ALBERT

Description: We present results from the KMOS Lens-Amplified Spectroscopic Survey (KLASS), an ESO Very Large Telescope (VLT) large program using gravitational lensing to study the spatially resolved kinematics of 44 star-forming galaxies at 0.6 〈 z 〈 2.3 with a stellar mass of 8.1 〈 log(M⋆/M⊙) 〈 11.0. These galaxies are located behind six galaxy clusters selected from the Hubble Space Telescope Grism Lens-Amplified Survey from Space (GLASS). We find that the majority of the galaxies show a rotating disc, but most of the rotation-dominated galaxies only have a low υ rot/σ0 ratio (median of υrot/σ0 ∼ 2.5). We explore the Tully–Fisher relation by adopting the circular velocity, $V_{mathrm{ circ}}=(upsilon _{mathrm{ rot}}^2+3.4sigma _0^2)^{1/2}$, to account for pressure support. We find that our sample follows a Tully–Fisher relation with a positive zero-point offset of +0.18 dex compared to the local relation, consistent with more gas-rich galaxies that still have to convert most of their gas into stars. We find a strong correlation between the velocity dispersion and stellar mass in the KLASS sample. When combining our data to other surveys from the literature, we see an increase of the velocity dispersion with stellar mass at all redshift. We obtain an increase of υrot/σ0 with stellar mass at 0.5 〈 z 〈 1.0. This could indicate that massive galaxies settle into regular rotating discs before the low-mass galaxies. For higher redshift (z 〉 1), we find a weak increase or flat trend. We find no clear trend between the rest-frame UV clumpiness and the velocity dispersion and υrot/σ0. This could suggest that the kinematic properties of galaxies evolve after the clumps formed in the galaxy disc or that the clumps can form in different physical conditions.

Description: We have measured the absolute proper motion of the Draco dwarf spheroidal galaxy using Subaru Suprime-Cam images taken at three epochs, with time baselines of 4.4 and 7 yr. The magnitude limit of the proper-motion study is i = 25, thus allowing for thousands of background galaxies and Draco stars to be used to perform extensive astrometric tests and to derive the correction to an inertial reference frame. The derived proper motion is (μ α , μ ) = (–0.284 ± 0.047, –0.289 ± 0.041) mas yr –1 . This motion implies an orbit that takes Draco to a pericentre of ~20 kpc; a somewhat disruptive orbit suggesting that tides might account for the rising velocity-dispersion profile of Draco seen in line-of-sight velocity studies. The orbit is only marginally consistent with Draco's membership to the vast polar structure of Galactic satellites, in contrast to a recent Hubble Space Telescope proper-motion measurement that finds alignment very likely. Our study is a test case to demonstrate that deep imaging with mosaic cameras of appropriate resolution can be used for high-accuracy, ground-based proper-motion measurement. As a useful by-product of the study, we also identify two faint brown-dwarf candidates in the foreground field.

Description: The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the wild-type KLI by other known KLIs using an innovative engineering method that combines rational and combinatorial approaches. A bioinformatic search of the protein data bank was initially performed to identify KLIs that are structurally similar to the one found in the VS ribozyme. Next, substrate/ribozyme (S/R) pairs that incorporate these alternative KLIs were kinetically and structurally characterized. Interestingly, several of the resulting S/R pairs allowed substrate cleavage with substantial catalytic efficiency, although with reduced activity compared to the reference S/R pair. Overall, this study describes an innovative approach for RNA engineering and establishes that the KLI of the trans VS ribozyme can be adapted to cleave other folded RNA substrates.

Description: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the selective death of motor neurons. Causative mutations in the global RNA-processing proteins TDP-43 and FUS among others, as well as their aggregation in ALS patients, have identified defects in RNA metabolism as an important feature in this disease. Lethal congenital contracture syndrome 1 and lethal arthrogryposis with anterior horn cell disease are autosomal recessive fetal motor neuron diseases that are caused by mutations in another global RNA-processing protein, hGle1. In this study, we carried out the first screening of GLE1 in ALS patients (173 familial and 760 sporadic) and identified 2 deleterious mutations (1 splice site and 1 nonsense mutation) and 1 missense mutation. Functional analysis of the deleterious mutants revealed them to be unable to rescue motor neuron pathology in zebrafish morphants lacking Gle1. Furthermore, in HeLa cells, both mutations caused a depletion of hGle1 at the nuclear pore where it carries out an essential role in nuclear export of mRNA. These results suggest a haploinsufficiency mechanism and point to a causative role for GLE1 mutations in ALS patients. This further supports the involvement of global defects in RNA metabolism in ALS.

Description: Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS [MIM 270550]) is an early-onset neurodegenerative disorder caused by mutations in the SACS gene. Over 170 SACS mutations have been reported worldwide and are thought to cause loss of function of sacsin, a poorly characterized and massive 520 kDa protein. To establish an animal model and to examine the pathophysiological basis of ARSACS, we generated Sacs knockout ( Sacs –/– ) mice. Null animals displayed an abnormal gait with progressive motor, cerebellar and peripheral nerve dysfunctions highly reminiscent of ARSACS. These clinical features were accompanied by an early onset, progressive loss of cerebellar Purkinje cells followed by spinal motor neuron loss and peripheral neuropathy. Importantly, loss of sacsin function resulted in abnormal accumulation of non-phosphorylated neurofilament (NF) bundles in the somatodendritic regions of vulnerable neuronal populations, a phenotype also observed in an ARSACS brain. Moreover, motor neurons cultured from Sacs –/– embryos exhibited a similar NF rearrangement with significant reduction in mitochondrial motility and elongated mitochondria. The data points to alterations in the NF cytoskeleton and defects in mitochondrial dynamics as the underlying pathophysiological basis of ARSACS.

