The transcription factor c-Maf induces the anti-inflammatory cytokine IL-10 in CD4+ T cells in vitro. However, the global effects of c-Maf on diverse immune responses in vivo are unknown. Here we show that c-Maf regulates IL-10 production in CD4+ T cells in TH1 (malaria), TH2 (allergy) and TH17 (autoimmunity) disease models in vivo. Although CD4-targeted Maf-deficient mice showed greater pathology in TH1 and TH2 responses, TH17-mediated pathology was reduced, with accompanying decreased TH17 and increased Foxp3+ regulatory T cells. Bivariate genomic footprinting elucidated the c-Maf transcription factor network, including enhanced NFAT activity, leading to the identification and validation of c-Maf as a negative regulator of IL-2. Decreased Rorc resulting from c-Maf deficiency was dependent on IL-2, explaining the in vivo observations. Thus, c-Maf is a positive and negative regulator of cytokine gene expression, with context-specific effects that allow each immune response to occur in a controlled yet effective manner.

FCP1 [transcription factor IIF (TFIIF)-associated carboxyl-terminal domain (CTD) phosphatase] is the only identified phosphatase specific for the phosphorylated CTD of RNA polymerase II (RNAP II).The phosphatase activity of FCP1 is enhanced in the presence of the large subunit of TFIIF (RAP74 in humans). It has been demonstrated that the CTD of RAP74 (cterRAP74; residues 436 -517) directly interacts with the highly acidic CTD of FCP1 (cterFCP; residues 879 -961 in human). In this manuscript, we have determined a high-resolution solution structure of a cterRAP74͞cterFCP complex by NMR spectroscopy. Interestingly, the cterFCP protein is completely disordered in the unbound state, but forms an ␣-helix (H1 ; E945-M961) in the complex. The cterRAP74͞cterFCP binding interface relies extensively on van der Waals contacts between hydrophobic residues from the H2 and H3 helices of cterRAP74 and hydrophobic residues from the H1 helix of cterFCP. The binding interface also contains two critical electrostatic interactions involving aspartic acid residues from H1 of cterFCP and lysine residues from both H2 and H3 of cterRAP74. There are also three additional polar interactions involving highly conserved acidic residues from the H1 helix. The cterRAP74͞cterFCP complex is the first highresolution structure between an acidic residue-rich domain from a holoenzyme-associated regulatory protein and a general transcription factor. The structure defines a clear role for both hydrophobic and acidic residues in protein͞protein complexes involving acidic residue-rich domains in transcription regulatory proteins. R NA polymerase II (RNAP II) is a multisubunit enzyme complex that enters the initiation complex with the carboxylterminal domain (CTD) of its largest subunit in an unphosphorylated form (RNAP IIA). The CTD contains a heptapeptide repeat (YSPTSPS) that becomes extensively phosphorylated (RNAP IIO) primarily at serine-2 and -5 during early stages of transcription (1-3). In the last several years, numerous protein kinases have been implicated in the phosphorylation of the CTD (4-8). This phosphorylation of the CTD enables RNAP II to progress from the initiation phase to a stable elongation complex, and the CTD remains extensively phosphorylated throughout the elongation phase of transcription (4-6). After completion of the transcription cycle, this same RNAP II must be in the unphosphorylated form (RNAP IIA) to be recruited back to the initiation complex (9). Therefore, dephosphorylation of the CTD by a phosphatase(s) is essential to generating a form of the polymerase (RNAP IIA) that is capable of reinitiating transcription.FCP1 [transcription factor IIF (TFIIF)-associating component of the CTD phosphatase], the only known RNAP II CTD-specific phosphatase, was originally partially purified from HeLa cell (10) and yeast (11) extracts. From experiments with this partially purified CTD phosphatase, it was determined that both general transcription factors IIB (TFIIB) and IIF (TFIIF) play important roles in regulating its activity (...

The timing of individual neuronal spikes is essential for biological brains to make fast responses to sensory stimuli. However, conventional artificial neural networks lack the intrinsic temporal coding ability present in biological networks. We propose a spiking neural network model that encodes information in the relative timing of individual spikes. In classification tasks, the output of the network is indicated by the first neuron to spike in the output layer. This temporal coding scheme allows the supervised training of the network with backpropagation, using locally exact derivatives of the postsynaptic spike times with respect to presynaptic spike times. The network operates using a biologically-plausible alpha synaptic transfer function. Additionally, we use trainable synchronisation pulses that provide bias, add flexibility during training and exploit the decay part of the alpha function. We show that such networks can be successfully trained on noisy Boolean logic tasks and on the MNIST dataset encoded in time. We show that the spiking neural network outperforms comparable spiking models on MNIST and achieves similar quality to fully connected conventional networks with the same architecture. The spiking network spontaneously discovers two operating modes, mirroring the accuracy-speed trade-off observed in human decision-making: a highly accurate but slow regime, and a fast but slightly lower-accuracy regime. These results demonstrate the computational power of spiking networks with biological characteristics that encode information in the timing of individual neurons. By studying temporal coding in spiking networks, we aim to create building blocks towards energy-efficient, state-based and more complex biologically-inspired neural architectures.

