In the era of 'Big Data' there is a pressing need for tools that provide human interpretable visualizations of emergent patterns in high-throughput high-dimensional data. Further, to enable insightful data exploration, such visualizations should faithfully capture and emphasize emergent structures and patterns without enforcing prior assumptions on the shape or form of the data. In this paper, we present PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) -an unsupervised low-dimensional embedding for visualization of data that is aimed at solving these issues. Unlike previous methods that are commonly used for visualization, such as PCA and tSNE, PHATE is able to capture and highlight both local and global structure in the data. In particular, in addition to clustering patterns, PHATE also uncovers and emphasizes progression and transitions (when they exist) in the data, which are often missed in other visualization-capable methods. Such 24, 2017; patterns are especially important in biological data that contain, for example, single-cell phenotypes at different phases of differentiation, patients at different stages of disease progression, and gut microbial compositions that vary gradually between individuals, even of the same enterotype.International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/120378 doi: bioRxiv preprint first posted online Mar.The embedding provided by PHATE is based on a novel informational distance that captures long-range nonlinear relations in the data by computing energy potentials of dataadaptive diffusion processes. We demonstrate the effectiveness of the produced visualization in revealing insights on a wide variety of biomedical data, including single-cell RNA-sequencing, mass cytometry, gut microbiome sequencing, human SNP data, Hi-C data, as well as non-biomedical data, such as facebook network and facial image data. In order to validate the capability of PHATE to enable exploratory analysis, we generate a new dataset of 31,000 single-cells from a human embryoid body differentiation system. Here, PHATE provides a comprehensive picture of the differentiation process, while visualizing major and minor branching trajectories in the data. We validate that all known cell types are recapitulated in the PHATE embedding in proper organization. Furthermore, the global picture of the system offered by PHATE allows us to connect parts of the developmental progression and characterize novel regulators associated with developmental lineages.

Colibactin is a gut microbiome metabolite of unknown structure that has been implicated in colorectal cancer formation. Several studies now suggest that the tumorgenicity of colibactin derives from interstrand cross-linking of host DNA. Here we use a combination of genetics, isotope labeling, tandem MS, and chemical synthesis to deduce the structure of colibactin. Our structural assignment accounts for all known biosynthetic data and suggests roles 5 for the final unaccounted enzymes in the colibactin gene cluster. DNA cross-link degradation products derived from synthetic and natural colibactin were indistinguishable by tandem MS analysis, thereby confirming the structure prediction. This work reveals the structure of colibactin, which has remained incompletely defined for over a decade. Main Text: 10Introduction.Colibactin is the product of the clb (also referred to as pks) biosynthetic gene cluster (BGC) that is commonly present within E. coli found in the human colon (1, 2). Intensive interest in colibactin has been fueled by reports that clb + E. coli induce DNA damage in eukaryotic cells in vitro (3) and in vivo (4), promote tumor formation in mouse models of 15 colorectal cancer (CRC) (5-7), and are more prevalent in CRC patients than healthy subjects (5, 8). However, despite intensive efforts, the structure of colibactin has remained unknown for over a decade (9-13).Traditionally, microbial natural products have been produced by large-scale fermentation of bacterial cultures, discovered via activity-guided isolation, and their structures determined by 20 well-established chemical spectroscopic methods. However, because colibactin has been recalcitrant to these classical isolation techniques, our knowledge of its structure and biological activity is derived from diverse interdisciplinary findings. Evaluating the biological effects of 3 clb + bacterial strains has revealed colibactin induces DNA damage in eukaryotic cells.Enzymology, bioinformatic analysis of the clb BGC, stable isotope feeding experiments, characterization of biosynthetic intermediates, and gene deletion and editing studies have given insights into many elements of colibactin's biosynthesis, biological activity, and cellular trafficking. Additionally, by employing chemical synthesis to access shunt metabolites and 5 putative biosynthetic intermediates, a mechanism of action model has been developed that defines the key structural elements of colibactin underling its DNA-damaging properties.Merging of this data forms a picture, albeit incomplete, of colibactin's biosynthesis, structure, and mode of genotoxicity. Colibactin is assembled in a linear prodrug form referred to as precolibactin (see 1, Fig. 1). Key structural elements of precolibactins include a terminal N-10 myristoyl-D-Asn amide (blue in 1) (14-16) and an aminocyclopropane residue (green in 1) (17)(18)(19). The terminal amide is cleaved in the periplasm by the pathway-dedicated serine protease, colibactin peptidase (ClbP) (20,21). The resulting amine 2 undergoes a series of s...

Streptozotocin (STZ)-induced diabetes causes an upregulation in the expression of endothelin (ET) receptors in the rat prostate (Eur J Pharmacol 310:197, 1996). We examined the effects of insulin treatment, started 8 weeks after the induction of diabetes, on the expression and distribution of ET receptors and their respective mRNAs in the rat prostate. The densities, pharmacological properties and distribution of ET receptors in the rat prostate were examined using radioligand receptor binding and autoradiographic studies, and gene expression of ET receptors was evaluated utilizing the reverse transcription-polymerase chain reaction (RT-PCR). STZ-injected rats had smaller prostates and reduced serum testosterone levels than control and insulin treated diabetic animals. ET receptor density was shown to be significantly higher in the prostate from diabetic rats than those from either control or insulin treated diabetic animals. The pharmacological profile of prostatic ET receptors was similar in all groups (approximately 80% ET(A); 20% ET(B) subtype). ET receptors were predominantly localized to the prostatic stroma. Induction of diabetes increased the expression of mRNA levels of ET(A) and ET receptors, and insulin treatment reversed this upregulation to control levels. These results indicate that (1) ET receptor subtypes are expressed in the rat prostate as transcription and translation products; (2) insulin can normalize the diabetes-induced upregulation in the expression of ET receptors and their respective mRNAs; and (3) diabetes-induced regression of the prostate may involve an alteration in ET receptors.