Biology subjects

Cameron, P.

Publications and source records attributed to Cameron, P..

5 recordsLinked to original sources

bioRxiv2026

Investigations into cyanobacteria, plant, and insect protein extracts as serum-replacement supplements for the expansion of cells for cultivated meat

Cultivated meat has undeniable potential to address some of the current detrimental impacts of animal farming, while addressing food security worldwide. However, one of the main challenges in cultivated meat production is manufacturing cost. The main contributor to cost is the culture media which comprises expensive components such as growth factors and animal-derived proteins. This study investigated alternative, food grade, high protein extracts as serum replacements in serum-free media formulations. The extracts were chosen to represent various sustainable sources of proteins: marine (spirulina e.g. cyanobacterium), plant (faba bean) and insect (mealworm flour). Different processing methods and different solvents were investigated for production of cell culture-compatible extracts which were then tested with mouse myoblasts (C2C12) and primary porcine myosatellites (pMyoSCs). A serum-free medium formulation containing 2.6% v/v spirulina extract was found to support long term growth of C2C12 cells for [~]10 population doublings compared to only [~]2 in the control. The processing steps were optimized, showing that a glycerine solution was best for free amino acid and protein yield (4950 {micro}M total free amino acids, 11.45 mg/mL protein concentration). This solution had a positive effect on C2C12 cells, increasing their growth by up to 20% when added to the B8 medium. However, this benefit did not translate to pMyoSCs, which showed no significant growth increases in short-term screening. This work demonstrates a method for converting food grade protein powders into effective culture media supplements and highlights the potential of spirulina-based extracts for the use in cultivated meat. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/702276v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@206658org.highwire.dtl.DTLVardef@11f28ceorg.highwire.dtl.DTLVardef@b00fd6org.highwire.dtl.DTLVardef@dfaaf4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Created in BioRender. Gordon-Petrovskii, W. (2025) https://BioRender.com/by7khs1 C_FIG

bioengineering↗

bioRxiv2025

Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data

CRISPR-Cas enzymes must recognize a protospacer-adjacent motif (PAM) to edit a genomic site, significantly limiting the range of targetable sequences in a genome. Machine learning-based protein engineering provides a powerful solution to efficiently generate Cas protein variants tailored to recognize specific PAMs. Here, we present Protein2PAM, an evolution-informed deep learning model trained on a dataset of over 45,000 CRISPR-Cas PAMs. Protein2PAM rapidly and accurately predicts PAM specificity directly from Cas proteins across Type I, II, and V CRISPR-Cas systems. Using in silico deep mutational scanning, we demonstrate that the model can identify residues critical for PAM recognition in Cas9 without utilizing structural information. As a proof of concept for protein engineering, we employ Protein2PAM to computationally evolve Nme1Cas9, generating variants with broadened PAM recognition and up to a 50-fold increase in PAM cleavage rates compared to the wild-type under in vitro conditions. This work represents the first successful application of machine learning to achieve customization of Cas enzymes for alternate PAM recognition, paving the way for personalized genome editing.

synthetic biology↗

bioRxiv2024

Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences

Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology, and human health. CRISPR-based gene editors derived from microbes, while powerful, often show significant functional tradeoffs when ported into non-native environments, such as human cells. Artificial intelligence (AI) enabled design provides a powerful alternative with potential to bypass evolutionary constraints and generate editors with optimal properties. Here, using large language models (LLMs) trained on biological diversity at scale, we demonstrate the first successful precision editing of the human genome with a programmable gene editor designed with AI. To achieve this goal, we curated a dataset of over one million CRISPR operons through systematic mining of 26 terabases of assembled genomes and meta-genomes. We demonstrate the capacity of our models by generating 4.8x the number of protein clusters across CRISPR-Cas families found in nature and tailoring single-guide RNA sequences for Cas9-like effector proteins. Several of the generated gene editors show comparable or improved activity and specificity relative to SpCas9, the prototypical gene editing effector, while being 400 mutations away in sequence. Finally, we demonstrate an AI-generated gene editor, denoted as OpenCRISPR-1, exhibits compatibility with base editing. We release OpenCRISPR-1 publicly to facilitate broad, ethical usage across research and commercial applications.

synthetic biology↗

bioRxiv2021

Structural basis for Cas9 off-target activity

The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, Cas9 can bind and cleave partially complementary off-target sequences, which raises safety concerns for its use in clinical applications. Here we report crystallographic structures of Cas9 bound to bona fide off-target substrates, revealing that off-target binding is enabled by a range of non-canonical base pairing interactions within the guide-off-target heteroduplex. Off-target sites containing single-nucleotide deletions relative to the guide RNA are accommodated by base skipping or multiple non-canonical base pairs rather than RNA bulge formation. Additionally, PAM-distal mismatches result in duplex unpairing and induce a conformational change of the Cas9 REC lobe that perturbs its conformational activation. Together, these insights provide a structural rationale for the off-target activity of Cas9 and contribute to the improved rational design of guide RNAs and off-target prediction algorithms.

biochemistry↗

bioRxiv2019

Fear Learning Induces Long-Lasting Changes in Gene Expression and Pathway Specific Presynaptic Growth

The stabilization or consolidation of long-term memories lasting more than a few hours requires new gene expression. While neural activity has been shown to induce expression of a variety of genes within several hours of learning, whether this leads to persistent changes in gene expression that lasts for days or weeks remains unclear. We developed a novel mouse line which expresses Cre recombinase in an inducible manner and used it to examine gene expression in learning-activated neurons of the medial prefrontal cortex (mPFC) one month following contextual fear conditioning. The mPFC is not required for the initial retrieval of contextual memory but becomes necessary after one month, suggesting a slowly developing plasticity. We found a variety of changes in gene expression in learning-activated neural ensembles that were specific to the mPFC. One group of transcriptional changes observed was the coordinated upregulation of presynaptic proteins suggesting a potential learning-induced elaboration of presynaptic terminals. We tested this idea by labeling the projections of mPFC neurons active during initial learning and found an increase in the number of terminals in neurons projecting to the basolateral amygdala at 1 month following training. These results suggest a presynaptic growth mechanism that could account for the enhanced role of the mPFC in fear memory retrieval at long time points after learning.

neuroscience↗