Complementary transcriptomic, lipidomic, and targeted functional genetic analyses in cultured Drosophila cells highlight the role of glycerophospholipid metabolism in Flock House virus RNA replication

Abstract Background Cellular membranes are crucial host components utilized by positive-strand RNA viruses for replication of their genomes. Published studies have suggested that the synthesis and distribution of membrane lipids are particularly important for the assembly and function of positive-strand RNA virus replication complexes. However, the impact of specific lipid metabolism pathways in this process have not been well defined, nor have potential changes in lipid expression associated with positive-strand RNA virus replication been examined in detail. Results In this study we used parallel and complementary global and targeted approaches to examine the impact of lipid metabolism on the replication of the well-studied model alphanodavirus Flock House virus (FHV). We found that FHV RNA replication in cultured Drosophila S2 cells stimulated the transcriptional upregulation of several lipid metabolism genes, and was also associated with increased phosphatidylcholine accumulation with preferential increases in lipid molecules with longer and unsaturated acyl chains. Furthermore, targeted RNA interference-mediated downregulation of candidate glycerophospholipid metabolism genes revealed a functional role of several genes in virus replication. In particular, we found that downregulation of Cct1 or Cct2, which encode essential enzymes for phosphatidylcholine biosynthesis, suppressed FHV RNA replication. Conclusion These results indicate that glycerophospholipid metabolism, and in particular phosphatidylcholine biosynthesis, plays an important role in FHV RNA replication. Furthermore, they provide a framework in which to further explore the impact of specific steps in lipid metabolism on FHV replication, and potentially identify novel cellular targets for the development of drugs to inhibit positive-strand RNA viruses.http://deepblue.lib.umich.edu/bitstream/2027.42/78268/1/1471-2164-11-183.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78268/2/1471-2164-11-183-S3.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78268/3/1471-2164-11-183-S2.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78268/4/1471-2164-11-183.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/78268/5/1471-2164-11-183-S4.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78268/6/1471-2164-11-183-S1.XLSPeer Reviewe

Characterizing analogue caldera collapse with computerized X-ray tomography

Analogue models of caldera collapse were imaged by computerized X-ray tomography (μCT). Interval μCT radiography sequences document ‘2.5D’ surface and internal model deformation in an unprecedented way, and carry the potential for a better understanding of the kinematics of various volcano-tectonic processes, of which caldera collapse is a mere illustration. A semi-automatic subsidence velocity analysis was carried out on radiographs. The developed method is a step towards the quantitative documentation of volcano-tectonic modelling that would render data interpretations immediately comparable to monitoring data available from recent deformation at natural volcanoes

Traces arising from regular inclusions

We study the problem of extending a state on an abelian $C^*$- subalgebra to a tracial state on the ambient $C^*$-algebra. We propose an approach that is well-suited to the case of regular inclusions, in which there is a large supply of normalizers of the subalgebra. Conditional expectations onto the subalgebra give natural extensions of a state to the ambient $C^*$-algebra; we prove that these extensions are tracial states if and only if certain invariance properties of both the state and conditional expectations are satisfied. In the example of a groupoid $C^*$-algebra, these invariance properties correspond to invariance of associated measures on the unit space under the action of bisections. Using our framework, we are able to completely describe the tracial state space of a Cuntz-Krieger graph algebra. Along the way we introduce certain operations called graph tightenings, which both streamline our description and provides connections to related finiteness questions in graph $C^*$-algebras. Our investigation has close connections with the so-called unique state extension property and its variants.Comment: 35 pages, submitted to Journal of the Australian Mathematical Societ

Beyond the photocycle-how cryptochromes regulate photoresponses in plants?