General transcription factor IIH (TFIIH) is recruited to the preinitiation complex (PIC) through direct interactions between its p62 (Tfb1) subunit and the carboxyl-terminal domain of TFIIEalpha. TFIIH has also been shown to interact with a number of transcriptional activator proteins through interactions with the same p62 (Tfb1) subunit. We have determined the NMR solution structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH (Tfb1(1-115)). Like the corresponding domain from the human p62 protein, Tfb1(1-115) contains a PH domain fold despite a low level of sequence identity between the two functionally homologous proteins. In addition, we have performed in vitro binding studies that demonstrate that the PH domains of Tfb1 and p62 specifically bind to monophosphorylated inositides [PtdIns(5)P and PtdIns(3)P]. NMR chemical shift mapping demonstrated that the PtdIns(5)P binding site on Tfb1 (p62) is located in the basic pocket formed by beta-strands beta5-beta7 of the PH domain fold. Interestingly, the structural composition of the PtdIns(5)P binding site is different from the composition of the binding sites for phosphoinositides on prototypic PH domains. We have also determined that the PH domains from Tfb1 and p62 are sufficient for binding to the activation domain of VP16. NMR chemical shift mapping demonstrated that the VP16 binding site within the PH domain of Tfb1 (p62) overlaps with the PtdIns(5)P binding site on Tfb1 (p62). These results provide new information about the recognition of phosphoinositides by PH domains, and point to a potential role for phosphoinositides in VP16 regulation.

An update on the JPEG XL standardization effort: JPEG XL is a practical approach focused on scalable web distribution and efficient compression of high-quality images. It will provide various benefits compared to existing image formats: significantly smaller size at equivalent subjective quality; fast, parallelizable decoding and encoding configurations; features such as progressive, lossless, animation, and reversible transcoding of existing JPEG; support for high-quality applications including wide gamut, higher resolution/bit depth/dynamic range, and visually lossless coding. Additionally, a royalty-free baseline is an important goal. The JPEG XL architecture is traditional block-transform coding with upgrades to each component. We describe these components and analyze decoded image quality.

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Melioidosis, a severe human disease caused by the bacterium Burkholderia pseudomallei, has a wide spectrum of clinical manifestations ranging from acute septicaemia to chronic localized illness or latent infection. Murine models have been widely used to study the pathogenesis of infection and to evaluate novel therapies or vaccines, but how faithfully they recapitulate the biology of human melioidosis at a molecular level is not known. Here, mice were intranasally infected with either high or low doses of B. pseudomallei to generate either acute, chronic or latent infection and host blood and tissue transcriptional profiles were generated. Acute infection was accompanied by a homogeneous signature associated with induction of multiple innate immune response pathways, such as IL10, TREM1 and IFN-signaling, largely found in both blood and tissue. The transcriptional profile in blood reflected the heterogeneity of chronic infection and quantitatively reflected the severity of disease. Genes associated with fibrosis and tissue remodelling, including MMPs and collagen, were upregulated in chronically infected mice with severe disease. Transcriptional signatures of both acute and chronic melioidosis revealed upregulation of iNOS in tissue, consistent with the expression of IFN-γ, but also Arginase-1, a functional antagonist of the iNOS pathway, and was confirmed by immunohistochemistry. Comparison of these mouse blood datasets by pathway and modular analysis with the blood transcriptional signature of patients with melioidosis showed that many genes were similarly perturbed, including Arginase-1, IL10, TREM1 and IFN-signaling, revealing the common immune response occurring in both mice and humans.

Analysis of the mouse transcriptional response to Listeria monocytogenes infection reveals that a large set of genes are perturbed in both blood and tissue and that these transcriptional responses are enriched for pathways of the immune response. Further we identified enrichment for both type I and type II interferon (IFN) signaling molecules in the blood and tissues upon infection. Since type I IFN signaling has been reported widely to impair bacterial clearance we examined gene expression from blood and tissues of wild type (WT) and type I IFNαβ receptor-deficient (Ifnar1-/-) mice at the basal level and upon infection with L. monocytogenes. Measurement of the fold change response upon infection in the absence of type I IFN signaling demonstrated an upregulation of specific genes at day 1 post infection. A less marked reduction of the global gene expression signature in blood or tissues from infected Ifnar1-/- as compared to WT mice was observed at days 2 and 3 after infection, with marked reduction in key genes such as Oasg1 and Stat2. Moreover, on in depth analysis, changes in gene expression in uninfected mice of key IFN regulatory genes including Irf9, Irf7, Stat1 and others were identified, and although induced by an equivalent degree upon infection this resulted in significantly lower final gene expression levels upon infection of Ifnar1-/- mice. These data highlight how dysregulation of this network in the steady state and temporally upon infection may determine the outcome of this bacterial infection and how basal levels of type I IFN-inducible genes may perturb an optimal host immune response to control intracellular bacterial infections such as L. monocytogenes.