Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells.

Epigenetic resetting in germ cells during development de-represses transposable elements (TEs). piRNAs protect fetal germ cells by targeted mRNA destruction and deposition of repressive epigenetic marks. Here, we provide the first evidence for an active piRNA pathway and TE repression in germ cells of human fetal testis.

Digital Quantum Simulation of Z_{2} Lattice Gauge Theories with Dynamical Fermionic Matter.

We propose a scheme for digital quantum simulation of lattice gauge theories with dynamical fermions. Using a layered optical lattice with ancilla atoms that can move and interact with the other atoms (simulating the physical degrees of freedom), we obtain a stroboscopic dynamics which yields the four-body plaquette interactions, arising in models with (2+1) and higher dimensions, without the use of perturbation theory. As an example we show how to simulate a Z_{2} model in (2+1) dimensions.

Lingunite-a high-pressure plagioclase polymorph at mineral interfaces in doleritic rock of the Lockne impact structure (Sweden).

Lingunite nanocrystals and amorphous plagioclase (maskelynite) are identified at the contacts between augite and labradorite wedge-shaped interfaces in the doleritic rocks of the Lockne impact structure in Sweden. The occurrence of lingunite suggests that the local pressure was above 19 GPa and the local temperature overwhelmed 1000 °C. These values are up to 10 times higher than previous values estimated numerically for bulk pressure and temperature.

Quantum simulations of lattice gauge theories using ultracold atoms in optical lattices.

Can high-energy physics be simulated by low-energy, non-relativistic, many-body systems such as ultracold atoms? Such ultracold atomic systems lack the type of symmetries and dynamical properties of high energy physics models: in particular, they manifest neither local gauge invariance nor Lorentz invariance, which are crucial properties of the quantum field theories which are the building blocks of the standard model of elementary particles. However, it turns out, surprisingly, that there are ways to configure an atomic system to manifest both local gauge invariance and Lorentz invariance. In particular, local gauge invariance can arise either as an effective low-energy symmetry, or as an exact symmetry, following from the conservation laws in atomic interactions.

Entanglement generation using discrete solitons in Coulomb crystals.

Laser-cooled and trapped ions can crystallize and feature discrete solitons that are nonlinear, topologically protected configurations of the Coulomb crystal. Such solitons, as their continuum counterparts, can move within the crystal, while their discreteness leads to the existence of a gap-separated, spatially localized motional mode of oscillation above the spectrum. Suggesting that these unique properties of discrete solitons can be used for generating entanglement between different sites of the crystal, we study a detailed proposal in the context of state-of-the-art experimental techniques.

hnRNP F complexes with tristetraprolin and stimulates ARE-mRNA decay.

The tristetraprolin (TTP) family of zinc-finger proteins, TTP, BRF1 and BRF2, regulate the stability of a subset of mRNAs containing 3'UTR AU-rich elements (AREs), including mRNAs coding for cytokines, transcription factors, and proto-oncogenes. To better understand the mechanism by which TTP-family proteins control mRNA stability in mammalian cells, we aimed to identify TTP- and BRF1-interacting proteins as potential TTP-family co-factors. This revealed hnRNP F as a prominent interactor of TTP and BRF1.

Trapping of topological-structural defects in Coulomb crystals.

We study experimentally and theoretically structural defects which are formed during the transition from a laser cooled cloud to a Coulomb crystal, consisting of tens of ions in a linear radio frequency trap. We demonstrate the creation of predicted topological defects ("kinks") in purely two-dimensional crystals and also find kinks which show novel dynamical features in a regime of parameters not considered before. The kinks are always observed at the center of the trap, showing a large nonlinear localized excitation, and the probability of their occurrence saturates at ∼0.

Cold-atom quantum simulator for SU(2) Yang-Mills lattice gauge theory.

Non-Abelian gauge theories play an important role in the standard model of particle physics, and unfold a partially unexplored world of exciting physical phenomena. In this Letter, we suggest a realization of a non-Abelian lattice gauge theory-SU(2) Yang-Mills in (1 + 1) dimensions, using ultracold atoms. Remarkably, and in contrast to previous proposals, in our model gauge invariance is a direct consequence of angular momentum conservation and thus is fundamental and robust.

