Modeling multidimensional effects in the propagation of radiative shocks

Radiative shocks (also called supercritical shocks) are high Mach number shock waves that photoionize the medium ahead of the shock front and give rise to a radiative precursor. They are generated in the laboratory using high-energy or high-power lasers and are frequently present in a wide range of astronomical objects. Their modelisation in one dimension has been the subject of numerous studies, but generalization to three dimensions is not straightforward. We calculate analyticaly the absorption of radiation in a grey uniform cylinder and show how it decreases with $\chi R$, the product of the opacity $\chi$ and of the cylinder radius $R$. Simple formulas, whose validity range increases when $\chi R$ diminishes, are derived for the radiation field on the axis of symmetry. Numerical calculations in three dimensions of the radiative energy density, flux and pressure created by a stationary shock wave show how the radiation decreases whith $R$. Finally, the bidimensional structures of both the precursor and the radiation field are calculated with time-dependent radiation hydrodynamics numerical simulations and the influence of two-dimensional effects on the electron density, the temperature, the shock velocity and the shock geometry are exhibited. These simulations show how the radiative precursor shortens, cools and slows down when $R$ is decreased

Protein Complexes are Central in the Yeast Genetic Landscape

If perturbing two genes together has a stronger or weaker effect than expected, they are said to genetically interact. Genetic interactions are important because they help map gene function, and functionally related genes have similar genetic interaction patterns. Mapping quantitative (positive and negative) genetic interactions on a global scale has recently become possible. This data clearly shows groups of genes connected by predominantly positive or negative interactions, termed monochromatic groups. These groups often correspond to functional modules, like biological processes or complexes, or connections between modules. However it is not yet known how these patterns globally relate to known functional modules. Here we systematically study the monochromatic nature of known biological processes using the largest quantitative genetic interaction data set available, which includes fitness measurements for ∼5.4 million gene pairs in the yeast Saccharomyces cerevisiae. We find that only 10% of biological processes, as defined by Gene Ontology annotations, and less than 1% of inter-process connections are monochromatic. Further, we show that protein complexes are responsible for a surprisingly large fraction of these patterns. This suggests that complexes play a central role in shaping the monochromatic landscape of biological processes. Altogether this work shows that both positive and negative monochromatic patterns are found in known biological processes and in their connections and that protein complexes play an important role in these patterns. The monochromatic processes, complexes and connections we find chart a hierarchical and modular map of sensitive and redundant biological systems in the yeast cell that will be useful for gene function prediction and comparison across phenotypes and organisms. Furthermore the analysis methods we develop are applicable to other species for which genetic interactions will progressively become more available

X-ray photodesorption of complex organic molecules in protoplanetary disks -- I. Acetonitrile CH3CN

X-rays emitted from pre-main-sequence stars at the center of protoplanetary disks can induce nonthermal desorption from interstellar ices populating the cold regions. This X-ray photodesorption needs to be quantified for complex organic molecules (COMs), including acetonitrile CH3CN, which has been detected in several disks. We experimentally estimate the X-ray photodesorption yields of neutral species from pure CH3CN ices and from interstellar ice analogs for which CH3CN is mixed either in a CO- or H2O-dominated ice. The ices were irradiated at 15 K by soft X-rays (400-600 eV) from synchrotron light (SOLEIL synchrotron). X-ray photodesorption was probed in the gas phase via quadrupole mass spectrometry. X-ray photodesorption yields were derived from the mass signals and were extrapolated to higher X-ray energies for astrochemical models. X-ray photodesorption of the intact CH3CN is detected from pure CH3CN ices and from mixed 13CO:CH3CN ices, with a yield of about 5x10^(-4) molecules/photon at 560 eV. When mixed in H2O-dominated ices, X-ray photodesorption of the intact CH3CN at 560 eV is below its detection limit, which is 10^(-4) molecules/photon. Yields associated with the desorption of HCN, CH4 , and CH3 are also provided. The derived astrophysical yields significantly depend on the local conditions expected in protoplanetary disks. They vary from 10^(-4) to 10(-6) molecules/photon for the X-ray photodesorption of intact CH3CN from CO-dominated ices. Only upper limits varying from 5x10^(-5) to 5x10^(-7) molecules/photon could be derived for the X-ray photodesorption of intact CH3CN from H2O-dominated ices. X-ray photodesorption of intact CH3CN from interstellar ices might in part explain the abundances of CH3CN observed in protoplanetary disks. The desorption efficiency is expected to vary with the local physical conditions, hence with the disk region

