Sox7 is dispensable for primitive endoderm differentiation from mouse ES cells

Abstract Background Primitive endoderm is a cell lineage segregated from the epiblast in the blastocyst and gives rise to parietal and visceral endoderm. Sox7 is a member of the SoxF gene family that is specifically expressed in primitive endoderm in the late blastocyst, although its function in this cell lineage remains unclear. Results Here we characterize the function of Sox7 in primitive endoderm differentiation using mouse embryonic stem (ES) cells as a model system. We show that ectopic expression of Sox7 in ES cells has a marginal effect on triggering differentiation into primitive endoderm-like cells. We also show that targeted disruption of Sox7 in ES cells does not affect differentiation into primitive endoderm cells in embryoid body formation as well as by forced expression of Gata6. Conclusions These data indicate that Sox7 function is supplementary and not essential for this differentiation from ES cells

Sox7 is dispensable for primitive endoderm differentiation from mouse ES cells.

BACKGROUND: Primitive endoderm is a cell lineage segregated from the epiblast in the blastocyst and gives rise to parietal and visceral endoderm. Sox7 is a member of the SoxF gene family that is specifically expressed in primitive endoderm in the late blastocyst, although its function in this cell lineage remains unclear. RESULTS: Here we characterize the function of Sox7 in primitive endoderm differentiation using mouse embryonic stem (ES) cells as a model system. We show that ectopic expression of Sox7 in ES cells has a marginal effect on triggering differentiation into primitive endoderm-like cells. We also show that targeted disruption of Sox7 in ES cells does not affect differentiation into primitive endoderm cells in embryoid body formation as well as by forced expression of Gata6. CONCLUSIONS: These data indicate that Sox7 function is supplementary and not essential for this differentiation from ES cells

Asteroid lightcurves from the Palomar Transient Factory survey: Rotation periods and phase functions from sparse photometry

We fit 54,296 sparsely-sampled asteroid lightcurves in the Palomar Transient Factory to a combined rotation plus phase-function model. Each lightcurve consists of 20+ observations acquired in a single opposition. Using 805 asteroids in our sample that have reference periods in the literature, we find the reliability of our fitted periods is a complicated function of the period, amplitude, apparent magnitude and other attributes. Using the 805-asteroid ground-truth sample, we train an automated classifier to estimate (along with manual inspection) the validity of the remaining 53,000 fitted periods. By this method we find 9,033 of our lightcurves (of 8,300 unique asteroids) have reliable periods. Subsequent consideration of asteroids with multiple lightcurve fits indicate 4% contamination in these reliable periods. For 3,902 lightcurves with sufficient phase-angle coverage and either a reliably-fit period or low amplitude, we examine the distribution of several phase-function parameters, none of which are bimodal though all correlate with the bond albedo and with visible-band colors. Comparing the theoretical maximal spin rate of a fluid body with our amplitude versus spin-rate distribution suggests that, if held together only by self-gravity, most asteroids are in general less dense than 2 g/cm$^3$, while C types have a lower limit of between 1 and 2 g/cm$^3$, in agreement with previous density estimates. For 5-20km diameters, S types rotate faster and have lower amplitudes than C types. If both populations share the same angular momentum, this may indicate the two types' differing ability to deform under rotational stress. Lastly, we compare our absolute magnitudes and apparent-magnitude residuals to those of the Minor Planet Center's nominal $G=0.15$, rotation-neglecting model; our phase-function plus Fourier-series fitting reduces asteroid photometric RMS scatter by a factor of 3.Comment: 35 pages, 29 figures. Accepted 15-Apr-2015 to The Astronomical Journal (AJ). Supplementary material including ASCII data tables will be available through the publishing journal's websit

ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis

Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated gene relationships based on co-expressed genes deduced from microarray data and the predicted cis elements. ATTED-II () includes the following features: (i) lists and networks of co-expressed genes calculated from 58 publicly available experimental series, which are composed of 1388 GeneChip data in A.thaliana; (ii) prediction of cis-regulatory elements in the 200 bp region upstream of the transcription start site to predict co-regulated genes amongst the co-expressed genes; and (iii) visual representation of expression patterns for individual genes. ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks