TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed.

Tumour necrosis factor alpha (TNFα) is a potent cytokine that signals through nuclear factor kappa B (NFκB) to activate a subset of human genes. It is usually assumed that this involves RNA polymerases transcribing responsive genes wherever they might be in the nucleus. Using primary human endothelial cells, variants of chromosome conformation capture (including 4C and chromatin interaction analysis with paired-end tag sequencing), and fluorescence in situ hybridization to detect single nascent transcripts, we show that TNFα induces responsive genes to congregate in discrete 'NFκB factories'. Some factories further specialize in transcribing responsive genes encoding micro-RNAs that target downregulated mRNAs. We expect all signalling pathways to contain this extra leg, where responding genes are transcribed in analogous specialized factories.

Transcription factories, chromatin loops, and the dysregulation of gene expression in malignancy.

Pathologists recognize and classify cancers according to nuclear morphology, but there remains little scientific explanation of why malignant nuclei possess their characteristic features, or how those features are related to dysregulated function. This essay will discuss a basic structure-function axis that connects one central architectural motif in the nucleus-the chromatin loop-to the vital nuclear function of transcription. The loop is attached to a "transcription factory" through components of the transcription machinery (either polymerases or transcriptional activators/repressors), and the position of a gene within a loop determines how often that gene is transcribed. Then, dysregulated transcription is tightly coupled to alterations in structure, and vice versa. We also speculate on how the experimental approaches being used to analyze loops and factories might be applied to study the problems of tumour initiation and progression.

The proteomes of transcription factories containing RNA polymerases I, II or III.

Human nuclei contain three RNA polymerases (I, II and III) that transcribe different groups of genes; the active forms of all three are difficult to isolate because they are bound to the substructure. Here we describe a purification approach for isolating active RNA polymerase complexes from mammalian cells. After isolation, we analyzed their protein content by mass spectrometry. Each complex represents part of the core of a transcription factory. For example, the RNA polymerase II complex contains subunits unique to RNA polymerase II plus various transcription factors but shares a number of ribonucleoproteins with the other polymerase complexes; it is also rich in polymerase II transcripts. We also describe a native chromosome conformation capture method to confirm that the complexes remain attached to the same pairs of DNA templates found in vivo.

Preparation and anti-icing behavior of superhydrophobic surfaces on aluminum alloy substrates.

It has been expected that superhydrophobic (SHP) surfaces could have potential anti-icing applications due to their excellent water-repellence properties. However, a thorough understanding on the anti-icing performance of such surfaces has never been reported; even systematic characterizations on icing behavior of various surfaces are still rare because of the lack of powerful instrumentations. In this study, we employed the electrochemical anodic oxidation and chemical etching methods to simplify the fabrication procedures for SHP surfaces on the aluminum alloy substrates, aiming at the anti-icing properties of SHP surfaces of various engineering materials. We found that the one-step chemical etching with FeCl3 and HCl as the etchants was the most effective for ideal SHP surfaces with a large contact angle (CA, 159.1°) and a small contact angle hysteresis (CAH, 4.0°). To systematically investigate the anti-icing behavior of the prepared SHP surfaces, we designed a robust apparatus with a real-time control system based on the two stage refrigerating method. This system can monitor the humidity, pressure, and temperature during the icing process on the surfaces. We demonstrated that the SHP surfaces exhibited excellent anti-icing properties, i.e., from the room temperature of 16.0 °C, the icing time on SHP surfaces can be postponed from 406s to 676s compared to the normal aluminum alloy surface if the surfaces were put horizontally, and the icing temperature can be decreased from -2.2 °C to -6.1 °C. If such surfaces were tilted, the sprayed water droplets on the normal surfaces iced up at the temperature of -3.9 °C, but bounced off the SHP surface even as the temperature reached as low as -8.0 °C. The present study therefore suggests a general, simple, and low-cost methodology for the promising anti-icing applications in various engineering materials and different fields (e.g., power lines and aircrafts).

