Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease, bioRxiv, 2019-08-06
AbstractAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with few avenues for treatment. Many proteins implicated in ALS associate with stress granules, which are examples of liquid-like compartments formed by phase separation. Aberrant phase transition of stress granules has been implicated in disease, suggesting that modulation of phase transitions could be a possible therapeutic route. Here, we combine cell-based and protein-based screens to show that lipoamide, and its related compound lipoic acid, reduce the propensity of stress granule proteins to aggregate in vitro. More significantly, they also prevented aggregation of proteins over the life time of Caenorhabditis elegans. Observations that they prevent dieback of ALS patient-derived (FUS mutant) motor neuron axons in culture and recover motor defects in Drosophila melanogaster expressing FUS mutants suggest plausibility as effective therapeutics. Our results suggest that altering phase behaviour of stress granule proteins in the cytoplasm could be a novel route to treat ALS.
biorxiv cell-biology 100-200-users 2019The critical role of mental imagery in human emotion insights from Aphantasia, bioRxiv, 2019-08-06
AbstractOne proposed function of imagery is to make thoughts more emotionally evocative through sensory simulations. Here we report a novel test of this theory utilizing a special population with no visual imagery Aphantasia. After using multi-method verification of aphantasia, we show that this condition, but not the general population, is associated with a flat-line physiological response to frightening written, but not perceptual scenarios, supporting imagery’s critical role in emotion.
biorxiv neuroscience 100-200-users 2019The Integrator complex terminates promoter-proximal transcription at protein-coding genes, bioRxiv, 2019-08-06
SUMMARYThe transition of RNA polymerase II (Pol II) from initiation to productive elongation is a central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in early elongation, remaining engaged with the 25-60 nucleotide-long nascent RNA for many minutes while awaiting signals for release into the gene body. However, a number of genes display highly unstable promoter Pol II, suggesting that paused polymerase might dissociate from template DNA at these promoters and release a short, non-productive mRNA. Here, we report that paused Pol II can be actively destabilized by the Integrator complex. Specifically, Integrator utilizes its RNA endonuclease activity to cleave nascent RNA and drive termination of paused Pol II. These findings uncover a previously unappreciated mechanism of metazoan gene repression, akin to bacterial transcription attenuation, wherein promoter-proximal Pol II is prevented from entering productive elongation through factor-regulated termination.Highlights<jatslist list-type=bullet><jatslist-item>The Integrator complex inhibits transcription elongation at ∼15% of mRNA genes<jatslist-item><jatslist-item>Integrator targets promoter-proximally paused Pol II for termination<jatslist-item><jatslist-item>The RNA endonuclease of Integrator subunit 11 is critical for gene attenuation<jatslist-item><jatslist-item>Integrator-repressed genes are enriched in signaling and growth-responsive pathways<jatslist-item>
biorxiv genomics 100-200-users 2019NAD+ repletion rescues female fertility during reproductive ageing, bioRxiv, 2019-08-03
AbstractFemale infertility is a common and devastating condition with life-long health, emotional and social consequences. There is currently no pharmacological therapy for preserving oocyte quality during aging, which is the strongest risk factor for infertility. This leads to an age dependent decline in natural conception and IVF success rates (1). Here, we show that this is due in part to declining levels of the metabolic cofactor nicotinamide adenine dinucleotide (NAD+), and that restoring NAD+ levels with its metabolic precursor nicotinamide mononucleotide (NMN) rejuvenates oocyte quality and quantity in aged animals, leading to improved fertility. These benefits extend to the developing embryo, where NMN supplementation in embryo culture media following IVF enhances blastocyst formation in older mice. The NAD+ dependent deacylase SIRT2 is sufficient, but not essential, to recapitulate the benefits of in vivo NMN treatment, and transgenic overexpression of SIRT2 maintains oocyte spindle assembly, accurate chromosome segregation, decreased oxidative stress and overall fertility with ageing. Pharmacological elevation of NAD+ may be an effective, non-invasive strategy for restoring and maintaining female fertility during ageing, and for improving the success of IVF.
biorxiv developmental-biology 0-100-users 2019Assembly methods for nanopore-based metagenomic sequencing a comparative study, bioRxiv, 2019-08-02
ABSTRACTBackgroundMetagenomic sequencing has lead to the recovery of previously unexplored microbial genomes. In this sense, short-reads sequencing platforms often result in highly fragmented metagenomes, thus complicating downstream analyses. Third generation sequencing technologies, such as MinION, could lead to more contiguous assemblies due to their ability to generate long reads. Nevertheless, there is a lack of studies evaluating the suitability of the available assembly tools for this new type of data.FindingsWe benchmarked the ability of different short-reads and long-reads tools to assembly two different commercially available mock communities, and observed remarkable differences in the resulting assemblies depending on the software of choice. Short-reads metagenomic assemblers proved unsuitable for MinION data. Among the long-reads assemblers tested, Flye and Canu were the only ones performing well in all the datasets. These tools were able to retrieve complete individual genomes directly from the metagenome, and assembled a bacterial genome in only two contigs in the best scenario. Despite the intrinsic high error of long-reads technologies, Canu and Flye lead to high accurate assemblies (~99.4-99.8 % of accuracy). However, errors still had an impact on the prediction of biosynthetic gene clusters.ConclusionsMinION metagenomic sequencing data proved sufficient for assembling low-complex microbial communities, leading to the recovery of highly complete and contiguous individual genomes. This work is the first systematic evaluation of the performance of different assembly tools on MinION data, and may help other researchers willing to use this technology to choose the most appropriate software depending on their goals. Future work is still needed in order to assess the performance of Oxford Nanopore MinION data on more complex microbiomes.
biorxiv bioinformatics 100-200-users 2019Genetic tool development in marine protists Emerging model organisms for experimental cell biology, bioRxiv, 2019-08-02
ABSTRACTMarine microbial eukaryotes underpin the largest food web on the planet and influence global biogeochemical cycles that maintain habitability. They are also remarkably diverse and provide insights into evolution, including the origins of complex life forms, as revealed through genome analyses. However, their genetic tractability has been limited to a few species that do not represent the broader diversity of eukaryotic life or some of the most environmentally relevant taxa. Here, we report on genetic systems developed as a community resource for experimental cell biology of aquatic protists from across the eukaryotic tree and primarily from marine habitats. We present evidence for foreign DNA delivery and expression in 14 species never before transformed, report on the advancement of genetic systems in 7 species, review of an already published transformation protocol in 1 species and discuss why the transformation of 17 additional species has not been achieved yet. For all protists studied in this community effort, we outline our methods, constructs, and genome-editing approaches in the context of published systems. The reported breakthroughs on genetic manipulation position the community to dissect cellular mechanisms from a breadth of protists, which will collectively provide insights into ancestral eukaryotic lifeforms, protein diversification and evolution of cellular pathways.
biorxiv ecology 100-200-users 2019