...providing many of the details not generally captured in the literature, scientists can use the Data Hub...commonly encountered in human gene therapy trials. Human Gene Therapy Methods, 26(2), 71–76. https://doi.org...Working with AAV vectors in the brain and peripheral nervous system presents a special challenge to scientists... process is often not detailed in the primary literature, and as a result can leave scientists under-informed...time and effort to test and optimize our vector - overall, I spent two years testing and reformulating our...dose–response and comparison to AAV PHP.B. Gene Therapy, 25(5), 392–400. https://doi.org/10.1038/s41434... Gene Delivery to the Hypothalamus. Human Gene Therapy, 21(6), 673–682. https://doi.org/10.1089/hum.2009.169...

...begin to use CRISPR as a therapy. Low frequency off-target effects may generate irreproducible data in ... CRISPR experiments, many are turning to next-generation sequencing options over older assays. Biased... search criteria are not exhaustive. Mismatch tolerance settings are often limited to off-target sites...sites of <4 bp. The off-target list is also generally weighted by the position of the mismatch along the ...CRISPR editing in the model cell line or organism. Several options exist for unbiased off-target detection...labeling, enrichment on streptavidin and next-generation sequencing (BLESS) (Crosetto et al. 2013). GUIDE-seq...consistent set of standards as the field seeks to generate reproducible, quality data on the role of genetic...

...FLEx cassette using next-generation sequencing (NGS) (Guerin, K. 2020). In general, we observe that 0.1 -... in the Central and Peripheral Nervous System and Relevance to Human Gene Therapy. Front Mol Neurosci ...FLEx Vectors Important Considerations When Using AAVs Three Key Considerations For Precise Neuronal Targeting...Vectors). While this strategy greatly reduced the overall level of off-target transgene expression, low levels...greater off-target expression just due to more overall viral particles getting into those cells. Therefore...transduces your cells of interest. We recommend testing several different serotypes to determine which one is the...course experiment to check expression levels over several weeks allows the researcher to determine when the...

...plasmids. Growth conditions The amount of aeration, temperature, culture volume, antibiotic, and medium ...survive within cells. The replicons of plasmids are generally different from the those used to replicate the... to make additional copies. ori sequences are generally high in As and Ts. Why, you ask? Well, A-T base...pairs can be separated more readily at lower temperatures and allows the replication machinery room to...few copies depending on how they are regulated. Generally, control of replication is referred to as "relaxed...exclusively in E. coli? Gram negative bacteria in general? Both Gram negatives and Gram positives? Will you...compatibility with one or more other plasmids. Generally speaking, plasmids with the same ori are incompatible...

... We’ve previously discussed some of the general considerations for performing behavioral tests, but now... modulating. Viral vectors, in contrast, are considerably more versatile and specific in how they manipulate...field box or a circular corridor apparatus using a camera or tracking software. Locomotion is a highly complex... of individual neurons and in terms of their interactions with one another. In addition to the neuronal...controlling muscle activity and coordinating movement, several additional brain areas that reflect motivational...sensitization and might open new ways for a novel therapeutic approach against drug addiction. Anxiety tests...rodents can be used to study anxiety levels in general, or anxiety associated with psychiatric diseases...

...One of the biggest barriers to gene therapy treatment of central nervous system (CNS) diseases is the...because in vivo transduction of AAV serotypes generally tracks between strains of mice. This suggests ... engineered PHP.B. PHP.B was created by first generating a diverse library of AAV9 mutants that had a ...inheritance pattern of PHP.B permissiveness. The first generation of outbred mice (F1) had half the level of CNS...transduction as their C57BL/6J parent. The second generation (F2) of outbred mice also showed a Mendelian ...galactose and AAVR to transduce cells. The Wilson Lab generated results similar to the Deverman Lab when they ...Transport across the Blood-Brain Barrier." Molecular Therapy 27.5 (2019): 912-921. PubMed PMID: 30819613. Hordeaux...

...microglia The REVeRT Dual AAV Vector System Neurodegeneration Collection updates   Multiplexed perturbation...2024 under a CC-BY-NC-ND license. In this iteration, the size of the lentiviral insert was minimized...ensure this tRNA processing only occurs on the RNA polymerase III transcript, the sgRNAs were encoded on the...recombinant versions of mouse monoclonal antibodies generated and characterized by the Geiss Lab in their effort...A122D mutation in the rhodopsin domain conferred several new improvements. The new variant has increased...valuable tool for microglia research and broader therapeutic applications.  Find microglia-targeting AAV plasmids...10.1101/2023.12.12.571321.  Revolutionizing Gene Therapy: The REVeRT Dual AAV Vector System By Vaibhav Kawde...

