The DanTIN project – creating a platform for describing the grammar of Danish talk-in-interaction

The article introduces a new website, samtalegrammatik.dk ('grammar of talk-in-interaction'), it describes the methods used for constructing the website, and it provides descriptions of three new grammatical phenomena in Danish talk-in-interaction. The website is a result of investigations carried out by the research group DanTIN ('Danish talk-in-interaction') since 2009. Until 2013, the group has published analyses of quite diverse phenomena, such as different versions of the word hvad 'what' that seem to belong to different word classes and have different functions in talk-ininteraction, the distribution of the hesitation marker øh(m) 'uh(m)', or different word orders after the conjunction fordi ('because'). These phenomena were selected because they were clearly different from written Danish. By launching the website samtalegrammatik.dk the group takes a step towards building a comprehensive grammar of Danish talk-in-interaction. It offers a template for a description of all aspects of the grammar of Danish talk-in-interaction, even though at the time of the launching only a little part of the entries will be filled in. The idea is that the investigations will be continued in many years to come, and, thus, the website will grow and become more complete. The three phenomena reported in some detail here all have intonation as an important part of their grammatical descriptions. They are (1) the particle nå (roughly 'oh'), (2) exaggerated pitch as a story ending device, and (3) the interjection ej, which is an intranslatable exclamation word. FGW – Publications without University Leiden contrac

Dynamic protein methylation in chromatin biology

Post-translational modification of chromatin is emerging as an increasingly important regulator of chromosomal processes. In particular, histone lysine and arginine methylation play important roles in regulating transcription, maintaining genomic integrity, and contributing to epigenetic memory. Recently, the use of new approaches to analyse histone methylation, the generation of genetic model systems, and the ability to interrogate genome wide histone modification profiles has aided in defining how histone methylation contributes to these processes. Here we focus on the recent advances in our understanding of the histone methylation system and examine how dynamic histone methylation contributes to normal cellular function in mammals

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts. Chiu et al. present a pan-cancer analysis of lncRNA regulatory interactions. They suggest that the dysregulation of hundreds of lncRNAs target and alter the expression of cancer genes and pathways in each tumor context. This implies that hundreds of lncRNAs can alter tumor phenotypes in each tumor context

Long-finned pilot whale population diversity and structure in Atlantic waters assessed through biogeochemical and genetic markers

Integration of ecological and genetic approaches is a particularly powerful strategy to identify natural population diversity and structure over different timescales. To investigate the potential occurrence of population differentiation in long-finned pilot whales Globicephala melas in the North Atlantic, both biogeochemical (fatty acids and stable isotopes) and genetic (mitochondrial DNA) markers were analyzed in animals from 4 regions within the North Atlantic: the northwestern Iberian Peninsula, the United Kingdom, the Faroe Islands and the United States of America. Genetic data revealed strong regional levels of divergence, although analysis of molecular variance revealed no differentiation between the northeastern and northwestern Atlantic. Results from biogeochemical tracers supported previous dietary studies, revealing geographic and ontogenetic dietary variation in pilot whales. Fatty acids revealed ecological differentiation between all regions analyzed, while stable isotopes showed an overlap between some sampling regions. These results suggest that both ecological and genetic factors may drive the levels of pilot whale differentiation in the North Atlantic. The ecological differentiation observed may be related to the exploitation of different foraging niches (e.g. oceanic vs. coastal), which can be highly influenced by prey distributions or oceanographic phenomena. Genetic differentiation may result from historical or contemporary processes or even limited dispersal mediated through the social structure displayed by this species and potential foraging specialization. These results highlight some problems when assessing population structure across multiple markers and the ecological vs. evolutionary timescales over which differences may accumulate. Notwithstanding, the data provide preliminary information about pilot whale diversity and stocks in the North Atlantic, giving essential baseline information for conservation plans