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The question of whether transcription factories containing RNA polymerases exist has been controversial, owing to the fact that they have not been isolated previously. Now, a method to carefully isolate these complexes and analyze their proteomes by mass spectrometry is described. 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 .

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.

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. TNFα alpha treatment induces congregation of both coding and non‐coding NFκB target genes in discrete transcription factories, leading to coordinated gene expression.

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. [PUBLICATION ABSTRACT]

In this paper, a remote FPGA-configuration method based on JTAG extension over optical fibers is presented. The method takes advantage of commercial components and ready-to-use software such as iMPACT and does not require any hardware or software development. The method combines the advantages of the slow remote JTAG configuration and the fast local flash memory configuration. The method has been verified successfully and used in the Demonstrator of Liquid-Argon Trigger Digitization Board (LTDB) for the ATLAS liquid argon calorimeter Phase-I trigger upgrade. All components on the FPGA side are verified to meet the radiation tolerance requirements.

A prototype Liquid-argon Trigger Digitizer Board (LTDB), called the LTDB Demonstrator, has been developed to demonstrate the functions of the ATLAS Liquid Argon Calorimeter Phase-I trigger electronics upgrade. Forty Analog-to-Digital converters and four FPGAs with embedded multi-gigabit-transceivers on each Demonstrator need high quality clocks. A clock distribution system based on commercial components has been developed for the Demonstrator. The design of the clock distribution system is presented. The performance of the clock distribution system has been evaluated. The components used in the clock distribution system have been qualified to meet radiation tolerance requirements of the Demonstrator.

The integration of a Verticle Cavity Surface-Emitting Laser (VCSEL) array and a driving Application-Specific Integrated Circuit (ASIC) in a custom optical array transmitter module (ATx) for operation in the detector front-end is constructed, assembled and tested. The ATx provides 12 parallel channels with each channel operating at 10 Gbps. The optical transmitter eye diagram passes the eye mask and the bit-error rate (BER) less than 1E-12 transmission is achieved at 10 Gbps/ch. The overall insertion loss including the radiation induced attenuation is sufficiently low to meet the proposed link budget requirement.

We present the design and test results of two optical data transmission ASICs for the High-Luminosity LHC (HL-LHC) experiments. These ASICs include a two-channel serializer (LOCs2) and a single-channel Vertical Cavity Surface Emitting Laser (VCSEL) driver (LOCld1V2). Both ASICs are fabricated in a commercial 0.25-um Silicon-on-Sapphire (SoS) CMOS technology and operate at a data rate up to 8 Gbps per channel. The power consumption of LOCs2 and LOCld1V2 are 1.25 W and 0.27 W at 8-Gbps data rate, respectively. LOCld1V2 has been verified meeting the radiation-tolerance requirements for HL-LHC experiments.

We propose a line code that has fast resynchronization capability and low latency. Both the encoder and decoder have been implemented in FPGAs. The encoder has also been implemented in an ASIC. The latency of the whole optical link (not including the optical fiber) is estimated to be less than 73.9 ns. In the case of radiation-induced link synchronization loss, the decoder can recover the synchronization in 25 ns. The line code will be used in the ATLAS liquid argon calorimeter Phase-I trigger upgrade and can also be potentially used in other LHC experiments.