The gene editing technique CRISPR/Cas9 has allowed researchers to make precise and impactful changes to an organism's DNA to fix mutations that cause genetic disease.
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BigField GEG Tech's curator insight,
March 8, 2022 6:06 AM
CROPSR is the first open source software tool for genome-wide design and evaluation of guide RNA (gRNA) sequences for CRISPR experiments, created by scientists at CABBI, a Department of Energy-funded Bioenergy Research Center (BRC). The genome-wide approach significantly shortens the time needed to design a CRISPR experiment, reducing the challenge of working with crops and speeding up the design, evaluation and validation of gRNA sequences, according to the study published in BMC Bioinformatics. To better meet the needs of crop geneticists, the team built software that lifts restrictions imposed by other packages on the design and evaluation of gRNA sequences, the guides used to locate targeted genetic material. Team members also developed a new machine learning model that would not avoid guides for repetitive genomic regions often found in plants, a problem with existing tools. The CROPSR scoring model provided much more accurate predictions, even in non-crop genomes. In the future, he hopes researchers will record their failures as well as their successes to help generate the data needed to train a non-specific model. |
BigField GEG Tech's curator insight,
September 22, 2023 6:29 AM
Researchers are improving non-invasive treatment options for degenerative disc disease, a condition that affects 3 million adults each year in the U.S. Stem cell therapy has been a viable field in regenerative technologies for many pathologies for several years. However, the degenerated intervertebral disc provides a hostile environment that is detrimental to stem cell survival, resulting in limited clinical success of stem cell therapy for the disc. Previous research has shown that stem cell-derived electrical vehicles contain many therapeutically beneficial proteins, lipids and nucleic acids and carry much of the regenerative potential of stem cells. However, by using CRISPR in mesenchymal stem cells, researchers have added to the growing field of regenerative medicine the process of producing cell-based therapies to alleviate pain and lack of mobility. In their study, the researchers target TSG6, an essential stem cell marker known to be linked to the regenerative and anti-inflammatory properties of these stem cells. Their hypothesis is that if they CRISPR-activate TSG6 in stem cells, they will not only increase TSG6 protein levels in the extracellular vesicle cargo, but potentially amplify the stem cells' anti-inflammatory and regenerative properties.
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CRISPR/Cas9 method can lead to unintended DNA mutations that can have negative effects. Recently, Japanese researchers have developed a new gene-editing technique that is as effective as CRISPR/Cas9, yet significantly reduces these unintended mutations. In a new study published in Nature Communications , researchers led by Osaka University have introduced a new technique called NICER, based on the creation of several small cuts in single DNA strands by an enzyme Cas 9 nickase. For their first experiments, the research team used human lymphoblastic cells with a known heterozygous mutation in a gene called TK1. When these cells were treated with nickase to induce a single cut in the TK1 region, TK1 activity was recovered at a low rate. However, when nickase induced multiple cuts in this region on both homologous chromosomes, the efficiency of gene correction was increased approximately seventeen-fold via activation of a cellular repair mechanism. Because the NICER method does not involve DNA double-strand breaks or the use of exogenous DNA, this technique appears to be a safe alternative to conventional CRISPR/Cas9 methods.