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Qi, Lei S.

Publications and source records attributed to Qi, Lei S..

A frugal CRISPR kit for equitable and accessible education in gene editing and synthetic biology

Equitable and accessible education in life sciences, bioengineering, and synthetic biology is crucial for training the next generation of scientists, fostering transparency in public decision-making, and ensuring biotechnology can benefit a wide-ranging population. As a groundbreaking technology for genome engineering, CRISPR has transformed research and therapeutics. However, hands-on exposure to this technology in educational settings remains limited due to the extensive resources required for CRISPR experiments. Here, we develop CRISPRkit, an affordable kit designed for gene editing and regulation in high school education. CRISPRkit eliminates the need for specialized equipment, prioritizes biosafety, and utilizes cost-effective reagents. By integrating CRISPRi gene regulation, colorful chromoproteins, cell-free transcription-translation systems, smartphone-based quantification, and an in-house automated algorithm (CRISPectra), our kit offers an inexpensive (~$2) and user-friendly approach to performing and analyzing CRISPR experiments, without the need for a traditional laboratory setup. Experiments conducted by high school students in classroom settings highlight the kit’s utility for reliable CRISPRkit experiments. Furthermore, CRISPRkit provides a modular and expandable platform for genome engineering, and we demonstrate its applications for controlling fluorescent proteins and metabolic pathways such as melanin production. We envision CRISPRkit will facilitate biotechnology education for communities of diverse socioeconomic and geographic backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗

Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro

A major challenge in coronavirus vaccination and treatment is to counteract rapid viral evolution and mutations. Here we demonstrate that CRISPR-Cas13d offers a broad-spectrum antiviral (BSA) to inhibit many SARS-CoV-2 variants and diverse human coronavirus strains with >99% reduction of the viral titer. We show that Cas13d-mediated coronavirus inhibition is dependent on the crRNA cellular spatial colocalization with Cas13d and target viral RNA. Cas13d can significantly enhance the therapeutic effects of diverse small molecule drugs against coronaviruses for prophylaxis or treatment purposes, and the best combination reduced viral titer by over four orders of magnitude. Using lipid nanoparticle-mediated RNA delivery, we demonstrate that the Cas13d system can effectively treat infection from multiple variants of coronavirus, including Omicron SARS-CoV-2, in human primary airway epithelium air-liquid interface (ALI) cultures. Our study establishes CRISPR-Cas13 as a BSA which is highly complementary to existing vaccination and antiviral treatment strategies.

60 APPLIED LIFE SCIENCES↗

Biodesign Research to Advance the Principles and Applications of Biosystems Design

Over the course of civilization, humans have increasingly expanded their freedom to live a better life. In comparison with the primitive society, our modern society has many more choices of life-supporting resources, such as year-round food supply, permanent shelters, diverse energy sources, and effective preventive and curing medicine. However, our society is currently still heavily relying on the resources provided by Mother Nature, which cannot meet the future global needs in terms of both quantity and quality under the pressure of population growth, natural resource reduction, and environmental deterioration. For example, the food sources originating from plants, animals, or microbes do not have the nutrition balance for optimal human health. Climate change and environmental deterioration threaten the food security. Increasingly, infectious diseases (e.g., HIV/AIDS), genetic diseases (e.g., cancer), and improper lifestyle-related disorders (e.g., obesity) become more prevalent and remain challenging to be prevented, controlled, and cured. Conventional medical technologies and modern medicine development are also meeting the ceiling. Antibiotic resistance is threatening the health of humans, animals, and environment. As the human lifespan continues to increase, aging-related diseases, disorders, and poor life quality are becoming global challenges. Plants, animals, and microbes in nature have evolved as part of our Earth ecosystem, not for benefiting humans. Even though humans have put forth tremendous efforts to domesticate plants, animals, and microbes based on random/induced mutations, hybridization, and limited genetic modifications via biological engineering, the improved food and industrial crop plants, animals, and microbial strains are still far from optimized for meeting the human needs. In other words, natural evolution and domestication in plants, animals, and microbes are tinkering processes and therefore cannot meet the ever-exploding population on the one hand and the unending appetite for living better quality life on the other. One promising strategy for solving these global challenges is to employ revolutionary biosystems design (also called biodesign), which is defined as predictable modification of existing organisms or creation of new organisms using rational engineering or automated design based on the theory and principles of biosystems design.

59 BASIC BIOLOGICAL SCIENCES↗

Methods and compositions for controlling gene expression by RNA processing

The present disclosure provides nucleic acids encoding an RNA recognition sequence positioned proximal to an insertion site for the insertion of a sequence of interest; and host cells genetically modified with the nucleic acids. The present disclosure also provides methods of modifying the activity of a target RNA, and kits and compositions for carrying out the methods.

59 BASIC BIOLOGICAL SCIENCES↗