Epidemiological evidence that indoor air pollution from cooking with solid fuels accelerates skin aging in Chinese women.

BACKGROUND: Recently, we showed that outdoor air pollution exposure from traffic and industry is associated with an increased risk of skin aging in Caucasian women. In China, indoor air pollution exposure caused by the use of solid fuels like coal is a major health problem and might also increase the risk of skin aging in Chinese women. OBJECTIVE: As cooking with solid fuels is a major source of indoor air pollution exposure in China, we aimed to test if cooking with solid fuels is associated with more pronounced skin aging in Chinese women. METHODS: We conducted two cross-sectional studies in China to assess the association between cooking with solid fuels and signs of skin aging. In Pingding (in northern China) we assessed N=405 and in Taizhou (in southern China) N=857 women between 30 and 90 years of age. Skin aging was evaluated by the SCINEXA score. Indoor air pollution exposure, sun exposure, smoking and other confounders were assessed by questionnaires. Associations were then tested by linear and logistic regression analyses adjusted for further confounders. RESULTS: The analysis showed that cooking with solid fuels was significantly associated with a 5-8% more severe wrinkle appearance on face and an 74% increased risk of having fine wrinkles on back of hands in both studies combined, independent of age and other influences on skin aging. CONCLUSION: The present studies thus corroborate our previous finding that air pollution is associated with skin aging and extend it by showing that indoor air pollution might be another risk factor for skin aging.

Protein interaction data set highlighted with human Ras-MAPK/PI3K signaling pathways.

The Ras-MAPK and PI3K-AKT pathways are conserved in metazoan organisms, which involve a series of signaling cascades and form the basis for numerous physiological and pathological processes. Here we report on yeast two hybrid screening results of a protein interaction network around the known components of human Ras-MAPK/PI3K pathways. A total of 42 independent cDNA library screenings resulted in 200 protein-protein interaction (PPI) pairs among 180 molecules. Most of the proteins formed a large cluster that contains 193 PPIs between 169 proteins. Seventy-four interactions indicate high-confidence according to bioinformatics analysis. The prey list contains high enrichment genes with specific Gene Ontology (GO) terms such as response to stress and response to external stimulus. Most interactions link the Ras signaling pathway with various cellular processes. Five interactions were validated by coimmunoprecipitation and colocalization assays in mammalian cells to confirm their in vivo interactions. This protein interaction network provides further insights into the molecular mechanism of Ras-MAPK/PI3K signaling pathways.

PACT is a negative regulator of p53 and essential for cell growth and embryonic development.

The tumor suppressor p53 regulates cell cycle progression and apoptosis in response to various types of stress, whereas excess p53 activity creates unwanted effects. Tight regulation of p53 is essential for maintaining normal cell growth. p53-associated cellular protein-testes derived (PACT, also known as P2P-R, RBBP6) is a 250-kDa Ring finger-containing protein that can directly bind to p53. PACT is highly up-regulated in esophageal cancer and may be a promising target for immunotherapy. However, the physiological role of the PACT-p53 interaction remains largely unclear. Here, we demonstrate that the disruption of PACT in mice leads to early embryonic lethality before embryonic day 7.5 (E7.5), accompanied by an accumulation of p53 and widespread apoptosis. p53-null mutation partially rescues the lethality phenotype and prolonged survival to E11.5. Endogenous PACT can interact with Hdm2 and enhance Hdm2-mediated ubiquitination and degradation of p53 as a result of the increase of the p53-Hdm2 affinity. Consequently, PACT represses p53-dependent gene transcription. Knockdown of PACT significantly attenuates the p53-Hdm2 interaction, reduces p53 polyubiquitination, and enhances p53 accumulation, leading to both apoptosis and cell growth retardation. Taken together, our data demonstrate that the PACT-p53 interaction plays a critical role in embryonic development and tumorigenesis and identify PACT as a member of negative regulators of p53.