Search

PDF file 146K, This file contains the legends to Supplementary Figures 1-7 and Supplementary methods

S1 XLSX file 63K, This Supplementary Table contains the results of ORF screen to identify genes that can rescue the suppression of TBK1 in a KRAS-dependent cell line

PDF file 1227K, This file contains Supplemental Figures 1-7, which provide additional supporting information for each of the main figures

Significant value can be achieved by optimizing production of a gas-lift network. Operators have traditionally performed this work manually using network models, but maintaining these models is often labor-intensive. To address this challenge, a closed-loop optimization system was developed that leverages both advanced analytics and physics-based techniques, as well as Internet of Things (IoT) Edge technology. The objectives of such system are to control and optimize the gas-lift network automatically, reduce downtime during compressor upsets, and mitigate any potential flare events. The new closed-loop gas-lift optimization algorithm consists of well and surface network models, optimization and regression solvers, and disturbance adaptation, all running in real time. The closed-loop optimizer works as follows: (1) in every cycle, the optimizer receives measurements; (2) disturbance adaptation compares the model's estimates with the measurements and adapts the surface network model to make it more accurate; (3) the adapted surface network model and well models are used to find the optimum lift gas setpoints; and (4) the calculated setpoints are sent to the automation system through IoT Edge technology. Integral to this system is a single-well nodal analysis model that automatically generates updated models daily for all gas-lift wells. This model is used both as a monitoring tool by the engineers and as part of the network model in the closed-loop gas-lift optimizer, which has been deployed in multiple fields and is running continuously (24/7). The optimizer has saved both production engineering time per network and well specialist time per compressor upset event. Field case studies have shown that the closed-loop optimizer has been successful in maintaining compressor station outlet pressure and optimizing the gas-lift networks during compressor upsets or potential flare events. A significant improvement in oil production has been achieved in fields using optimizer due to both optimized lift gas distribution and reduced downtime. This new algorithm can optimize gas-lift networks during normal operating conditions, compressor upsets, or potential flare events, while simultaneously controlling compressor station outlet pressure within an acceptable range in real time. Significantly, disturbance adaptation is used for the first time to improve the surface model accuracy immediately as additional measurements are received.

The detection of near Earth space objects and potentially threatening asteroids is a challenging problem. The goal of this paper is to present a new method useful for detecting objects in space and to prove that it is more efficient than other existing methods. Instead of simply looking at a single, specified point in an image, this new method would use vectors created by summing across the rows and columns of the CCD array. The data is processed by a likelihood ratio test designed to process vector data under Poisson noise assumptions. The summing is done on the chip before readout noise is added to the image, so this method might have a higher signal to noise ratio than other techniques. Using this method, it is possible to search the same amount of space as you would with other techniques, while using less data. In order to prove that this method is more efficient, a likelihood ratio test will be derived and compared to the same kind of test using simulated data. It will be shown that this new method has a higher detection probability and lower false alarm rate than other methods under certain conditions; and that it will be more useful for detecting potentially deadly asteroids or other space objects that would threaten national security.

We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stranded DNA in its ATP-bound state and single-stranded DNA in its apo state. RarA ATPase activity is stimulated by single-stranded DNA gaps and double-stranded DNA ends. At these double-stranded DNA ends, RarA couples the energy of ATP binding and hydrolysis to separating the strands of duplex DNA, creating flaps. We hypothesize that the creation of a flap at the site of a leading strand discontinuity could, in principle, allow DnaB and the associated replisome to continue DNA synthesis without impediment, with leading strand re-priming by DnaG. Replication forks could thus be rescued in a manner that does not involve replisome disassembly or reassembly, albeit with loss of one of the two chromosomal products of a replication cycle.

