ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data

ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage of two unique properties of ChIP-chip data: the single-tailed nature of the data, caused by specific enrichment but not specific depletion of genomic fragments; and the predictable enrichment of DNA fragments adjacent to sites of direct protein-DNA interaction. Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction

The Sloan Digital Sky Survey Stripe 82 Imaging Data: Depth-Optimized Co-adds Over 300 Deg^2 in Five Filters

We present and release co-added images of the Sloan Digital Sky Survey (SDSS) Stripe 82. Stripe 82 covers an area of 300 deg^2 on the Celestial Equator, and has been repeatedly scanned 70-90 times in the ugriz bands by the SDSS imaging survey. By making use of all available data in the SDSS archive, our co-added images are optimized for depth. Input single-epoch frames were properly processed and weighted based on seeing, sky transparency, and background noise before co-addition. The resultant products are co-added science images and their associated weight images that record relative weights at individual pixels. The depths of the co-adds, measured as the 5 sigma detection limits of the aperture (3.2 arcsec diameter) magnitudes for point sources, are roughly 23.9, 25.1, 24.6, 24.1, and 22.8 AB magnitudes in the five bands, respectively. They are 1.9-2.2 mag deeper than the best SDSS single-epoch data. The co-added images have good image quality, with an average point-spread function FWHM of ~1 arcsec in the r, i, and z bands. We also release object catalogs that were made with SExtractor. These co-added products have many potential uses for studies of galaxies, quasars, and Galactic structure. We further present and release near-IR J-band images that cover ~90 deg^2 of Stripe 82. These images were obtained using the NEWFIRM camera on the NOAO 4-m Mayall telescope, and have a depth of about 20.0--20.5 Vega magnitudes (also 5 sigma detection limits for point sources).Comment: 19 pages, 17 figures, accepted for publication in ApJ

Baryon structure in a quark-confining non-local NJL model

We study the nucleon and diquarks in a non-local Nambu-Jona-Lasinio model. For certain parameters the model exhibits quark confinement, in the form of a propagator without real poles. After truncation of the two-body channels to the scalar and axial-vector diquarks, a relativistic Faddeev equation for nucleon bound states is solved in the covariant diquark-quark picture. The dependence of the nucleon mass on diquark masses is studied in detail. We find parameters that lead to a simultaneous reasonable description of pions and nucleons. Both the diquarks contribute attractively to the nucleon mass. Axial-vector diquark correlations are seen to be important, especially in the confining phase of the model. We study the possible implications of quark confinement for the description of the diquarks and the nucleon. In particular, we find that it leads to a more compact nucleon.Comment: 21 pages (RevTeX), 18 figures (eps

A chromatin-mediated mechanism for specification of conditional transcription factor targets

Organisms respond to changes in their environment, and many such responses are initiated at the level of gene transcription. Here, we provide evidence for a previously undiscovered mechanism for directing transcriptional regulators to new binding targets in response to an environmental change. We show that repressor-activator protein 1 (Rap1), a master regulator of yeast metabolism, binds to an expanded target set after glucose depletion despite decreasing protein levels and no evidence of posttranslational modification. Computational analysis predicts that proteins capable of recruiting the chromatin regulator Tup1 act to restrict the binding distribution of Rap1 in the presence of glucose. Deletion of the gene(s) encoding Tup1, recruiters of Tup1 or chromatin regulators recruited by Tup1 cause Rap1 to bind specifically and inappropriately to low-glucose targets. These data, combined with whole-genome measurements of nucleosome occupancy and Tup1 distribution, provide evidence for a mechanism of dynamic target specification that coordinates the genome-wide distribution of intermediate-affinity DNA sequence motifs with chromatin-mediated regulation of accessibility to those sites

Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen

<p>Abstract</p> <p>Background</p> <p>Studies of nuclear function in many organisms, especially those with tough cell walls, are limited by lack of availability of simple, economical methods for large-scale preparation of clean, undamaged nuclei.</p> <p>Findings</p> <p>Here we present a useful method for nuclear isolation from the important model organism, the fission yeast, <it>Schizosaccharomyces pombe</it>. To preserve <it>in vivo </it>molecular configurations, we flash-froze the yeast cells in liquid nitrogen. Then we broke their tough cell walls, without damaging their nuclei, by grinding in a precision-controlled motorized mortar-and-pestle apparatus. The cryo-ground cells were resuspended and thawed in a buffer designed to preserve nuclear morphology, and the nuclei were enriched by differential centrifugation. The washed nuclei were free from contaminating nucleases and have proven well-suited as starting material for genome-wide chromatin analysis and for preparation of fragile DNA replication intermediates.</p> <p>Conclusions</p> <p>We have developed a simple, reproducible, economical procedure for large-scale preparation of endogenous-nuclease-free, morphologically intact nuclei from fission yeast. With appropriate modifications, this procedure may well prove useful for isolation of nuclei from other organisms with, or without, tough cell walls.</p

