The Seventh Data Release of the Sloan Digital Sky Survey

This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11663 deg^2 of imaging data, with most of the roughly 2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry over 250 deg^2 along the Celestial Equator in the Southern Galactic Cap. A coaddition of these data goes roughly two magnitudes fainter than the main survey. The spectroscopy is now complete over a contiguous area of 7500 deg^2 in the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog (UCAC-2), reducing the rms statistical errors at the bright end to 45 milli-arcseconds per coordinate. A systematic error in bright galaxy photometr is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat-fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities. (Abridged)Comment: 20 pages, 10 embedded figures. Accepted to ApJS after minor correction

Is Female Sexual Dysfunction Related to Personality and Coping? An Exploratory Study

AbstractIntroductionSexual disorders impact up to 43% of women. However, the relationship between sexual dysfunction and psychological variables such as personality traits and coping mechanisms is not well understood.AimTo examine personality domains and coping strategies utilized by women with sexual dysfunction in a clinical sample.MethodsPatients seeking care for female sexual dysfunction (FSD) from a sexual medicine specialist were identified using International Classification of Diseases, Ninth Revision codes. Packets containing informed consent, Female Sexual Function Index (FSFI), Female Sexual Distress Scale‐Revised (FSDS‐R), Ten Item Personality Index (TIPI), and Brief COPE were mailed to subjects.Main Outcome MeasuresCorrelations among FSFI, FSDS‐R, TIPI, and Brief COPE.ResultsOf 79 eligible subjects, 50 (63.2%) returned completed questionnaires. The mean age was 40 years (standard deviation 14). Total FSFI and FSDS‐R scores confirmed FSD. Correlations between the FSFI and TIPI illustrated trends with the domain of extraversion, suggesting better function in those exhibiting more of this trait (r = 0.285, P = 0.079). Similarly, FSDS‐R scores correlated with openness to experience (r = −0.305, P = 0.037) and approached significance for extraversion (r = −0.258, P = 0.080), indicating lower distress in such personality types. When assessing the Brief COPE, use of emotional support, a positive coping strategy, correlated with better orgasm (r = 0.303, P = 0.048) and higher satisfaction (r = 0.331, P = 0.03). Finally, when evaluating TIPI with COPE scores, several significant associations were noted, establishing that personality may influence these adaptive behaviors.ConclusionMany notable relationships between sexual function, personality, and coping are presented. These support a role for consideration of psychological variables when evaluating women presenting for sexual dysfunction. Crisp CC, Vaccaro CM, Pancholy A, Kleeman S, Fellner AN, and Pauls R. Is female sexual dysfunction related to personality and coping? An exploratory study. Sex Med 2013;1:69–75

Roundup Ready® soybean gene concentrations in field soil aggregate size classes

Roundup Ready® (RR) soybeans containing recombinant Agrobacterium spp. CP4 5-enol-pyruvyl-shikimate-3-phosphate synthase (cp4 epsps) genes tolerant to the herbicide glyphosate are extensively grown worldwide. The concentration of recombinant DNA from RR soybeans in soil aggregates was studied due to the possibility of genetic transformation of soil bacteria. This study used real-time PCR to examine the concentration of cp4 epsps in four field soil aggregate size classes (>2000 μm, 2000–500 μm, 500–250 μm and < 2000 μm fraction contained between 66.62% and 99.18% of total gene copies, although it only accounted for about 30.00% of the sampled soil. Aggregate formation may facilitate persistence of recombinant DNA

An empirical approach to target DNA quantification in environmental samples using real-time polymerase chain reactions

Recent advances in molecular techniques have allowed for the routine examination of nucleic acids in environmental samples. Although current methodologies are very sensitive, accurate target DNA quantification from environmental samples remains challenging. To facilitate high-throughput DNA quantification from environmental samples, we developed a novel DNA quantification method based on a non-linear curve-fitting approach to extract additional information from quantitative PCR amplification curves and used the fitted parameters to develop multiple regression standard equations for target DNA quantification. A 3-parameter sigmoidal function performed superior to a 4-parameter Weibull function for generating the multiple regression standard equations. In a verification experiment, target DNA was quantified in a series of ‘unknown’ samples in three soils using this approach and the results were compared to target DNA values determined using corrected and uncorrected Ct-based (threshold cycle) methods. For each method, the deviations from the expected target DNA content were determined. Results clearly showed that over all DNA concentrations, target DNA content determined by the non-linear curve-fitting method was more accurate and more precise than values predicted by all other methods. Analysis of variance conducted on the predicted DNA contents also revealed fewer statistical artifacts with the non-linear curve fitting method compared to the conventional Ct-based methods. The novel approach described here is accurate, inexpensive, and very amenable for automation and high-throughput applications

Cycling of extracellular DNA in the soil environment

Upon entering the soil environment, extracellular DNA is subjected to dynamic biological, physical, and chemical factors that determine its fate. This review concerns the fate of both recombinant and non-recombinant sources of DNA. A schematic of DNA cycling coupled with genetic transformation is presented to understand its behavior in soil. Extracellular DNA may persist through cation bridging onto soil minerals and humic substances, be enzymatically degraded and restricted by DNases of microbial origin, and/or enter the microbial DNA cycle through natural transformation of competent bacteria. Lateral gene transfer may disseminate DNA through the microbial community. An understanding of DNA cycling is fundamental to elucidating the fate of extracellular DNA in the soil environment

Mycorrhizal and Rhizobial Colonization of Genetically Modified and Conventional Soybeans▿

We grew plants of nine soybean varieties, six of which were genetically modified to express transgenic cp4-epsps, in the presence of Bradyrhizobium japonicum and arbuscular mycorrhizal fungi. Mycorrhizal colonization and nodule abundance and mass differed among soybean varieties; however, in no case was variation significantly associated with the genetic modification

Real-time polymerase chain reaction monitoring of recombinant DNA entry into soil from decomposing Roundup Ready leaf biomass

Glyphosate-tolerant, Roundup Ready (RR) soybeans account for about 57% of all genetically modified (GM) crops grown worldwide. The entry of recombinant DNA into soil from GM crops has been identified as an environmental concern due to the possibility of their horizontal transfer to soil microorganisms. RR soybeans contain recombinant gene sequences that can be differentiated from wild-type plant and microbial genes in soil by using a sequence-specific molecular beacon and real-time polymerase chain reaction (PCR). A molecular beacon-based real-time PCR system to quantify a wild-type soybean lectin (le1) gene was designed to compare amounts of endogenous soybean genes to recombinant DNA in soil. Microcosm studies were carried out to develop methodologies for the detection of recombinant DNA from RR soybeans in soil. RR soybean leaf litterbags were imbedded in the soil under controlled environmental conditions (60% water holding capacity, 10/15 °C, and 8/16 h day/night) for 30 days. The soybean biomass decomposition was described using a single-phase exponential equation, and the DNA concentration in planta and in soil was quantified using real-time PCR using sequence-specific molecular beacons for the recombinant cp4 epsps and endogenous soybean lectin (le1) genes. The biomass of RR soybean leaves was 8.6% less than nontransgenic (NT) soybean leaves after 30 days. The pooled half-disappearance time for cp4 epsps and le1 in RR and of le1 in NT soybean leaves was 1.4 days. All genes from leaves were detected in soil after 30 days. This study provides a methodology for monitoring the entry of RR and NT soybean DNA into soil from decomposing plant residues