Absorption Systems In Radio-Selected QSO Surveys

Radio-selected samples of quasars with complete optical identifications offer an ideal dataset with which to investigate dust bias associated with intervening absorption systems. Here, we review our work on the Complete Optical and Radio Absorption Line System (CORALS) survey whose aim is to quantify this bias and assess the impact of dust on absorber statistics. First, we review previously published results on the number density and gas content of high column density absorbers over the redshift range 0.6 < z < 3.5. We then present the latest results from CORALS which focus on measuring the metal content of our unbiased absorber sample and an investigation of their optical--IR colours. Overall we find that although dust is unarguably present in absorption galaxies, the level appears to be low enough that the statistics of previous magnitude limited samples have not been severely affected and that the subsequent reddening of background QSOs is small.Comment: Proceedings of IAUC199, Probing Galaxies through Quasar Absorption Lines, P. R. Williams, C. Shu, and B. Menard, ed

In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus.

Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump their genome into a preformed capsid, single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host 'sex pilus' (F-pilus); it was the first fully sequenced organism and is a model system for studies of translational gene regulation, RNA-protein interactions, and RNA virus assembly. Its positive-sense ssRNA genome of 3,569 bases is enclosed in a capsid with one maturation protein monomer and 89 coat protein dimers arranged in a T = 3 icosahedral lattice. The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection, but how the genome is organized and delivered is not known. Here we describe the MS2 structure at 3.6 Å resolution, determined by electron-counting cryo-electron microscopy (cryoEM) and asymmetric reconstruction. We traced approximately 80% of the backbone of the viral genome, built atomic models for 16 RNA stem-loops, and identified three conserved motifs of RNA-coat protein interactions among 15 of these stem-loops with diverse sequences. The stem-loop at the 3' end of the genome interacts extensively with the maturation protein, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus and joins 89 coat protein dimers to form a capsid. This atomic description of genome-capsid interactions in a spherical ssRNA virus provides insight into genome delivery via the host sex pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires speculation about the links between nucleoprotein complexes and the origins of viruses

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.ImportanceTo fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available

Developing an instrument for Iranian EFL learners' listening comprehension problems and listening strategies

In the body of literature on listening strategies to EFL learners, what seems to be lacking is that the focus is on teaching listening strategies to learners with little attention to their listening comprehension problems. No local research has been conducted on the nature of the Iranian tertiary level students' EFL listening comprehension problems or strategies. Therefore, no instrument is available to investigate these constructs. This paper reports the findings of a study that made an attempt to develop and test an instrument that will aid researchers identify students’ specific listening problems and listening strategy repertoire. The instrument was developed by integrating and validating the available instruments in the related literature. The two developed questionnaires were: the Listening Comprehension Problems Questionnaire (LCPQ) and the Listening Strategy Use Questionnaire (LSUQ). Problems related to designing and testing this instrument is shared and the modifications made to it are presented. The instrument is expected to be useful for researchers interested to study the area of EFL listening in a similar setting

Iranian EFL Students’ Listening Comprehension Problems

English as a Foreign Language (EFL) listening skill is considered a problematic skill particularly in a foreign language context where practice opportunities are limited. This study aimed to explore the listening comprehension problems of a group of EFL learners. Survey method was followed to collect data from a group of Iranian tertiary level EFL learners (n = 100) using the Listening Comprehension Processing Problems Questionnaire. The results indicated that the learners experienced moderate to high levels of difficulty in all three categories of listening comprehension problems, namely perception, parsing, and utilization. The findings are expected to have useful implications for syllabus designers and teachers who intend to address the listening comprehension problems of EFL learners

Comparison of bicarbonate values from venous blood gas and chemistry panels measured at the time of diagnosis and resolution of diabetes ketoacidosis

