Pulsed extraction of ionization from helium buffer gas

The migration of intense ionization created in helium buffer gas under the influence of applied electric fields is considered. First the chemical evolution of the ionization created by fast heavy-ion beams is described. Straight forward estimates of the lifetimes for charge exchange indicate a clear suppression of charge exchange during ion migration in low pressure helium. Then self-consistent calculations of the migration of the ions in the electric field of a gas-filled cell at the National Superconducting Cyclotron Laboratory (NSCL) using a Particle-In-Cell computer code are presented. The results of the calculations are compared to measurements of the extracted ion current caused by beam pulses injected into the NSCL gas cell.Comment: Accepted for pubilication in Nucl. Instrum. Meth. B, 14 pages, 8 figure

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia

Ubiquitin charging of human class III ubiquitin-conjugating enzymes triggers their nuclear import

Ubiquitin is a small polypeptide that is conjugated to proteins and commonly serves as a degradation signal. The attachment of ubiquitin (Ub) to a substrate proceeds through a multi-enzyme cascade involving an activating enzyme (E1), a conjugating enzyme (E2), and a protein ligase (E3). We previously demonstrated that a murine E2, UbcM2, is imported into nuclei by the transport receptor importin-11. We now show that the import mechanism for UbcM2 and two other human class III E2s (UbcH6 and UBE2E2) uniquely requires the covalent attachment of Ub to the active site cysteine of these enzymes. This coupling of E2 activation and transport arises from the selective interaction of importin-11 with the Ub-loaded forms of these enzymes. Together, these findings reveal that Ub charging can function as a nuclear import trigger, and identify a novel link between E2 regulation and karyopherin-mediated transport

Molecular recording of mammalian embryogenesis.

Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. This field is particularly challenging in mammals, owing to the indeterminate relationship between self-renewal and differentiation, variation in progenitor field sizes, and internal gestation in these animals. Here we present a flexible, high-information, multi-channel molecular recorder with a single-cell readout and apply it as an evolving lineage tracer to assemble mouse cell-fate maps from fertilization through gastrulation. By combining lineage information with single-cell RNA sequencing profiles, we recapitulate canonical developmental relationships between different tissue types and reveal the nearly complete transcriptional convergence of endodermal cells of extra-embryonic and embryonic origins. Finally, we apply our cell-fate maps to estimate the number of embryonic progenitor cells and their degree of asymmetric partitioning during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems, which will facilitate the construction of a quantitative framework for understanding developmental processes

The aggregation of cytochrome C may be linked to its flexibility during refolding

Large-scale expression of biopharmaceutical proteins in cellular hosts results in production of large insoluble mass aggregates. In order to generate functional product, these aggregates require further processing through refolding with denaturant, a process in itself that can result in aggregation. Using a model folding protein, cytochrome C, we show how an increase in final denaturant concentration decreases the propensity of the protein to aggregate during refolding. Using polarised fluorescence anisotropy, we show how reduced levels of aggregation can be achieved by increasing the period of time the protein remains flexible during refolding, mediated through dilution ratios. This highlights the relationship between the flexibility of a protein and its propensity to aggregate. We attribute this behaviour to the preferential urea-residue interaction, over self-association between molecules

Tackling an intractable problem: can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?

The relationships among and within the families that comprise the orthopteran superfamily Stenopelmatoidea (suborder Ensifera) remain poorly understood. We developed a phylogenetic hypothesis based on Bayesian analysis of two nuclear ribosomal and one mitochondrial gene for 118 individuals (84 de novo and 34 from GenBank). These included Gryllacrididae from North, Central, and South America, South Africa and Madagascar, Australia and Papua New Guinea; Stenopelmatidae from North and Central America and South Africa; Anostostomatidae from North and Central America, Papua New Guinea, New Zealand, Australia, and South Africa; members of the Australian endemic Cooloola (three species); and a representative of Lezina from the Middle East. We also included representatives of all other major ensiferan families: Prophalangopsidae, Rhaphidophoridae, Schizodactylidae, Tettigoniidae, Gryllidae, Gryllotalpidae and Myrmecophilidae and representatives of the suborder Caelifera as outgroups. Bayesian analyses of concatenated sequence data supported a clade of Stenopelmatoidea inclusive of all analyzed members of Gryllacrididae, Stenopelmatidae, Anostostomatidae, Lezina and Cooloola. We found Gryllacrididae worldwide to be monophyletic, while we did not recover a monophyletic Stenopelmatidae nor Anostostomatidae. Australian Cooloola clustered in a clade composed of Australian, New Zealand, and some (but not all) North American Anostostomatidae. Lezina was included in a clade of New World Anostostomatidae. Finally, we compiled and compared karyotypes and sound production characteristics for each supported group. Chromosome number, centromere position, drumming, and stridulation differed among some groups, but also show variation within groups. This preliminary trait information may contribute toward future studies of trait evolution. Despite greater taxon sampling within Stenopelmatoidea than previous efforts, some relationships among the families examined continue to remain elusive

