Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies

The rapid (< 1 ms) transport of biological material to and from the cell nucleus is regulated by the nuclear pore complex (NPC). At the core of the NPC is a permeability barrier consisting of intrinsically disordered Phe-Gly (FG) nucleoporins (FG Nups). Various types of nuclear transport receptors (NTRs) facilitate transport by partitioning in the FG Nup assembly, overcoming the barrier by their affinity to the FG Nups, and comprise a significant fraction of proteins in the NPC barrier. In previous work Zahn et al. (2016), we revealed a universal physical behaviour in the experimentally observed binding of two well-characterized NTRs, NTF2 and the larger Importin-ᵝ, to different planar assemblies of FG Nups, with the binding behaviour defined by negative cooperativity. This was further validated by a minimal physical model that treated the FG Nups as flexible homopolymers and the NTRs as uniformly cohesive spheres. Here, we build upon our original study by first parametrizing our model to experimental data, and next predicting the effects of crowding by different types of NTRs. We show how varying the amounts of one type of NTR modulates how the other NTR penetrates the FG Nup assembly. Notably, at similar and physiologically relevant NTR concentrations, our model predicts demixed phases of NTF2 and Imp-ᵝ within the FG Nup assembly. The functional implication of NTR phase separation is that NPCs may sustain separate transport pathways that are determined by inter-NTR competition

Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics

In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events

Comparative genomics of the genus porphyromonas identifies adaptations for heme synthesis within the prevalent canine oral species porphyromonas cangingivalis

© 2015 The Author(s). Porphyromonads play an important role inhuman periodontal disease and recently have been shownto be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions characterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from18Porphyromonad species fromdogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to synthesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. Other pathway differences such as the ability to synthesize siroheme and vitamin B12 point to enhanced metabolic flexibility for P. cangingivalis, which may underlie its prevalence in the canine oral cavity

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment

© 2019 Coil et al. Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy was revisited through a manual process using a combination of average nucleotide identity (ANI), concatenated marker gene phylogenies, and 16S rRNA gene phylogenies. This taxonomy was then compared to the automated taxonomic assignment given by the recently proposed Genome Taxonomy Database (GTDB). We found the results of all three methods to be similar (25 out of the 33 had matching genera), but the GTDB approach required fewer subjective decisions, and required far less labor. The primary differences in the non-identical taxonomic assignments involved cases where GTDB has proposed taxonomic revisions

Shifts in national land use and food production in Great Britain after a climate tipping point

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordData availability: The modelled output data that support the findings of this study are openly available from: Smith, G. S. & Ritchie, P. D. L. (NERC Environmental Information Data Centre: 639 doi.org/10.5285/e1c1dbcf-2f37-429b-af19-a730f98600f6, 2019).Climate change is expected to impact agricultural land use. Steadily accumulating changes in temperature and water availability can alter the relative profitability of different farming activities and promote land use changes. There is also potential for high-impact ‘climate tipping points’ where abrupt, non-linear change in climate occurs - such as the potential collapse of the Atlantic Meridional Overturning Circulation (AMOC). Here, using data from Great Britain, we develop a methodology to analyse the impacts of a climate tipping point on land use and economic outcomes for agriculture. We show that economic/land use impacts of such a tipping point are likely to include widespread cessation of arable farming with losses of agricultural output, an order of magnitude larger than the impacts of climate change without an AMOC collapse. The agricultural effects of AMOC collapse could be ameliorated by technological adaptations such as widespread irrigation, but the amount of water required and the costs appear prohibitive in this instance.Natural Environment Research Council (NERC)Alan Turing Institut

Refactoring bacteriophage T7

Natural biological systems are selected by evolution to continue to exist and evolve. Evolution likely gives rise to complicated systems that are difficult to understand and manipulate. Here, we redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. Our initial design goals were to physically separate and enable unique manipulation of primary genetic elements. Implicit in our design are the hypotheses that overlapping genetic elements are, in aggregate, nonessential for T7 viability and that our models for the functions encoded by elements are sufficient. To test our initial design, we replaced the left 11 515 base pairs (bp) of the 39 937 bp wild-type genome with 12 179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention

Primary myxoid liposarcoma of the supraglottic larynx

Sarcomas are a rare occurrence accounting for roughly 1% of all cancer cases reported. Of these, 9–18% will be identified as liposarcoma. Overall, only 4–9% of all liposarcomas occur in the head and neck region. As such, it is a rare event to see a primary liposarcoma of the aerodigestive tract. These tumors are typically misdiagnosed secondary to their indolent, asymptomatic course and similarities in appearance to other benign lesions. An understanding of these lesions will help clinicians appropriately manage their patients. We present a case of a 60-year male with a primary supraglottic myxoid liposarcoma, and provide relevant information about liposarcomas

The stability of educational achievement across school years is largely explained by genetic factors.

Little is known about the etiology of developmental change and continuity in educational achievement. Here, we study achievement from primary school to the end of compulsory education for 6000 twin pairs in the UK-representative Twins Early Development Study sample. Results showed that educational achievement is highly heritable across school years and across subjects studied at school (twin heritability ~60%; SNP heritability ~30%); achievement is highly stable (phenotypic correlations ~0.70 from ages 7 to 16). Twin analyses, applying simplex and common pathway models, showed that genetic factors accounted for most of this stability (70%), even after controlling for intelligence (60%). Shared environmental factors also contributed to the stability, while change was mostly accounted for by individual-specific environmental factors. Polygenic scores, derived from a genome-wide association analysis of adult years of education, also showed stable effects on school achievement. We conclude that the remarkable stability of achievement is largely driven genetically even after accounting for intelligence