Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

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Online and Local Television Networks: A new pedagogy for a changing media.

To investigate campus-based and local TV focused on innovative opportunities for students, employers and community groups to contribute to the design of learning pedagogies and course structures. To utilize the strong element of collaboration within and across creative courses in the UPC Partnership encouraging students to explore the medium of TV and establish new learning cultures that broaden the context of the student experience, encouraging creative work-based/related collaboration with local communities and employers. Research outcomes will enhance understanding of a fluid and dynamic growth area for a new media, new educational and employment possibilities and arts practice, which in turn will inform new curriculum structures, pedagogic models of practice and contribute to an understanding of how local TV can achieve relevance to a community and economic viability. To develop into a shared online TV channel, managed and developed by students and the wider community (PUTALS, 2012: Key Theme 10) which will contribute to the development of a model for students and staff engaged in local TV initiatives. To enhance employability skills for students. The fluid and dynamic growth area of new media, new educational and employment possibilities and arts practice inform new curriculum structures, pedagogic models of practice and contribute to an understanding of how local TV can achieve relevance to a community and achieve economic viability. Hence the traditional models of teaching and learning are challenged by the movements in media distributions, technologies and their application and use. This is particularly true in models that do not rely on a central broadcaster strongly mediating content and creating schedules. One of the key aims, to develop a shared online TV channel managed and developed by students and the wider community, was based on research into similar initiatives in Europe and the USA. The aim was however, not to simply replicate these structure, but to research how new media opportunities may affect content, practice and eventually pedagogy.TFA

Spectroscopic analysis of diversity of arabinoxylan structures in endosperm cell walls of wheat cultivars (Triticum aestivum) in the HEALTHGRAIN diversity collection

Fifty bread wheat (Triticum aestivum L.) cultivars were selected from the HEALTHGRAIN germplasm collection based on variation in their contents of total and water-extractable arabinoxylan. FT-IR spectroscopic mapping of thin transverse sections of grain showed variation in cell wall arabinoxylan composition between the cultivars, from consisting almost entirely of low-substituted arabinoxylan (e.g., T.aestivum Claire) to almost entirely of highly substituted arabinoxylan (e.g., T.aestivum Manital) and a mixture of the two forms (e.g., T.aestivum Hereward). Complementary data were obtained using endoxylanase digestion of flour followed by HP-AEC analysis of the arabinoxylan oligosaccharides. This allowed the selection of six cultivars for more detailed analysis using FT-IR and 1H NMR spectroscopy to determine the proportions of mono-, di-, and unsubstituted xylose residues. The results of the two analyses were consistent, showing that variation in the composition and structure of the endosperm cell wall arabinoxylan is present between bread wheat cultivars. The heterogeneity and spatial distribution of the arabinoxylan in endosperm cell walls may be exploited in wheat processing as it may allow the production of mill streams enriched in various arabinoxylan fractions which have beneficial effects on health

The ALPK1/TIFA/NF-κB axis links a bacterial carcinogen to R-loop-induced replication stress

Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double strand breaks. Here, we show that H. pylori-induced DNA damage occurs co-transcriptionally in S-phase cells that activate NF-κB signaling upon innate immune recognition of the lipopolysaccharide biosynthetic intermediate β-ADP-heptose by the ALPK1/TIFA signaling pathway. DNA damage depends on the bi-functional RfaE enzyme and the Cag pathogenicity island of H. pylori, is accompanied by replication fork stalling and can be observed also in primary cells derived from gastric organoids. Importantly, H. pylori-induced replication stress and DNA damage depend on the presence of co-transcriptional RNA/DNA hybrids (R-loops) that form in infected cells during S-phase as a consequence of β-ADP-heptose/ ALPK1/TIFA/NF-κB signaling. H. pylori resides in close proximity to S-phase cells in the gastric mucosa of gastritis patients. Taken together, our results link bacterial infection and NF-κB-driven innate immune responses to R-loop-dependent replication stress and DNA damage

Social partnership agreements in Britain: labor cooperation and compliance

This article reviews evidence on the outcomes of British social partnership agreements using matched comparisons. It concludes that in industries marked by employment decline, partnership firms often have shed jobs at a faster rate than nonpartnership firms. However, in expanding sectors, partnership firms have created jobs at a faster rate than nonpartnership rivals. There is no discernible impact of partnership on either wage settlements or union density. It is argued that we need evidence on information sharing, trust, and power and suggested that partnership agreements are unlikely to contribute significantly to union revitalization

Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers.

Understanding viral tropism is an essential step towards reducing SARS-CoV-2 transmission, decreasing mortality from COVID-19, and limiting opportunities for mutant strains to arise. Currently, little is known about the extent to which distinct tissue sites in the human head & neck region and proximal respiratory tract selectively permit SARS-CoV-2 infection and replication. In this translational study, we discover key variabilities in the expression of ACE2 and TMPRSS2, essential SARS-CoV-2 entry factors, among the mucosal tissues of the human proximal airways. We show that SARS-CoV-2 infection is present in all examined head & neck tissues, with a notable tropism for the nasal cavity and tracheal mucosa. Finally, we uncover an association between smoking and higher SARS-CoV-2 viral infection in the human proximal airway, which may explain the increased susceptibility of smokers to developing severe COVID-19. This is at least partially explained by differences in IFN-β1 levels between smokers and non-smokers