Mutagenesis-based protein structure determination

Two-dimensional nanostructures based '-onics' and '-omics' in personalized medicine

With the maturing techniques for advanced synthesis and engineering of two-dimensional (2D) materials, its nanocomposites, hybrid nanostructures, alloys, and heterostructures, researchers have been able to create materials with improved as well as novel functionalities. One of the major applications that have been taking advantage of these materials with unique properties is biomedical devices, which currently prefer to be decentralized and highly personalized with good precision. The unique properties of these materials, such as high surface to volume ratio, a large number of active sites, tunable bandgap, nonlinear optical properties, and high carrier mobility is a boon to 'onics' (photonics/electronics) and 'omics' (genomics/exposomics) technologies for developing personalized, low-cost, feasible, decentralized, and highly accurate medical devices. This review aims to unfold the developments in point-of-care technology, the application of 'onics' and 'omics' in point-of-care medicine, and the part of two-dimensional materials. We have discussed the prospects of photonic devices based on 2D materials in personalized medicine and briefly discussed electronic devices for the same.

UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution

The success of protein evolution campaigns is strongly dependent on the sequence context in which mutations are introduced, stemming from pervasive non-additive interactions between a protein's amino acids ('intra-gene epistasis'). Our limited understanding of such epistasis hinders the correct prediction of the functional contributions and adaptive potential of mutations. Here we present a straightforward unique molecular identifier (UMI)-linked consensus sequencing workflow (UMIC-seq) that simplifies mapping of evolutionary trajectories based on full-length sequences. Attaching UMIs to gene variants allows accurate consensus generation for closely related genes with nanopore sequencing. We exemplify the utility of this approach by reconstructing the artificial phylogeny emerging in three rounds of directed evolution of an amine dehydrogenase biocatalyst via ultrahigh throughput droplet screening. Uniquely, we are able to identify lineages and their founding variant, as well as non-additive interactions between mutations within a full gene showing sign epistasis. Access to deep and accurate long reads will facilitate prediction of key beneficial mutations and adaptive potential based on in silico analysis of large sequence datasets.

Rewriting Human History and Empowering Indigenous Communities with Genome Editing Tools

Appropriate empirical-based evidence and detailed theoretical considerations should be used for evolutionary explanations of phenotypic variation observed in the field of human population genetics (especially Indigenous populations). Investigators within the population genetics community frequently overlook the importance of these criteria when associating observed phenotypic variation with evolutionary explanations. A functional investigation of population-specific variation using cutting-edge genome editing tools has the potential to empower the population genetics community by holding "just-so" evolutionary explanations accountable. Here, we detail currently available precision genome editing tools and methods, with a particular emphasis on base editing, that can be applied to functionally investigate population-specific point mutations. We use the recent identification of thrifty mutations in the CREBRF gene as an example of the current dire need for an alliance between the fields of population genetics and genome editing.

Omics Meeting Onics: Towards the Next Generation of Spectroscopic-Based Technologies in Personalized Medicine

This article aims to discuss the recent development of integrated point-of-care spectroscopic-based technologies that are paving the way for the next generation of diagnostic monitoring technologies in personalized medicine. Focusing on the nuclear magnetic resonance (NMR) technologies as the leading example, we discuss the emergence of -onics technologies (e.g., photonics and electronics) and how their coexistence with -omics technologies (e.g., genomics, proteomics, and metabolomics) can potentially change the future technological landscape of personalized medicine. The idea of an open-source (e.g., hardware and software) movement is discussed, and we argue that technology democratization will not only promote the dissemination of knowledge and inspire new applications, but it will also increase the speed of field implementation.