Synthesis and properties of oligonucleotides containing a 2,6-diamino-3-deazapurine:furanopyrimidine base pair.

Furanopyrimidine (FPy) and 2,6-diamino-3-deazapurine (DC3Pu) nucleosides with the ability to interact in DDD and AAA H-bonding patterns, respectively, were prepared. The N-1 pKa value of the DC3Pu nucleoside was estimated to be 6.4, which is due to the lack of a nitrogen atom at the 3-position, suggesting that DC3Pu acts as a base interacting in a DDD H-bonding pattern under near physiological conditions. As DC3Pu and FPy are expected to form a thermally stable DDD:AAA type of base pair in an oligodeoxynucleotide (ODN) duplex, they were incorporated into ODNs, and the Tm value of the ODN duplex was determined. However, the ODN duplex containing a DC3Pu:FPy pair has a lower thermal stability than that containing a G:C pair does, although its thermal stability is equal to that of an ODN duplex with an A:T pair even under acidic conditions.

Anisotropic Gaussian kernel adaptive filtering by Lie-group dictionary learning.

The present paper proposes a novel kernel adaptive filtering algorithm, where each Gaussian kernel is parameterized by a center vector and a symmetric positive definite (SPD) precision matrix, which is regarded as a generalization of scalar width parameter. In fact, different from conventional kernel adaptive systems, the proposed filter is structured as a superposition of non-isotropic Gaussian kernels, whose non-isotropy makes the filter more flexible. The adaptation algorithm will search for optimal parameters in a wider parameter space. This generalization brings the need of special treatment of parameters that have a geometric structure. In fact, the main contribution of this paper is to establish update rules for precision matrices on the Lie group of SPD matrices in order to ensure their symmetry and positive-definiteness. The parameters of this filter are adapted on the basis of a least-squares criterion to minimize the filtering error, together with an ℓ1-type regularization criterion to avoid overfitting and to prevent the increase of dimensionality of the dictionary. Experimental results confirm the validity of the proposed method.

Classification of familiarity based on cross-correlation features between EEG and music.

An approach to recognize the familiarity of a listener with music using both the electroencephalogram (EEG) signals and the music signal is proposed in this paper. Eight participants listened to melodies produced by piano sounds as simple natural stimuli. We classified the familiarity of each participant using cross-correlation values between EEG and the envelope of the music signal as features of the support vector machine (SVM) or neural network used. Here, we report that the maximum classification accuracy was 100% obtained by the SVM. These results suggest that the familiarity of music can be classified by cross-correlation values. The proposed approach can be used to recognize high-level brain states such as familiarity, preference, and emotion.

Groove modification of siRNA duplexes to elucidate siRNA-protein interactions using 7-bromo-7-deazaadenosine and 3-bromo-3-deazaadenosine as chemical probes.

Elucidation of dynamic interactions between RNA and proteins is essential for understanding the biological processes regulated by RNA, such as RNA interference (RNAi). In this study, the logical chemical probes, comprising 7-bromo-7-deazaadenosine (Br7C7A) and 3-bromo-3-deazaadenosine (Br3C3A), to investigate small interfering RNA (siRNA)-RNAi related protein interactions, were developed. The bromo substituents of Br7C7A and Br3C3A are expected to be located in the major and the minor grooves, respectively, and to act as a steric hindrance in each groove when these chemical probes are incorporated into siRNAs. A comprehensive investigation using siRNAs containing these chemical probes revealed that (i) Br3C3A(s) at the 5'-end of the passenger strand enhanced their RNAi activity, and (ii) the direction of RISC assembly is determined by the interaction between Argonaute2, which is the main component of RISC, and siRNA in the minor groove near the 5'-end of the passenger strand. Utilization of these chemical probes enables the investigation of the dynamic interactions between RNA and proteins.

Coat protein mutations in an attenuated Cucumber mosaic virus encoding mutant 2b protein that lacks RNA silencing suppressor activity induces chlorosis with photosynthesis gene repression and chloroplast abnormalities in infected tobacco plants.

In tobacco plants, the Cucumber mosaic virus (CMV) pepo strain induces mosaic symptoms, including pale green chlorosis and malformed tissues. Here, we characterized the involvement of 2b protein and coat protein (CP) in the development of mosaic symptoms. A 2b mutant (R46C) that lacks viral suppressor of RNA silencing (VSR) activity showed an asymptomatic phenotype with low levels of virus accumulation. Tomato spotted wilt virus NSs protein did not complement the virulence of the R46C, although it did restore high-level virus accumulation. However, R46C mutants expressing mutated CP in which the amino acid P129 was mutated to A, E, C, Q, or S induced chlorosis that was associated with reduced expression of chloroplast and photosynthesis related genes (CPRGs) and abnormal chloroplasts with fewer thylakoid membranes. These results suggest that the CP of the CMV pepo strain acquires virulence by amino acid mutations, which causes CPRG repression and chloroplast abnormalities.