1/f Noise and Extreme Value Statistics

We study the finite-size scaling of the roughness of signals in systems displaying Gaussian 1/f power spectra. It is found that one of the extreme value distributions (Gumbel distribution) emerges as the scaling function when the boundary conditions are periodic. We provide a realistic example of periodic 1/f noise, and demonstrate by simulations that the Gumbel distribution is a good approximation for the case of nonperiodic boundary conditions as well. Experiments on voltage fluctuations in GaAs films are analyzed and excellent agreement is found with the theory.Comment: 4 pages, 4 postscript figures, RevTe

Design of intelligent mesoscale periodic array structures utilizing smart hydrogel

Mesoscale Periodic Array Structures (MPAS, also known as crystalline colloidal arrays), composed of aqueous or nonaqueous dispersions of self-assembled submicron colloidal spheres are emerging toward the development of advanced optical devices for technological applications. This is because of their unique optical diffraction properties and the ease with which these intriguing properties can be modulated experimentally. Moreover our recent advancements in this area which include 'locking' the liquid MPAS into solid or semisolid polymer matrices for greater stability with longer life span, and incorporation of CdS quantum dots and laser dyes into colloidal spheres to obtain nonlinear optical (NLO) responses further corroborate the use of MPAS in optical technology. Our long term goal is fabrication of all-optical and electro-optical devices such as spatial light modulators for optical signal processing and flat panel display devices by utilizing intelligent nonlinear periodic array structural materials. Here we show further progress in the design of novel linear MPAS which have the ability to sense and respond to an external source such as temperature. This is achieved by combining the self-assembly properties of polymer colloidal spheres and thermoshrinking properties of smart polymer gels. At selected temperatures the periodic array efficiently Bragg diffracts light and transmits most of the light at other temperatures. Hence these intelligent systems are of potential use as fixed notch filters optical switches or limiters to protect delicate optical sensors from high intensity laser radiation

Interacting Random Walkers and Non-Equilibrium Fluctuations

We introduce a model of interacting Random Walk, whose hopping amplitude depends on the number of walkers/particles on the link. The mesoscopic counterpart of such a microscopic dynamics is a diffusing system whose diffusivity depends on the particle density. A non-equilibrium stationary flux can be induced by suitable boundary conditions, and we show indeed that it is mesoscopically described by a Fourier equation with a density dependent diffusivity. A simple mean-field description predicts a critical diffusivity if the hopping amplitude vanishes for a certain walker density. Actually, we evidence that, even if the density equals this pseudo-critical value, the system does not present any criticality but only a dynamical slowing down. This property is confirmed by the fact that, in spite of interaction, the particle distribution at equilibrium is simply described in terms of a product of Poissonians. For mesoscopic systems with a stationary flux, a very effect of interaction among particles consists in the amplification of fluctuations, which is especially relevant close to the pseudo-critical density. This agrees with analogous results obtained for Ising models, clarifying that larger fluctuations are induced by the dynamical slowing down and not by a genuine criticality. The consistency of this amplification effect with altered coloured noise in time series is also proved.Comment: 8 pages, 7 figure

An Optical Readout TPC (O-TPC) for Studies in Nuclear Astrophysics With Gamma-Ray Beams at HIgS

We report on the construction, tests, calibrations and commissioning of an Optical Readout Time Projection Chamber (O-TPC) detector operating with a CO2(80%) + N2(20%) gas mixture at 100 and 150 Torr. It was designed to measure the cross sections of several key nuclear reactions involved in stellar evolution. In particular, a study of the rate of formation of oxygen and carbon during the process of helium burning will be performed by exposing the chamber gas to intense nearly mono-energetic gamma-ray beams at the High Intensity Gamma Source (HIgS) facility. The O-TPC has a sensitive target-drift volume of 30x30x21 cm^3. Ionization electrons drift towards a double parallel grid avalanche multiplier, yielding charge multiplication and light emission. Avalanche induced photons from N2 emission are collected, intensified and recorded with a Charge Coupled Device (CCD) camera, providing two-dimensional track images. The event's time projection (third coordinate) and the deposited energy are recorded by photomultipliers and by the TPC charge-signal, respectively. A dedicated VME-based data acquisition system and associated data analysis tools were developed to record and analyze these data. The O-TPC has been tested and calibrated with 3.183 MeV alpha-particles emitted by a 148Gd source placed within its volume with a measured energy resolution of 3.0%. Tracks of alpha and 12C particles from the dissociation of 16O and of three alpha-particles from the dissociation of 12C have been measured during initial in-beam test experiments performed at the HIgS facility at Duke University. The full detection system and its performance are described and the results of the preliminary in-beam test experiments are reported.Comment: Supported by the Richard F. Goodman Yale-Weizmann Exchange Program, ACWIS, NY, and USDOE grant Numbers: DE-FG02-94ER40870 and DE-FG02-97ER4103