...structural studies of E3 ligase cereblon By Mike Lacy Several types of drugs target the ubiquitin E3 ligase cereblon...Lon and TBD domains, part of the HB domain, and several mutations to improve solubility and stability (...and mScarlet-I3, Oliver Hobert’s lab recently generated new constructs specifically for C. elegans (Cao...showed greater photostability and also matured considerably faster, with expression levels comparable to...notorious for its high resistance to antibiotics. Several CRISPR/Cas-based systems have been developed for...mechanosensor called PILATeS, Pulling-Induced Luciferase Association Tension Sensor (Zhong et al., 2024...sensor STReTCh, the 11-amino acid BiT fragment of luciferase is embedded in the I10 domain of the human titin...

...that stably express a gene of interest. While the general approach for using lentivirus, infect and select...consider is the age of your culture post thaw. In general, the higher the passage number of a culture the...routinely test for mycoplasma contamination. There are several commercially available mycoplasma detection kits...parameters. For example, while freeze thaw is generally not recommended, Holic et al. found that lentivirus...your target cells Labs tend to follow the same general procedure for lentiviral infections, produce the...earliest steps in lentiviral transduction is the interaction between the viral envelop and the receptors on... on the target cell surface. The possible interactions and hence possible targets for a lentivirus are...

...in Steve Pollard’s lab at the MRC Centre for Regenerative Medicine (CRM), Edinburgh. Most commercial antibodies...therefore, critical to understand how proteins interact with one another (or with DNA) to perform diverse...the most popular approaches to study protein interactions is the pull-down assay, wherein a protein of...analysed by mass spectrometry to identify the interacting proteins. Similarly, in ChIP-seq assays, chromatin...however, to these IP-based assays is to find (or generate in-house) a pre-validated antibody for each target...throughput because numerous cell lines can be generated, each with a different tagged protein of interest...these factors prevent stem cell researchers from generating clonal knock-in lines, especially for ambitious...

...enhancers, and cross-cassette interactions in gene expression, and to generate multi-gene knockouts. Mammalian...MoClo background MoClo is a clever way to assemble several DNA parts in a specific orientation using Type ...2011). It can be performed at multiple levels to generate anything from individual transcription units (...products without the undesirable side products generated during chemical synthesis of these molecules. ...bacteria. If your yeast experimental goals are more general in nature, or you aren’t planning on using K. phaffii...Multiplex Yeast Toolkit builds on the YTK and adds several additional capabilities, including conditional ...., 2014). This kit is a great starter for your general plant cloning experiments. Addgene also has two...

...photobleaching. Interaction with receptors: Understanding how fluorescent dyes interact with specific receptors...intermolecular FRET for ligand-receptor interactions, require specific considerations regarding the choice of fluorescent...crucial in the world of biological research, medical therapy, and even drug development (Grimm & Lavis, 2022...targets through fluorescent labeling. There are several advantages to using these self-labeling proteins...is bound through green light emission. Key considerations in selecting fluorescent dyes/ligands Effects...best practice to determine optimal DOL is through several small-batch experimental labeling. Size is also...under certain conditions, which is an important consideration for assay design (Breen et al., 2016). When ...

...Chamberlain JS (2011) Gene Therapy of mdx Mice With Large Truncated Dystrophins Generated by Recombination Using... reassemble fragmented genomes is the basis of several split vector approaches developed in the early ...full-length transgene (Chamberlain et al., 2016). It’s generally accepted that some form of homologous recombination...exact mechanism is not yet known. Drawbacks:  Generally an overlapping split vector has equal or higher...is currently no one ideal split vector system. Overall the efficiency of transgene expression from split... of Adeno-Associated Virus Capsids. Human Gene Therapy Methods 27:1–12 . https://doi.org/10.1089/hgtb.2015.140...Capacity in a Transgene-independent Manner. Molecular Therapy 16:124–130 . https://doi.org/10.1038/sj.mt.6300322...

