Transcriptome Analyses of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed with Transposable Elements

Background: Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined. Results: Here we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated expression across broad classes of TEs. Despite this co-expression within tissues, there are individual TE loci that exhibit tissue-specific expression patterns, when compared across tissues. The core TE modules were negatively correlated with other gene modules that consisted of immune response genes in interferon signaling. KRAB Zinc Finger Proteins (KZFPs) were over-represented gene members of the TE modules, showing positive correlation across multiple tissues. But we did not find overlap between TE-KZFP pairs that are co-expressed and TE-KZFP pairs that are bound in published ChIP-seq studies. Conclusions: We find unexpected variation in TE derived transcripts, within and across non-tumorous tissues. We describe a broad view of the RNA state for non-tumorous tissues exhibiting higher level of TE transcripts. Tissues with higher level of TE transcripts have a broad range of TEs co-expressed, with high expression of a large number of KZFPs, and lower RNA levels of immune genes

A Comparative Study of Three Different Chemical Vapor Deposition Techniques of Carbon Nanotube Growth on Diamond Films

This paper compares between the methods of growing carbon nanotubes (CNTs) on diamond substrates and evaluates the quality of the CNTs and the interfacial strength. One potential application for these materials is a heat sink/spreader for high-power electronic devices. The CNTs and diamond substrates have a significantly higher specific thermal conductivity than traditional heat sink/spreader materials making them good replacement candidates. Only limited research has been performed on these CNT/diamond structures and their suitability of different growth methods. This study investigates three potential chemical vapor deposition (CVD) techniques for growing CNTs on diamond: thermal CVD (T-CVD), microwave plasma-enhanced CVD (MPE-CVD), and floating catalyst thermal CVD (FCT-CVD). Scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (TEM) were used to analyze the morphology and topology of the CNTs. Raman spectroscopy was used to assess the quality of the CNTs by determining the ID/IG peak intensity ratios. Additionally, the CNT/diamond samples were sonicated for qualitative comparisons of the durability of the CNT forests. T-CVD provided the largest diameter tubes, with catalysts residing mainly at the CNT/diamond interface. The MPE-CVD process yielded non uniform defective CNTs, and FCT-CVD resulted in the smallest diameter CNTs with catalyst particles imbedded throughout the length of the nanotubes

Estimating the environmental impact of dairy cattle breeding programs through emission intensity.

A recently developed methodological approach for determining the greenhouse gas emissions impact of national breeding programs was applied to measure the effects of current and future breeding goals on the emission intensity (EI) of the Canadian dairy industry. Emission intensity is the ratio of greenhouse gas outputted in comparison to the product generated. Traits under investigation affected EI by either decreasing the direct emissions yield (i.e. increasing feed performance), changing herd structure (i.e. prolonging herd life) or through the dilution effect of increased production (i.e. increasing fat yield). The intensity value (IV) of each trait, defined as the change in emissions' intensity per unit change in each trait, was calculated for each of the investigated traits. The IV trend of these traits was compared for the current and prospective selection index, as well as for a system with and without quota (the supply management policy designed to prevent overproduction). The overall EI of the average genetic merit Canadian dairy herd per breeding female was 5.07 kg CO2eq/kg protein equivalent output. The annual reduction in EI due to the improvement of production traits was -0.027, -0.018 and -0.006 for fat, protein and milk other solids, respectively. The functional traits, herd life and mastitis resistance, had more modest effects (-0.008 and -0.001, respectively). These results are consistent with international studies that identified traits related to production, survival, health and fertility as having the largest impact on the environmental footprint of dairy cattle. Overall, the dairy industry is becoming more efficient by reducing its EI through selection of environmentally favorable traits, with a 1% annual reduction of EI in Canada

Correction to: Transcriptome Analyses of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed with Transposable Elements

Following publication of the original article [1], the authors reported errors in Table 2 wherein all “KZFP” in the gene names should be changed to “ZNF”

A Synthetic Chloride Channel Restores Chloride Conductance in Human Cystic Fibrosis Epithelial Cells

Mutations in the gene-encoding cystic fibrosis transmembrane conductance regulator (CFTR) cause defective transepithelial transport of chloride (Cl−) ions and fluid, thereby becoming responsible for the onset of cystic fibrosis (CF). One strategy to reduce the pathophysiology associated with CF is to increase Cl− transport through alternative pathways. In this paper, we demonstrate that a small synthetic molecule which forms Cl− channels to mediate Cl− transport across lipid bilayer membranes is capable of restoring Cl− permeability in human CF epithelial cells; as a result, it has the potential to become a lead compound for the treatment of human diseases associated with Cl− channel dysfunction

Permafrost Landscape History Shapes Fluvial Chemistry, Ecosystem Carbon Balance, and Potential Trajectories of Future Change

