Metapopulation dynamics over 25 years of a beetle, Osmoderma eremita, inhabiting hollow oaks

Osmoderma eremita is a species of beetle that inhabits hollows in ancient trees, which is a habitat that has decreased significantly during the last century. In southeastern Sweden, we studied the metapopulation dynamics of this beetle over a 25 year period, using capture-mark-recapture. The metapopulation size had been rather stable over time, but in most of the individual trees there had been a positive or negative trend in population development. The probability of colonisation was higher in well-connected trees with characteristics reflecting earlier successional stages, and the probability of extinction higher in trees with larger diameter (i.e. in later successional stages), which is expected from a habitat-tracking metapopulation. The annual tree mortality and fall rates (1.1% and 0.4%, respectively) are lower than the colonisation and extinction rates (5-7%), indicating that some of the metapopulation dynamics are due to the habitat dynamics, but many colonisations and extinctions take place for other reasons, such as stochastic events in small populations. The studied metapopulation occurs in an area with a high density of hollow oaks and where the oak pastures are still managed by grazing. In stands with fewer than ten suitable trees, the long-term extinction risk may be considerable, since only a small proportion of all hollow trees harbours large populations, and the population size in trees may change considerably during a decade

Comparing Star Formation on Large Scales in the c2d Legacy Clouds: Bolocam 1.1 mm Dust Continuum Surveys of Serpens, Perseus, and Ophiuchus

We have undertaken an unprecedentedly large 1.1 millimeter continuum survey of three nearby star forming clouds using Bolocam at the Caltech Submillimeter Observatory. We mapped the largest areas in each cloud at millimeter or submillimeter wavelengths to date: 7.5 sq. deg in Perseus (Paper I), 10.8 sq. deg in Ophiuchus (Paper II), and 1.5 sq. deg in Serpens with a resolution of 31", detecting 122, 44, and 35 cores, respectively. Here we report on results of the Serpens survey and compare the three clouds. Average measured angular core sizes and their dependence on resolution suggest that many of the observed sources are consistent with power-law density profiles. Tests of the effects of cloud distance reveal that linear resolution strongly affects measured source sizes and densities, but not the shape of the mass distribution. Core mass distribution slopes in Perseus and Ophiuchus (alpha=2.1+/-0.1 and alpha=2.1+/-0.3) are consistent with recent measurements of the stellar IMF, whereas the Serpens distribution is flatter (alpha=1.6+/-0.2). We also compare the relative mass distribution shapes to predictions from turbulent fragmentation simulations. Dense cores constitute less than 10% of the total cloud mass in all three clouds, consistent with other measurements of low star-formation efficiencies. Furthermore, most cores are found at high column densities; more than 75% of 1.1 mm cores are associated with Av>8 mag in Perseus, 15 mag in Serpens, and 20-23 mag in Ophiuchus.Comment: 32 pages, including 18 figures, accepted for publication in Ap

Dispersal and spatiotemporal distribution of Protapion fulvipes in white clover fields: implications for pest management

Yield loss caused by insect pests remains a substantial problem in agriculture. Chemical control, with potential negative effects on non-target organisms, is still the main tool for pest management. For pest species with limited dispersal capacity, rotation of the crop in time and space has potential as an alternative management measure. This is particularly important in organic farming, where most agrochemicals are prohibited, but also relevant as a complementary pest management strategy in conventional agriculture. Clover is an important crop used for animal feed and as green manure; however, seed-eating weevils can severely limit the seed yield. We hypothesized that the previous year's clover seed fields constitute the major sources of weevil pests. Consequently, a greater distance to, and a smaller pest load from, this source should reduce the number of weevils colonizing the new seed fields. To map population dynamics and dispersal range of Protapion fulvipes, an economically important seed weevil specialized on white clover, we conducted field studies over four years in 45 white clover seed fields. We found that P. fulvipes overwinters close to its source field and disperses to new fields in early spring the following year. Pest abundance increased with pest load in the previous year's seed field, but decreased by 68% per km distance to the previous year's field. Thus, separation of seed production fields between years by 2-3 km would create a spatiotemporal pest management tool to reduce the pest infestation below the estimated economic injury level

Integrerat växtskydd i vitklöverfröodling: flytta fält mellan år för att minska angrepp av fröätande skadegörare

Tillgång på alternativa växtskyddsmetoder är viktiga för att kunna tillämpa integrerat växtskydd. I detta projekt undersökte vi hur förekomst av fröskadegörare och fröproduktion hos vitklöver påverkas av att flytta fält kortare respektive längre avstånd mellan år

Ethanol production of semi-simultaneous saccharification and fermentation from mixture of cotton gin waste and recycled paper sludge

Ethanol production from the steam-exploded mixture of 75% cotton gin waste and 25% recycled paper sludge in various conditions was investigated by semi-simultaneous saccharification and fermentation (SSSF) consisting of a pre-hydrolysis and a simultaneous saccharification and fermentation (SSF). Four cases were studied: 24-h pre-hydrolysis + 48-h SSF (SSSF 24), 12-h pre-hydrolysis + 60-h SSF (SSSF 12), 72-h SSF, and 48-h hydrolysis + 24-h fermentation (SHF). The ethanol concentration, yield, and productivity of SSSF 24 were higher than those of the other operations. A model of SSF was used to simulate the data for four components in SSF. The analysis of the reaction rates of cellobiose, glucose, cell, and ethanol using the model and the parameters from the experiments showed that there was a transition point of the rate-controlling step at which the cell growth control in the initial 2 h was changed to the cellobiose reaction control in later period during ethanol production of SSF from the mixture

Locus Reference Genomic sequences: an improved basis for describing human DNA variants

As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specific purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-file record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)-approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants affecting human health. Further information can be found on the LRG web site: http://www.lrg-sequence.org

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

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

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

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