PUMA amplifies necroptosis signaling by activating cytosolic DNA sensors.

Necroptosis, a form of regulated necrotic cell death, is governed by RIP1/RIP3-mediated activation of MLKL. However, the signaling process leading to necroptotic death remains to be elucidated. In this study, we found that PUMA, a proapoptotic BH3-only Bcl-2 family member, is transcriptionally activated in an RIP3/MLKL-dependent manner following induction of necroptosis. The induction of PUMA, which is mediated by autocrine TNF-α and enhanced NF-κB activity, contributes to necroptotic death in RIP3-expressing cells with caspases inhibited. On induction, PUMA promotes the cytosolic release of mitochondrial DNA and activation of the DNA sensors DAI/Zbp1 and STING, leading to enhanced RIP3 and MLKL phosphorylation in a positive feedback loop. Furthermore, deletion of PUMA partially rescues necroptosis-mediated developmental defects in FADD-deficient embryos. Collectively, our results reveal a signal amplification mechanism mediated by PUMA and cytosolic DNA sensors that is involved in TNF-driven necroptotic death in vitro and in vivo

A domain ontology for the non-coding RNA field

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology

The Performance of the Construction of a Water Ecological Civilization City: International Assessment and Comparison

The water ecological environment problems brought about by rapid urbanization have prompted the proposal and implementation of different approaches to urban water ecological construction, such as eco-cities, best management practices (BMPs), and low-impact development (LID). As one of the most representative urban water ecological management policies in China, the Water Ecological Civilization City (WECC) was proposed in 2013, and 105 cities were selected for pilot construction. Many studies have evaluated the effectiveness of WECC construction, but international quantitative comparison is lacking. To address this, an urban Water-Human-Health (WHH) Assessment Model, considering water resources, ecological environment, economic and social development level, and water resources utilization, was developed and applied to five WECC pilot cities in China and 10 other cities worldwide, in which mainstream urban water ecological construction modes have been used. Principal component analysis of the index values in the assessment system was used to evaluate the current status of water ecosystem health in the 15 cities, showing that Sydney, Cleveland, and Hamburg were the most advanced in urban water ecological management. The two cities with the best evaluation results (Sydney and Cleveland), and the WECC city with the highest score (Wuhan) were selected for documentary analysis of their water ecological construction documents to identify similarities and differences to inform best practice internationally for urban water ecological construction. The results showed that Sydney and Cleveland attach similar emphasis across most constituents of urban water ecological construction, while, for Wuhan, greater importance is attached to water resource management and water culture. The advantages and disadvantages of WECC construction and international experience are discussed. The WHH assessment model proposed in this study provides a new quantitative evaluation method for international urban water ecological health evaluation, which could be further improved by including an urban flood risk indicator

The development of non-coding RNA ontology

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data

Density of States and Conductivity of Granular Metal or Array of Quantum Dots

The conductivity of a granular metal or an array of quantum dots usually has the temperature dependence associated with variable range hopping within the soft Coulomb gap of density of states. This is difficult to explain because neutral dots have a hard charging gap at the Fermi level. We show that uncontrolled or intentional doping of the insulator around dots by donors leads to random charging of dots and finite bare density of states at the Fermi level. Then Coulomb interactions between electrons of distant dots results in the a soft Coulomb gap. We show that in a sparse array of dots the bare density of states oscillates as a function of concentration of donors and causes periodic changes in the temperature dependence of conductivity. In a dense array of dots the bare density of states is totally smeared if there are several donors per dot in the insulator.Comment: 13 pages, 15 figures. Some misprints are fixed. Some figures are dropped. Some small changes are given to improve the organizatio

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl

Estimating the Occurrence of Wind-Driven Coastal Upwelling Associated with “Aoshio” on the Northeast Shore of Tokyo Bay, Japan: An Analytical Model

“Aoshio” in Tokyo Bay is a hydroenvironmental phenomenon in which seawater appears milky blue due to reflection of sunshine off surface water which contains lots of sulfur particles. Its appearance is due to coastal upwelling of bottom oxygen-depleted water, which causes many deaths of shellfish and other aquatic animals around the bay. In this study, we derived some analytical solutions in the context of a two-layered fluid and used them to make a simple analytical model to estimate the occurrence of “Aoshio” phenomenon on the northeast shore of Tokyo Bay. Comparison with observation data suggested that this model was valid to a certain degree

Estimating the Occurrence of Wind-Driven Coastal Upwelling Associated with “Aoshio” on the Northeast Shore of Tokyo Bay, Japan: An Analytical Model

“Aoshio” in Tokyo Bay is a hydroenvironmental phenomenon in which seawater appears milky blue due to reflection of sunshine off surface water which contains lots of sulfur particles. Its appearance is due to coastal upwelling of bottom oxygen-depleted water, which causes many deaths of shellfish and other aquatic animals around the bay. In this study, we derived some analytical solutions in the context of a two-layered fluid and used them to make a simple analytical model to estimate the occurrence of “Aoshio” phenomenon on the northeast shore of Tokyo Bay. Comparison with observation data suggested that this model was valid to a certain degree