The Second Data Release of the Sloan Digital Sky Survey

The Sloan Digital Sky Survey (SDSS) has validated and made publicly available its Second Data Release. This data release consists of 3324 deg2 of five-band (ugriz) imaging data with photometry for over 88 million unique objects, 367,360 spectra of galaxies, quasars, stars, and calibrating blank sky patches selected over 2627 deg2 of this area, and tables of measured parameters from these data. The imaging data reach a depth of r ≈ 22.2 (95% completeness limit for point sources) and are photometrically and astrometrically calibrated to 2% rms and 100 mas rms per coordinate, respectively. The imaging data have all been processed through a new version of the SDSS imaging pipeline, in which the most important improvement since the last data release is fixing an error in the model fits to each object. The result is that model magnitudes are now a good proxy for point-spread function magnitudes for point sources, and Petrosian magnitudes for extended sources. The spectroscopy extends from 3800 to 9200 Å at a resolution of 2000. The spectroscopic software now repairs a systematic error in the radial velocities of certain types of stars and has substantially improved spectrophotometry. All data included in the SDSS Early Data Release and First Data Release are reprocessed with the improved pipelines and included in the Second Data Release. Further characteristics of the data are described, as are the data products themselves and the tools for accessing them

The First Data Release of the Sloan Digital Sky Survey

The Sloan Digital Sky Survey has validated and made publicly available its First Data Release. This consists of 2099 square degrees of five-band (u, g, r, i, z) imaging data, 186,240 spectra of galaxies, quasars, stars and calibrating blank sky patches selected over 1360 square degrees of this area, and tables of measured parameters from these data. The imaging data go to a depth of r ~ 22.6 and are photometrically and astrometrically calibrated to 2% rms and 100 milli-arcsec rms per coordinate, respectively. The spectra cover the range 3800--9200 A, with a resolution of 1800--2100. Further characteristics of the data are described, as are the data products themselves.Comment: Submitted to The Astronomical Journal. 16 pages. For associated documentation, see http://www.sdss.org/dr

A novel retinoic acid-response element requires an enhancer element mediator for transcriptional activation

The Col11a2 gene codes for α2(XI), a subunit of type XI collagen that is a critical component of the cartilage extracellular matrix. The 5′ regulatory region of Col11a2 was subjected to deletional analysis to detect any regulatory element in addition to the two known chondrocyte-specific enhancer elements B/C and D/E. Deletion of the region from −342 to −242 bp reduced transcriptional activity to less than 50% of wild-type, but the sequence showed no independent ability to increase transcription from a minimal promoter. When cloned downstream of the D/E enhancer, however, a subsection of the sequence nearly doubled transcriptional activity and produced an additional 3-fold activation in response to RA (retinoic acid). A 6-bp direct repeat, separated by 4 bp (a DR-4 element) near the 5′-end of this region, was found to be essential for its activity, and was further shown to bind the RA X receptor β in electrophoretic mobility-shift assays. The present study has revealed a novel RA-response element in Col11a2 that does not interact directly with the promoter, but instead requires the D/E enhancer to mediate transcriptional activation. Proteins bound at the enhancer, therefore, would be expected to affect the transcriptional response to RA. Such a system of regulation, particularly if found to be operating in other cartilage genes, could explain the conflicting responses RA produces in chondrocytes under different experimental conditions

The First Data Release of the Sloan Digital Sky Survey

The Sloan Digital Sky Survey (SDSS) has validated and made publicly available its First Data Release. This consists of 2099 deg2 of five-band (u, g, r, i, z) imaging data, 186,240 spectra of galaxies, quasars, stars and calibrating blank sky patches selected over 1360 deg2 of this area, and tables of measured parameters from these data. The imaging data go to a depth of r ≈ 22.6 and are photometrically and astrometrically calibrated to 2% rms and 100 mas rms per coordinate, respectively. The spectra cover the range 3800–9200 Å, with a resolution of 1800–2100. This paper describes the characteristics of the data with emphasis on improvements since the release of commissioning data (the SDSS Early Data Release) and serves as a pointer to extensive published and on-line documentation of the survey.Astronom

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field