Genetic Engineering seminars

David Baker presents recent advances in designing proteins for functions that natural evolution has not been required to solve. The approach begins with a desired structure or activity and uses deep learning to propose amino acid sequences expected to realise it. The resulting designs are translated into synthetic genes, produced as proteins and tested experimentally. The lecture connects computational design with laboratory characterisation, explaining how the combination can create new molecular functions relevant to medicine, technology and sustainability. Its focus is the construction and evaluation of proteins from scratch, extending the protein-design research recognised by the 2024 chemistry prize.

My research uses electrophysiological techniques to evaluate normal retinal function, dysfunction caused by blinding retinal diseases and the restoration of function using a variety of therapeutic strategies. We can use our understanding or normal retinal function and disease-related changes to construct optimal therapeutic strategies and evaluate how they ameliorate the effects of disease. Retinitis pigmentosa (RP) is a family of blinding eye diseases caused by photoreceptor degeneration. The absence of the cells that for this primary signal leads to blindness. My interest in RP involves the evaluation of therapies to restore vision: replacing degenerated photoreceptors either with: (1) new stem or other embryonic cells, manipulated to become photoreceptors or (2) prosthetics devices that replace the photoreceptor signal with an electronic signal to light. Glaucoma is caused by increased intraocular pressure and leads to ganglion cell death, which eliminates the link between the retinal output and central visual processing. We are parsing out of the effects of increased intraocular pressure and aging on ganglion cells. Congenital Stationary Night Blindness (CSNB) is a family of diseases in which signaling is eliminated between rod photoreceptors and their postsynaptic targets, rod bipolar cells. This deafferents the retinal circuit that is responsible for vision under dim lighting. My interest in CSNB involves understanding the basic interplay between excitation and inhibition in the retinal circuit and its normal development. Because of the targeted nature of this disease, we are hopeful that a gene therapy approach can be developed to restore night vision. My work utilizes rodent disease models whose mutations mimic those found in human patients. While molecular manipulation of rodents is a fairly common approach, we have recently developed a mutant NIH miniature swine model of a common form of autosomal dominant RP (Pro23His rhodopsin mutation) in collaboration with the National Swine Resource Research Center at University of Missouri. More genetically modified mini-swine models are in the pipeline to examine other retinal diseases.

Dr. Looger will present updates on a variety of molecular tools for studying & manipulating neural circuits & other preparations. Topics include genetically encoded calcium indicators (including the new ultra-fast jGCaMP8 variants), neurotransmitter sensors (improved versions for following glutamate, GABA, acetylcholine, serotonin), optogenetic effectors including the new “enhanced Magnets” dimerizers, AAV serotypes for retrograde labeling & altered tropism, probes for correlative light-electron microscopy, chemical gene switches, etc. He will make all his slides freely available - so don’t worry about hurriedly taking notes; instead focus on questions and ideas for collaboration. Please bring your suggestions for molecular tools that would be transformative for the field.

Modern day “neurohackers” are radically self-experimenting, attempting genomic modification with CRISPR-Cas9 constructs and electrode insertion into their cortex amongst a host of other things. Institutions wanting to avoid the risks bought on by these procedures, generally avoid involvement with self-experimenting research. Modern day “neurohackers” are radically self-experimenting, attempting genomic modification with CRISPR-Cas9 constructs and electrode insertion into their cortex amongst a host of other things. Institutions wanting to avoid the risks bought on by these procedures, generally avoid involvement with self-experimenting research. But what is the ethical thing to do? Should researchers be allowed or encouraged to self-experiment? Should institutions support or hinder them? Where do you think that this process of self-experimentation could take us? This presentation by Dr Matt Lennon and Professor Zoltan Molnar of the University of Oxford, will explore the history, future and ethics of self-experimentation. It will explore notable examples of self-experimenters including Isaac Newton, Angelo Ruffini and Oliver Sacks and how a number of these pivotal experiments created paradigm shifts in neuroscience. The presentation will open up a forum for all participants to be involved asking key ethical questions around what should and should not be allowed in self-experimentation research.

Emmanuelle Charpentier and Jennifer Doudna explain the discovery and biochemical development of CRISPR-Cas9 as a programmable tool for modifying DNA. The scientific story begins with bacterial defence against invading genetic material and the role of tracrRNA in the CRISPR system. It proceeds through the reconstruction and simplification of the RNA-guided machinery and the demonstration that a chosen guide can direct DNA cleavage to a specified sequence. The lectures connect basic research on microbes and RNA with a method that transformed experimental genetics. They explain the molecular logic of the system and the possibilities it opened for studying gene function, engineering organisms and developing therapeutic approaches.

Human genes associated with brain-related diseases are being discovered at an accelerating pace. A major challenge is an identification of the mechanisms through which these genes act, and of potential therapeutic strategies. To elucidate such mechanisms in human cells, we established a CRISPR-based platform for genetic screening in human iPSC-derived neurons, astrocytes and microglia. Our approach relies on CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa), in which a catalytically dead version of the bacterial Cas9 protein recruits transcriptional repressors or activators, respectively, to endogenous genes to control their expression, as directed by a small guide RNA (sgRNA). Complex libraries of sgRNAs enable us to conduct genome-wide or focused loss-of-function and gain-of-function screens. Such screens uncover molecular players for phenotypes based on survival, stress resistance, fluorescent phenotypes, high-content imaging and single-cell RNA-Seq. To uncover disease mechanisms and therapeutic targets, we are conducting genetic modifier screens for disease-relevant cellular phenotypes in patient-derived neurons and glia with familial mutations and isogenic controls. In a genome-wide screen, we have uncovered genes that modulate the formation of disease-associated aggregates of tau in neurons with a tauopathy-linked mutation (MAPT V337M). CRISPRi/a can also be used to model and functionally evaluate disease-associated changes in gene expression, such as those caused by eQTLs, haploinsufficiency, or disease states of brain cells. We will discuss an application to Alzheimer’s Disease-associated genes in microglia.