Is the Correlation between Storage Capacity and Matrix Reasoning Driven by the Storage of Partial Solutions? A Pilot Study of an Experimental Approach

Working memory capacity (WMC) and reasoning abilities—as assessed by figural matrices tests—are substantially correlated. It is controversially discussed whether this correlation is only caused by controlled attention or also by storage capacity. This study aims at investigating storage of partial solutions as a possible mechanism by which storage capacity may contribute to solving figural matrices tests. For this purpose, we analyzed how an experimental manipulation of storage demands changes the pattern of correlations between WMC and performance in a matrix task. We manipulated the storage demands by applying two test formats: one providing the externalization of partial solutions and one without the possibility of externalization. Storage capacity was assessed by different types of change detection tasks. We found substantial correlations between storage capacity and matrices test performance, but they were of comparable size for both test formats. We take this as evidence that the necessity to store partial solutions is not the limiting factor which causes the association between storage capacity and matrices test. It is discussed how this approach can be used to investigate alternative mechanisms by that storage may influence performance in matrices tests

The Complex Evolutionary History of Aminoacyl-tRNA Synthetases

Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of \u3e2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. In the course of this analysis, highly conserved protein motifs and domains within each of the AARS loci were identified and used to build a web-based computational tool for the genome-wide detection of AARS coding sequences. This is based on hidden Markov models (HMMs) and is available together with a cognate database that may be used for specific analyses. The bioinformatics tools that we have developed may also help to identify new antibiotic agents and targets using these essential enzymes. These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code

Sampling a Littoral Fish Assemblage: Comparison of Small-Mesh Fyke Netting and Boat Electrofishing

We compared small-mesh (4-mm) fyke netting and boat electrofishing for sampling a littoral fish assemblage in Muskegon Lake, Michigan. We hypothesized that fyke netting selects for small-bodied fishes and electrofishing selects for large-bodied fishes. Three sites were sampled during May (2004 and 2005), July (2005 only), and September (2004 and 2005). We found that the species composition of captured fish differed considerably between fyke netting and electrofishing based on nonmetric multidimensional scaling (NMDS). Species strongly associated with fyke netting (based on NMDS and relative abundance) included the brook silverside Labidesthes sicculus, banded killifish Fundulus diaphanus, round goby Neogobius melanostomus, mimic shiner Notropis volucellus, and bluntnose minnow Pimephales notatus, whereas species associated with electrofishing included the Chinook salmon Oncorhynchus tshawytscha, catostomids (Moxostoma spp. and Catostomus spp.), freshwater drum Aplodinotus grunniens, walleye Sander vitreus, gizzard shad Dorosoma cepedianum, and common carp Cyprinus carpio. The total length of fish captured by electrofishing was 12.8 cm (95% confidence interval ¼ 5.5– 17.2 cm) greater than that of fish captured by fyke netting. Size selectivity of the gears contributed to differences in species composition of the fish captured, supporting our initial hypothesis. Thus, small-mesh fyke nets and boat electrofishers provided complementary information on a littoral fish assemblage. Our results support use of multiple gear types in monitoring and research surveys of fish assemblages. Copyright by the American Fisheries Society 2007, Originally published in the North American Journal of Fisheries Management 27: 825-831, 2007

The heterotrimeric Thermus thermophilus Asp-tRNAAsn amidotransferase can also generate Gln-tRNAGln

AbstractThermus thermophilus strain HB8 is known to have a heterodimeric aspartyl-tRNAAsn amidotransferase (Asp-AdT) capable of forming Asn-tRNAAsn [Becker, H.D. and Kern, D. (1998) Proc. Natl. Acad. Sci. USA 95, 12832–12837]. Here we show that, like other bacteria, T. thermophilus possesses the canonical set of amidotransferase (AdT) genes (gatA, gatB and gatC). We cloned and sequenced these genes, and constructed an artificial operon for overexpression in Escherichia coli of the thermophilic holoenzyme. The overproduced T. thermophilus AdT can generate Gln-tRNAGln as well as Asn-tRNAAsn. Thus, the T. thermophilus tRNA-dependent AdT is a dual-specific Asp/Glu-AdT resembling other bacterial AdTs. In addition, we observed that removal of the 44 carboxy-terminal amino acids of the GatA subunit only inhibits the Asp-AdT activity, leaving the Glu-AdT activity of the mutant AdT unaltered; this shows that Asp-AdT and Glu-AdT activities can be mechanistically separated

Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases

Yeast mitochondrial Gln-mtRNAGln is synthesized by the transamidation of mischarged Glu-mtRNAGln by a non-canonical heterotrimeric tRNA-dependent amidotransferase (AdT). The GatA and GatB subunits of the yeast AdT (GatFAB) are well conserved among bacteria and eukaryota, but the GatF subunit is a fungi-specific ortholog of the GatC subunit found in all other known heterotrimeric AdTs (GatCAB). Here we report the crystal structure of yeast mitochondrial GatFAB at 2.0 Å resolution. The C-terminal region of GatF encircles the GatA-GatB interface in the same manner as GatC, but the N-terminal extension domain (NTD) of GatF forms several additional hydrophobic and hydrophilic interactions with GatA. NTD-deletion mutants displayed growth defects, but retained the ability to respire. Truncation of the NTD in purified mutants reduced glutaminase and transamidase activities when glutamine was used as the ammonia donor, but increased transamidase activity relative to the full-length enzyme when the donor was ammonium chloride. Our structure-based functional analyses suggest the NTD is a trans-acting scaffolding peptide for the GatA glutaminase active site. The positive surface charge and novel fold of the GatF-GatA interface, shown in this first crystal structure of an organellar AdT, stand in contrast with the more conventional, negatively charged bacterial AdTs described previousl

The Peculiar SN 2005hk: Do Some Type Ia Supernovae Explode as Deflagrations?

We present extensive u'g'r'i'BVRIYJHKs photometry and optical spectroscopy of SN 2005hk. These data reveal that SN 2005hk was nearly identical in its observed properties to SN 2002cx, which has been called ``the most peculiar known type Ia supernova.'' Both supernovae exhibited high ionization SN 1991T-like pre-maximum spectra, yet low peak luminosities like SN 1991bg. The spectra reveal that SN 2005hk, like SN 2002cx, exhibited expansion velocities that were roughly half those of typical type Ia supernovae. The R and I light curves of both supernovae were also peculiar in not displaying the secondary maximum observed for normal type Ia supernovae. Our YJH photometry of SN 2005hk reveals the same peculiarity in the near-infrared. By combining our optical and near-infrared photometry of SN 2005hk with published ultraviolet light curves obtained with the Swift satellite, we are able to construct a bolometric light curve from ~10 days before to ~60 days after B maximum. The shape and unusually low peak luminosity of this light curve, plus the low expansion velocities and absence of a secondary maximum at red and near-infrared wavelengths, are all in reasonable agreement with model calculations of a 3D deflagration which produces ~0.25 M_sun of 56Ni.Comment: Accepted by PASP, to appear in April 2007 issue, 63 pages, 16 figures, 11 table

Muon Track Reconstruction and Data Selection Techniques in AMANDA

The Antarctic Muon And Neutrino Detector Array (AMANDA) is a high-energy neutrino telescope operating at the geographic South Pole. It is a lattice of photo-multiplier tubes buried deep in the polar ice between 1500m and 2000m. The primary goal of this detector is to discover astrophysical sources of high energy neutrinos. A high-energy muon neutrino coming through the earth from the Northern Hemisphere can be identified by the secondary muon moving upward through the detector. The muon tracks are reconstructed with a maximum likelihood method. It models the arrival times and amplitudes of Cherenkov photons registered by the photo-multipliers. This paper describes the different methods of reconstruction, which have been successfully implemented within AMANDA. Strategies for optimizing the reconstruction performance and rejecting background are presented. For a typical analysis procedure the direction of tracks are reconstructed with about 2 degree accuracy.Comment: 40 pages, 16 Postscript figures, uses elsart.st

On the selection of AGN neutrino source candidates for a source stacking analysis with neutrino telescopes

The sensitivity of a search for sources of TeV neutrinos can be improved by grouping potential sources together into generic classes in a procedure that is known as source stacking. In this paper, we define catalogs of Active Galactic Nuclei (AGN) and use them to perform a source stacking analysis. The grouping of AGN into classes is done in two steps: first, AGN classes are defined, then, sources to be stacked are selected assuming that a potential neutrino flux is linearly correlated with the photon luminosity in a certain energy band (radio, IR, optical, keV, GeV, TeV). Lacking any secure detailed knowledge on neutrino production in AGN, this correlation is motivated by hadronic AGN models, as briefly reviewed in this paper. The source stacking search for neutrinos from generic AGN classes is illustrated using the data collected by the AMANDA-II high energy neutrino detector during the year 2000. No significant excess for any of the suggested groups was found.Comment: 43 pages, 12 figures, accepted by Astroparticle Physic

Calibration and Characterization of the IceCube Photomultiplier Tube

Over 5,000 PMTs are being deployed at the South Pole to compose the IceCube neutrino observatory. Many are placed deep in the ice to detect Cherenkov light emitted by the products of high-energy neutrino interactions, and others are frozen into tanks on the surface to detect particles from atmospheric cosmic ray showers. IceCube is using the 10-inch diameter R7081-02 made by Hamamatsu Photonics. This paper describes the laboratory characterization and calibration of these PMTs before deployment. PMTs were illuminated with pulses ranging from single photons to saturation level. Parameterizations are given for the single photoelectron charge spectrum and the saturation behavior. Time resolution, late pulses and afterpulses are characterized. Because the PMTs are relatively large, the cathode sensitivity uniformity was measured. The absolute photon detection efficiency was calibrated using Rayleigh-scattered photons from a nitrogen laser. Measured characteristics are discussed in the context of their relevance to IceCube event reconstruction and simulation efforts.Comment: 40 pages, 12 figure