Simulating (2+1)-dimensional lattice QED with dynamical matter using ultracold atoms.

We suggest a method to simulate compact quantum electrodynamics using ultracold atoms in optical lattices, which includes dynamical Dirac fermions in 2+1 dimensions. This allows us to test the dynamical effects of confinement as well as the deformations and breaking of two-dimensional flux loops, and to observe the Wilson-loop area law.

Simulating compact quantum electrodynamics with ultracold atoms: probing confinement and nonperturbative effects.

Recently, there has been much interest in simulating quantum field theory effects of matter and gauge fields. In a recent work, a method for simulating compact quantum electrodynamics (CQED) using Bose-Einstein condensates has been suggested. We suggest an alternative approach, which relies on single atoms in an optical lattice, carrying 2l + 1 internal levels, which converges rapidly to CQED as l increases.

Confinement and lattice quantum-electrodynamic electric flux tubes simulated with ultracold atoms.

We propose a method for simulating (2+1)D compact lattice quantum-electrodynamics, using ultracold atoms in optical lattices. In our model local Bose-Einstein condensates' (BECs) phases correspond to the electromagnetic vector potential, and the local number operators represent the conjugate electric field. The well-known gauge-invariant Kogut-Susskind Hamiltonian is obtained as an effective low-energy theory.

Regulated and quality-control mRNA turnover pathways in eukaryotes.

Gene expression can be regulated at multiple levels, including transcription, RNA processing, RNA localization, translation and, finally, RNA turnover. RNA degradation may occur at points along the processing pathway or during translation as it undergoes quality control by RNA surveillance systems. Alternatively, mRNAs may be subject to regulated degradation, often mediated by cis-encoded determinants in the mRNA sequence that, through the recruitment of trans factors, determine the fate of the mRNA.

Hawking radiation from an acoustic black hole on an ion ring.

In this Letter we propose to simulate acoustic black holes with ions in rings. If the ions are rotating with a stationary and inhomogeneous velocity profile, regions can appear where the ion velocity exceeds the group velocity of the phonons. In these regions phonons are trapped like light in black holes, even though we have a discrete field theory and a nonlinear dispersion relation.

Superfast laser cooling.

Currently, laser cooling schemes are fundamentally based on the weak coupling regime. This requirement sets the trap frequency as an upper bound to the cooling rate. In this work we present a numerical study that shows the feasibility of cooling in the strong-coupling regime which then allows cooling rates that are faster than the trap frequency with experimentally feasible parameters.

Quantum coherence of discrete kink solitons in ion traps.

We propose to realize quantized discrete kinks with cold trapped ions. We show that long-lived solitonlike configurations are manifested as deformations of the zigzag structure in the linear Paul trap, and are topologically protected in a circular trap with an odd number of ions. We study the quantum-mechanical time evolution of a high-frequency, gap separated internal mode of a static kink and find long coherence times when the system is cooled to the Doppler limit.

Methods for detecting acceleration radiation in a Bose-Einstein condensate.

We propose and study methods for detecting Unruh-like acceleration radiation effects in a Bose-Einstein condensate in a (1+1)-dimensional setup. The Bogoliubov vacuum of a Bose-Einstein condensate is used to simulate a scalar field theory, and accelerated atom dots or optical lattices serve as detectors of phonon radiation due to acceleration effects. In particular, we study the dispersive effects of the Bogoliubov spectrum on the ideal case of exact thermalization.

Selective apoptosis of breast cancer cells by siRNA targeting of BORIS.

Brother of the regulator of imprinted sites (BORIS) is an epigenetically acting transcription factor which represses the tumor inhibitor functions of the tumor suppressor protein CTCF. BORIS expression has not been documented in adult females, making it an exciting molecular target for drug development in breast cancer. Previously, we demonstrated that vaccination of mice with zing-finger (ZF)-deleted non-functional BORIS results in regression of breast cancer and generation of potent anti-tumor immune responses.

