Multiplexed Illumina sequencing libraries from picogram quantities of DNA

Background: High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. Results: We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Conclusions: Application of this method allows whole genome studies from samples where material or yields are limiting

What Next-Generation 21 cm Power Spectrum Measurements Can Teach Us About the Epoch of Reionization

A number of experiments are currently working towards a measurement of the 21 cm signal from the Epoch of Reionization. Whether or not these experiments deliver a detection of cosmological emission, their limited sensitivity will prevent them from providing detailed information about the astrophysics of reionization. In this work, we consider what types of measurements will be enabled by a next-generation of larger 21 cm EoR telescopes. To calculate the type of constraints that will be possible with such arrays, we use simple models for the instrument, foreground emission, and the reionization history. We focus primarily on an instrument modeled after the $\sim 0.1~\rm{km}^2$ collecting area Hydrogen Epoch of Reionization Array (HERA) concept design, and parameterize the uncertainties with regard to foreground emission by considering different limits to the recently described "wedge" footprint in k-space. Uncertainties in the reionization history are accounted for using a series of simulations which vary the ionizing efficiency and minimum virial temperature of the galaxies responsible for reionization, as well as the mean free path of ionizing photons through the IGM. Given various combinations of models, we consider the significance of the possible power spectrum detections, the ability to trace the power spectrum evolution versus redshift, the detectability of salient power spectrum features, and the achievable level of quantitative constraints on astrophysical parameters. Ultimately, we find that $0.1~\rm{km}^2$ of collecting area is enough to ensure a very high significance ($\gtrsim30\sigma$) detection of the reionization power spectrum in even the most pessimistic scenarios. This sensitivity should allow for meaningful constraints on the reionization history and astrophysical parameters, especially if foreground subtraction techniques can be improved and successfully implemented.Comment: 27 pages, 18 figures, updated SKA numbers in appendi

High-resolution Xist binding maps reveal 2-step spreading during X-inactivation

The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes1-3. During XCI, Xist coats the future inactive X (Xi)4 and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic)5. How Xist spreads silencing on a 150 Mb scale is unclear. Here we generate high-resolution maps of Xist binding on the X chromosome across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism, initially targeting gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but may concentrate near escapee boundaries. Xist binding is linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped off Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time-scale of hours instead of days, suggesting a previously primed Xi chromatin state. We conclude that Xist spreading takes distinct stage-specific forms: During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and -poor regions

Saccadic Eye Movement Characteristics in Adult Niemann-Pick Type C Disease: Relationships with Disease Severity and Brain Structural Measures

Niemann-Pick Type C disease (NPC) is a rare genetic disorder of lipid metabolism. A parameter related to horizontal saccadic peak velocity was one of the primary outcome measures in the clinical trial assessing miglustat as a treatment for NPC. Neuropathology is widespread in NPC, however, and could be expected to affect other saccadic parameters. We compared horizontal saccadic velocity, latency, gain, antisaccade error percentage and self-paced saccade generation in 9 adult NPC patients to data from 10 age-matched controls. These saccadic measures were correlated with appropriate MRI-derived brain structural measures (e.g., dorsolateral prefrontal cortex, frontal eye fields, supplemental eye fields, parietal eye fields, pons, midbrain and cerebellar vermis) and with measures of disease severity and duration. The best discriminators between groups were reflexive saccade gain and the two volitional saccade measures. Gain was also the strongest correlate with disease severity and duration. Most of the saccadic measures showed strongly significant correlations with neurophysiologically appropriate brain regions. While our patient sample is small, the apparent specificity of these relationships suggests that as new diagnostic methods and treatments become available for NPC, a broader range of saccadic measures may be useful tools for the assessment of disease progression and treatment efficacy.No external funding was received for this study. JCLL self-funded computational, travel and accommodation costs to conduct his component of this research in Melbourne

Relativity, rank and the utility of income

This is the accepted version of the following article: Rablen, M. D. (2008), Relativity, Rank and the Utility of Income. The Economic Journal, 118: 801–821, which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/j.1468-0297.2008.02143.x/abstract.Relative utility has become an important concept in several disjoint areas of economics. I present a cardinal model of income utility based on the supposition that agents care about their rank in the income distribution and that utility is subject to adaptation over time. Utility levels correspond to the Leyden Individual Welfare Function while utility differences yield a version of the prospect theory value function, thereby providing a new and shared derivation of each. I offer an explanation of some long-standing paradoxes in the wellbeing literature and an insight into the links between relative comparisons and loss aversion.ESR

Representations of the family in postwar British amateur film: family histories in the Lane and Scrutton collection at the East Anglian Film Archive

This article examines the construction of the postwar British family in amateur film with reference to the Sidney Lane and Cecil Scrutton collection held at the East Anglian Film Archive (EAFA), particularly the films covering 1948 – 1961. Heather Norris Nicholson argues that home movies contribute to 'an understanding of leisure and visual-related practices of consumption as well as the social processes by which people came to give themselves, and others, identities' in the mid-twentieth century (Nicholson, 2004, p. 323). By considering the social and historical contexts in which these home movies were produced, and using accompanying notes by one of the filmmaker’s sons, the leisure time films of Lane and Scrutton can be analysed in order to understand how the amateur cine hobby ideologically constructed family, community and national identity in postwar Britain. The images of Christmas parties, daytrips and holidays in these films reveal much about this particular family, and are therefore very illuminating to the social historian and film scholar of today

Argyres-Douglas theories, the Macdonald index, and an RG inequality

We conjecture closed-form expressions for the Macdonald limits of the super-conformal indices of the (A1, A2n − 3) and (A1, D2n) Argyres-Douglas (AD) theories in terms of certain simple deformations of Macdonald polynomials. As checks of our conjectures, we demonstrate compatibility with two S-dualities, we show symmetry enhancement for special values of n, and we argue that our expressions encode a non-trivial set of renormalization group flows. Moreover, we demonstrate that, for certain values of n, our conjectures imply simple operator relations involving composites built out of the SU(2)R currents and flavor symmetry moment maps, and we find a consistent picture in which these relations give rise to certain null states in the corresponding chiral algebras. In addition, we show that the Hall-Littlewood limits of our indices are equivalent to the corresponding Higgs branch Hilbert series. We explain this fact by considering the S1 reductions of our theories and showing that the equivalence follows from an inequality on monopole quantum numbers whose coefficients are fixed by data of the four-dimensional parent theories. Finally, we comment on the implications of our work for more general (Formula presented.) superconformal field theories

Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin