24 research outputs found

    The Current State and Future of CRISPR-Cas9 gRNA Design Tools

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    Recent years have seen the development of computational tools to assist researchers in performing CRISPR-Cas9 experiment optimally. More specifically, these tools aim to maximize on-target activity (guide efficiency) while also minimizing potential off-target effects (guide specificity) by analyzing the features of the target site. Nonetheless, currently available tools cannot robustly predict experimental success as prediction accuracy depends on the approximations of the underlying model and how closely the experimental setup matches the data the model was trained on. Here, we present an overview of the available computational tools, their current limitations and future considerations. We discuss new trends around personalized health by taking genomic variants into account when predicting target sites as well as discussing other governing factors that can improve prediction accuracy

    MicroRNA-22 Controls Aberrant Neurogenesis and Changes in Neuronal Morphology After Status Epilepticus

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    Prolonged seizures (status epilepticus, SE) may drive hippocampal dysfunction and epileptogenesis, at least partly, through an elevation in neurogenesis, dysregulation of migration and aberrant dendritic arborization of newly-formed neurons. MicroRNA-22 was recently found to protect against the development of epileptic foci, but the mechanisms remain incompletely understood. Here, we investigated the contribution of microRNA-22 to SE-induced aberrant adult neurogenesis. SE was induced by intraamygdala microinjection of kainic acid (KA) to model unilateral hippocampal neuropathology in mice. MicroRNA-22 expression was suppressed using specific oligonucleotide inhibitors (antagomir-22) and newly-formed neurons were visualized using the thymidine analog iodo-deoxyuridine (IdU) and a green fluorescent protein (GFP)-expressing retrovirus to visualize the dendritic tree and synaptic spines. Using this approach, we quantified differences in the rate of neurogenesis and migration, the structure of the apical dendritic tree and density and morphology of dendritic spines in newly-formed neurons.SE resulted in an increased rate of hippocampal neurogenesis, including within the undamaged contralateral dentate gyrus (DG). Newly-formed neurons underwent aberrant migration, both within the granule cell layer and into ectopic sites. Inhibition of microRNA-22 exacerbated these changes. The dendritic diameter and the density and average volume of dendritic spines were unaffected by SE, but these parameters were all elevated in mice in which microRNA-22 was suppressed. MicroRNA-22 inhibition also reduced the length and complexity of the dendritic tree, independently of SE. These data indicate that microRNA-22 is an important regulator of morphogenesis of newly-formed neurons in adults and plays a role in supressing aberrant neurogenesis associated with SE

    Severe Intraperitoneal Haemorrhage following Suprapubic Catheter Insertion in a Patient Treated with Iloprost

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    Suprapubic catheter (SPC) insertion is a common urological procedure, performed both in the elective and emergency settings. The authors present an unusual case of severe intraperitoneal bleeding following the insertion of an SPC under direct vision, where the use of prostacyclin analogue may have been a contributing factor

    Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning

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    Editing individual nucleotides is a crucial component for validating genomic disease association. It is currently hampered by CRISPR-Cas-mediated “base editing” being limited to certain nucleotide changes, and only achievable within a small window around CRISPR-Cas target sites. The more versatile alternative, HDR (homology directed repair), has a 3-fold lower efciency with known optimization factors being largely immutable in experiments. Here, we investigated the variable efciency-governing factors on a novel mouse dataset using machine learning. We found the sequence composition of the single-stranded oligodeoxynucleotide (ssODN), i.e. the repair template, to be a governing factor. Furthermore, diferent regions of the ssODN have variable infuence, which refects the underlying mechanism of the repair process. Our model improves HDR efciency by 83% compared to traditionally chosen targets. Using our fndings, we developed CUNE (Computational Universal Nucleotide Editor), which enables users to identify and design the optimal targeting strategy using traditional base editing or – for-the-frst-time–HDR-mediated nucleotide changes.This work was supported by the National Collaborative Research Infrastructure (NCRIS) via the Australian Phenomics Network (APN). We thank Alex Whan and Daniel Layton for critical reading of the document

    Table_1_The Current State and Future of CRISPR-Cas9 gRNA Design Tools.DOCX

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    <p>Recent years have seen the development of computational tools to assist researchers in performing CRISPR-Cas9 experiment optimally. More specifically, these tools aim to maximize on-target activity (guide efficiency) while also minimizing potential off-target effects (guide specificity) by analyzing the features of the target site. Nonetheless, currently available tools cannot robustly predict experimental success as prediction accuracy depends on the approximations of the underlying model and how closely the experimental setup matches the data the model was trained on. Here, we present an overview of the available computational tools, their current limitations and future considerations. We discuss new trends around personalized health by taking genomic variants into account when predicting target sites as well as discussing other governing factors that can improve prediction accuracy.</p
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