The Cech Symposium: a celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom.

The Cech Symposium was held in Boulder, Colorado, on July 12-13, 2007, to celebrate a triple anniversary: 25 years since the first publication reporting RNA self-splicing, 10 years since the identification of reverse transcriptase motifs in the catalytic subunit of telomerase, and 60 years since the birth of Thomas R. Cech. Past and present members of the Cech laboratory presented on their current research, which branched into many categories of study including RNA-mediated catalysis, telomerase and telomeres, new frontiers in nucleic acids, alternative splicing, as well as scientific research with direct medical applications.

Molecular cloning of the baboon UDP-glucuronosyltransferase 1A gene family: evolution of the primate UGT1 locus and relevance for models of human drug metabolism.

Background: Glucuronidation by the UDP glucuronosyltransferase 1A enzymes (UGT1As) is a major pathway for elimination of drugs and endogenous substances, such as bilirubin.

Objective: To identify the baboon UGT1A gene family, compare it with that of the human, and evaluate the baboon as a model for human glucuronidation.

Methods And Results: Aligning the human and baboon UGT1 loci identified rearrangements occurring since the divergence of baboons and humans.

An improved method for angular-resolved characterization of the optical anisotropy of pyrolytic carbon.

A description is given of an experimental technique that improves the accuracy of the measurement of light extinctions by polarized light microscopy from deposits of pyrolytic carbon. The measurements were performed using a specially developed digital photometric image-analysis procedure providing high spatial and angular resolution of light extinctions over the reflecting optical domains with a high dynamic range of grey levels. The digital image acquisition and data processing are illustrated using circular-shaped pyrolytic carbon matrices of infiltrated carbon fibre felts and planar layers of pyrolytic graphite.

Induction of antitumor immunity through xenoplacental immunization.

Historically cancer vaccines have yielded suboptimal clinical results. We have developed a novel strategy for eliciting antitumor immunity based upon homology between neoplastic tissue and the developing placenta. Placenta formation shares several key processes with neoplasia, namely: angiogenesis, activation of matrix metalloproteases, and active suppression of immune function.

Fetal morphine metabolism and clearance are constant during late gestation.

Fetal metabolism significantly contributes to the clearance of drugs from the fetus. To understand how the changes in fetal metabolism expected in late gestation alter fetal drug clearance, serial measurements of morphine metabolism were made in the fetal baboon over the latter third of gestation. Clearance and metabolism were evaluated in the context of fetal growth, onset of labor, and the administration of classical enzyme induction agents.

Evaluation of a novel kit for the rapid detection of extended-spectrum beta-lactamases.

Since a method of rapidly detecting extended-spectrum beta-lactamase (ESBL) production in gram-negative isolates from patients with severe infection is urgently required, the present study of a novel commercial kit was conducted. The Cica-Beta Test I (Kanto Chemical, Tokyo, Japan) is designed for the rapid detection of ESBL in gram-negative bacteria directly from isolated colonies in a 15-min protocol. In this study, a total of 304 strains of Klebsiella spp.

Detecting vacuum entanglement in a linear ion trap.

We propose and study a method for detecting ground-state entanglement in a chain of trapped ions. We show that the entanglement between single ions or groups of ions can be swapped to the internal levels of two ions by sending laser pulses that couple the internal and motional degrees of freedom. This allows us to entangle two ions without actually performing gate operations.

Microstructure analysis of a carbon-carbon composite using argon ion etching.

The microstructure of carbon-carbon composites obtained by chemical vapor infiltration of a carbon fiber felt was comparatively studied by reflection light microscopy, transmission electron microscopy (TEM), scanning electron microscopy (SEM), atomic force microscopy (AFM), and laser scanning confocal microscopy (LSCM). Ar+ ion etching was used to reveal and distinguish structural units of the pyrolytic carbon matrix. Mechanically polished samples, polished and subsequently ion etched samples, and fractured samples were compared.