Wavelength-Dependent UV Photodesorption of Pure N2N_2 and O2O_2 Ices

Context: Ultraviolet photodesorption of molecules from icy interstellar grains can explain observations of cold gas in regions where thermal desorption is negligible. This non-thermal desorption mechanism should be especially important where UV fluxes are high. Aims: $N_2$ and $O_2$ are expected to play key roles in astrochemical reaction networks, both in the solid state and in the gas phase. Measurements of the wavelength-dependent photodesorption rates of these two infrared-inactive molecules provide astronomical and physical-chemical insights into the conditions required for their photodesorption. Methods: Tunable radiation from the DESIRS beamline at the SOLEIL synchrotron in the astrophysically relevant 7 to 13.6 eV range is used to irradiate pure $N_2$ and $O_2$ thin ice films. Photodesorption of molecules is monitored through quadrupole mass spectrometry. Absolute rates are calculated by using the well-calibrated CO photodesorption rates. Strategic $N_2$ and $O_2$ isotopolog mixtures are used to investigate the importance of dissociation upon irradiation. Results: $N_2$ photodesorption mainly occurs through excitation of the $b^1\sqcap_u$ state and subsequent desorption of surface molecules. The observed vibronic structure in the $N_2$ photodesorption spectrum, together with the absence of $N_3$ formation, supports that the photodesorption mechanism of $N_2$ is similar to CO, i.e., an indirect DIET (Desorption Induced by Electronic Transition) process without dissociation of the desorbing molecule. In contrast, $O_2$ photodesorption in the 7−13.6 eV range occurs through dissociation and presents no vibrational structure. Conclusions: Photodesorption rates of $N_2$ and $O_2$ integrated over the far-UV field from various star-forming environments are lower than for CO. Rates vary between $10^{-3}$ and $10^{-2}$ photodesorbed molecules per incoming photon.Astronom

Bringing order to protein disorder through comparative genomics and genetic interactions

Abstract Background Intrinsically disordered regions are widespread, especially in proteomes of higher eukaryotes. Recently, protein disorder has been associated with a wide variety of cellular processes and has been implicated in several human diseases. Despite its apparent functional importance, the sheer range of different roles played by protein disorder often makes its exact contribution difficult to interpret. Results We attempt to better understand the different roles of disorder using a novel analysis that leverages both comparative genomics and genetic interactions. Strikingly, we find that disorder can be partitioned into three biologically distinct phenomena: regions where disorder is conserved but with quickly evolving amino acid sequences (flexible disorder); regions of conserved disorder with also highly conserved amino acid sequences (constrained disorder); and, lastly, non-conserved disorder. Flexible disorder bears many of the characteristics commonly attributed to disorder and is associated with signaling pathways and multi-functionality. Conversely, constrained disorder has markedly different functional attributes and is involved in RNA binding and protein chaperones. Finally, non-conserved disorder lacks clear functional hallmarks based on our analysis. Conclusions Our new perspective on protein disorder clarifies a variety of previous results by putting them into a systematic framework. Moreover, the clear and distinct functional association of flexible and constrained disorder will allow for new approaches and more specific algorithms for disorder detection in a functional context. Finally, in flexible disordered regions, we demonstrate clear evolutionary selection of protein disorder with little selection on primary structure, which has important implications for sequence-based studies of protein structure and evolution

The dorsoventral regulatory gene cassette spätzle/Toll/cactus controls the potent antifungal response in Drosophila adults

