Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells

<p>Abstract</p> <p>Background</p> <p>Recently, we demonstrated that human mesenchymal stem cells (hMSC) stimulated with dexamethazone undergo gene focusing during osteogenic differentiation (<it>Stem Cells Dev </it>14(6): 1608–20, 2005). Here, we examine the protein expression profiles of three additional populations of hMSC stimulated to undergo osteogenic differentiation via either contact with pro-osteogenic extracellular matrix (ECM) proteins (collagen I, vitronectin, or laminin-5) or osteogenic media supplements (OS media). Specifically, we annotate these four protein expression profiles, as well as profiles from naïve hMSC and differentiated human osteoblasts (hOST), with known gene ontologies and analyze them as a tensor with modes for the expressed proteins, gene ontologies, and stimulants.</p> <p>Results</p> <p>Direct component analysis in the gene ontology space identifies three components that account for 90% of the variance between hMSC, osteoblasts, and the four stimulated hMSC populations. The directed component maps the differentiation stages of the stimulated stem cell populations along the differentiation axis created by the difference in the expression profiles of hMSC and hOST. Surprisingly, hMSC treated with ECM proteins lie closer to osteoblasts than do hMSC treated with OS media. Additionally, the second component demonstrates that proteomic profiles of collagen I- and vitronectin-stimulated hMSC are distinct from those of OS-stimulated cells. A three-mode tensor analysis reveals additional focus proteins critical for characterizing the phenotypic variations between naïve hMSC, partially differentiated hMSC, and hOST.</p> <p>Conclusion</p> <p>The differences between the proteomic profiles of OS-stimulated hMSC and ECM-hMSC characterize different transitional phenotypes en route to becoming osteoblasts. This conclusion is arrived at via a three-mode tensor analysis validated using hMSC plated on laminin-5.</p

Fundamental Parameters and Abundances of Metal-Poor Stars: The SDSS Standard BD +17 4708

The atmospheric parameters and iron abundance of the Sloan Digital Sky Survey (SDSS) spectrophotometric standard star BD +17 4708 are critically examined using up-to-date Kurucz model atmospheres, LTE line formation calculations, and reliable atomic data. We find Teff = 6141+-50 K, log g = 3.87+-0.08, and [Fe/H]=-1.74+-0.09. The line-of-sight interstellar reddening, bolometric flux, limb-darkened angular diameter, stellar mass, and the abundances of Mg, Si, and Ca are also obtained. This star is a unique example of a moderately metal-poor star for which the effective temperature can be accurately constrained from the observed spectral energy distribution (corrected for reddening). Such analysis leads to a value that is higher than most spectroscopic results previously reported in the literature (~5950 K). We find that the ionization balance of Fe lines is satisfied only if a low Teff (~5950 K) is adopted. With our preferred Teff (6141 K), the mean iron abundance we obtain from the FeII lines is lower by about 0.15 dex than that from the FeI lines, and therefore, the discrepancy between the mean iron abundance from FeI and FeII lines cannot be explained by overionization by UV photons as the main non-LTE effect. We also comment on non-LTE effects and the importance of inelastic collisions with neutral H atoms in the determination of oxygen abundances in metal-poor stars from the 777 nm OI triplet. (Abridged)Comment: A&A in pres

Glucagonoma Masquerading as a Mucinous Cancer of the Ovary: Lessons from Cell Biology

High-grade mucinous ovarian cancer (HGMOC) is often a misnomer as the majority of cases are metastatic disease with a gastro-intestinal origin. The standard platinum-based ovarian cancer (OC) chemotherapy regimens are often ineffective, and there are insufficient data to support the use of colorectal cancer (CRC) chemotherapy regimens due to the rarity of HGMOC. We described a cohort of four consecutive suspected HGMOC cases treated at the Royal Women’s Hospital, Melbourne in 2012. Two cases were treated as primary MOC, whereas the other two were considered to be metastatic CRC based on histopathological and clinical evidence. From the RNAseq analysis, we identified two cases of HGMOC whose gene expression profiles were consistent with mucinous epithelial OC, one case that was treated as metastatic CRC with gene expression profile correlated with CRC and one case with neuroendocrine (NET) gene expression features. Interestingly, glucagon was over-expressed in this tumor that was subsequently confirmed by immunohistochemistry. These findings suggest a rare glucagonoma-like NET appendiceal tumor that had metastasized to the surface of ovary and were unresponsive to CRC chemotherapy regimens. In summary, a carefully curated panel of expression markers and selected functional genomics could provide diagnosis and treatment guidance for patients with possible HGMOC

