Nonsynchronous, episodic incision: Evidence of threshold exceedance and complex response as controls of terrace formation

Terrace sequences can represent regional or continental scale factors such as climatic fluctuations, neotectonic activity, and base-level change. However, they can also reflect random incision events brought about by local scale, geomorphic threshold exceedance, and subsequent complex response. This study explores the formative processes of three discontinuous, but adjacent, late Pleistocene to late Holocene stepterrace sequences in southeastern Australia. Correlation of river terrace fills was undertaken by comparing terrace remnants based on topography, morphology, sedimentology, stratigraphy, and chronology. A geomorphic model of floodplain abandonment and terrace formation for this valley setting is presented. Most of southeastern Australia has shown no evidence of tectonic uplift during the late Quaternary. Bedrock bars on the Hunter River isolate the study reach from downstream base-level changes. The nonsynchronous, episodic behavior of incision events in this catchment strongly indicates that climate is not a dominant control on terrace formation. With the exclusion of climatic fluctuations, tectonic uplift and base-level change as causes of incision, catastrophic floods, and the exceedance of geomorphic thresholds emerge as the dominant controls of terrace formation. Crow

Targeted DamID reveals differential binding of mammalian pluripotency factors.

The precise control of gene expression by transcription factor networks is crucial to organismal development. The predominant approach for mapping transcription factor-chromatin interactions has been chromatin immunoprecipitation (ChIP). However, ChIP requires a large number of homogeneous cells and antisera with high specificity. A second approach, DamID, has the drawback that high levels of Dam methylase are toxic. Here, we modify our targeted DamID approach (TaDa) to enable cell type-specific expression in mammalian systems, generating an inducible system (mammalian TaDa or MaTaDa) to identify genome-wide protein/DNA interactions in 100 to 1000 times fewer cells than ChIP-based approaches. We mapped the binding sites of two key pluripotency factors, OCT4 and PRDM14, in mouse embryonic stem cells, epiblast-like cells and primordial germ cell-like cells (PGCLCs). PGCLCs are an important system for elucidating primordial germ cell development in mice. We monitored PRDM14 binding during the specification of PGCLCs, identifying direct targets of PRDM14 that are key to understanding its crucial role in PGCLC development. We show that MaTaDa is a sensitive and accurate method for assessing cell type-specific transcription factor binding in limited numbers of cells

Exact and Truncated Dynamics in Nonequilibrium Field Theory

Nonperturbative dynamics of quantum fields out of equilibrium is often described by the time evolution of a hierarchy of correlation functions, using approximation methods such as Hartree, large N, and nPI-effective action techniques. These truncation schemes can be implemented equally well in a classical statistical system, where results can be tested by comparison with the complete nonlinear evolution obtained by numerical methods. For a 1+1 dimensional scalar field we find that the early-time behaviour is reproduced qualitatively by the Hartree dynamics. The inclusion of direct scattering improves this to the quantitative level. We show that the emergence of nonthermal temperature profiles at intermediate times can be understood in terms of the fixed points of the evolution equations in the Hartree approximation. The form of the profile depends explicitly on the initial ensemble. While the truncated evolution equations do not seem to be able to get away from the fixed point, the full nonlinear evolution shows thermalization with a (surprisingly) slow relaxation.Comment: 30 pages with 12 eps figures, minor changes; to appear in Phys.Rev.

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu\ua0(SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization

Formation of topological defects in gauge field theories

When a symmetry gets spontaneously broken in a phase transition, topological defects are typically formed. The theoretical picture of how this happens in a breakdown of a global symmetry, the Kibble-Zurek mechanism, is well established and has been tested in various condensed matter experiments. However, from the viewpoint of particle physics and cosmology, gauge field theories are more relevant than global theories. In recent years, there have been significant advances in the theory of defect formation in gauge field theories, which make precise predictions possible, and in experimental techniques that can be used to test these predictions in superconductor experiments. This opens up the possibility of carrying out relatively simple and controlled experiments, in which the non-equilibrium phase transition dynamics of gauge field theories can be studied. This will have a significant impact on our understanding of phase transitions in the early universe and in heavy ion collider experiments. In this paper, I review the current status of the theory and the experiments in which it can be tested.Comment: Review article, 43 pages, 7 figures. Minor changes, some references added. Final version to appear in IJMP

The molecular and cellular basis of rhodopsin retinitis pigmentosa reveals potential strategies for therapy

Inherited mutations in the rod visual pigment, rhodopsin, cause the degenerative blinding condition, retinitis pigmentosa (RP). Over 150 different mutations in rhodopsin have been identified and, collectively, they are the most common cause of autosomal dominant RP (adRP). Mutations in rhodopsin are also associated with dominant congenital stationary night blindness (adCSNB) and, less frequently, recessive RP (arRP). Recessive RP is usually associated with loss of rhodopsin function, whereas the dominant conditions are a consequence of gain of function and/or dominant negative activity. The in-depth characterisation of many rhodopsin mutations has revealed that there are distinct consequences on the protein structure and function associated with different mutations. Here we categorise rhodopsin mutations into seven discrete classes; with defects ranging from misfolding and disruption of proteostasis, through mislocalisation and disrupted intracellular traffic to instability and altered function. Rhodopsin adRP offers a unique paradigm to understand how disturbances in photoreceptor homeostasis can lead to neuronal cell death. Furthermore, a wide range of therapies have been tested in rhodopsin RP, from gene therapy and gene editing to pharmacological interventions. The understanding of the disease mechanisms associated with rhodopsin RP and the development of targeted therapies offer the potential of treatment for this currently untreatable neurodegeneration

Unquenched large orbital magnetic moment in NiO

Magnetic properties of NiO are investigated by incorporating the spin-orbit interaction in the LSDA+U scheme. It is found that the large part of orbital moment remains unquenched in NiO. The orbital moment contributes about mu_L = 0.29 mu_B to the total magnetic moment of M = 1.93 mu_B, as leads to the orbital-to-spin angular momentum ratio of L/S = 0.36. The theoretical values are in good agreement with recent magnetic X-ray scattering measurements.Comment: 4 pages, 2 figure

Nonequilibrium Quantum Dynamics of Second Order Phase Transitions

We use the so-called Liouville-von Neumann (LvN) approach to study the nonequilibrium quantum dynamics of time-dependent second order phase transitions. The LvN approach is a canonical method that unifies the functional Schr\"{o}dinger equation for the quantum evolution of pure states and the LvN equation for the quantum description of mixed states of either equilibrium or nonequilibrium. As nonequilibrium quantum mechanical systems we study a time-dependent harmonic and an anharmonic oscillator and find the exact Fock space and density operator for the harmonic oscillator and the nonperturbative Gaussian Fock space and density operator for the anharmonic oscillator. The density matrix and the coherent, thermal and coherent-thermal states are found in terms of their classical solutions, for which the effective Hamiltonians and equations of motion are derived. The LvN approach is further extended to quantum fields undergoing time-dependent second order phase transitions. We study an exactly solvable model with a finite smooth quench and find the two-point correlation functions. Due to the spinodal instability of long wavelength modes the two-point correlation functions lead to the $t^{1/4}$-scaling relation during the quench and the Cahn-Allen scaling relation $t^{1/2}$ after the completion of quench. Further, after the finite quench the domain formation shows a time-lag behavior at the cubic power of quench period. Finally we study the time-dependent phase transition of a self-interacting scalar field.Comment: discussion on back-reaction added, typos corrected, references added, final version for PR