A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis

Transcriptional enhancers integrate the contributions of multiple classes of transcription factors (TFs) to orchestrate the myriad spatio-temporal gene expression programs that occur during development. A molecular understanding of enhancers with similar activities requires the identification of both their unique and their shared sequence features. To address this problem, we combined phylogenetic profiling with a DNA–based enhancer sequence classifier that analyzes the TF binding sites (TFBSs) governing the transcription of a co-expressed gene set. We first assembled a small number of enhancers that are active in Drosophila melanogaster muscle founder cells (FCs) and other mesodermal cell types. Using phylogenetic profiling, we increased the number of enhancers by incorporating orthologous but divergent sequences from other Drosophila species. Functional assays revealed that the diverged enhancer orthologs were active in largely similar patterns as their D. melanogaster counterparts, although there was extensive evolutionary shuffling of known TFBSs. We then built and trained a classifier using this enhancer set and identified additional related enhancers based on the presence or absence of known and putative TFBSs. Predicted FC enhancers were over-represented in proximity to known FC genes; and many of the TFBSs learned by the classifier were found to be critical for enhancer activity, including POU homeodomain, Myb, Ets, Forkhead, and T-box motifs. Empirical testing also revealed that the T-box TF encoded by org-1 is a previously uncharacterized regulator of muscle cell identity. Finally, we found extensive diversity in the composition of TFBSs within known FC enhancers, suggesting that motif combinatorics plays an essential role in the cellular specificity exhibited by such enhancers. In summary, machine learning combined with evolutionary sequence analysis is useful for recognizing novel TFBSs and for facilitating the identification of cognate TFs that coordinate cell type–specific developmental gene expression patterns

Sexual dimorphism in cancer.

The incidence of many types of cancer arising in organs with non-reproductive functions is significantly higher in male populations than in female populations, with associated differences in survival. Occupational and/or behavioural factors are well-known underlying determinants. However, cellular and molecular differences between the two sexes are also likely to be important. In this Opinion article, we focus on the complex interplay that sex hormones and sex chromosomes can have in intrinsic control of cancer-initiating cell populations, the tumour microenvironment and systemic determinants of cancer development, such as the immune system and metabolism. A better appreciation of these differences between the two sexes could be of substantial value for cancer prevention as well as treatment

Generation and Relaxation of Microstrains in GaN Nanocrystals under Extreme Pressures

Nanocrystalline powders of GaN with grain sizes ranging from 2 to 30 nm were examined under high external pressures by in situ diffraction techniques in a diamond anvil cell at DESY (HASYLAB, Station F3). The experiments on densification of pure powders under high pressure were performed without a pressure medium. The mechanism of generation and relaxation of internal strains and their distribution in nanoparticles was deduced from the Bragg reflections recorded in situ under high pressures at room temperature. The microstrain was calculated from the full-width at half-maximum (FWHM) values of the Bragg lines. It was found that microstrains in GaN crystallites are generated and subsequently relaxed by two mechanisms: generation of stacking faults and change of the size and shape of the grains occurring under external stress

Generation and Relaxation of Microstrains in GaN Nanocrystals under Extreme Pressures

Nanocrystalline powders of GaN with grain sizes ranging from 2 to 30 nm were examined under high external pressures by in situ diffraction techniques in a diamond anvil cell at DESY (HASYLAB, Station F3). The experiments on densification of pure powders under high pressure were performed without a pressure medium. The mechanism of generation and relaxation of internal strains and their distribution in nanoparticles was deduced from the Bragg reflections recorded in situ under high pressures at room temperature. The microstrain was calculated from the full-width at half-maximum (FWHM) values of the Bragg lines. It was found that microstrains in GaN crystallites are generated and subsequently relaxed by two mechanisms: generation of stacking faults and change of the size and shape of the grains occurring under external stress