Heterogeneity and expression of the zein storage protein gene family of maize : (zein, maize, multiple gene families, in vitro processing, protein synthesis, cloning, low molecular weight PAGE)

The storage protein zein is synthesized by polysomes on the endoplasmic reticulum in certain cells of the maize seed. As zein accumulates within the membrane lumen the cisternae are transformed into vesiculate protein bodies. Zein is comprised of a large family of structurally related polypeptides that fall into two classes of 19,000 and 25,000 daltons. On two-dimensional IEF:SDS polyacrylamide gels, the number and positions of the electromorphs within each class differ greatly from one strain to another. Typically, however, there may be 8-12 spots for each class. Within any strain that has been examined the polypeptides constricting each molecular weight class have a similar amino-terminal sequence, but there are a number of position differences when the sequences are compared between strains. Zeins are made as preproteins that are 1,000 and 2,000 daltons larger than the respective mature light and heavy zein polypeptide class. As the growing preprotein chain is moved through the ER membrane, the leader sequence is removed by an exopeptidase. One glucose residue is added to the mature portion of the molecule at this time. An in vitro system using maize endosperm membranes has been developed to study the synthesis and processing of maize preproteins. Assessment of the products made indicates that the method faithfully reproduces the in vitro processes. Cloned cDNA zein sequences were employed to examine the extent of genetic heterogeneity. Based on restriction analyses and dot hybridizations, eighteen zein clones could be divided into three classes for the light zein class and two for the heavy zein class. The Southern transfer hybridizations showed a very complex picture that suggests that zein is encoded by many genomic sequences which share partial polypeptides but until more is known about the structures of the different zein genes, an estimate of the number of copies in the maize genome by hybridization with cloned sequences cannot be made.FRANCES BURR and BENJAMIN BURR, Department of Biology, Brookhaven National Laboratory, Upton, N.Y

Morphology of fluvial networks on Titan: Evidence for structural control

Although Titan’s surface shows clear evidence of erosional modification, such as fluvial incision, evidence for tectonism has been less apparent. On Earth, fluvial networks with strongly preferred orientations are often associated with structural features, such as faults or joints, that influence flow or erodibility. We delineated and classified the morphologies of fluvial drainages on Titan and discovered evidence of structural control. Fluvial networks were delineated both on synthetic aperture radar (SAR) images covering ∼40% of Titan from the Cassini Titan Radar Mapper up through T71 and on visible light images of the Huygens landing site collected by the Descent Imager/Spectral Radiometer (DISR). The delineated networks were assigned to one of three morphologic classes—dendritic, parallel or rectangular—using a quantitative terrestrial drainage pattern classification algorithm modified for use with Titan data. We validated our modified algorithm by applying it to synthetic fluvial networks produced by a landscape evolution model with no structural control of drainage orientations, and confirmed that only a small fraction of the networks are falsely identified as structurally controlled. As a second validation, we confirmed that our modified algorithm correctly classifies terrestrial networks that are classified in multiple previous works as rectangular. Application of this modified algorithm to our Titan networks results in a classification of rectangular for one-half of the SAR and DISR networks. A review of the geological context of the four terrestrial rectangular networks indicates that tensional stresses formed the structures controlling those terrestrial drainages. Based on the similar brittle response of rock and cryogenic ice to stress, we infer that structures formed under tension are the most likely cause of the rectangular Titan networks delineated here. The distribution of these rectangular networks suggests that tensional stresses on Titan may have been widespread.United States. National Aeronautics and Space Administration (NASA Cassini Data Analysis Program Grant NNX08BA81G

The Scikit HEP Project -- overview and prospects

Scikit-HEP is a community-driven and community-oriented project with the goal of providing an ecosystem for particle physics data analysis in Python. Scikit-HEP is a toolset of approximately twenty packages and a few "affiliated" packages. It expands the typical Python data analysis tools for particle physicists. Each package focuses on a particular topic, and interacts with other packages in the toolset, where appropriate. Most of the packages are easy to install in many environments; much work has been done this year to provide binary "wheels" on PyPI and conda-forge packages. The Scikit-HEP project has been gaining interest and momentum, by building a user and developer community engaging collaboration across experiments. Some of the packages are being used by other communities, including the astroparticle physics community. An overview of the overall project and toolset will be presented, as well as a vision for development and sustainability.Comment: 6 pages, 3 figures, Proceedings of the 24th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2019), Adelaide, Australia, 4-8 November 201

A Forward Genetic Screen Reveals Novel Independent Regulators of Ulbp1, an Activating Ligand for Natural Killer Cells

Recognition and elimination of tumor cells by the immune system is crucial for limiting tumor growth. Natural killer (NK) cells become activated when the receptor NKG2D is engaged by ligands that are frequently upregulated in primary tumors and on cancer cell lines. However, the molecular mechanisms driving NKG2D ligand expression on tumor cells are not well defined. Using a forward genetic screen in a tumor-derived human cell line, we identified several novel factors supporting expression of the NKG2D ligand ULBP1. Our results show stepwise contributions of independent pathways working at multiple stages of ULBP1 biogenesis. Deeper investigation of selected hits from the screen showed that the transcription factor ATF4 drives ULBP1 gene expression in cancer cell lines, while the RNA-binding protein RBM4 supports ULBP1 expression by suppressing a novel alternatively spliced isoform of ULBP1 mRNA. These findings offer insight into the stress pathways that alert the immune system to danger

