Semicontinuous Bioreactor Production of Recombinant Butyrylcholinesterase in Transgenic Rice Cell Suspension Cultures.

An active and tetrameric form of recombinant butyrylcholinesterase (BChE), a large and complex human enzyme, was produced via semicontinuous operation in a transgenic rice cell suspension culture. After transformation of rice callus and screening of transformants, the cultures were scaled up from culture flask to a lab scale bioreactor. The bioreactor was operated through two phases each of growth and expression. The cells were able to produce BChE during both expression phases, with a maximum yield of 1.6 mg BChE/L of culture during the second expression phase. Cells successfully regrew during a 5-day growth phase. A combination of activity assays and Western blot analysis indicated production of an active and fully assembled tetramer of BChE

A panchromatic view of PKS 0558-504: an ideal laboratory to study the disk-jet link

PKS 0558-504 is the brightest radio-loud Narrow-Line Seyfert 1 galaxy at X-ray energies. Here we present results from the radio, optical, UV, and X-ray bands obtained with Swift, XMM, and ATCA during a 10-day monitoring campaign in September 2008. The simultaneous coverage at several wavelengths makes it possible to investigate in detail the broadband spectral energy distribution (SED) and the energetic of this source. The main results can be summarized as follows. The ATCA reveals the presence of an extended radio emission in PKS 0558-504 with two lobe-like structures at ~7" from the bright central source. The extended radio structure and the low value of the radio-loudness similar to radio-quiet Seyfert galaxies coupled with constraints from higher energy bands argue against a jet-dominated emission. The study of the SED, which is dominated by a nearly constant optical-UV emission, supports the conclusion that PKS 0558-504 is accreting at super-Eddington rate. This conclusion was reached assuming M_BH=2.5e8 M_sun, which was obtained with a new scaling method based on X-ray spectral variability results. A comparison between the accretion luminosity and the kinetic power associated with the jet suggests that in this source the accretion power dominates in agreement with the results obtained from Radiation-MHD simulations of Galactic black holes (GBHs) accreting at the Eddington rate. The combined findings from this panchromatic investigation strongly suggest that PKS 0558-504 is a large-scale analog of GBHs in their highly accreting intermediate state. Importantly, PKS 0558-504 may also be the prototype of the parent population of the very radio-loud NLS1s recently detected at gamma-ray energies.Comment: 11 pages, 5 figures, 3 tables, accepted for publication in Ap

The HSV-1 ICP27 RGG box specifically binds flexible, GC-rich sequences but not G-quartet structures

Herpes simplex virus 1 (HSV-1) protein ICP27, an important regulator for viral gene expression, directly recognizes and exports viral RNA through an N-terminal RGG box RNA binding motif, which is necessary and sufficient for RNA binding. An ICP27 N-terminal peptide, including the RGG box RNA binding motif, was expressed and its binding specificity was analyzed using EMSA and SELEX. DNA oligonucleotides corresponding to HSV-1 glycoprotein C (gC) mRNA, identified in a yeast three-hybrid analysis, were screened for binding to the ICP27 N-terminal peptide in EMSA experiments. The ICP27 N-terminus was able to bind most gC substrates. Notably, the ICP27 RGG box was unable to bind G-quartet structures recognized by the RGG domains of other proteins. SELEX analysis identified GC-rich RNA sequences as a common feature of recognition. NMR analysis of SELEX and gC sequences revealed that sequences able to bind to ICP27 did not form secondary structures and conversely, sequences that were not able to bind to ICP27 gave spectra consistent with base-pairing. Therefore, the ICP27 RGG box is unique in its recognition of nucleic acid sequences compared to other RGG box proteins; it prefers flexible, GC-rich substrates that do not form stable secondary structures

