Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency

The nonhomologous DNA end-joining (NHEJ) pathway is a key mechanism for repairing dsDNA breaks that occur often in eukaryotic cells. In the simplest model, these breaks are first recognized by Ku, which then interacts with other NHEJ proteins to improve their affinity at DNA ends. These include DNA-PK$_{cs}$ and Artemis for trimming the DNA ends; DNA polymerase μ and λ to add nucleotides; and the DNA ligase IV complex to ligate the ends with the additional factors, XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor/Cernunos), and PAXX (paralog of XRCC4 and XLF). $\textit{In vivo}$ studies have demonstrated the degrees of importance of these NHEJ proteins in the mechanism of repair of dsDNA breaks, but interpretations can be confounded by other cellular processes. $\textit{In vitro}$ studies with NHEJ proteins have been performed to evaluate the nucleolytic resection, polymerization, and ligation steps, but a complete system has been elusive. Here we have developed a NHEJ reconstitution system that includes the nuclease, polymerase, and ligase components to evaluate relative NHEJ efficiency and analyze ligated junctional sequences for various types of DNA ends, including blunt, 5' overhangs, and 3' overhangs. We find that different dsDNA end structures have differential dependence on these enzymatic components. The dependence of some end joining on only Ku and XRCC4·DNA ligase IV allows us to formulate a physical model that incorporates nuclease and polymerase components as needed.National Institutes of Health, Cancer Research UK Program Grant IDs: C6/A11224, C6946/A14492), Wellcome Trust (Grant IDs: WT092096, WT093167

Prospects for Spin Physics at RHIC

Colliding beams of 70% polarized protons at up to $\sqrt{s}$=500 GeV, with high luminosity, L=2$\times10^{{\rm 32}}$ cm$^{-2}$sec$^{-1}$, will represent a new and unique laboratory for studying the proton. RHIC-Spin will be the first polarized-proton collider and will be capable of copious production of jets, directly produced photons, and $W$ and $Z$ bosons. Features will include direct and precise measurements of the polarization of the gluons and of $\bar{u}$, $\bar{d}$, $u$, and $d$ quarks in a polarized proton. Parity violation searches for physics beyond the standard model will be competitive with unpolarized searches at the Fermilab Tevatron. Transverse spin will explore transversity for the first time, as well as quark-gluon correlations in the proton. Spin dependence of the total cross section and in the Coulomb nuclear interference region will be measured at collider energies for the first time. These qualitatively new measurements can be expected to deepen our understanding of the structure of matter and of the strong interaction.Comment: 51 pages, 22 figures. Scheduled to appear in the Annual Review of Nuclear and Particle Science Vol. 50, to be published in December 2000 by Annual Reviews, http://AnnualReviews.or

A hybrid constructed wetland for organic-material and nutrient removal from sewage: Process performance and multi-kinetic models

© 2018 Elsevier Ltd A pilot-scale hybrid constructed wetland with vertical flow and horizontal flow in series was constructed and used to investigate organic material and nutrient removal rate constants for wastewater treatment and establish a practical predictive model for use. For this purpose, the performance of multiple parameters was statistically evaluated during the process and predictive models were suggested. The measurement of the kinetic rate constant was based on the use of the first-order derivation and Monod kinetic derivation (Monod) paired with a plug flow reactor (PFR) and a continuously stirred tank reactor (CSTR). Both the Lindeman, Merenda, and Gold (LMG) analysis and Bayesian model averaging (BMA) method were employed for identifying the relative importance of variables and their optimal multiple regression (MR). The results showed that the first-order–PFR (M2) model did not fit the data (P > 0.05, and R2 0.5). The pollutant removal rates in the case of M1 were 0.19 m/d (CODCr) and those for M3 were 25.2 g/m2∙d for CODCr and 2.63 g/m2∙d for NH4-N. By applying a multi-variable linear regression method, the optimal empirical models were established for predicting the final effluent concentration of five days' biochemical oxygen demand (BOD5) and NH4-N. In general, the hydraulic loading rate was considered an important variable having a high value of relative importance, which appeared in all the optimal predictive models

What is the psychological impact of self-weighing? A meta-analysis

© 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. ABSTRACT: Many people self-weigh and many interventions addressing weight-related problems such as obesity promote self-weighing. However, while self-weighing has been associated with weight loss, there is mixed evidence regarding the psychological impact of this behaviour. The present review aimed to quantify the relationship between self-weighing and: (i) affect (e.g., anxiety, depression); (ii) psychological functioning (e.g., self-esteem); (iii) body-related attitudes and (iv) disordered eating. A computerized search of scientific databases in September 2014 and subsequent ancestry and citation searches identified 29 independent tests of the relationship between self-weighing on psychological outcomes. Meta-analysis was used to quantify the size of the association across the tests. Results indicated that there was no association between self-weighing and affect, body-related attitudes or disordered eating. There was, however, a small-sized negative association between self-weighing and psychological functioning. The age of participants, obesity status, the extent of weight loss, duration of self-weighing and study design (RCT versus correlational) were found to influence at least some of the psychological outcomes of self-weighing. The findings suggest that, for the most part, self-weighing is not associated with adverse psychological outcomes. However, in some cases the association between self-weighing and psychological outcomes may be more negative than in others