The Star Formation History and Dust Content in the Far Outer Disc of M31

We present a detailed analysis of two fields located 26 kpc (~5 scalelengths) from the centre of M31. One field samples the major axis populations--the Outer Disc field--while the other is offset by ~18' and samples the Warp in the stellar disc. The CMDs based on HST/ACS imaging reach old main-sequence turn-offs (~12.5 Gyr). We apply the CMD-fitting technique to the Warp field to reconstruct the star formation history (SFH). We find that after undergoing roughly constant SF until about 4.5 Gyr ago, there was a rapid decline in activity and then a ~1.5 Gyr lull, followed by a strong burst lasting 1.5 Gyr and responsible for 25% of the total stellar mass in this field. This burst appears to be accompanied by a decline in metallicity which could be a signature of the inflow of metal-poor gas. The onset of the burst (~3 Gyr ago) corresponds to the last close passage of M31 and M33 as predicted by detailed N-body modelling, and may have been triggered by this event. We reprocess the deep M33 outer disc field data of Barker et al. (2011) in order to compare consistently-derived SFHs. This reveals a similar duration burst that is exactly coeval with that seen in the M31 Warp field, lending further support to the interaction hypothesis. The complex SFHs and the smoothly-varying age-metallicity relations suggest that the stellar populations observed in the far outer discs of both galaxies have largely formed in situ rather than migrated from smaller galactocentric radii. The strong differential reddening affecting the CMD of the Outer Disc field prevents derivation of the SFH. Instead, we quantify this reddening and find that the fine-scale distribution of dust precisely follows that of the HI gas. This indicates that the outer HI disc of M31 contains a substantial amount of dust and therefore suggests significant metal enrichment in these parts, consistent with inferences from our CMD analysis.Comment: Abstract shortened. 17 pages, 12 figures (+ 6 pages & 5 figures in Appendix). MNRAS, in pres

Limits on the gravity wave contribution to microwave anisotropies

We present limits on the fraction of large angle microwave anisotropies which could come from tensor perturbations. We use the COBE results as well as smaller scale CMB observations, measurements of galaxy correlations, abundances of galaxy clusters, and Lyman alpha absorption cloud statistics. Our aim is to provide conservative limits on the tensor-to-scalar ratio for standard inflationary models. For power-law inflation, for example, we find T/S<0.52 at 95% confidence, with a similar constraint for phi^p potentials. However, for models with tensor amplitude unrelated to the scalar spectral index it is still currently possible to have T/S>1.Comment: 23 pages, 7 figures, accepted for publication in Phys. Rev. D. Calculations extended to blue spectral index, Fig. 6 added, discussion of results expande

The Fifth Data Release of the Sloan Digital Sky Survey

This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through June 2005 and represents the completion of the SDSS-I project (whose successor, SDSS-II will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 square degrees, and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 square degrees of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.Comment: ApJ Supp, in press, October 2007. This paper describes DR5. The SDSS Sixth Data Release (DR6) is now public, available from http://www.sdss.or

Activation of PI3K/mTOR pathway occurs in most adult low-grade gliomas and predicts patient survival

Recent evidence suggests the Akt-mTOR pathway may play a role in development of low-grade gliomas (LGG). We sought to evaluate whether activation of this pathway correlates with survival in LGG by examining expression patterns of proteins within this pathway. Forty-five LGG tumor specimens from newly diagnosed patients were analyzed for methylation of the putative 5′-promoter region of PTEN using methylation-specific PCR as well as phosphorylation of S6 and PRAS40 and expression of PTEN protein using immunohistochemistry. Relationships between molecular markers and overall survival (OS) were assessed using Kaplan-Meier methods and exact log-rank test. Correlation between molecular markers was determined using the Mann-Whitney U and Spearman Rank Correlation tests. Eight of the 26 patients with methylated PTEN died, as compared to 1 of 19 without methylation. There was a trend towards statistical significance, with PTEN methylated patients having decreased survival (P = 0.128). Eight of 29 patients that expressed phospho-S6 died, whereas all 9 patients lacking p-S6 expression were alive at last follow-up. There was an inverse relationship between expression of phospho-S6 and survival (P = 0.029). There was a trend towards decreased survival in patients expressing phospho-PRAS40 (P = 0.077). Analyses of relationships between molecular markers demonstrated a statistically significant positive correlation between expression of p-S6(235) and p-PRAS40 (P = 0.04); expression of p-S6(240) correlated positively with PTEN methylation (P = 0.04) and negatively with PTEN expression (P = 0.03). Survival of LGG patients correlates with phosphorylation of S6 protein. This relationship supports the use of selective mTOR inhibitors in the treatment of low grade glioma

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

The Sloan Digital Sky Survey (SDSS) started a new phase in August 2008, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Ly alpha forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg^2 in the Southern Galactic Cap, bringing the total footprint of the SDSS imaging to 14,555 deg^2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Evolution (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameters pipeline, which has better determination of metallicity for high metallicity stars.Comment: Astrophysical Journal Supplements, in press (minor updates from submitted version

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