Cell-free prediction of protein expression costs for growing cells

Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any given gene is a major challenge, as multiple processes and factors combine to determine translation efficiency. To enable prediction of the cost of gene expression in bacteria, we describe here a standard cell-free lysate assay that provides a relative measure of resource consumption when a protein coding sequence is expressed. These lysate measurements can then be used with a computational model of translation to predict the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway

Magnetic induction mapping of magnetite chains in magnetotactic bacteria at room temperature and close to the Verwey transition using electron holography

Off-axis electron holography in the transmission electron microscope is used to record magnetic induction maps of closely spaced magnetite crystals in magnetotactic bacteria at room temperature and after cooling the sample using liquid nitrogen. The magnetic microstructure is related to the morphology and crystallography of the particles, and to interparticle interactions. At room temperature, the magnetic signal is dominated by interactions and shape anisotropy, with highly parallel and straight field lines following the axis of each chain of crystals closely. In contrast, at low temperature the magnetic induction undulates along the length of the chain. This behaviour may result from a competition between interparticle interactions and an easy axis of magnetisation that is no longer parallel to the chain axis. The quantitative nature of electron holography also allows the change in magnetisation in the crystals with temperature to be measured

Non-adiabatic spin torque investigated using thermally activated magnetic domain wall dynamics

Using transmission electron microscopy, we investigate the thermally activated motion of domain walls (DWs) between two positions in permalloy (Ni80Fe20) nanowires at room temperature. We show that this purely thermal motion is well described by an Arrhenius law, allowing for a description of the DW as a quasi-particle in a 1D potential landscape. By injecting small currents, the potential is modified, allowing for the determination of the non-adiabatic spin torque: the non-adiabatic coefficient is 0.010 +/- 0.004 for a transverse DW and 0.073 +/- 0.026 for a vortex DW. The larger value is attributed to the higher magnetization gradients present

Mass scaling and non-adiabatic effects in photoassociation spectroscopy of ultracold strontium atoms

We report photoassociation spectroscopy of ultracold $^{86}$Sr atoms near the intercombination line and provide theoretical models to describe the obtained bound state energies. We show that using only the molecular states correlating with the $^1S_0$$+$$^3P_1$ asymptote is insufficient to provide a mass scaled theoretical model that would reproduce the bound state energies for all isotopes investigated to date: $^{84}$Sr, $^{86}$Sr and $^{88}$Sr. We attribute that to the recently discovered avoided crossing between the $^1S_0$$+$$^3P_1$ $0_u^+$ ($^3\Pi_u$) and $^1S_0$$+$$^1D_2$ $0_u^+$ ($^1\Sigma^+_u$) potential curves at short range and we build a mass scaled interaction model that quantitatively reproduces the available $0_u^+$ and $1_u$ bound state energies for the three stable bosonic isotopes. We also provide isotope-specific two-channel models that incorporate the rotational (Coriolis) mixing between the $0_u^+$ and $1_u$ curves which, while not mass scaled, are capable of quantitatively describing the vibrational splittings observed in experiment. We find that the use of state-of-the-art ab initio potential curves significantly improves the quantitative description of the Coriolis mixing between the two -8 GHz bound states in $^{88}$Sr over the previously used model potentials. We show that one of the recently reported energy levels in $^{84}$Sr does not follow the long range bound state series and theorize on the possible causes. Finally, we give the Coriolis mixing angles and linear Zeeman coefficients for all of the photoassociation lines. The long range van der Waals coefficients $C_6(0_u^+)=3868(50)$~a.u. and $C_6(1_u)=4085(50)$~a.u. are reported.Comment: 14 pages, 7 tables, 5 figures. Submitted to Phys. Rev.

Characterization of Fe-N nanocrystals and nitrogen–containing inclusions in (Ga,Fe)N thin films using transmission electron microscopy

Nanometric inclusions filled with nitrogen, located adjacent to FenN (n¼3 or 4) nanocrystals within (Ga,Fe)N layers, are identified and characterized using scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS). High-resolution STEM images reveal a truncation of the Fe-N nanocrystals at their boundaries with the nitrogen-containing inclusions. A controlled electron beam hole drilling experiment is used to release nitrogen gas from an inclusion in situ in the electron microscope. The density of nitrogen in an individual inclusion is measured to be 1.460.3 g/cm3. These observations provide an explanation for the location of surplus nitrogen in the (Ga,Fe)N layers, which is liberated by the nucleation of FenN (n>1) nanocrystals during growth

Hydrothermal synthesis, off-axis electron holography and magnetic properties of Fe3_{3}O4_{4} nanoparticles

The hydrothermal synthesis of Fe3O4 nanoparticles (NPs) (< 50 nm) from mixed FeCl3 / FeCl2 precursor solution at pH ~ 12 has been confirmed using complementary characterisation techniques of transmission electron microscopy and X-ray diffractometry. Off-axis electron holography allowed for visualisation of their single domain (SD) nature, as well as inter-particle interactions, with the latter attributed to explain the pseudo-SD/multi-domain behaviour demonstrated by bulk magnetic measurements

Chandra Imaging and Spectroscopy of the Eastern XA Region of the Cygnus Loop Supernova Remnant

The XA region of the Cygnus Loop is a bright knot of X-ray emission on the eastern edge of the supernova remnant resulting from the interaction of the supernova blast wave with density enhancements at the edge of a precursor formed cavity. To study the nature and origin of the X-ray emission we use high spatial resolution images from Chandra. Our goal is to probe the density of various spectral extraction regions to form a picture of the cavity wall and characterize the interaction between this supernova and the local interstellar medium. We find that a series of regions along the edge of the X-ray emission appears to trace out the location of the cavity wall. The best fit plasma models result in two temperature component equilibrium models for each region. The low temperature components have densities that are an order of magnitude higher than the high temperature components. The high density plasma may exist in the cavity wall where it equilibrates rapidly and cools efficiently. The low density plasma is interior to the enhancement and heated further by a reverse shock from the wall. Calculations of shock velocities and timescales since shock heating are consistent with this interpretation. Furthermore, we find a bright knot of emission indicative of a discrete interaction of the blast wave with a high density cloud in the cavity wall with a size scale ~0.1 pc. Aside from this, other extractions made interior to the X-ray edge are confused by line of sight projection of various components. Some of these regions show evidence of detecting the cavity wall but their location makes the interpretation difficult. In general, the softer plasmas are well fit at temperatures kT~0.11 keV, with harder plasmas at temperatures of kT~0.27 keV. All regions display consistent metal depletions most notably in N, O, and Ne at an average of 0.54, 0.55, and 0.36 times solar