Experimental research during the last few decades has provided evidence that language is embedded in a mosaic of cognitive functions. An account of how language interfaces with memory, perception, action and control is no longer beyond the scope of linguistics, and can now be seen as part of an explanation of linguistic structure itself. However, although our view of language has changed, linguistic methodology is lagging behind. This chapter is a sustained argument for a diversification of the kinds of evidence applicable to linguistic questions at di↵erent levels of theory, and a defense of the role of linguistics in experimental cognitive science. 1.1 Linguistic methodology and cognitive science At least two conceptual issues are raised by current interactions between linguistics and cognitive science. One is whether the structures and rules described by linguists are cognitively real. There exist several opinions in this regard, that occupy di↵erent positions on the mentalism/anti-mentalism spectrum. At one extreme is cognitive linguistics [ Croft and Cruse, 2004 ] , endorsing both theoretical and methodological mentalism. The former is the idea that linguistic structures are related formally and causally to other mental entities. The latter calls for a revision of traditional linguistic methodology, and emphasizes the role of cognitive data in linguistics. At the opposite side of the spectrum lies formal semantics which, partly inspired by Frege’s anti-psychologistic stance on meaning and thought [ Frege, 1980; Lewis, 1970; Burge, 2005 ] , rejects both versions of mentalism. Somewhere between the two poles is Chomsky’s [ Chomsky, 1965 ] theoretical mentalism, which sees linguistic rules as ultimately residing in the brain of speakers. However, his commitment to the cognitive reality of grammar does not imply a revision of linguistic methodology, which is maintained in its traditional form based on native speakers’ intuitions and the competence/performance distinction. The second problem, in part dependent on the first, is whether experimental data on language acquisition, comprehension and production have any bearing on linguistic theory. On this point too, there is no consensus among linguists. The division between competence and performance has often been used to secure linguistics from experimental evidence of various sorts [ Bunge, 1984 ] , while

Bacterial “maintenance of genome stability protein A” (MgsA) and related eukaryotic enzymes play important roles in cellular responses to stalled DNA replication processes. Sequence information identifies MgsA enzymes as members of the clamp loader clade of AAA+ proteins, but structural information defining the family has been limited. Here, the x-ray crystal structure of Escherichia coli MgsA is described, revealing a homotetrameric arrangement for the protein that distinguishes it from other clamp loader clade AAA+ proteins. Each MgsA protomer is composed of three elements as follows: ATP-binding and helical lid domains (conserved among AAA+ proteins) and a tetramerization domain. Although the tetramerization domains bury the greatest amount of surface area in the MgsA oligomer, each of the domains participates in oligomerization to form a highly intertwined quaternary structure. Phosphate is bound at each AAA+ ATP-binding site, but the active sites do not appear to be in a catalytically competent conformation due to displacement of Arg finger residues. E. coli MgsA is also shown to form a complex with the single-stranded DNA-binding protein through co-purification and biochemical studies. MgsA DNA-dependent ATPase activity is inhibited by single-stranded DNA-binding protein. Together, these structural and biochemical observations provide insights into the mechanisms of MgsA family AAA+ proteins.

International audience; L’article s’interroge sur l’inexistence du roman comme genre littéraire dans la littérature hébraïque de l’Europe d’Ancien régime, alors qu’il existe de nombreuses similitudes avec le reste de la littérature européenne pour la poésie, le théâtre, la philosophie. Il faut attribuer ce phénomène à la réticence des milieux rabbiniques à l’égard d’un genre considéré comme mondain. Il existe cependant une prose romanesque au sein des communautés juives dans les récits de voyage.

Although the roles of mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K) signaling in KRAS-driven tumorigenesis are well established, KRAS activates additional pathways required for tumor maintenance, the inhibition of which are likely to be necessary for effective KRAS-directed therapy. Here, we show that the IκB kinase (IKK)–related kinases Tank-binding kinase-1 (TBK1) and IKKϵ promote KRAS-driven tumorigenesis by regulating autocrine CCL5 and interleukin (IL)-6 and identify CYT387 as a potent JAK/TBK1/IKKϵ inhibitor. CYT387 treatment ablates RAS-associated cytokine signaling and impairs Kras-driven murine lung cancer growth. Combined CYT387 treatment and MAPK pathway inhibition induces regression of aggressive murine lung adenocarcinomas driven by Kras mutation and p53 loss. These observations reveal that TBK1/IKKϵ promote tumor survival by activating CCL5 and IL-6 and identify concurrent inhibition of TBK1/IKKϵ, Janus-activated kinase (JAK), and MEK signaling as an effective approach to inhibit the actions of oncogenic KRAS. Significance: In addition to activating MAPK and PI3K, oncogenic KRAS engages cytokine signaling to promote tumorigenesis. CYT387, originally described as a selective JAK inhibitor, is also a potent TBK/IKKϵ inhibitor that uniquely disrupts a cytokine circuit involving CCL5, IL-6, and STAT3. The efficacy of CYT387-based treatment in murine Kras-driven lung cancer models uncovers a novel therapeutic approach for these refractory tumors with immediate translational implications. Cancer Discov; 4(4); 452–65. ©2014 AACR. This article is highlighted in the In This Issue feature, p. 377