Cryptochromes (CRYs) are blue light receptors that mediate light regulation of plant growth and development. Land plants possess various numbers of cryptochromes, CRY1 and CRY2, which serve overlapping and partially redundant functions in different plant species. Cryptochromes exist as physiologically inactive monomers in darkness; photoexcited cryptochromes undergo homodimerization to increase their affinity to the CRY-signaling proteins, such as CIBs (CRY2-interacting bHLH), PIFs (Phytochrome-Interacting Factors), AUX/IAA (Auxin/INDOLE-3-ACETIC ACID), and the COP1-SPAs (Constitutive Photomorphogenesis 1-Suppressors of Phytochrome A) complexes. These light-dependent protein-protein interactions alter the activity of the CRY-signaling proteins to change gene expression and developmental programs in response to light. In the meantime, photoexcitation also changes the affinity of cryptochromes to the CRY-regulatory proteins, such as BICs (Blue-light Inhibitors of CRYs) and PPKs (Photoregulatory Protein Kinases), to modulate the activity, modification, or abundance of cryptochromes and photosensitivity of plants in response to the changing light environment

The structural design for a "canted cosine-theta" Superconducting dipole coil and magnet structure-CCT

The Superconducting Magnet Group, at Lawrence Berkeley National Laboratory (LBNL), has been developing a canted cosine-theta (CCT) superconducting dipole coil as well as the coil's supporting magnet structure. This contribution reports on the progress in the development of the coil's winding mandrel and its fabrication options. A comprehensive study of the coil's Lorentz forces was performed to validate the winding mandrel's "stress interception" attributes. The design of the external structure and the application of the "Bladder & Key" technology is also discussed. Additionally, the application of these studies to a curved ion-therapy CCT dipole magnet is reported

Canted-cosine-theta magnet (CCT)-A concept for high field accelerator magnets

Canted-Cosine-Theta (CCT) magnet is an accelerator magnet that superposes fields of nested and tilted solenoids that are oppositely canted. The current distribution of any canted layer generates a pure harmonic field as well as a solenoid field that can be cancelled with a similar but oppositely canted layer. The concept places windings within mandrel's ribs and spars that simultaneously intercept and guide Lorentz forces of each turn to prevent stress accumulation. With respect to other designs, the need for pre-stress in this concept is reduced by an order of magnitude making it highly compatible with the use of strain sensitive superconductors such as Nb3Sn or HTS. Intercepting large Lorentz forces is of particular interest in magnets with large bores and high field accelerator magnets like the one foreseen in the future high energy upgrade of the LHC. This paper describes the CCT concept and reports on the construction of CCT1 a "proof of principle" dipole

Semi-compositional Method for Synonym Extraction of Multi-Word Terms

International audienceAutomatic synonyms and semantically related word extraction is a challenging task, useful in many NLP applications such as question answering, search query expansion, text summarization, etc. While different studies addressed the task of word synonym extraction, only a few investigations tackled the problem of acquiring synonyms of multi-word terms (MWT) from specialized corpora. To extract pairs of synonyms of multi-word terms, we propose in this paper an unsupervised semi-compositional method that makes use of distributional semantics and exploit the compositional property shared by most MWT. We show that our method outperforms significantly the state-of-the-art

Vaccinia-Related Kinase 2 Mediates Accumulation of Polyglutamine Aggregates via Negative Regulation of the Chaperonin TRiC

Misfolding of proteins containing abnormal expansions of polyglutamine (polyQ) repeats is associated with cytotoxicity in several neurodegenerative disorders, including Huntington's disease. Recently, the eukaryotic chaperonin TRiC hetero-oligomeric complex has been shown to play an important role in protecting cells against the accumulation of misfolded polyQ protein aggregates. It is essential to elucidate how TRiC function is regulated to better understand the pathological mechanism of polyQ aggregation. Here, we propose that vaccinia-related kinase 2 (VRK2) is a critical enzyme that negatively regulates TRiC. In mammalian cells, overexpression of wild-type VRK2 decreased endogenous TRiC protein levels by promoting TRiC ubiquitination, but a VRK2 kinase-dead mutant did not. Interestingly, VRK2-mediated downregulation of TRiC increased aggregate formation of a polyQ-expanded huntingtin fragment. This effect was ameliorated by rescue of TRiC protein levels. Notably, small interference RNA-mediated knockdown of VRK2 enhanced TRiC protein stability and decreased polyQ aggregation. The VRK2-mediated reduction of TRiC protein levels was subsequent to the recruitment of COP1 E3 ligase. Among the members of the COP1 E3 ligase complex, VRK2 interacted with RBX1 and increased E3 ligase activity on TRiC in vitro. Taken together, these results demonstrate that VRK2 is crucial to regulate the ubiquitination-proteosomal degradation of TRiC, which controls folding of polyglutamine proteins involved in Huntington's disease.open118Ysciescopu