... for Autoinhibition Release of Methyltransferase (CHARM), with several advantages over the earlier system...and stimulate the endogenous methyltransferase. The strategy is generalizable to a variety of DNA-targeting...Arimura et al. used MagIC-cryo-EM to determine several structures (at < 5 Å resolution) of the linker ....    Figure 2: A) When proteins (blue) interact with the air-water interface (AWI) before vitrification... 2024). The best-performing variant yielded an average integration efficiency of 23%, a more than four-fold...editor consisting of dCas9 fused to a DNA methyltransferase — that can drive lasting transcriptional silencing...  Rather than overexpressing an exogenous methyltransferase for epigenetic silencing, which can be toxic...

...mouse inner ear. Fourth-generation cytosine base editors The fourth-generation base editors, BE4, reduce...variety of targets in human cell lines, with an average indel frequency of only 1.1%. These numbers are...over Cas9-mediated HDR for the loci tested, where average HDR-mediated editing frequency was only 0.5%, and...18 bases upstream of the PAM.  David Liu’s lab generated BE3 variants with other deaminases: AID, CDA1,...these three improvements represent the fourth generation of base editors. Compared to BE3, BE4 offers ...ABE7.10 is the most active editor, displaying an average editing efficiency of 53% with an editing window... phage-assisted evolution selection systems to generate ABE8e(TadA-8e V106W), which edits ~590-fold faster...

.... To overcome this limitation, we created a generalizable tag-based strategy, which we refer to as the... target degradation (Figure 1). Plasmids: We generated a series of plasmids that are available from Addgene...of N- or C-terminally FKBP12F36V-tagged fusion chimeras or locus-specific knock-in of FKBP12F36V. Detailed...or Jay Bradner ([email protected]). Considerations when getting the dTAG system up and running...your lab Confirm the functionality of your fusion chimeras For each protein-of-interest, it is important ...FKBP12F36V tag without disrupting protein function. A literature search can help determine which terminus is favorable... evaluate degradation of the FKBP12F36V-fusion chimera of interest. In the cell lines we have evaluated...

...Fragments generation After you’ve designed your cloning scheme, you’re now ready to generate fragments... specific, there are few general parameters that you can adjust: temperature and time of incubation, and...fragments. You can generate the parts of DNA that you want to assemble together in a combination of different...multiple digestion be sure that the buffers and temperature are compatible between the different enzymes....genome organisms like mouse or human. There are several online tools that can help you with that, they ...companies selling PCR reagents. Nowadays commercial polymerases are very efficient, but if you are having difficulties...conditions. Purifying DNA fragments Once you’ve generated your DNA fragments, it is always a good habit ...

...organism. These features make AAV ideal for human therapies and in vivo laboratory experiments ranging from...terminal repeats – the sequences that flank the deliverable DNA) are removed, resulting in recombinant AAVs... over 4.7 kb. Co-infection rates for AAVs are generally high enough for this approach to work, although...some mammalian tissues has shown expression for several years (Wonjo et al., 2013). Remember that AAVs ...As a starting point, we recommend checking the literature and our AAV data hub to see if others have used...transduction independently of DNA synthesis." Gene therapy 8.16 (2001). PubMed PMID: 11509958. Vandenberghe...adeno-associated virus manufacturing." Human gene therapy 21.10 (2010): 1251-1257. PubMed PMID: 20649475....

...separation is maintained by 2 sets of interactions : 1. Interactions between the non-target strand and a... through interactions between the non-target strand and the HNH/RuvC groove, and interactions between ...weakening interaction sbetween the non-target strand and Cas9, Kleinstiver et al disrupted interactions between...by the Cas9 HNH and RuvC nuclease domains 2. Interactions between the target strand and the gRNA (see ... the HNH/RuvC groove, then they could weaken interactions between the groove and the negatively charged...that if they could weaken sequence independent interactions between Cas9 and DNA, then they could diminish...effect on specificity was similar; SpCas9-HF1 generated fewer off-target cuts when compared to WT SpCas9...

...to base transition editing, we can expect several generations of optimization before the field begins to...review how CRISPR-derived base editing works in general. Base editors use either catalytically dead Cas9... Beyond UNG: Optimizing C → G editors Now that several labs had shown that preferential C → G editing ...rXRCC1, or the DNA binding and lyase domain of DNA polymerase β (PB) (Chen et al., 2021). Both of these fusion... Sun and Erwei Zuo labs tested and implemented several of these advances for CGBEs (Yuan et al., 2021)...efficiency and produced fewer indels than first-generation editors. This team also demonstrated that different... proteins whose fusion improved the CGBE: DNA polymerase D2 (POLD2), exonuclease 1 (EXO1), and RNA binding...