Intensifying permafrost thaw alters carbon cycling by mobilizing large amounts of terrestrial substrate into aquatic ecosystems. Yet, few studies have measured aquatic carbon fluxes and constrained drivers of ecosystem carbon balance across heterogeneous Arctic landscapes. Here, we characterized hydrochemical and landscape controls on fluvial carbon cycling, quantified fluvial carbon fluxes, and estimated fluvial contributions to ecosystem carbon balance across 33 watersheds in four ecoregions in the continuous permafrost zone of the western Canadian Arctic: unglaciated uplands, ice-rich moraine, and organic-rich lowlands and till plains. Major ions, stable isotopes, and carbon speciation and fluxes revealed patterns in carbon cycling across ecoregions defined by terrain relief and accumulation of organics. In previously unglaciated mountainous watersheds, bicarbonate dominated carbon export (70% of total) due to chemical weathering of bedrock. In lowland watersheds, where soil organic carbon stores were largest, lateral transport of dissolved organic carbon (50%) and efflux of biotic CO2 (25%) dominated. In watersheds affected by thaw-induced mass wasting, erosion of ice-rich tills enhanced chemical weathering and increased particulate carbon fluxes by two orders of magnitude. From an ecosystem carbon balance perspective, fluvial carbon export in watersheds not affected by thaw-induced wasting was, on average, equivalent to 6%–16% of estimated net ecosystem exchange (NEE). In watersheds affected by thaw-induced wasting, fluvial carbon export approached 60% of NEE. Because future intensification of thermokarst activity will amplify fluvial carbon export, determining the fate of carbon across diverse northern landscapes is a priority for constraining trajectories of permafrost region ecosystem carbon balance

First-level trigger systems for LHC experiments

We propose to carry out a broad-based programme of R&D on level-1 trigger systems for LHC experiments. We will consider the overall level-1 which coordinates different subtriggers and which interacts with the front end electronics and with the level-2 system. Careful attention will be paid to systems aspects and problems of synchronization within the pipelined processor system. Trigger algorithms for selecting events with high-pt electrons, photons, muons, jets and large missing Et will be evaluated by physics simulation studies. We will study possible implementations of such trigger algorithms in fast electronics by making conceptual design studies and using behavioural simulation models. For critical areas more detailed design studies will be made, and prototypes of some key elements will be constructed and tested. The proposed R&D project builds on existing studies and will complement other R&D projects already funded by the DRDC

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here we present our largest increase in plant, metazoan and fungal genomes since the project’s inception creating one of the world’s most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We also detail our new efforts in gene annotation, our emerging support for pangenome analysis and efforts to accelerate data dissemination through the Ensembl Rapid Release resource. We also present our new AlphaFold visualisation. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl’s release cycle

The Structure of Spatial Localization

Material objects, such as tables and chairs, have an intimate relationship with space. They have to be somewhere. They must possess an address at which they are found. Under this aspect, they are in good company. Events, too, such as Caesar’s death and John’s buttering of the toast, and more elusive entities, such as the surface of the table, have an address, difficult as it may be to specify. A stronger notion presents itself, though. Some entities may not only be located at an address; they may also own (as it were) the place at which they are located, so as to exclude other entities from being located at the same address. Thus, for certain kinds of entities, no two tokens of the same kind can be located at the same place at the same time. This is typically the case with material objects. Likewise, no two particularized properties of the same level or degree of determinacy can be located at the same place at the same time (although particularized properties of different degree, such as the red of this table and the color of this table, can). Other entities seem to evade the restriction. Two events can be perfectly co-located without competing for their address. Or, to use a different terminology, events do not occupy the spatial region at which they are located, and can therefore share it with other events. The rotation of the Earth and the cooling down of the Earth take place at exactly the same regio

Mucociliary and long-term particle clearance in airways of patients with immotile cilia

Spherical monodisperse ferromagnetic iron oxide particles of 1.9 μm geometric and 4.2 μm aerodynamic diameter were inhaled by seven patients with primary ciliary dyskinesia (PCD) using the shallow bolus technique, and compared to 13 healthy non-smokers (NS) from a previous study. The bolus penetration front depth was limiting to the phase1 dead space volume. In PCD patients deposition was 58+/-8 % after 8 s breath holding time. Particle retention was measured by the magnetopneumographic method over a period of nine months. Particle clearance from the airways showed a fast and a slow phase. In PCD patients airway clearance was retarded and prolonged, 42+/-12 % followed the fast phase with a mean half time of 16.8+/-8.6 hours. The remaining fraction was cleared slowly with a half time of 121+/-25 days. In healthy NS 49+/-9 % of particles were cleared in the fast phase with a mean half time of 3.0+/-1.6 hours, characteristic of an intact mucociliary clearance. There was no difference in the slow clearance phase between PCD patients and healthy NS. Despite non-functioning cilia the effectiveness of airway clearance in PCD patients is comparable to healthy NS, with a prolonged kinetics of one week, which may primarily reflect the effectiveness of cough clearance. This prolonged airway clearance allows longer residence times of bacteria and viruses in the airways and may be one reason for increased frequency of infections in PCD patients