Joint profiling of DNA methylation and chromatin architecture in single cells.

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues

A Close Nuclear Black Hole Pair in the Spiral Galaxy NGC 3393

The current picture of galaxy evolution advocates co-evolution of galaxies and their nuclear massive black holes (MBHs), through accretion and merging. Quasar pairs (6,000-300,000 light-years separation) exemplify the first stages of this gravitational interaction. The final stages, through binary MBHs and final collapse with gravitational wave emission, are consistent with the sub-light-year separation MBHs inferred from optical spectra and light-variability of two quasars. The double active nuclei of few nearby galaxies with disrupted morphology and intense star formation (e.g., NGC 6240 and Mkn 463; ~2,400 and ~12,000 light-years separation respectively) demonstrate the importance of major mergers of equal mass spirals in this evolution, leading to an elliptical galaxy, as in the case of the double radio nucleus (~15 light-years separation) elliptical 0402+379. Minor mergers of galaxies with a smaller companion should be a more common occurrence, evolving into spiral galaxies with active MBH pairs, but have hitherto not been seen. Here we report the presence of two active MBHs, separated by ~430 light-years, in the Seyfert galaxy NGC 3393. The regular spiral morphology and predominantly old circum-nuclear stellar population of this galaxy, and the closeness of the MBHs embedded in the bulge, suggest the result of minor merger evolution.Comment: Preprint (not final) version of a paper to appear in Natur

Multiplex Detection and SNP Genotyping in a Single Fluorescence Channel

Probe-based PCR is widely used for SNP (single nucleotide polymorphism) genotyping and pathogen nucleic acid detection due to its simplicity, sensitivity and cost-effectiveness. However, the multiplex capability of hydrolysis probe-based PCR is normally limited to one target (pathogen or allele) per fluorescence channel. Current fluorescence PCR machines typically have 4–6 channels. We present a strategy permitting the multiplex detection of multiple targets in a single detection channel. The technique is named Multiplex Probe Amplification (MPA). Polymorphisms of the CYP2C9 gene (cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2C9*2) and human papillomavirus sequences HPV16, 18, 31, 52 and 59 were chosen as model targets for testing MPA. The allele status of the CYP2C9*2 determined by MPA was entirely concordant with the reference TaqMan® SNP Genotyping Assays. The four HPV strain sequences could be independently detected in a single fluorescence detection channel. The results validate the multiplex capacity, the simplicity and accuracy of MPA for SNP genotyping and multiplex detection using different probes labeled with the same fluorophore. The technique offers a new way to multiplex in a single detection channel of a closed-tube PCR

Invasive Lionfish Drive Atlantic Coral Reef Fish Declines

Indo-Pacific lionfish (Pterois volitans and P. miles) have spread swiftly across the Western Atlantic, producing a marine predator invasion of unparalleled speed and magnitude. There is growing concern that lionfish will affect the structure and function of invaded marine ecosystems, however detrimental impacts on natural communities have yet to be measured. Here we document the response of native fish communities to predation by lionfish populations on nine coral reefs off New Providence Island, Bahamas. We assessed lionfish diet through stomach contents analysis, and quantified changes in fish biomass through visual surveys of lionfish and native fishes at the sites over time. Lionfish abundance increased rapidly between 2004 and 2010, by which time lionfish comprised nearly 40% of the total predator biomass in the system. The increase in lionfish abundance coincided with a 65% decline in the biomass of the lionfish's 42 Atlantic prey fishes in just two years. Without prompt action to control increasing lionfish populations, similar effects across the region may have long-term negative implications for the structure of Atlantic marine communities, as well as the societies and economies that depend on them

A Study in Red: The Overlooked Role of Azo‐Moieties in Polymeric Carbon Nitride Photocatalysts with Strongly Extended Optical Absorption

The unique optical and photoredox properties of heptazine-based polymeric carbon nitride (PCN) materials make them promising semiconductors for driving various productive photocatalytic conversions. However, their typical absorption onset at ca. 430–450 nm is still far from optimum for efficient sunlight harvesting. Despite many reports of successful attempts to extend the light absorption range of PCNs, the determination of the structural features responsible for the red shift of the light absorption edge beyond 450 nm has often been obstructed by the highly disordered structure of PCNs and/or low content of the moieties responsible for changes in optical and electronic properties. In this work, we implement a high-temperature (900 °C) treatment procedure for turning the conventional melamine-derived yellow PCN into a red carbon nitride. This approach preserves the typical PCN structure but incorporates a new functionality that promotes visible light absorption. A detailed characterization of the prepared material reveals that partial heptazine fragmentation accompanied by de-ammonification leads to the formation of azo-groups in the red PCN, a chromophore moiety whose role in shifting the optical absorption edge of PCNs has been overlooked so far. These azo moieties can be activated under visible-light (470 nm) for H₂ evolution even without any additional co-catalyst, but are also responsible for enhanced charge-trapping and radiative recombination, as shown by spectroscopic studies