Description: Human herpesvirus-6A (HHV-6A) and HHV-6B integrate their genomes into the telomeres of human chromosomes, however, the mechanisms leading to integration remain unknown. HHV-6A/B encode a protein that has been proposed to be involved in integration termed U94, an ortholog of adeno-associated virus type 2 (AAV-2) Rep68 integrase. In this report, we addressed whether purified recombinant maltose-binding protein (MBP)-U94 fusion proteins of HHV-6A/B possess biological functions compatible with viral integration. We could demonstrate that MBP-U94 efficiently binds both dsDNA and ssDNA containing telomeric repeats using gel shift assay and surface plasmon resonance. MBP-U94 is also able to hydrolyze adenosine triphosphate (ATP) to ADP, providing the energy for further catalytic activities. In addition, U94 displays a 3' to 5' exonuclease activity on dsDNA with a preference for 3'-recessed ends. Once the DNA strand reaches 8–10 nt in length, the enzyme dissociates it from the complementary strand. Lastly, MBP-U94 compromises the integrity of a synthetic telomeric D-loop through exonuclease attack at the 3' end of the invading strand. The preferential DNA binding of MBP-U94 to telomeric sequences, its ability to hydrolyze ATP and its exonuclease/helicase activities suggest that U94 possesses all functions required for HHV-6A/B chromosomal integration.

Description: Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systematically review and compare different approaches to map probes across seven platforms from different vendors: U95A, U133A and U133 Plus 2.0 from Affymetrix, Inc.; HT-12 v1, HT-12v2 and HT-12v3 from Illumina, Inc.; and 4112A from Agilent, Inc. We use a unique data set, which contains 56 lung cancer cell line samples—each of which has been measured by two different microarray platforms—to evaluate the consistency of expression measurement across platforms using different approaches. Based on the evaluation from the empirical data set, the BLAST alignment of the probe sequences to a recent revision of the Transcriptome generated better results than using annotations provided by Vendors or from Bioconductor's Annotate package. However, a combination of all three methods (deemed the ‘Consensus Annotation’) yielded the most consistent expression measurement across platforms. To facilitate data integration across microarray platforms for the research community, we develop a user-friendly web-based tool, an API and an R package to map data across different microarray platforms from Affymetrix, Illumina and Agilent. Information on all three can be found at http://qbrc.swmed.edu/software/probemapper/ .

Description: Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing–loop interaction important for substrate recognition. To rapidly characterize the substrate specificity ( k cat /K M ) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing–loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.

Description: The surface nuclear magnetic resonance (SNMR) method is a geophysical method designed for non-invasive groundwater investigations. Inversion of experimental data provides the spatial distribution of the water content in the subsurface. However, SNMR inversion is ill-posed and admits many solutions because of the imaging equation properties that are compounded by experimental error. SNMR data sets are conveniently presented as complex numbers, thus possessing phase and amplitude components. Subsurface electroconductive formations and fluctuations of the Earth's magnetic field cause non-negligible phase shifts. Consequently, the forward modelling of the SNMR signal generated by 3-D water saturated formations is achieved in the complex domain. Nevertheless, in many cases, phase measurements are less reliable than amplitude measurements and water content rendering cannot be carried out using the complex SNMR signal. This problem is resolved by performing inversion using complex forward modelling whose resulting signal amplitude is used for comparison with the data. Along with water content boundaries ranging from 0 to 1, this property turns the linear initial value inversion problem into a non-linear one. In such a situation, the comprehensive analysis of inversion uncertainties is achieved by performing a solution space exploration based on a Monte Carlo approach. An adapted Metropolis–Hastings algorithm has been used on SNMR 3-D data sets to perform such an exploration. Computing time depends on the problem dimensions. With a standard laptop computer about 10 hr were necessary for the inversion of our field data set. The resulting model collection is used to calculate the probability density functions of the water content. From there, it is possible to estimate the uncertainty of the water content imagery. Using both synthetic and experimental data, we show that our routine provides robust estimates of the spatial distribution of the water content for the SNMR 3-D initial amplitude inversion.

Description: We discuss the results of cross-correlating catalogues of bright X-ray binaries with the Yale Southern Proper Motion Catalog (version 4.0). Several objects already known to have large proper motions from Hipparcos are recovered. Two additional objects are found which show substantial proper motions, both of which are unusual in their X-ray properties. One is IGR J17544–2619, one of the supergiant fast X-ray transients. Assuming the quoted distances in the literature for this source of about 3 kpc are correct, this system has a peculiar velocity of about 275 km s –1 – greater than the velocity of a Keplerian orbit at its location of the Galaxy and in line with the expectations formed from suggestions that the supergiant fast X-ray transients should be highly eccentric. We discuss the possibility that these objects may help explain the existence of short gamma-ray bursts outside the central regions of galaxies. The other is the source 2A 1822–371, which is a member of the small class of objects which are low-mass X-ray binaries and long (i.e. 〉100 ms) X-ray pulsars. This system also shows both an anomalously high X-ray luminosity and a large orbital period derivative for a system with its orbital period, and some possible indications of an eccentric orbit. A coherent picture can be developed by adding in the proper motion information in which this system formed in the Perseus spiral arm of the Galaxy about 3 Myr ago and retains a slightly eccentric orbit which leads to enhanced mass transfer.