Single-cell analysis of the 3D topologies of genomic loci using genome architecture mapping

Although each cell within an organism contains a nearly identical genome sequence, the three-dimensional (3D) packing of the genome varies among individual cells, influencing cell-type-specific gene expression. Genome Architecture Mapping (GAM) is the first genome-wide experimental method for capturing 3D proximities between any number of genomic loci without ligation. GAM overcomes several limitations of 3C-based methods by sequencing DNA from a large collection of thin sections sliced from individual nuclei. The GAM technique measures locus co-segregation, extracts radial positions, infers chromatin compaction, requires small numbers of cells, does not depend on ligation, and provides rich single-cell information. However, previous analyses of GAM data focused exclusively on population averages, neglecting the variation in 3D topology among individual cells. We present the first single-cell analysis of GAM data, demonstrating that the slices from individual cells reveal intercellular heterogeneity in chromosome conformation. By simultaneously clustering both slices and genomic loci, we identify topological variation among single cells, including differential compaction of cell cycle genes. We also develop a geometric model of the nucleus, allowing prediction of the 3D positions of each slice. Using GAM data from mouse embryonic stem cells, we make new discoveries about the structure of the major mammalian histone gene locus, which is incorporated into the Histone Locus Body (HLB), including structural fluctuations and putative causal molecular mechanisms. Our methods are packaged as SluiceBox, a toolkit for mining GAM data. Our approach represents a new method of investigating variation in 3D genome topology among individual cells across space and time

Hubble expansion and structure formation in the "running FLRW model" of the cosmic evolution

A new class of FLRW cosmological models with time-evolving fundamental parameters should emerge naturally from a description of the expansion of the universe based on the first principles of quantum field theory and string theory. Within this general paradigm, one expects that both the gravitational Newton's coupling, G, and the cosmological term, Lambda, should not be strictly constant but appear rather as smooth functions of the Hubble rate. This scenario ("running FLRW model") predicts, in a natural way, the existence of dynamical dark energy without invoking the participation of extraneous scalar fields. In this paper, we perform a detailed study of these models in the light of the latest cosmological data, which serves to illustrate the phenomenological viability of the new dark energy paradigm as a serious alternative to the traditional scalar field approaches. By performing a joint likelihood analysis of the recent SNIa data, the CMB shift parameter, and the BAOs traced by the Sloan Digital Sky Survey, we put tight constraints on the main cosmological parameters. Furthermore, we derive the theoretically predicted dark-matter halo mass function and the corresponding redshift distribution of cluster-size halos for the "running" models studied. Despite the fact that these models closely reproduce the standard LCDM Hubble expansion, their normalization of the perturbation's power-spectrum varies, imposing, in many cases, a significantly different cluster-size halo redshift distribution. This fact indicates that it should be relatively easy to distinguish between the "running" models and the LCDM cosmology using realistic future X-ray and Sunyaev-Zeldovich cluster surveys.Comment: Version published in JCAP 08 (2011) 007: 1+41 pages, 6 Figures, 1 Table. Typos corrected. Extended discussion on the computation of the linearly extrapolated density threshold above which structures collapse in time-varying vacuum models. One appendix, a few references and one figure adde

The Intentional Use of Service Recovery Strategies to Influence Consumer Emotion, Cognition and Behaviour

Service recovery strategies have been identified as a critical factor in the success of. service organizations. This study develops a conceptual frame work to investigate how specific service recovery strategies influence the emotional, cognitive and negative behavioural responses of . consumers., as well as how emotion and cognition influence negative behavior. Understanding the impact of specific service recovery strategies will allow service providers' to more deliberately and intentionally engage in strategies that result in positive organizational outcomes. This study was conducted using a 2 x 2 between-subjects quasi-experimental design. The results suggest that service recovery has a significant impact on emotion, cognition and negative behavior. Similarly, satisfaction, negative emotion and positive emotion all influence negative behavior but distributive justice has no effect

Energy Flow in the Hadronic Final State of Diffractive and Non-Diffractive Deep-Inelastic Scattering at HERA

An investigation of the hadronic final state in diffractive and non--diffractive deep--inelastic electron--proton scattering at HERA is presented, where diffractive data are selected experimentally by demanding a large gap in pseudo --rapidity around the proton remnant direction. The transverse energy flow in the hadronic final state is evaluated using a set of estimators which quantify topological properties. Using available Monte Carlo QCD calculations, it is demonstrated that the final state in diffractive DIS exhibits the features expected if the interaction is interpreted as the scattering of an electron off a current quark with associated effects of perturbative QCD. A model in which deep--inelastic diffraction is taken to be the exchange of a pomeron with partonic structure is found to reproduce the measurements well. Models for deep--inelastic $ep$ scattering, in which a sizeable diffractive contribution is present because of non--perturbative effects in the production of the hadronic final state, reproduce the general tendencies of the data but in all give a worse description.Comment: 22 pages, latex, 6 Figures appended as uuencoded fil

A Search for Selectrons and Squarks at HERA

Data from electron-proton collisions at a center-of-mass energy of 300 GeV are used for a search for selectrons and squarks within the framework of the minimal supersymmetric model. The decays of selectrons and squarks into the lightest supersymmetric particle lead to final states with an electron and hadrons accompanied by large missing energy and transverse momentum. No signal is found and new bounds on the existence of these particles are derived. At 95% confidence level the excluded region extends to 65 GeV for selectron and squark masses, and to 40 GeV for the mass of the lightest supersymmetric particle.Comment: 13 pages, latex, 6 Figure

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve ‘active’ regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain ‘inactive’ regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies

Comparison of CyTOF assays across sites: Results of a six-center pilot study.

For more than five years, high-dimensional mass cytometry has been employed to study immunology. However, these studies have typically been performed in one laboratory on one or few instruments. We present the results of a six-center study using healthy control human peripheral blood mononuclear cells (PBMCs) and commercially available reagents to test the intra-site and inter-site variation of mass cytometers and operators. We used prestained controls generated by the primary center as a reference to compare against samples stained at each individual center. Data were analyzed at the primary center, including investigating the effects of two normalization methods. All six sites performed similarly, with CVs for both Frequency of Parent and median signal intensity (MSI) values<30%. Increased background was seen when using the premixed antibody cocktail aliquots at each site, suggesting that cocktails are best made fresh. Both normalization methods tested performed adequately for normalizing MSI values between centers. Clustering algorithms revealed slight differences between the prestained and the sites-stained samples, due mostly to the increased background of a few antibodies. Therefore, we believe that multicenter mass cytometry assays are feasible

Kiyang-yang, a West-African Postwar Idiom of Distress

In 1984, a healing cult for young barren women in southern Guinea Bissau developed into a movement, Kiyang-yang, that shook society to its foundations and had national repercussions. “Idiom of distress” is used here as a heuristic tool to understand how Kiyang-yang was able to link war and post-war-related traumatic stress and suffering on both individual and group levels. An individual experience born from a traumatic origin may be generalized into an idiom that diverse sectors of society could embrace for a range of related reasons. We argue that, for an idiom to be understood and appropriated by others, there has to be resonance at the level of symbolic language and shared experiences as well as at the level of the culturally mediated contingent emotions it communicates. We also argue that through its symbolic references to structural causes of suffering, an idiom of distress entails a danger for those in power. It can continue to exist only if its etiology is not exposed or the social suffering it articulates is not eliminated. We finally argue that idioms of distress are not to be understood as discrete diagnostic categories or as monodimensional expressions of “trauma” that can be addressed