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Abstract Polycomb repressive complex 2 (PRC2) is a chromatin-modifying enzyme that catalyses the methylation of histone H3 at lysine 27 (H3K27me1/2/3). This complex maintains gene transcriptional repression and plays an essential role in the maintenance of cellular identity as well as normal organismal development. The activity of PRC2, including its genomic targeting and catalytic activity, is controlled by various signals. Recent studies have revealed that these signals involve cis chromatin features, PRC2 facultative subunits and post-translational modifications (PTMs) of PRC2 subunits. Overall, these findings have provided insight into the biochemical signals directing PRC2 function, although many mysteries remain.

Camels bear unique genotypes and phenotypes for adaptation in their environment, and as such could be very useful in the weather extremes accelerated by global climate change. Published sequences of Camelidae genomes provide an opportunity to elucidate the genomic architecture of these animals. CpG islands (CGIs) sequence patterns in complex genomes play important roles in gene regulation via epigenetic change. Comparative large-scale genome analysis of CGIs in Camelidae was carried out using five different CGI detection algorithms, evaluating numbers of CGIs, CGI density and CGI length distribution in Camelidae. All algorithms identified the alpaca genome as having the largest number of CGIs, CGI density and average length of CGIs, though, the CGI length distribution and their number could be implicitly attributed to the characteristics of an algorithm for CGI identification rather than that of the species. In addition, high algorithm-to-algorithm variability of the observed CGI properties was shown. It was well expected, since there is no clear definition of a CGI and different algorithms could identify different genome regions as CGIs. Comparison with other mammalian genomes (human, mouse, dog, horse and cow) shows that CGIs features in cow were most similar to camelid genomes. Further analysis of camelid genomes may shed more light on molecular origins and mechanisms of adaptation in these extreme heat-adapted animals. [ABSTRACT FROM AUTHOR]

Drawing on Stephen Prince's concept of "perceptual realism"' to examine the use of computer-generated images in two megahit Korean blockbuster films of 2014, The Admiral: Roaring Currents and Ode to My Father, this article underlines these films' impression of reality as the nexus of the complex intersections between Korea's national history and identity, and the industrial and aesthetic transnationality of Korean popular cinema. [ABSTRACT FROM AUTHOR]

Imprinted genes are characterized by monoallelic expression that is dependent on parental origin. Comparative analysis of imprinted genes between species is a powerful tool for understanding the biological significance of genomic imprinting. The slc38a4 gene encodes a neutral amino acid transporter and is identified as imprinted in mice. In this study, the imprinting status of SLC38A4 was assessed in bovine adult tissues and placenta using a polymorphism-based approach. Results indicate that SLC38A4 is not imprinted in eight adult bovine tissues including heart, liver, spleen, lung, kidney, muscle, fat, and brain. It was interesting to note that SLC38A4 showed polymorphic status in five heterogeneous placentas, with three exhibiting paternal monoallelic expression and two exhibiting biallelic expression. Monoallelic expression of imprinted genes is generally associated with allele-specific differentially methylation regions (DMRs) of CpG islands (CGIs)-encompassed promoter; therefore, the DNA methylation statuses of three CGIs in the SLC38A4 promoter and exon 1 region were tested in three placentas (two exhibiting paternal monoallelic and one showing biallelic expression of SLC38A4) and their corresponding paternal sperms. Unexpectedly, extreme hypomethylation (< 3%) of the DNA was observed in all the three detected placentas and their corresponding paternal sperms. The absence of DMR in bovine SLC38A4 promoter region implied that DNA methylation of these three CGIs does not directly or indirectly affect the polymorphic imprinting of SLC38A4 in bovine placenta. This suggested other epigenetic features other than DNA methylation are needed in regulating the imprinting of bovine SLC38A4, which is different from that of mouse with respect to a DMR existence at the mouse’s slc38a4 promoter region. Although further work is needed, this first characterization of polymorphic imprinting status of SLC38A4 in cattle placenta provides valuable information on investigating the genomic imprinting phenomenon itself. [ABSTRACT FROM AUTHOR]

The rules of k-mer non-random usage and the biological functions are worthy of special attention. Firstly, the article studied human 8-mer spectra and found that only the spectra of cytosine-guanine (CG) dinucleotide classification formed independent unimodal distributions when the 8-mers were classified into three subsets under 16 dinucleotide classifications. Secondly, the distribution rules were reproduced by other seven species including yeast, which showed that the evolution phenomenon had species universality. It followed that we proposed two theoretical conjectures: (1) CG motifs (8-mers including 1 CG) are the nucleosome-binding motifs. (2) CG motifs (8-mers including two or more than two CG) are the modular units of CpG islands. Our conjectures were confirmed in yeast by the following results: a maximum of average area under the receiver operating characteristic (AUC) resulted from CG information during nucleosome core sequences, and linker sequences were distinguished by three CG subsets; there was a one-to-one relationship between abundant CG signal regions and histone positions; the sequence changing of squeezed nucleosomes was relevant with the strength of CG signals; and the AUC value of 0.986 was based on CG information when CpG islands and non-CpG islands were distinguished by the three CG subsets. [ABSTRACT FROM AUTHOR]

