Towards Accurate Genotype-Phenotype Correlations in the CYP2D6 Gene

Generalizable Metamaterials Design Techniques Inspire Efficient Mycelial Materials Inverse Design

Fungal mycelial materials can mimic numerous nonrenewable materials; they are even capable of outperforming certain materials at their own applications. Fungi's versatility makes mock leather, bricks, wood, foam, meats, and many other products possible. That said, there is currently a critical need to develop efficient mycelial materials design techniques. In mycelial materials, and the wider field of biomaterials, design is primarily limited to costly forward techniques. New mycelial materials could be developed faster and cheaper with robust inverse design techniques, which are not currently used within the field. However, computational inverse design techniques will not be tractable unless clear and concrete design parameters are defined for fungi, derived from genotype and bulk phenotype characteristics. Through mycelial materials case studies and a comprehensive review of metamaterials design techniques, we identify three critical needs that must be addressed to implement computational inverse design in mycelial materials. These critical needs are the following: 1) heuristic search/optimization algorithms, 2) efficient mathematical modeling, and 3) dimensionality reduction techniques. Metamaterials researchers already use many of these computational techniques that can be adapted for mycelial materials inverse design. Then, we suggest mycelium-specific parameters as well as how to measure and use them. Ultimately, based on a review of metamaterials research and the current state of mycelial materials design, we synthesize a generalizable inverse design paradigm that can be applied to mycelial materials or related design fields.

Global perspectives on CYP2D6 associations with primaquine metabolism and Plasmodium vivax radical cure

Clinical trial and individual patient treatment outcomes have produced accumulating evidence that effective primaquine (PQ) treatment of Plasmodium vivax and P. ovale liver stage hypnozoites is associated with genetic variation in the human cytochrome P450 gene, CYP2D6. Successful PQ treatment of individual and population-wide infections by the Plasmodium species that generate these dormant liver stage forms is likely to be necessary to reach elimination of malaria caused by these parasites globally. Optimizing safe and effective PQ treatment will require coordination of efforts between the malaria and pharmacogenomics research communities.

Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein

The functional and pathological implications of the enormous genetic diversity of the human genome are mostly unknown, primarily due to our unability to predict pathogenicity in a high-throughput manner. In this work, we characterized the phenotypic consequences of eight naturally-occurring missense variants on the multifunctional and disease-associated NQO1 protein using biophysical and structural analyses on several protein traits. Mutations found in both exome-sequencing initiatives and in cancer cell lines cause mild to catastrophic effects on NQO1 stability and function. Importantly, some mutations perturb functional features located structurally far from the mutated site. These effects are well rationalized by considering the nature of the mutation, its location in protein structure and the local stability of its environment. Using a set of 22 experimentally characterized mutations in NQO1, we generated experimental scores for pathogenicity that correlate reasonably well with bioinformatic scores derived from a set of commonly used algorithms, although the latter fail to semiquantitatively predict the phenotypic alterations caused by a significant fraction of mutations individually. These results provide insight into the propagation of mutational effects on multifunctional proteins, the implementation of in silico approaches for establishing genotype-phenotype correlations and the molecular determinants underlying loss-of-function in genetic diseases.