River Invertebrate Classification Tool

Background to research The Regulatory Agencies in the UK (the Environment Agency; Scottish Environment Protection Agency; and the Environment & Heritage Service) currently use RIVPACS III+ software to classify the ecological quality of rivers. However, because RIVPACS III+ pre-dates the WFD, there has been a requirement to ensure that the RIVPACS reference sites are fully WFD compliant, to add new biotic indices to the RIVPACS models, and to improve the robustness of the RIVPACS software to fully meet the needs of the Agencies in their delivery of WFD monitoring. These issues have been addressed in this project and have led to the development of new RIVPACS IV predictive models that will be programmed into a new River Invertebrate Classification Tool being built by SEPA. This new system will be based on a modern software programming language, be compatible with the agencies’ computer systems and include the ability to predict new biological indices, produce biological status assessments based on these new indices and be able to estimate the errors involved in using these new indices. Because access to the new system will be essential for the UK Agencies to be able to implementation the WFD, the new tool will be readily and freely available to anyone who might seek to use it. Objectives of research • The overall objective of the project was to produce a new set of RIVPACS predictive models for use within a new River Invertebrate Classification Tool that will be used to classify the ecological status of rivers for Water Framework Directive compliance monitoring • The new RIVPACS models constructed with this project required considerably enhanced functionality compared to RIVPACS III+ to properly address the monitoring requirements of the UK Agencies in their implementation of the Water Framework Directive. Key findings and recommendations This project has produced new RIVPACS IV models with considerably enhanced functionality compared to RIVPACS III+. These models incorporate: • A full revision of the taxonomic framework of RIVPACS to bring the taxonomy up-to-date and enable compatiability across the revised Miatland, Furse code and National Biodiversity Network taxon coding systems used across the UK Agencies and beyond • Predictions that fully satisfy the WFD definition of ‘reference condition’ by adjusting predictions for certain stream types and by removal of sites that were not in reference condition when sampled • Allocation of actual abundance values to family level records in the RIVPACS reference data set. Lack of actual abundance data, especially at family level, has affected all versions of RIVPACS and has constrained the types of biotic indices that RIVPACS can predict • Extension to the suite of biotic indices so that the new system can predict a wider range of reference state “expected” index values. This enables full WFD quality reporting capabilities as well as providing the system with the general functionality to predict a much wider range of indices e.g. intercalibration indices (e.g. ICMi), stress-specific indices, and ecological and functional trait indices • Extension of the uncertainty/errors module to estimate and assess uncertainty in (i) assignment to status class and (ii) comparison of samples for temporal change in quality and status. This needs to be done for a wider range of biotic indices (including those incorporating abundance data) These new RIVPACS IV models can be used by the UK Agencies across Great Britain and Northern Ireland in their WFD compliance monitoring. All of the algorithms, variables and data necessary to build these models have been provided to SEPA for programming into a new River Invertebrate Classification Tool that will be disseminated made free of charge to all interested user

The Parkes quarter-Jansky flat-spectrum sample 2. New Optical Spectra and Redshift Measurements

We present optical spectra and redshift measurements for 178 flat-spectrum objects from the Parkes quarter-Jansky flat-spectrum sample. These spectra were obtained in order to compile a complete sample of quasars for use in a study of quasar evolution. We present a composite optical spectrum made from the subset of 109 quasars that have flux densities in the range 0.25Jy < S(2.7GHz)< 0.5Jy, and make a comparison with a composite for radio-quiet QSOs from the Large Bright Quasar Survey. Our large sample of radio-loud quasars allows us to strengthen previous reports that the Ly-alpha and CIV emission lines have larger equivalent width in radio-loud quasars than radio-quiet QSOs to greater than the 3-sigma level. However we see no significant difference in the equivalent widths of CIII] or MgII. We also show that the flux decrements across the Lyman-alpha line (D_A) measured from these spectra show the same trend with redshift as for optically selected QSOs.Comment: 20 pages, 8 figures. Accepted for publication in Astronomy and Astrophysic

Hubble Space Telescope NICMOS Imaging of the Core of M87

We present broad-band 1.1, 1.6 and 2.2 micron images and a 2.37 micron narrow-band image of the inner 19" of the nearby radio galaxy M87, obtained with the Near Infrared Camera and Multi-Object Spectrometer of the Hubble Space Telescope (HST). The isophotes of the broad-band images are almost perfectly circular to within approximately 0.5" (~ 50 pc) of the active nucleus, and an r**1/4 law provides a good fit to the galaxy profile to within the same distance. This result agrees with predictions that the nuclear supermassive black hole will produce a nearly spherical distribution of the surrounding stars within a galaxy crossing time. A difference image formed from the 1.6 micron image and a V-band image obtained with the HST Wide Field Planetary Camera 2 does not show any clear evidence of a physically thick dusty torus around the nucleus, consistent with its lack of strong thermal infrared emission. The images and associated colors also confirm that the regions beyond the nucleus do not contain strongly concentrated dust,in contrast to many other radio galaxies. In combination with other recent observations, these results indicate that M87 represents the dynamically evolved product of past galaxy mergers, and suggest that its nucleus is in the final stages of activity.Comment: Accepted for publication in the Astronomical Journa

A sample of radio-loud QSOs at redshift ~ 4

We obtained spectra of 60 red, starlike objects (E< 18.8) identified with FIRST radio sources, S_{1.4GHz} > 1 mJy. Eight are QSOs with redshift z> 3.6.Combined with our pilot search (Benn et al 2002), our sample of 121 candidates yields a total of 18 z > 3.6 QSOs (10 of these with z > 4.0). 8% of candidates with S_{1.4GHz} 10 mJy are QSOs with z > 3.6. The surface density of E 1mJy, z> 4 QSOs is 0.003 deg^{-2}. This is currently the only well-defined sample of radio-loud QSOs at z ~ 4 selected independently of radio spectral index. The QSOs are highly luminous in the optical (8 have M_B < -28, q_0 = 0.5, H_0 = 50 kms^{-1}Mpc^{-1}). The SEDs are as varied as those seen in optical searches for high-redshift QSOs, but the fraction of objects with weak (strongly self-absorbed) Ly alpha emission is marginally higher (3 out of 18) than for high-redshift QSOs from SDSS (5 out of 96).Comment: Accepted for publication in MNRAS, 9 pages, Latex, 5 postscript figures, 1 landscape table (postscript

Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis

Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. CFS were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression.Comment: 18 pages, accepted for publication in BMC Bioinformatic