Dual Requirement for Yeast hnRNP Nab2p in mRNA poly(A) Tail Length Control and Nuclear Export

Recent studies of mRNA export factors have provided additional evidence for a mechanistic link between mRNA 3′‐end formation and nuclear export. Here, we identify Nab2p as a nuclear poly(A)‐binding protein required for both poly(A) tail length control and nuclear export of mRNA. Loss of NAB2 expression leads to hyperadenylation and nuclear accumulation of poly(A)+ RNA but, in contrast to mRNA export mutants, these defects can be uncoupled in a nab2 mutant strain. Previous studies have implicated the cytoplasmic poly(A) tail‐binding protein Pab1p in poly(A) tail length control during polyadenylation. Although cells are viable in the absence of NAB2 expression when PAB1 is overexpressed, Pab1p fails to resolve the nab2Δ hyperadenylation defect even when Pab1p is tagged with a nuclear localization sequence and targeted to the nucleus. These results indicate that Nab2p is essential for poly(A) tail length control in vivo, and we demonstrate that Nab2p activates polyadenylation, while inhibiting hyperadenylation, in the absence of Pab1p in vitro. We propose that Nab2p provides an important link between the termination of mRNA polyadenylation and nuclear export

Overview of the 6m HIAD Inflatable Structure and Flexible TPS Static Load Test Series

To support NASAs long term goal of landing humans on Mars, technologies which enable the landing of heavy payloads are being developed. Current entry, decent, and landing technologies are not practical for this class of payloads due to geometric constraints dictated by current launch vehicle fairing limitations. Therefore, past and present technologies are now being explored to provide a mass and volume efficient solution to atmospheric entry, including Hypersonic Inflatable Aerodynamic Decelerators (HIADs). At the beginning of 2014, a 6m HIAD inflatable structure with an integrated flexible thermal protection system (TPS) was subjected to a static load test series to verify the designs structural performace. The 6m HIAD structure was constructed in a stacked toroid configuration using nine inflatable torus segments composed of fiber reinforced thin films, which were joined together using adhesives and high strength textile woven structural straps to help distribute the loads throughout the inflatable structure. The 6m flexible TPS was constructed using multiple layers of high performance materials to protect the inflatable structure from heat loads that would be seen during atmospheric entry. To perform the static load test series, a custom test fixture was constructed. The fixture consisted of a structural tub rim with enough height to allow for displacement of the inflatable structure as loads were applied. The bottom of the tub rim had an airtight seal with the floor. The centerbody of the inflatable structure was attached to a pedestal mount as seen in Figure 1. Using an impermeable membrane seal draped over the test article, partial vacuum was pulled beneath the HIAD, resulting in a uniform static pressure load applied to the outer surface. During the test series an extensive amount of instrumentation was used to provide many data sets including: deformed shape, shoulder deflection, strap loads, cord loads, inflation pressures, and applied static load.In this overview, the 6m HIAD static load test series will be discussed in detail, including the 6m HIAD inflatable structure and flexible TPS design, test setup and execution, and finally initial results and conclusions from the test series

APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane

Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

A Landscape Plan Based on Historical Fire Regimes for a Managed Forest Ecosystem: the Augusta Creek Study

The Augusta Creek project was initiated to establish and integrate landscape and watershed objectives into a landscape plan to guide management activities within a 7600-hectare (19,000-acre) planning area in western Oregon. Primary objectives included the maintenance of native species, ecosystem processes and structures, and long-term ecosystem productivity in a federally managed landscape where substantial acreage was allocated to timber harvest. Landscape and watershed management objectives and prescriptions were based on an interpreted range of natural variability of landscape conditions and disturbance processes. A dendrochronological study characterized fire patterns and regimes over the last 500 years. Changes in landscape conditions throughout the larger surrounding watershed due to human uses (e.g., roads in riparian areas, widespread clearcutting, a major dam, and portions of a designated wilderness and an unroaded area) also were factored into the landscape plan. Landscape prescriptions include an aquatic reserve system comprised of small watersheds distributed throughout the planning area and major valley-bottom corridor reserves that connect the small-watershed reserves. Where timber harvest was allocated, prescriptions derived from interpretations of fire regimes differ in rotation ages (100 to 300 years), green-tree retention levels (15- to 50-percent canopy cover), and spatial patterns of residual trees. General prescriptions for fire management also were based on interpretations of past fire regimes. All these prescriptions were linked to specific blocks of land to provide an efficient transition to site-level planning and project implementation. Landscape and watershed conditions were projected 200 years into the future and compared with conditions that would result from application of standards, guidelines, and assumptions in the Northwest Forest Plan prior to adjustments resulting from watershed analyses. The contrasting prescriptions for aquatic reserves and timber harvest (rotation lengths, green-tree retention levels, and spatial patterns) in these two approaches resulted in strikingly different potential future landscapes. These differences have significant implications for some ecosystem processes and habitats. We view this management approach as a potential post watershed analysis implementation of the Northwest Forest Plan and offer it as an example of how ecosystem management could be applied in a particular landscape by using the results of watershed analysis

Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

Duplicated genes can contribute to the evolution of new functions and they are common in eukaryotic genomes. After duplication, genes can show divergence in their sequence and/or expression patterns. Qualitative complementary expression, or reciprocal expression, is when only one copy is expressed in some organ or tissue types and only the other copy is expressed in others, indicative of regulatory subfunctionalization or neofunctionalization. From analyses of two microarray data sets with 83 different organ types, developmental stages, and cell types in Arabidopsis thaliana, we determined that 30% of whole-genome duplicate pairs and 38% of tandem duplicate pairs show reciprocal expression patterns. We reconstructed the ancestral state of expression patterns to infer that considerably more cases of reciprocal expression resulted from gain of a new expression pattern (regulatory neofunctionalization) than from partitioning of ancestral expression patterns (regulatory subfunctionalization). Pollen was an especially common organ type for expression gain, resulting in contrasting expression of some duplicates in pollen. Many of the gene pairs with reciprocal expression showed asymmetric sequence rate evolution, consistent with neofunctionalization, and the more rapidly evolving copy often showed a more restricted expression pattern. A gene with reciprocal expression in pollen, involved in brassinosteroid signal transduction, has evolved more rapidly than its paralog, and it shows evidence for a new function in pollen. This study indicates the evolutionary importance of reciprocal expression patterns between gene duplicates, showing that they are common, often associated with regulatory neofunctionalization, and may be a factor allowing for retention and divergence of duplicated genes