The Design and Operation of The Keck Observatory Archive

The Infrared Processing and Analysis Center (IPAC) and the W. M. Keck Observatory (WMKO) operate an archive for the Keck Observatory. At the end of 2013, KOA completed the ingestion of data from all eight active observatory instruments. KOA will continue to ingest all newly obtained observations, at an anticipated volume of 4 TB per year. The data are transmitted electronically from WMKO to IPAC for storage and curation. Access to data is governed by a data use policy, and approximately two-thirds of the data in the archive are public.Comment: 12 pages, 4 figs, 4 tables. Presented at Software and Cyberinfrastructure for Astronomy III, SPIE Astronomical Telescopes + Instrumentation 2014. June 2014, Montreal, Canad

RNA Recognition by the DNA End-Binding Ku Heterodimer

Most nucleic acid-binding proteins selectively bind either DNA or RNA, but not both nucleic acids. The Saccharomyces cerevisiae Ku heterodimer is unusual in that it has two very different biologically relevant binding modes: (1) Ku is a sequence-nonspecific double-stranded DNA end-binding protein with prominent roles in nonhomologous end-joining and telomeric capping, and (2) Ku associates with a specific stem–loop of TLC1, the RNA subunit of budding yeast telomerase, and is necessary for proper nuclear localization of this ribonucleoprotein enzyme. TLC1 RNA-binding and dsDNA-binding are mutually exclusive, so they may be mediated by the same site on Ku. Although dsDNA binding by Ku is well studied, much less is known about what features of an RNA hairpin enable specific recognition by Ku. To address this question, we localized the Ku-binding site of the TLC1 hairpin with single-nucleotide resolution using phosphorothioate footprinting, used chemical modification to identify an unpredicted motif within the hairpin secondary structure, and carried out mutagenesis of the stem–loop to ascertain the critical elements within the RNA that permit Ku binding. Finally, we provide evidence that the Ku-binding site is present in additional budding yeast telomerase RNAs and discuss the possibility that RNA binding is a conserved function of the Ku heterodimer

Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials

Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to the centroid of the Voronoi cell in which the particle resides. These vectors tend to point in toward regions of high free volume and away from regions of low free volume, reminiscent of sinks and sources in a vector field. We compute the local divergence of these vectors, where positive values correspond to overpacked regions and negative values identify underpacked regions within the material. Distributions of this divergence are nearly Gaussian with zero mean, allowing for structural characterization using only the moments of the distribution. We explore how the standard deviation and skewness vary with the packing fraction for simulations of bidisperse systems and find a kink in these moments that coincides with the jamming transition

Treatment intensity and characteristics of MRSA infection in CF

Background: Prevalence of methicillin-resistant Staphylococcus aureus (MRSA) and interchange of hospital-associated strains carrying the staphylococcal chromosomal cassette mec-II (SCCmec-II) with those in the community (SCCmec-IV) has increased. This study assesses the impact of MRSA and different MRSA types on clinical outcomes, medication use, and antibiotic sensitivities. Methods: MRSA isolates from CF patients at our center were typed by SCCmec- and pvl status. Patient characteristics, lung function and nutrition are compared between MRSA types and to age, gender and Pseudomonas aeruginosa matched patients with chronic methicillin sensitive S. aureus (MSSA) infection. Results: Seventy-two percent of patients carry pvl negative SCCmec-II isolates. Seventeen percent of all MRSA were SCCmec-IV pvl positive (USA300). These patients were younger and fewer had chronic P. aeruginosa infection, whereas pvl-negative SCCmec-IV isolates show highest antibiotic resistance. Nutritional outcomes and FEV1 percent predicted (75.1±2.7 versus 77.9±2.7) did not differ in patients with MRSA compared to those with MSSA but MRSA patients received more pulmonary maintenance but not oral antibiotic medications. Conclusion: Patients with chronic MRSA are treated more intensely than age, gender and Pseudomonas aeruginosa matched MSSA-positive patients but clinical characteristics within MRSA patients vary depending on MRSA types

Closing the brief case: A Fatal Case of Necrotizing Fasciitis Due to Multidrug-Resistant Acinetobacter baumannii

ANSWERS TO SELF-ASSESSMENT QUESTIONS 1. What is the most common etiology of monomicrobial (type 2) necrotizing fasciitis? a. Acinetobacter baumannii b. Staphylococcus aureus c. Streptococcus pyogenes d. Vibrio vulnificus Answer: c. Although all of the organisms listed cause type 2 necrotizing fasciitis, the most common cause is still S. pyogenes, with an incidence of 0.4 per 100,000 in the United States. Due to variations in reporting practices, the exact incidences of other etiologies are not known, but they are less common than S. pyogenes

Interactions of HMGB Proteins with the Genome and the Impact on Disease

High Mobility Group Box (HMGB) proteins are small architectural DNA binding proteins that regulate multiple genomic processes such as DNA damage repair, nucleosome sliding, telomere homeostasis, and transcription. In doing so they control both normal cellular functions and impact a myriad of disease states, including cancers and autoimmune diseases. HMGB proteins bind to DNA and nucleosomes to modulate the local chromatin environment, which facilitates the binding of regulatory protein factors to the genome and modulates higher order chromosomal organization. Numerous studies over the years have characterized the structure and function of interactions between HMGB proteins and DNA, both biochemically and inside cells, providing valuable mechanistic insight as well as evidence these interactions influence pathological processes. This review highlights recent studies supporting the roles of HMGB1 and HMGB2 in global organization of the genome, as well as roles in transcriptional regulation and telomere maintenance via interactions with G-quadruplex structures. Moreover, emerging models for how HMGB proteins function as RNA binding proteins are presented. Nuclear HMGB proteins have broad regulatory potential to impact numerous aspects of cellular metabolism in normal and disease states. &nbsp;</p

Interstellar Polarization and the Position Angle Orientations of Seyfert 1 Galaxies

We comment on recent spectropolarimetric studies that compare the observed polarization position angles (PAs) of Seyfert 1 galaxies near H alpha with the observed orientations of their radio source axes on the sky. For a Seyfert galaxy in which scattering occurs mainly in an equatorial scattering region, one expects the polarization PA to be parallel to the radio axis, while in a case in which light scatters predominantly in the polar regions, the H alpha polarization PA should be perpendicular to the radio axis. In practice, these correlations are difficult to establish because a Galactic interstellar polarization contribution can introduce a significant uncertainty into the polarization PA determination, even when the magnitude of interstellar polarization is small. We show how such uncertainties may affect the analysis of PA alignments and present spectropolarimetric observations of a probe star along the line of sight to the Seyfert 1 galaxy Mrk 871 that allow us to assess the intrinsic H alpha polarization and PA of Mrk 871. These results suggest that spectropolarimetric observations of such probe stars should form an integral part of future Seyfert galaxy polarization studies.Comment: 15 pages, 3 figures, accepted by MNRAS; made small corrections to the derived ISP of Mrk 871 and other minor revisions in response to the referee's recommendation

Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity.

Transcription by RNA polymerase II (Pol II) is a complex process that requires general transcription factors and Pol II to assemble on DNA into preinitiation complexes that can begin RNA synthesis upon binding of NTPs (nucleoside triphosphate). The pathways by which preinitiation complexes form, and how this impacts transcriptional activity are not completely clear. To address these issues, we developed a single molecule system using TIRF (total internal reflection fluorescence) microscopy and purified human transcription factors, which allows us to visualize transcriptional activity at individual template molecules. We see that stable interactions between polymerase II (Pol II) and a heteroduplex DNA template do not depend on general transcription factors; however, transcriptional activity is highly dependent upon TATA-binding protein, TFIIB and TFIIF. We also found that subsets of general transcription factors and Pol II can form stable complexes that are precursors for functional transcription complexes upon addition of the remaining factors and DNA. Ultimately we found that Pol II, TATA-binding protein, TFIIB and TFIIF can form a quaternary complex in the absence of promoter DNA, indicating that a stable network of interactions exists between these proteins independent of promoter DNA. Single molecule studies can be used to learn how different modes of preinitiation complex assembly impact transcriptional activity

Scopolamine and Pavlovian fear conditioning in rats: dose-effect analysis

Muscarinic-cholinergic antagonism produces learning and memory deficits in a wide variety of hippocampal-dependent tasks. Hippocampal lesions produce both acquisition deficits and retrograde amnesia of contextual fear (fear of the place of conditioning), but do not impact fear conditioning to discrete cues (such as a tone). In order to examine the effects of muscarinic antagonism in this paradigm, rats were given 0.01 to 100 mg/kg of scopolamine (or methylscopolamine) either before or after a fear conditioning session in which tones were paired with aversive footshocks. Fear to the context and the tone were assessed by measuring freezing in separate tests. It was found that pretraining, but not post-training, scopolamine severely impaired fear conditioning; methylscopolamine was ineffective in disrupting conditioning. Although contextual fear conditioning was more sensitive to cholinergic disruption, high doses of scopolamine also disrupted tone conditioning. Scopolamine did not affect footshock reactivity, but did produce high levels of activity. However, hyperactivity was not directly responsible for deficits in conditioning. It was concluded that scopolamine disrupts CS-US association formation or CS processing, perhaps through an attenuation of hippocampal theta rhythm.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/56239/1/anagNPHARM99.pd

Gene therapy approaches for equine osteoarthritis

With an intrinsically low ability for self-repair, articular cartilage injuries often progress to cartilage loss and joint degeneration resulting in osteoarthritis (OA). Osteoarthritis and the associated articular cartilage changes can be debilitating, resulting in lameness and functional disability both in human and equine patients. While articular cartilage damage plays a central role in the pathogenesis of OA, the contribution of other joint tissues to the pathogenesis of OA has increasingly been recognized thus prompting a whole organ approach for therapeutic strategies. Gene therapy methods have generated significant interest in OA therapy in recent years. These utilize viral or non-viral vectors to deliver therapeutic molecules directly into the joint space with the goal of reprogramming the cells' machinery to secrete high levels of the target protein at the site of injection. Several viral vector-based approaches have demonstrated successful gene transfer with persistent therapeutic levels of transgene expression in the equine joint. As an experimental model, horses represent the pathology of human OA more accurately compared to other animal models. The anatomical and biomechanical similarities between equine and human joints also allow for the use of similar imaging and diagnostic methods as used in humans. In addition, horses experience naturally occurring OA and undergo similar therapies as human patients and, therefore, are a clinically relevant patient population. Thus, further studies utilizing this equine model would not only help advance the field of human OA therapy but also benefit the clinical equine patients with naturally occurring joint disease. In this review, we discuss the advancements in gene therapeutic approaches for the treatment of OA with the horse as a relevant patient population as well as an effective and commonly utilized species as a translational model