Breaking Synchrony by Heterogeneity in Complex Networks

For networks of pulse-coupled oscillators with complex connectivity, we demonstrate that in the presence of coupling heterogeneity precisely timed periodic firing patterns replace the state of global synchrony that exists in homogenous networks only. With increasing disorder, these patterns persist until they reach a critical temporal extent that is of the order of the interaction delay. For stronger disorder these patterns cease to exist and only asynchronous, aperiodic states are observed. We derive self-consistency equations to predict the precise temporal structure of a pattern from the network heterogeneity. Moreover, we show how to design heterogenous coupling architectures to create an arbitrary prescribed pattern.Comment: 4 pages, 3 figure

Role of melt supply in oceanic detachment faulting and formation of megamullions

Author Posting. © Geological Society of America, 2008. This article is posted here by permission of Geological Society of America for personal use, not for redistribution. The definitive version was published in Geology 36 (2008): 455-458, doi:10.1130/G24639A.1.Normal faults are ubiquitous on mid-ocean ridges and are expected to develop increasing offset with reduced spreading rate as the proportion of tectonic extension increases. Numerous long-lived detachment faults that form megamullions with large-scale corrugations have been identified on magma-poor mid-ocean ridges, but recent studies suggest, counterintuitively, that they may be associated with elevated magmatism. We present numerical models and geological data to show that these detachments occur when ~30%–50% of total extension is accommodated by magmatic accretion and that there is significant magmatic accretion in the fault footwalls. Under these low-melt conditions, magmatism may focus unevenly along the spreading axis to create an irregular brittle-plastic transition where detachments root, thus explaining the origin of the enigmatic corrugations. Morphological and compositional characteristics of the oceanic lithosphere suggested by this study provide important new constraints to assess the distribution of magmatic versus tectonic extension along mid-ocean ridges.This research was supported by the National Science Foundation and by the Henry Bryant Bigelow Chair in Oceanography to Tucholke at Woods Hole Oceanographic Institution

Query Health: standards-based, cross-platform population health surveillance

Objective: Understanding population-level health trends is essential to effectively monitor and improve public health. The Office of the National Coordinator for Health Information Technology (ONC) Query Health initiative is a collaboration to develop a national architecture for distributed, population-level health queries across diverse clinical systems with disparate data models. Here we review Query Health activities, including a standards-based methodology, an open-source reference implementation, and three pilot projects. Materials and methods Query Health defined a standards-based approach for distributed population health queries, using an ontology based on the Quality Data Model and Consolidated Clinical Document Architecture, Health Quality Measures Format (HQMF) as the query language, the Query Envelope as the secure transport layer, and the Quality Reporting Document Architecture as the result language. Results: We implemented this approach using Informatics for Integrating Biology and the Bedside (i2b2) and hQuery for data analytics and PopMedNet for access control, secure query distribution, and response. We deployed the reference implementation at three pilot sites: two public health departments (New York City and Massachusetts) and one pilot designed to support Food and Drug Administration post-market safety surveillance activities. The pilots were successful, although improved cross-platform data normalization is needed. Discussions This initiative resulted in a standards-based methodology for population health queries, a reference implementation, and revision of the HQMF standard. It also informed future directions regarding interoperability and data access for ONC's Data Access Framework initiative. Conclusions: Query Health was a test of the learning health system that supplied a functional methodology and reference implementation for distributed population health queries that has been validated at three sites

The Pennsylvania Environmental Resource Consortium: A State-Wide Collaborative Network for Sustainable, Outreach, Education, and Action

This paper explores the organizational theory, programs, and concomitant challenges faced by a state-level higher education consortium for sustainability in the United States, the Pennsylvania Environmental Resource Consortium (PERC). We provide insights for other institutions of higher education that may want to form consortia or consider changes to existing consortia. PERC members collaborate to advance sustainability on member campuses, in local communities, and across the Commonwealth. PERC envisions thriving, just communities on a healthy planet, and seeks to inspire higher education communities throughout the Commonwealth to lead transformational sustainability efforts through example, expertise, and collaboration. This chapter provides a brief theoretical background in PERC as a collaborative. It shares history and context for PERC’s mission and activities as well as an overview of its programs. It includes reflections on challenges to collaboration and coordination, including from COVID-19, changing digital technology, disparities among PERC institutions, accelerating sustainability challenges in the Anthropocene, anti-intellectualism and hyperpartisanship in the Commonwealth and the United States, and PERC’s own staffing, volunteerism, participation, and funding challenges. The chapter closes by revisiting the organization’s 2021–2025 Strategic Plan as an invitation to consider how cooperation, coordination, and collaboration among higher education institutions can positively impact sustainability across sectors