The cytokine-induced activation cascade of NF-kappaB in mammals and the activation of the morphogen dorsal in Drosophila embryos show striking structural and functional similarities (Toll/IL-1, Cactus/I-kappaB, and dorsal/NF-kappaB). Here we demonstrate that these parallels extend to the immune response of Drosophila. In particular, the intracellular components of the dorsoventral signaling pathway (except for dorsal) and the extracellular Toll ligand, spätzle, control expression of the antifungal peptide gene drosomycin in adults. We also show that mutations in the Toll signaling pathway dramatically reduce survival after fungal infection. Antibacterial genes are induced either by a distinct pathway involving the immune deficiency gene (imd) or by combined activation of both imd and dorsoventral pathways

Spectrally-resolved UV photodesorption of CH4 in pure and layered ices

Context. Methane is among the main components of the ice mantles of insterstellar dust grains, where it is at the start of a rich solid-phase chemical network. Quantification of the photon-induced desorption yield of these frozen molecules and understanding of the underlying processes is necessary to accurately model the observations and the chemical evolution of various regions of the interstellar medium. Aims. This study aims at experimentally determining absolute photodesorption yields for the CH4 molecule as a function of photon energy. The influence of the ice composition is also investigated. By studying the methane desorption from layered CH4:CO ice, indirect desorption processes triggered by the excitation of the CO molecules is monitored and quantified. Methods. Tunable monochromatic VUV light from the DESIRS beamline of the SOLEIL synchrotron is used in the 7 - 13.6 eV (177 - 91 nm) range to irradiate pure CH4 or layers of CH4 deposited on top of CO ice samples. The release of species in the gas phase is monitored by quadrupole mass spectrometry and absolute photodesorption yields of intact CH4 are deduced. Results. CH4 photodesorbs for photon energies higher than ~9.1 eV (~136 nm). The photodesorption spectrum follows the absorption spectrum of CH4, which confirms a desorption mechanism mediated by electronic transitions in the ice. When it is deposited on top of CO, CH4 desorbs between 8 and 9 eV with a pattern characteristic of CO absorption, indicating desorption induced by energy transfer from CO molecules. Conclusions. The photodesorption of CH4 from the pure ice in various interstellar environments is around 2.0 x 10^-3 molecules per incident photon. Results on CO-induced indirect desorption of CH4 provide useful insights for the generalization of this process to other molecules co-existing with CO in ice mantles

Parallel In Vivo and In Vitro Melanoma RNAi Dropout Screens Reveal Synthetic Lethality between Hypoxia and DNA Damage Response Inhibition

SummaryTo identify factors preferentially necessary for driving tumor expansion, we performed parallel in vitro and in vivo negative-selection short hairpin RNA (shRNA) screens. Melanoma cells harboring shRNAs targeting several DNA damage response (DDR) kinases had a greater selective disadvantage in vivo than in vitro, indicating an essential contribution of these factors during tumor expansion. In growing tumors, DDR kinases were activated following hypoxia. Correspondingly, depletion or pharmacologic inhibition of DDR kinases was toxic to melanoma cells, including those that were resistant to BRAF inhibitor, and this could be enhanced by angiogenesis blockade. These results reveal that hypoxia sensitizes melanomas to targeted inhibition of the DDR and illustrate the utility of in vivo shRNA dropout screens for the identification of pharmacologically tractable targets

A recessive mutation, immune deficiency (imd), defines two distinct control pathways in the Drosophila host defense

In this paper we report a recessive mutation, immune deficiency (imd), that impairs the inducibility of all genes encoding antibacterial peptides during the immune response of Drosophila. When challenged with bacteria, flies carrying this mutation show a lower survival rate than wild-type flies. We also report that, in contrast to the antibacterial peptides, the antifungal peptide drosomycin remains inducible in a homozygous imd mutant background. These results point to the existence of two different pathways leading to the expression of two types of target genes, encoding either the antibacterial peptides or the antifungal peptide drosomycin