Surface plasmon resonance (SPR) is a widely employed technique for studying protein-protein interactions. Here, we describe a method for the analysis of single-stranded DNA binding protein (SSB)-heterologous protein interactions by SPR. This method avoids several pitfalls often associated with SPR, particularly difficulties in immobilizing the protein while still allowing for facile regeneration of the sensor chip surface for subsequent experiments. Essentially, the method entails immobilizing a biotinylated single-stranded DNA oligo onto the chip surface, which is then bound by SSB prior to analyte addition to the SSB-coated chip. This allows for rapid qualitative and detailed quantitative analysis of both equilibrium and kinetic parameters of the SSB-protein interaction.

Surface plasmon resonance (SPR) is a widely employed technique for studying protein-protein interactions. Here, we describe a method for the analysis of single-stranded DNA binding protein (SSB)-heterologous protein interactions by SPR. This method avoids several pitfalls often associated with SPR, particularly difficulties in immobilizing the protein while still allowing for facile regeneration of the sensor chip surface for subsequent experiments. Essentially, the method entails immobilizing a biotinylated single-stranded DNA oligo onto the chip surface, which is then bound by SSB prior to analyte addition to the SSB-coated chip. This allows for rapid qualitative and detailed quantitative analysis of both equilibrium and kinetic parameters of the SSB-protein interaction.

Using an ensemble approach, we demonstrate that an oligomeric RecA species is required for the extension phase of RecA filament formation. The RecA K72R mutant protein can bind but not hydrolyze ATP or dATP. When mixed with other RecA variants, RecA K72R causes a drop in the rate of ATP hydrolysis and has been used to study disassembly of hydrolysis-proficient RecA protein filaments. RecA K72R filaments do not form in the presence of ATP but do so when dATP is provided. We demonstrate that in the presence of ATP, RecA K72R is defective for extension of RecA filaments on DNA. This defect is partially rescued when the mutant protein is mixed with sufficient levels of wild type RecA protein. Functional extension complexes form most readily when wild type RecA is in excess of RecA K72R. Thus, RecA K72R inhibits hydrolysis-proficient RecA proteins by interacting with them in solution and preventing the extension phase of filament assembly.

International audience; Toute analyse littéraire se concentrant uniquement sur la forme et le mode stylistique des lamentations hébraïques (qinot) mettra l’accent sur les conventions poétiques statiques et répétitives utilisées par les auteurs, du Moyen Âge au début de la période moderne. Pourtant, si l’on prête attention aux circonstances ayant servi de prétexte à l’écriture du qinot, on remarque un changement d’attitude progressif envers ce qui était considéré comme un événement funèbre, et donc digne d’être commémoré en vers. Jusqu’à ce que les Juifs italiens soient circonscrits dans des ghettos au XVIe siècle, les lamentations étaient habituellement provoquées par des catastrophes d’ordre politique (invasions étrangères, guerres, persécutions, expulsions). Au contraire, l’époque des ghettos fut dominée jusqu’à la fin du XVIIIe siècle par des complaintes commémorant des nouvelles du quotidien (l’effondrement du toit d’une synagogue, un feu, un tremblement de terre). Cet article propose des témoignages qui appuient ces observations, au moins en Italie, et suggère des pistes d’analyse pour expliquer ce changement d’attitude.

Many indexicals can pick out referents from a context other than the context of use, contrary to David Kaplan's predictions. English `actual', `here', and `now', along with Amharic `I' and Chinese `ziji' can shift contexts. We propose that indexicals should be understood anaphorically. Indexicals trigger presuppositions which search for antecedents. Using DRT, we show that they search the global context first (the outermost DRS), but when binding in the global context leads to inconsistency, they will search within a local context. If binding fails entirely, accommodation will often produce an antecedent. This account is simpler than Philippe Schlenker's in that it relies entirely on existing mechanisms in dynamic semantics and DRT to explain the behavior of shifting indexicals.