Personal Aesthetic Values Development as the Basis for a Modern Musician’s Spiritual Formation

This article proves the necessity of personal aesthetic foundations development, proposes mechanisms for the formation of aesthetic values, studies the "aesthetic" category in the aspect of the problem of the individual’s spiritual world formation. Musical activity is considered as a basis for the development of aesthetic consciousness and the most important factor in the formation of aesthetic culture of the modern musician. In Methods section, a four-complex model of individual’s spiritual self-determination and self-actualization is provided. DOI: 10.5901/mjss.2015.v6n5s1p56

Draft Genome Sequences of Strains \u3ci\u3eSalinicola socius\u3c/i\u3e SMB35\u3csup\u3eT\u3c/sup\u3e, \u3ci\u3eSalinicola\u3c/i\u3e sp. MH3R3-1 and \u3ci\u3eChromohalobacter\u3c/i\u3e sp. SMB17 From the Verkhnekamsk Potash Mining Region of Russia

Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75–90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches

DNA/RNA structure and processing in vitro and in cells: from probing to prediction

Human DNA sequence determines the cellular fate through transcription to RNA and translation to proteins. DNA and RNA undergo extensive processing in the cells based on the sequence and cellular state, where alternative splicing in particular determines RNA isoform choice. In the recent years, in addition to the sequence of nucleic acid, its structure and epigenetic landscape have been shown to play important roles in cellular functions. For example, DNA and RNA G-quadruplex (G4) structures were found to affect oncogene expression and to be attractive therapeutic targets. This thesis mainly focuses on the DNA and RNA G4 structure formation and RNA splicing in cellular contexts. First, I analyse the formation of irregular G4 forming motifs using reported experimental data on DNA G4 in cells. I find possible correlations of DNA G4 formation with contextual epigenetic features using neural networks and propose a deep learning-based method for G4 prediction in cells. Motivated by the scarcity of RNA G4 probing methods, I additionally propose a method for detection of RNA G-quadruplexes in long RNA with direct nanopore sequencing. Contextual machine learning is further applied to predict alternative RNA splicing in cells using RNA-binding protein (RBP) levels. In summary, I have developed deep learning methods for prediction of G4 structure formation and RNA splicing in cells, which will help to advance our understanding of DNA/RNA structure and processing in different cellular contexts.Doctor of Philosoph

epiG4NN

epiG4NN is a novel deep learning framework for G-quadruplex prediction using epigenetic data</p

Prediction of G4 formation in live cells with epigenetic data: a deep learning approach

G-quadruplexes (G4s) are secondary structures abundant in DNA that may play regulatory roles in cells. Despite the ubiquity of the putative G-quadruplex-forming sequences (PQS) in the human genome, only a small fraction forms G4 structures in cells. Folded G4, histone methylation and chromatin accessibility are all parts of the complex cis regulatory landscape. We propose an approach for prediction of G4 formation in cells that incorporates epigenetic and chromatin accessibility data. The novel approach termed epiG4NN efficiently predicts cell-specific G4 formation in live cells based on a local epigenomic snapshot. Our results confirm the close relationship between H3K4me3 histone methylation, chromatin accessibility and G4 structure formation. Trained on A549 cell data, epiG4NN was then able to predict G4 formation in HEK293T and K562 cell lines. We observe the dependency of model performance with different epigenetic features on the underlying experimental condition of G4 detection. We expect that this approach will contribute to the systematic understanding of correlations between structural and epigenomic feature landscape.Nanyang Technological UniversityPublished versionFunding: Nanyang Technological University (NTU Singapore) grants (to A.T.P.). Funding for open access charge: Nanyang Technological University

RNA alternative splicing prediction with discrete compositional energy network

A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers. Alternative splicing is determined by the gene's primary sequence and other regulatory factors such as RNA-binding protein levels. With these as input, we formulate the prediction of RNA splicing as a regression task and build a new training dataset (CAPD) to benchmark learned models. We propose discrete compositional energy network (DCEN) which leverages the hierarchical relationships between splice sites, junctions and transcripts to approach this task. In the case of alternative splicing prediction, DCEN models mRNA transcript probabilities through its constituent splice junctions' energy values. These transcript probabilities are subsequently mapped to relative abundance values of key nucleotides and trained with ground-truth experimental measurements. Through our experiments on CAPD1, we show that DCEN outperforms baselines and ablation variants.Nanyang Technological UniversityNational Research Foundation (NRF)Published versionThis work is supported by the Data Science and Artificial Intelligence Research Center (DSAIR), the School of Computer Science and Engineering at Nanyang Technological University and the Singapore National Research Foundation Investigatorship (NRFNRFI2017-09)

Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia

Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75-90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.CC BY 4.0</p

Colloidal suspensions in external rotating electric field: experimental studies and prospective applications in physics, material science, and biomedicine

Colloidal suspensions and tunable self-assembly of colloidal particles attract a great interest in recent years. In this paper, we propose a new setup and technology for studies of self-assembly of colloidal particles, interection of which between themselves is tuned by external rotating electric fields. We reveal wide prospectives of electric field employment for tunable self-assembly, from suspensions of inorganic particles to ensembles of biological cells. These results make enable particle-resolved studies of various collective phenomena and fundamental processes in many-particle systems in equilibrium state and far from it, while the dynamics can be resolved at the level of individual particles using video microscopy. For the first time, we demonstrate that, apart from ability to prepare photonic crystalline films of inorganic silica particles, the tunable self-assembly provides a novel technological way for manipulation with ensembles of biological cells by control of interactions between them

LISA Definition Study Report

International audienceThe Laser Interferometer Space Antenna (LISA) is the first scientific endeavour to detect and study gravitational waves from space. LISA will survey the sky for Gravitational Waves in the 0.1 mHz to 1 Hz frequency band which will enable the study of a vast number of objects ranging from Galactic binaries and stellar mass black holes in the Milky Way, to distant massive black-hole mergers and the expansion of the Universe. This definition study report, or Red Book, presents a summary of the very large body of work that has been undertaken on the LISA mission over the LISA definition phase