Objective: To determine if bicarbonate values from venous blood gas (VBG) and plasma chemistry samples provided agreement in determining the bicarbonate criteria for the diagnosis and/or resolution of diabetic ketoacidosis (DKA). Methods: A retrospective chart review of data from patients admitted to a tertiary care hospital with a diagnosis of DKA over a four year period was performed. Paired bicarbonate values from a VBG and chemistry panel, if drawn within 60minutes of each other, were compared. Results: At the time of diagnosis of DKA, 197 paired bicarbonate values were available for analysis with the mean difference between the two methods of testing of 2.5mmol/L. 16 of the 197 (8%) paired values were discordant in meeting criteria for diagnosis of DKA. At the time of resolution of DKA, 83 paired bicarbonate samples were compared. The mean difference was 2.3mmol/L. 20 of the 83 (24%) paired bicarbonate values showed discordance with regards to meeting the bicarbonate criteria for resolution of DKA. Conclusion: Discordance between bicarbonate results from different analysis methods may lead to different determinations as to whether or not a patient meets the biochemical definition for diagnosis and resolution of DKA

Efficient Prodrug Activator Gene Therapy by Retroviral Replicating Vectors Prolongs Survival in an Immune-Competent Intracerebral Glioma Model.

Prodrug activator gene therapy mediated by murine leukemia virus (MLV)-based retroviral replicating vectors (RRV) was previously shown to be highly effective in killing glioma cells both in culture and in vivo. To avoid receptor interference and enable dual vector co-infection with MLV-RRV, we have developed another RRV based on gibbon ape leukemia virus (GALV) that also shows robust replicative spread in a wide variety of tumor cells. We evaluated the potential of GALV-based RRV as a cancer therapeutic agent by incorporating yeast cytosine deaminase (CD) and E. coli nitroreductase (NTR) prodrug activator genes into the vector. The expression of CD and NTR genes from GALV-RRV achieved highly efficient delivery of these prodrug activator genes to RG-2 glioma cells, resulting in enhanced cytotoxicity after administering their respective prodrugs 5-fluorocytosine and CB1954 in vitro. In an immune-competent intracerebral RG-2 glioma model, GALV-mediated CD and NTR gene therapy both significantly suppressed tumor growth with CB1954 administration after a single injection of vector supernatant. However, NTR showed greater potency than CD, with control animals receiving GALV-NTR vector alone (i.e., without CB1954 prodrug) showing extensive tumor growth with a median survival time of 17.5 days, while animals receiving GALV-NTR and CB1954 showed significantly prolonged survival with a median survival time of 30 days. In conclusion, GALV-RRV enabled high-efficiency gene transfer and persistent expression of NTR, resulting in efficient cell killing, suppression of tumor growth, and prolonged survival upon CB1954 administration. This validates the use of therapeutic strategies employing this prodrug activator gene to arm GALV-RRV, and opens the door to the possibility of future combination gene therapy with CD-armed MLV-RRV, as the latter vector is currently being evaluated in clinical trials

The Coiled-coil Domain Is the Structural Determinant for Mammalian Homologues of Drosophila Sina-mediated Degradation of Promyelocytic Leukemia Protein and Other Tripartite Motif Proteins by the Proteasome

Mammalian homologues of Drosophila Seven in Absentia (SIAHs) target for proteasome-mediated degradation several factors involved in cell growth and tumorigenesis. Here we show that SIAH-1/2 binds and targets for proteasome-mediated degradation the putative tumor suppressor and tripartite motif (TRIM) family member PML, leading to the loss of its transcriptional co-activating properties and a reduction in the number of endogenous PML nuclear bodies. Association with PML requires the substrate-binding domain (SBD) of SIAH-1/2 through an interacting surface apparently distinct from those predicted by the structural studies, or shown experimentally to mediate binding to SIAH-associated factors. Within PML, the coiled-coil domain is required for Siah- and proteasome-mediated degradation, and deletions of regions critical for the integrity of this region impair the ability of Siah to trigger PML-RAR degradation. Fusion of the coiled-coil domain to heterologous proteins resulted in the capacity of mSiah-2 to target their degradation. All of the TRIM proteins tested were degraded upon mSiah-2 overexpression. Finally, we show that the fusion protein PML-RAR (that retains the coiled-coil domain), which causes acute promyelocytic leukemias, is also a potential substrate of mSiah-2. As a result of mSiah-2 overexpression and subsequent degradation of the fusion protein, the arrest in hematopoietic differentiation because of expression of PML-RAR is partially rescued. These results identify PML and other TRIMs as new factors post-translationally regulated by SIAH and involve the coiled-coil region of PML and of other SIAH substrates as a novel structural determinant for targeted degradation