Conformational Targeting of Fibrillar Polyglutamine Proteins in Live Cells Escalates Aggregation and Cytotoxicity

Misfolding- and aggregation-prone proteins underlying Parkinson's, Huntington's and Machado-Joseph diseases, namely alpha-synuclein, huntingtin, and ataxin-3 respectively, adopt numerous intracellular conformations during pathogenesis, including globular intermediates and insoluble amyloid-like fibrils. Such conformational diversity has complicated research into amyloid-associated intracellular dysfunction and neurodegeneration. To this end, recombinant single-chain Fv antibodies (scFvs) are compelling molecular tools that can be selected against specific protein conformations, and expressed inside cells as intrabodies, for investigative and therapeutic purposes.Using atomic force microscopy (AFM) and live-cell fluorescence microscopy, we report that a human scFv selected against the fibrillar form of alpha-synuclein targets isomorphic conformations of misfolded polyglutamine proteins. When expressed in the cytoplasm of striatal cells, this conformation-specific intrabody co-localizes with intracellular aggregates of misfolded ataxin-3 and a pathological fragment of huntingtin, and enhances the aggregation propensity of both disease-linked polyglutamine proteins. Using this intrabody as a tool for modulating the kinetics of amyloidogenesis, we show that escalating aggregate formation of a pathologic huntingtin fragment is not cytoprotective in striatal cells, but rather heightens oxidative stress and cell death as detected by flow cytometry. Instead, cellular protection is achieved by suppressing aggregation using a previously described intrabody that binds to the amyloidogenic N-terminus of huntingtin. Analogous cytotoxic results are observed following conformational targeting of normal or polyglutamine-expanded human ataxin-3, which partially aggregate through non-polyglutamine domains.These findings validate that the rate of aggregation modulates polyglutamine-mediated intracellular dysfunction, and caution that molecules designed to specifically hasten aggregation may be detrimental as therapies for polyglutamine disorders. Moreover, our findings introduce a novel antibody-based tool that, as a consequence of its general specificity for fibrillar conformations and its ability to function intracellularly, offers broad research potential for a variety of human amyloid diseases

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations

We tested whether DNA-methylation profiles account for inter-individual variation in body mass index (BMI) and height and whether they predict these phenotypes over and above genetic factors. Genetic predictors were derived from published summary results from the largest genome-wide association studies on BMI (n ∼ 350,000) and height (n ∼ 250,000) to date. We derived methylation predictors by estimating probe-trait effects in discovery samples and tested them in external samples. Methylation profiles associated with BMI in older individuals from the Lothian Birth Cohorts (LBCs, n = 1,366) explained 4.9% of the variation in BMI in Dutch adults from the LifeLines DEEP study (n = 750) but did not account for any BMI variation in adolescents from the Brisbane Systems Genetic Study (BSGS, n = 403). Methylation profiles based on the Dutch sample explained 4.9% and 3.6% of the variation in BMI in the LBCs and BSGS, respectively. Methylation profiles predicted BMI independently of genetic profiles in an additive manner: 7%, 8%, and 14% of variance of BMI in the LBCs were explained by the methylation predictor, the genetic predictor, and a model containing both, respectively. The corresponding percentages for LifeLines DEEP were 5%, 9%, and 13%, respectively, suggesting that the methylation profiles represent environmental effects. The differential effects of the BMI methylation profiles by age support previous observations of age modulation of genetic contributions. In contrast, methylation profiles accounted for almost no variation in height, consistent with a mainly genetic contribution to inter-individual variation. The BMI results suggest that combining genetic and epigenetic information might have greater utility for complex-trait prediction

Investigating model evolution in a collaborative BIM environment

As the adoption and implementation of building information modeling (BIM) continues to gain momentum, the benefits and challenges of its implementation and use are becoming better defined. However, there still lacks an understanding into the reconfiguration of practice that is being induced by BIM within multi-disciplinary project teams. Part of this reconfiguration of practice involves the development of the model through the generation, authoring and exchange of project information. This paper presents the finding of a research project that investigated the evolution of a BIM developed by a vertically integrated project team on a large institutional project for design and construction purposes. The objective of the research project was to develop measures to investigate the evolution of a BIM in a collaborative and multi-disciplinary project setting. The research team analyzed the bi-weekly iterations of the models produced by the design team following a rigorous protocol. Timesheets were obtained for all project team members involved in the modeling process. The measures developed adopt both the product and the process perspective of BIM. These measures were tested to verify how they correlated to one another and to the overall time spent in the project and in BIM. Four categories of measure are developed: measures of information quantity, measures of information content, measures of information representation and measures of product evolution. These measures can serve as a benchmark to evaluate the efficiency of the modeling and ultimately the project delivery process.Applied Science, Faculty ofCivil Engineering, Department ofNon UBCUnreviewedFacultyOthe

Structuring the adoption and implementation of BIM and integrated approaches to project delivery across the Canadian AECO industry : key drivers from abroad

The architecture, engineering, construction and owners (AECO) industry plays a vital role in a country’s economy, and has a great impact on its society and on the local and global environment. Focussing on the performance and the impact of their respective AECO industries, government bodies around the world are increasingly pushing to transform current practices to maximise the value generated by this industry. Recent innovative approaches, notably building information modeling (BIM), integrated approaches (either integrated project delivery (IPD) or integrated design processes (IDP)) and Lean construction, show promise in providing many improvements. However, many challenges and obstacles are hindering the deployment of these approaches; a lack of strong client demand chiefly among them. In response to this, many countries have developed strategies to encourage and accelerate the pace of adoption of these innovative approaches. This often is prompted by requirements for suppliers to implement one or more of these innovations on all their publicly procured projects. The various levels of governments in Canada however have yet to follow suit in this regard. As a consequence, the Canadian AECO industry is seen to be lagging in its adoption of BIM and integrated approaches to project delivery. While certain projects have emerged as beacons of enlightened practice in the Canadian context, it remains that the vast majority of projects are still being delivered in a traditional fashion, with the well-known limitations this entails. This paper investigates the contextual challenges in adoption and implementation of BIM and integrated approaches in the Canadian AECO industry. The objective is to identify challenges and opportunities to create favourable context that ensures that the Canadian AECO industry remain competitive in the face of increasing global competition by leveraging the potential significant benefits of these innovative approaches. This paper is based on a review of the literature of various initiatives around the world. The paper lays out six key factors, which are seen as drivers for the adoption and implementation of BIM and integrated approaches in other countries, and discusses their implication in the Canadian context. Notably, the need for a national policy that structures the adoption and implementation BIM and integrated approaches; the need for leadership from the public sector; the importance of constituent organizations acting as a voice for industry; and the need for investments in research and development.Non UBCUnreviewedFacultyOthe