Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

Superconducting Properties in Metallic Phase of NbS3

Metallic phase of NbS₃ was synthesized by heating the crystal of semiconducting NbS₃. Metallic NbS₃ undergoes superconducting transition around 2 K. The analysis of the angular dependence of the upper critical magnetic field suggests that the effect of filmy or fibrous morphology plays an important role in the superconducting properties.     

Some triplet energy-transfer reactions initiated by photoexcitation of triplet excited state of dibenz[a,h]anthracene to the higher triplet excited states

Some triplet energy-transfer reactions initiated by photoexcitation of the triplet excited state of dibenz[a,h]anthracene to higher triplet excited states (DBA(T_n)) were observed in the presence of the triplet energy quenchers (Q) such as naphthalene, biphenyl, p-dichlorobenzene, and o-dicyanobenzene. In the case of carbon tetrachloride (CCl₄) as Q, DBA(T_n)-sensitized decomposition of CCl₄ occurred.     

Essential of Proline and Valine Residues in the Peptide Derived from Lactoferrin for Angiotensin Converting Enzyme Inhibition

We synthesized Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu, the peptide contained in lactoferrin (Lf), to identify the angiotensin converting enzyme (ACE) inhibition. In an attempt to know the structure‐activity relationship of this peptide, we replaced Pro (the third amino acid residues from N‐terminal) or Val (the fourth amino acid residues from N‐terminal) with Ala (neutral amino acid), Glu (acidic amino acid) or Lys (basic amino acid) to produce six peptides. From the in vitro ACE inhibition (IC₅₀) of these synthesized peptides, the original peptide (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu) showed higher ACE inhibition than the replaced six peptides. Thus, replacement of Pro at the third amino acid residues or Val at the fourth position with Ala, Glu or Lys revealed the ACE inhibition to be lower than the original form of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu. Otherwise, we added one peptide at the C‐terminal of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu and found both products with an addition of Val (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Val) or Ile (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Ile) showing a lower ACE inhibition than the original one. The ACE inhibitions produced by both replaced peptides were without significance. Also, deletion of the last peptide at the C‐terminal (Leu‐Arg‐Pro‐Val‐Ala‐Ala) failed to produce a marked change of ACE inhibition as compared to the original one. These results suggest that Pro and Val are essential in the peptide for inhibition of ACE activity.     

Properties of hadron and quark matter studied with molecular dynamics

We study the hadron-quark phase transition in a molecular dynamics (MD) of quark degrees of freedom. The hadron state at low density and temperature, and the deconfined quark state at high density and temperature are observed in our model. We investigate the equations of state and draw the phase diagram at wide baryon density and temperature range. We also discuss the transport property, e.g. viscosity, of $q\bar q$ matter. It is found that the ratio of the shear viscosity to the entropy density is less than one for quark matter.     

Preparation of telechelic oligomers by thermal degradation of propylene copolymers

The reactive end groups of nonvolatile oligomers obtained by controlled thermal degradation of poly(propylene-ran-ethylene) and poly(propylene-ran-1-butene) were determined by ¹H and ¹³C NMR spectroscopy. The molar ratio of unsaturated to saturated end groups was found to be about 9:1. The average number of unsaturated end groups per molecule was between 1.6 and 1.8, indicating that 60–80 mol% of the oligomer molecules were telechelic, having two terminal unsaturated end groups. These oligomers had a lower polydispersity than the raw material, despite their lower molecular weight and melting temperature. Although the end groups resulting from each monomer unit could be detected by ¹³C NMR, the end group composition differed from that of the main chains of the raw materials. The end group composition was satisfactorily explained by the differences in bond dissociation energy and activation energy of elementary reactions that occurred during thermal degradation, based on the monomer composition of the raw materials.     

Multi-Terabit Long-Haul Transmission System Utilizing Distributed Raman Amplification Technologies

Here we summarize multi-terabit long-haul transmission experiment and distributed Raman amplification (DRA) technologies. As well, we investigate the configuration of dispersion-managed fibers for the DRA-based system from the viewpoint of the fiber non-linear effect and required pumping power.     

Photoluminescence characteristics of nitrogen atomic-layer-doped GaAs grown by MOVPE

Nitrogen atomic-layer-doped and uniformly doped GaAs were grown by MOVPE using dimethylhydrazine on a (001) plane. They showed several sharp photoluminescence lines with a full width at half maximum less than 1 meV at 8 K. Compared with uniformly doped GaAs, the photoluminescence intensity of the nitrogen-related line at the longest wavelength is enhanced in nitrogen atomic-layer-doped GaAs, suggesting that it is easier to form nitrogen pairs during atomic layer doping. To investigate the sharp nitrogen-related lines, we also grew GaAs with double atomic-layer-doped planes and varied the distance between the two planes. When the two planes are brought close to 1 nm, two new lines, NN_C and NN_D, appear between the two nitrogen-related lines, NN_A and NN_B, observed in a single nitrogen atomic-layer-doped GaAs. The NN_C and NN_D lines are also observed in uniformly doped GaAs. Therefore, NN_A and NN_B originate from excitons bound to pairs of nitrogen atoms, both of which are in the (001) plane, while NN_C and NN_D originate from those bound to pairs of nitrogen atoms, of which pairing directions are not included in the (001) plane. From the photoluminescence characteristics, distances between nitrogen atoms of a pair are estimated for each line.     

Bayesian analysis of lymphatic spreading patterns in cancer of the thoracic esophagus

For the treatment of patients with cancer of the thoracic esophagus, lymphatic spreading is one important factor to infer how advanced their cancer is. We introduced a one-dimensional scale based on lymphatic spreading patterns, the stage of cancer, to express how advanced their cancer is, and we proposed a method to infer each patient's stage from his lymphatic spreading pattern by applying a Bayesian model. Our Bayesian model was built based on the assumption that lymphatic spreading in cancer could be explained as what was brought about by the advance of stage. In the modeling, we introduced the probability of what stage each patient was in as a prior distribution. We also introduced distribution functions of Weibull distributions to express the relation between the advance of stage and the increase of the probability of metastasis. Our model was applied to the data of nodal involvement obtained from 103 patients with cancer of the thoracic esophagus and the parameters were estimated with the maximum likelihood method. AIC was used to check that the data had enough information to be divided into the stages of a clinically reasonable number. With the estimated parameters, we inferred the probability of metastasis to each lymph node in each stage and calculated by Bayes' theorem with 31 new patients the probability of what stage they were in. The results well represented some characteristics of the lymphatic spreading and suggested the appropriateness of our approach.The present study was carried out under the ISM Cooperative Research Program (91-ISM·CRP-18).