Methane storms as a driver of Titan's dune orientation

Titan's equatorial regions are covered by eastward propagating linear dunes. This direction is opposite to mean surface winds simulated by Global Climate Models (GCMs), which are oriented westward at these latitudes, similar to trade winds on Earth. Different hypotheses have been proposed to address this apparent contradiction, involving Saturn's gravitational tides, large scale topography or wind statistics, but none of them can explain a global eastward dune propagation in the equatorial band. Here we analyse the impact of equinoctial tropical methane storms developing in the superrotating atmosphere (i.e. the eastward winds at high altitude) on Titan's dune orientation. Using mesoscale simulations of convective methane clouds with a GCM wind profile featuring superrotation, we show that Titan's storms should produce fast eastward gust fronts above the surface. Such gusts dominate the aeolian transport, allowing dunes to extend eastward. This analysis therefore suggests a coupling between superrotation, tropical methane storms and dune formation on Titan. Furthermore, together with GCM predictions and analogies to some terrestrial dune fields, this work provides a general framework explaining several major features of Titan's dunes: linear shape, eastward propagation and poleward divergence, and implies an equatorial origin of Titan's dune sand.Comment: Published online on Nature Geoscience on 13 April 201

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Write-rationing garbage collection for hybrid memories

Emerging Non-Volatile Memory (NVM) technologies offer high capacity and energy efficiency compared to DRAM, but suffer from limited write endurance and longer latencies. Prior work seeks the best of both technologies by combining DRAM and NVM in hybrid memories to attain low latency, high capacity, energy efficiency, and durability. Coarse-grained hardware and OS optimizations then spread writes out (wear-leveling) and place highly mutated pages in DRAM to extend NVM lifetimes. Unfortunately even with these coarse-grained methods, popular Java applications exact impractical NVM lifetimes of 4 years or less. This paper shows how to make hybrid memories practical, without changing the programming model, by enhancing garbage collection in managed language runtimes. We find object write behaviors offer two opportunities: (1) 70% of writes occur to newly allocated objects, and (2) 2% of objects capture 81% of writes to mature objects. We introduce writerationing garbage collectors that exploit these fine-grained behaviors. They extend NVM lifetimes by placing highly mutated objects in DRAM and read-mostly objects in NVM. We implement two such systems. (1) Kingsguard-nursery places new allocation in DRAM and survivors in NVM, reducing NVM writes by 5x versus NVM only with wear-leveling. (2) Kingsguard-writers (KG-W) places nursery objects in DRAM and survivors in a DRAM observer space. It monitors all mature object writes and moves unwritten mature objects from DRAM to NVM. Because most mature objects are unwritten, KG-W exploits NVM capacity while increasing NVM lifetimes by 11x. It reduces the energy-delay product by 32% over DRAM-only and 29% over NVM-only. This work opens up new avenues for making hybrid memories practical

The duration of a co-occurring sound modulates visual detection performance in humans.

The duration of sounds can affect the perceived duration of co-occurring visual stimuli. However, it is unclear whether this is limited to amodal processes of duration perception or affects other non-temporal qualities of visual perception

An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer.

Loss of MHC class I (MHC-I) antigen presentation in cancer cells can elicit immunotherapy resistance. A genome-wide CRISPR/Cas9 screen identified an evolutionarily conserved function of polycomb repressive complex 2 (PRC2) that mediates coordinated transcriptional silencing of the MHC-I antigen processing pathway (MHC-I APP), promoting evasion of T cell-mediated immunity. MHC-I APP gene promoters in MHC-I low cancers harbor bivalent activating H3K4me3 and repressive H3K27me3 histone modifications, silencing basal MHC-I expression and restricting cytokine-induced upregulation. Bivalent chromatin at MHC-I APP genes is a normal developmental process active in embryonic stem cells and maintained during neural progenitor differentiation. This physiological MHC-I silencing highlights a conserved mechanism by which cancers arising from these primitive tissues exploit PRC2 activity to enable immune evasion.Cancer Research UK Clinician Scientist Fellowship C53779/A20097 (M.L.B), Leukaemia Foundation Australia Senior Fellowship and Howard Hughes Medical Institute International Research Scholarship 55008729 (M.A.D), Peter and Julie Alston Centenary fellowship (K.D.S.), Wellcome Trust Principal Research Fellowship 101835/Z/13/Z (P.J.L), Peter MacCallum Postgraduate Scholarship (C.E.S), NHMRC Postgraduate Scholarship (K.L.C.), Maddie Riewoldt's Vision 064728 (Y-C.C), Victorian Cancer Agency (E.Y.N.L), CSL Centenary fellowship (S-J.D), National Breast Cancer Foundation Fellowship ECF-17-005 (P.A.B.), Addenbrooke’s Charitable Trust and NIHR Cambridge BRC (M.L.B., P.J.L), NHMRC grant 1085015, 1106444 (M.A.D) and 1128984 (M.A.D, S-J.D)

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13