramidal QD. We also found that the multiple wetting layers around the columnar-shaped QD structure act as a strain-reducing layer, so that the improvement of symmetry is dependent on the average indium composition of the multiple wetting/interval layers. The symmetry improvement was explained by the wavefunction overflow outside the QDs. We found that, to achieve highly symmetric wavefunction, the strain-reducing-layer-embedded QDs are adequate more than the columnar-shaped QDs. These results will aid in the development of an entangled-photon generator that requires symmetric in-plane QD structure.

Insecticidal bacteria isolated from predatory larvae of the antlion species Myrmeleon bore (Neuroptera: Myrmeleontidae).

Various bacterial species were isolated from the crop (digestive organ) of the antlion species Myrmeleon bore and tested for their insecticidal activity against caterpillars by injection. Sixty-eight isolates from the antlion crop were grouped into twenty-four species based on homologies of 16S rRNA gene sequences and biochemical properties. Isolated Bacillus cereus, Bacillus sphaericus, Morganella morganii, Serratia marcescens and a Klebsiella species killed 80% or more cutworms when injected at a dose of 5x10(5)cells per insect. In addition, cutworms killed by these isolates resembled observations made of caterpillars attacked by antlions. A culture-independent analysis showed that the isolated bacterial species are likely to be frequently present in the antlion crop. These results suggest that insecticidal microorganisms associate with antlions, and may promote the death of prey.

Cloning, functional characterization, and mode of action of a novel insecticidal pore-forming toxin, sphaericolysin, produced by Bacillus sphaericus.

An insecticidal protein produced by Bacillus sphaericus A3-2 was purified to elucidate its structure and mode of action. The active principle purified from the culture broth of A3-2 was a protein with a molecular mass of 53 kDa that rapidly intoxicated German cockroaches (Blattela germanica) at a dose of about 100 ng when injected. The insecticidal protein sphaericolysin possessed the undecapeptide motif of cholesterol-dependent cytolysins and had a unique N-terminal sequence. The recombinant protein expressed in Escherichia coli was equally as potent as the native protein. Sphaericolysin-induced hemolysis resulted from the protein's pore-forming action. This activity as well as the insecticidal activity was markedly reduced by a Y159A mutation. Also, coapplication of sphaericolysin with cholesterol abolished the insecticidal action, suggesting that cholesterol binding plays an important role in insecticidal activity. Sphaericolysin-lysed neurons dissociated from the thoracic ganglia of the German cockroaches. In addition, sphaericolysin's activity in ganglia was suppressed by the Y159A mutation. The sphaericolysin-induced damage to the cockroach ganglia was greater than the damage to the ganglia of common cutworms (Spodoptera litura), which accounts, at least in part, for the higher sensitivity to sphaericolysin displayed by the cockroaches than that displayed by cutworms.

Theoretical study on controllability of quantum state energy in an InGaAs/GaAs quantum dot buried in InGaAs.

We theoretically studied the relationship between quantum energy states and structural parameters of an InGaAs/GaAs quantum dot (QD) buried in strained InGaAs, emitting at 1.1 to 1.4 em. The crystal distortion of the buried QD structure in three dimensions was computed based on the three-dimensional finite element method. Under the computed strain fields, the Schrödinger equation was solved to obtain wavefunctions and eigenenergies. By calculating the dependence on structural parameters, we investigated the controllable range of the ground state energy and the energy separation between the ground state and the first excited state. We found that the energy separation exhibited a maximum value as a function of QD composition, enabling us to identify the composition of the QD structure. The effects of the burying layer composition and QD diameter were also investigated to expand the controllable range of the state energy. We also showed that the wavefunction symmetry was improved by burying the QD in the InGaAs layer. Our results will be useful in developing advanced devices for optical telecommunications and quantum information technology.