Superfluid vs Ferromagnetic Behaviour in a Bose Gas of Spin-1/2 Atoms

We study the thermodynamic phases of a gas of spin-1/2 atoms in the Hartree-Fock approximation. Our main result is that, for repulsive or weakly-attractive inter-component interaction strength, the superfluid and ferromagnetic phase transitions occur at the same temperature. For strongly-attractive inter-component interaction strength, however, the ferromagnetic phase transition occurs at a higher temperature than the superfluid phase transition. We also find that the presence of a condensate acts as an effective magnetic field that polarizes the normal cloud. We finally comment on the validity of the Hartree-Fock approximation in describing different phenomena in this system.Comment: 10 pages, 2 figure

Coherent multi-flavour spin dynamics in a fermionic quantum gas

Microscopic spin interaction processes are fundamental for global static and dynamical magnetic properties of many-body systems. Quantum gases as pure and well isolated systems offer intriguing possibilities to study basic magnetic processes including non-equilibrium dynamics. Here, we report on the realization of a well-controlled fermionic spinor gas in an optical lattice with tunable effective spin ranging from 1/2 to 9/2. We observe long-lived intrinsic spin oscillations and investigate the transition from two-body to many-body dynamics. The latter results in a spin-interaction driven melting of a band insulator. Via an external magnetic field we control the system's dimensionality and tune the spin oscillations in and out of resonance. Our results open new routes to study quantum magnetism of fermionic particles beyond conventional spin 1/2 systems.Comment: 9 pages, 5 figure

Coherent spinor dynamics in a spin-1 Bose condensate

Collisions in a thermal gas are perceived as random or incoherent as a consequence of the large numbers of initial and final quantum states accessible to the system. In a quantum gas, e.g. a Bose-Einstein condensate or a degenerate Fermi gas, the phase space accessible to low energy collisions is so restricted that collisions be-come coherent and reversible. Here, we report the observation of coherent spin-changing collisions in a gas of spin-1 bosons. Starting with condensates occupying two spin states, a condensate in the third spin state is coherently and reversibly created by atomic collisions. The observed dynamics are analogous to Josephson oscillations in weakly connected superconductors and represent a type of matter-wave four-wave mixing. The spin-dependent scattering length is determined from these oscillations to be -1.45(18) Bohr. Finally, we demonstrate coherent control of the evolution of the system by applying differential phase shifts to the spin states using magnetic fields.Comment: 19 pages, 3 figure

Energy Considerations for Estimating Displacements of Oscillators with Different Hysteresis Shapes

This paper evaluates the number of cycles of deformation, Nc, of single degree of freedom (SDOF) structures with different hysteresis loop shapes subjected to earthquake loading because this influences both the peak displacement and the damage in a structure. The open-source software OpenSEES was modified to allow flagshaped hysteresis loops ranging from elastic bilinear (with no energy dissipation) to traditional bilinear. To address the current inconsistency in the literature the concept of oscillation resistance ratio (ORR) has been introduced before. A relationship to estimate (ORR) for oscillators with different displacement ductility and a flag-shaped hysteresis loop is developed under free vibration, assuming no damping and no strain hardening. This relationship, initially developed using simple mechanics considerations, is then compared with that found from a time history analysis. The relationship is then extended to consider the effects of tangent stiffness proportional damping. The number of oscillation cycles, Nc, is defined as the number of post-initial elastic displacement excursions obtained during shaking to the number in one full cycle to the same peak displacement. Relationships between Nc and ORR were developed for structures with lateral force reduction factor, R, period, T, and damping assuming no strain hardening using a suite of 9 earthquakes records. It was found that estimated ORR for the mechanics-based method and time history analysis considering free vibration were identical for all flag shape loop shapes. For a damping ratio of 5%, the ORR obtained increased by less than 12% compared to 0% damping for the flag-shaped parameters greater than 0.2. As a result, the ORR for a loop with no damping was used in the remainder of the paper. In general, as the ORR decreased to less than 0.3 (i.e. the hysteresis loop had less energy dissipation), Nc increased. It was found that Nc was insensitive to the lateral force reduction factor, but increased for lower damping when ORR was less than 0.3. Also, it increased for shorter period oscillators when ORR was less than 0.3, but the trends were less clear with greater ORR