Characterisation of CCT271850, a selective, oral and potent MPS1 inhibitor, used to directly measure in vivo MPS1 inhibition vs therapeutic efficacy

BACKGROUND: The main role of the cell cycle is to enable error-free DNA replication, chromosome segregation and cytokinesis. One of the best characterised checkpoint pathways is the spindle assembly checkpoint, which prevents anaphase onset until the appropriate attachment and tension across kinetochores is achieved. MPS1 kinase activity is essential for the activation of the spindle assembly checkpoint and has been shown to be deregulated in human tumours with chromosomal instability and aneuploidy. Therefore, MPS1 inhibition represents an attractive strategy to target cancers. METHODS: To evaluate CCT271850 cellular potency, two specific antibodies that recognise the activation sites of MPS1 were used and its antiproliferative activity was determined in 91 human cancer cell lines. DLD1 cells with induced GFP-MPS1 and HCT116 cells were used in in vivo studies to directly measure MPS1 inhibition and efficacy of CCT271850 treatment. RESULTS: CCT271850 selectively and potently inhibits MPS1 kinase activity in biochemical and cellular assays and in in vivo models. Mechanistically, tumour cells treated with CCT271850 acquire aberrant numbers of chromosomes and the majority of cells divide their chromosomes without proper alignment because of abrogation of the mitotic checkpoint, leading to cell death. We demonstrated a moderate level of efficacy of CCT271850 as a single agent in a human colorectal carcinoma xenograft model. CONCLUSIONS: CCT271850 is a potent, selective and orally bioavailable MPS1 kinase inhibitor. On the basis of in vivo pharmacodynamic vs efficacy relationships, we predict that more than 80% inhibition of MPS1 activity for at least 24 h is required to achieve tumour stasis or regression by CCT271850

Rapid Discovery of Pyrido[3,4- d ]pyrimidine Inhibitors of Monopolar Spindle Kinase 1 (MPS1) Using a Structure-Based Hybridization Approach

Monopolar spindle 1 (MPS1) plays a central role in the transition of cells from metaphase to anaphase and is one of the main components of the spindle assembly checkpoint. Chromosomally unstable cancer cells rely heavily on MPS1 to cope with the stress arising from abnormal numbers of chromosomes and centrosomes and are thus more sensitive to MPS1 inhibition than normal cells. We report the discovery and optimization of a series of new pyrido[3,4-d]pyrimidine based inhibitors via a structure-based hybridization approach from our previously reported inhibitor CCT251455 and a modestly potent screening hit. Compounds in this novel series display excellent potency and selectivity for MPS1, which translates into biomarker modulation in an in vivo human tumor xenograft mode

High-quality habitat and facilitation ameliorate competitive effects of prior residents on new settlers

Many species disperse during their lifetime. Two factors that can affect the performance of individuals following dispersal are the presence of conspecifics and intrinsic habitat quality at the settlement site. Detecting the influence of these factors can be difficult for at least two reasons: (1) the outcomes of interactions with conspecifics are often variable including both competition and facilitation, and (2) selection of high quality habitats often leads to positive covariance between habitat quality and density. In this study, I investigate positive and negative effects of resident blue streak cleaner wrasse (Labroides dimidiatus) on the growth and survival of recently settled conspecifics while accounting for habitat quality. Juvenile L. dimidiatus settle near adult conspecifics, but likely have to compete with resident adults for access to food. However, field experiments indicate that settlers have access to more resources at occupied sites, and as a result, grow faster despite evidence for competition with residents. This result is a direct consequence of two factors: (1) resident conspecifics facilitate settlers by attracting client fish, and (2) resident conspecifics are strongly associated with high quality habitat. These results highlight the need to simultaneously consider habitat quality and competitive and facilitative interactions between conspecifics when making inferences about ecological processes from spatial patterns of individual performance