In this paper, copper–gallium–indium–sulfide (CGIS) nanocrystals with different Ga/In ratios, i.e., CuGa x In 5 –x S 8 , where x = 0–5, were synthesized and investigated for visible-light-driven hydrogen (H 2 ) evolution from aqueous solutions that contain sulfide/sulfite ions. The synthesized CGIS nanocrystals were characterized by diffuse reflectance spectroscopy (DRS), X-ray diffraction (XRD), transmission electron microscopy (TEM), and photoluminescence spectroscopy (PL). With 1.0 wt.% Ru as a co-catalyst, the H 2 evolution rate on CuGa 2 In 3 S 8 (CGIS hereafter) showed the highest activity. The CGIS nanocrystals were deposited onto a TiO 2 surface via a unique solvent-induced deposition method. The CGIS/TiO 2 photocatalyst showed comparable activity to that obtained using bare CGIS nanocrystals when the photocatalyst amount was sufficient in the photoreactor system, suggesting that TiO 2 remains intact in terms of photocatalytic activity. The quantity of CGIS nanocrystals, however, required to achieve the rate-plateau condition at saturation was much lower in the presence of TiO 2 . The enhanced activities at low CGIS loadings observed in the presence of TiO 2 were explained by the improved dispersion of the powder suspension and optical path in the photoreactor. This TiO 2 supported photocatalyst lowers the required amount of CGIS, which is beneficial from an economic point of view. [ABSTRACT FROM AUTHOR]

Background: Studies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies between different functional and structural components of genes and genomes. Using whole-genome bisulfite sequencing data we here describe both CpG and non-CpG methylation profiles of whole blood and brain tissue in relation to gene features, CpG-islands (CGIs), transposable elements (TE), and their functional roles in an ecological model species, the great tit (Parus major). Results: We show that hypomethylation at the transcription start site (TSS) is enriched in genes with functional classes that relate directly to processes specific to each tissue type. We find that 6877 (~21 %) of the CGIs are differentially methylated between blood and brain, of which 1186 and 2055 are annotated to promoter and intragenic regions, respectively. We observe that CGI methylation in promoter regions is more conserved between tissues compared to CGI methylation in intra and inter-genic regions. Differentially methylated CGIs in promoter and intragenic regions are overrepresented in genomic loci linked to development, suggesting a distinct role for CGI methylation in regulating expression during development. Additionally, we find significant non-CpG methylation in brain but not in blood with a strong preference for methylation at CpA dinucleotide sites. Finally, CpG hypermethylation of TEs is significantly stronger in brain compared to blood, but does not correlate with TE activity. Surprisingly, TEs showed significant hypomethylation in non-CpG contexts which was negatively correlated with TE expression. Conclusion: The discovery that TSS methylation levels are directly linked to functional classes related to each tissue provides new insights in the regulatory role of DNA-methylation patterns. The dominant sequence motifs for brain non-CpG methylation, similar to those found in mammals, suggests that a conserved non-CpG regulatory mechanism was already present in the amniote ancestor. The negative correlation between brain non-CpG methylation and TE activity (not found for CpG methylation) suggests that non-CpG is the dominant regulatory form of methylation in TE silencing. [ABSTRACT FROM AUTHOR]

CpG Islands (CGIs) are compositionally defined short genomic stretches, which have been studied in the human, mouse, chicken and later in several other genomes. Initially, they were assigned the role of transcriptional regulation of protein-coding genes, especially the house-keeping ones, while more recently there is found evidence that they are involved in several other functions as well, which might include regulation of the expression of RNA genes, DNA replication etc. Here, an investigation of their distributional characteristics in a variety of genomes is undertaken for both whole CGI populations as well as for CGI subsets that lie away from known genes (gene-unrelated or “orphan” CGIs). In both cases power-law-like linearity in double logarithmic scale is found. An evolutionary model, initially put forward for the explanation of a similar pattern found in gene populations is implemented. It includes segmental duplication events and eliminations of most of the duplicated CGIs, while a moderate rate of non-duplicated CGI eliminations is also applied in some cases. Simulations reproduce all the main features of the observed inter-CGI chromosomal size distributions. Our results on power-law-like linearity found in orphan CGI populations suggest that the observed distributional pattern is independent of the analogous pattern that protein coding segments were reported to follow. The power-law-like patterns in the genomic distributions of CGIs described herein are found to be compatible with several other features of the composition, abundance or functional role of CGIs reported in the current literature across several genomes, on the basis of the proposed evolutionary model. [ABSTRACT FROM AUTHOR]

Objectives We studied the effect of quetiapine in drug-induced psychosis (DIP) in Parkinson's disease (PD) patients with dementia (PDDEM) and without dementia (PDNODEM) in a 6-month open study. Methods Thirty-five consecutive PD patients with DIP (19 of them demented [DSMIV criteria]) were examined. Assessment included Mini-Mental State Examination (MMSE), UPDRS (motor part), Brief Psychiatric Rating Scale (BPRS), Clinical Global Improvement Scale (CGIS) and Hamilton test (for depression). Quetiapine was administered in a flexible dose 25–600 mg daily. Out of the 35 patients included in the study, 24 completed treatment with quetiapine (14 demented and 10 without dementia). Treatment was stopped in 11 patients (5 demented). Results Intention to treat patient (ITT) analysis did not show a significant quetiapine effect (BPRS), although in about 30% a good outcome was reported by the family (CGIS).Among the patients who completed the study (n=24), in the PDNODEM group (n=10) BPRS improved almost significantly (p=0.06) while in the PDDEM group the BPRS did not change. According to the CGIS, a good improvement was observed in 50% of the PDDEM group (7/14) and 40% of the PDNODEM group (4/10).Motor features of PD patients worsened mildly (p=0.05) in the PDDEM group. Conclusions In this open trial, quetiapine was not beneficial in the ITT group using the BPRS, although families reported improvement in about 30% of patients (CGIS).Among patients who completed the study, quetiapine was more effective in the PDNODEM group. A double blind study with quetiapine is required. [ABSTRACT FROM AUTHOR]