Characterization of the cork oak transcriptome dynamics during acorn development

Background: Cork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water. Results: A total of 80,357 expressed sequence tags (ESTs) were de novo assembled from RNA-Seq libraries representative of the several acorn developmental stages. Approximately 7.6 % of the total number of transcripts present in Q. suber transcriptome was identified as acorn specific. The analysis of expression profiles during development returned 2,285 differentially expressed (DE) transcripts, which were clustered into six groups. The stage of development corresponding to the mature acorn exhibited an expression profile markedly different from other stages. Approximately 22 % of the DE transcripts putatively code for transcription factors (TF) or transcriptional regulators, and were found almost equally distributed among the several expression profile clusters, highlighting their major roles in controlling the whole developmental process. On the other hand, carbohydrate metabolism, the biological pathway most represented during acorn development, was especially prevalent in mid to late stages as evidenced by enrichment analysis. We further show that genes related to response to water, water deprivation and transport were mostly represented during the early (S2) and the last stage (S8) of acorn development, when tolerance to water desiccation is possibly critical for acorn viability. Conclusions: To our knowledge this work represents the first report of acorn development transcriptomics in oaks. The obtained results provide novel insights into the developmental biology of cork oak acorns, highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for adaptation. It is expected that this knowledge can be transferred to other oak species of great ecological value.Fundação para a Ciência e a Tecnologi

Muon Fluence Measurements for Homeland Security Applications

This report focuses on work conducted at Pacific Northwest National Laboratory to better characterize aspects of backgrounds in RPMs deployed for homeland security purposes. Two polyvinyl toluene scintillators were utilized with supporting NIM electronics to measure the muon coincidence rate. Muon spallation is one mechanism by which background neutrons are produced. The measurements performed concentrated on a broad investigation of the dependence of the muon flux on a) variations in solid angle subtended by the detector; b) the detector inclination with the horizontal; c) depth underground; and d) diurnal effects. These tests were conducted inside at Building 318/133, outdoors at Building 331G, and underground at Building 3425 at Pacific Northwest National Laboratory

Superconductor digital electronics: Scalability and energy efficiency issues (Review Article)

Superconductor digital electronics using Josephson junctions as ultrafast switches and magnetic-flux encoding of information was proposed over 30 years ago as a sub-terahertz clock frequency alternative to semiconductor electronics based on complementary metal-oxide-semiconductor (CMOS) transistors. Recently, interest in developing superconductor electronics has been renewed due to a search for energy saving solutions in applications related to high-performance computing. The current state of superconductor electronics and fabrication processes are reviewed in order to evaluate whether this electronics is scalable to a very large scale integration (VLSI) required to achieve computation complexities comparable to CMOS processors. A fully planarized process at MIT Lincoln Laboratory, perhaps the most advanced process developed so far for superconductor electronics, is used as an example. The process has nine superconducting layers: eight Nb wiring layers with the minimum feature size of 350 nm, and a thin superconducting layer for making compact high-kinetic-inductance bias inductors. All circuit layers are fully planarized using chemical mechanical planarization (CMP) of SiO₂ interlayer dielectric. The physical limitations imposed on the circuit density by Josephson junctions, circuit inductors, shunt and bias resistors, etc., are discussed. Energy dissipation in superconducting circuits is also reviewed in order to estimate whether this technology, which requires cryogenic refrigeration, can be energy efficient. Fabrication process development required for increasing the density of superconductor digital circuits by a factor of ten and achieving densities above 10⁷ Josephson junctions per cm² is described