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..., and deletions) without introducing DNA double-strand breaks (Anzalone et al., 2019; Chen & Liu, 2023...typically a Cas9 H840A nickase fused to a reverse transcriptase) together with a prime editing guide RNA (pegRNA...containing a primer binding site and a reverse transcription template (RTT). The design of the pegRNA has...provides users with different designs of pegRNAs, ranked by their PRIDICT/PRIDICT2.0 score. For the best...editing strategies) based on a DeepSpCas9 score ranking (Kim et al., 2019). PRIDICT saves time and resources...doi.org/10.1016/J.CELL.2013.07.018 Anzalone, A. V., Randolph, P. B., Davis, J. R., Sousa, A. A., Koblan, L....Search-and-replace genome editing without double-strand breaks or donor DNA. Nature, 576(7785), 149–157...

...number of transformants); the greater the number of inserts, the lower the number of transformants. To compensate...containing the transformants onto the selection plate. Figure 2 shows representative transformation plates obtained...high levels of transformants and low backgrounds – so much so that there was little range for detectable...the number of transformants while maintaining high levels of correct assemblies) translate to faster assembly...background by antibiotic selection. Screening of transformants by colony PCR confirmed the insertion of the...volume of the 1 ml outgrowth spread on each transformation plate can be manipulated to result in appropriate...

...genome edits. But have you heard of another double-stranded break repair mechanism: MMEJ (microhomology-mediated...primary methods for repairing DNA after a double-stranded break. HDR copies the sequence from a repair template...are chewed back to reveal homology, allowing the strands to anneal. DNA synthesis then fills in the gaps...5-25 bp) regions of homology flanking a double-stranded break yield precise deletion of the sequence between...locus flanking the GFP-Puro cassette. Three double stranded breaks are necessary for knock-in: one on either...an insertion locus-specific gRNA. These double stranded breaks allow for two sets of microhomologies (...PITCh-gRNA binding sites. This PITCh plasmic is cotransfected with a plasmid carrying Cas9, the PITCh-gRNA...

...microscopy coupled with techniques that make tissues transparent are enabling microscopes to visualize the cellular...the cortico spinal tract, CST, spinal cord and cranial nerve afferents labelled with a AAV8 expressing...sectioning (OPFOS) (2). Arne Voie, David Burns and Francis Spelman focused a laser beam into a thin sheet ...of clear specimens and for in vivo imaging of transparent organisms. Advances in tissue clearing Similar...attempt to render fixed anatomical preparations transparent was done by Walter Spalteholtz (10).  He used...green fluorescent protein (GFP) (6).   The Dodt and Frank Bradke laboratories later developed the 3DISCO (...spinal cords by combining Ultramicroscopy with tetrahydrofuran-based tissue clearing (13,14). A few years ...

...Science describing the development of “transcriptors,” transistor-like digital genetic switches that enable...comprised of well-characterized bacterial transcription and translation initiation elements. Open science with...dogma - replication of DNA, transcription of DNA to make RNA, translation of RNA to make proteins. That's...reliable gene expression via standard transcription and translation initiation." Nature Methods. 10, 354...cellular computing. These logic gates built from transcriptors are available at Addgene as a BIOFAB kit comprised...genetically encoded sensors. Those sensors could transduce otherwise invisible molecules into regulation ...

...-1 Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Cowan CA, Talkowski ME, Musunuru... efficacious to target the coding or non-coding strand of DNA. As a rule of thumb, we avoid target sites..., 2020). is not limited to single nucleotide transitions but still requires a nearby PAM, although these... modulating gene expression at the level of transcription – CRISPRa (activation) and CRISPRi (inhibition...most-efficacious to target a ~100nt window upstream of the transcription start site (TSS), while for CRISPRi, a ~100nt...of producing the guide (synthetic, in vitro transcription, or lentiviral delivery) can affect the accuracy...examined whenever possible when using knockout or transcriptional modulation approaches. Avoiding off-target ...

...and they had been shown to to transduce the retina but only transiently. However new viral vectors capable...adenovirus (AdV) and lentivirus (LV) are known to transduce retinal cells, AAV quickly became the vector of...due to its considerable immunogenicity and its transient expression. LV results in long term expression... in dividing and non-dividing cells due to its (random) integration into the genome, and its large DNA... packaging capacity is well suited for larger transgenes. Unfortunately it has limited tropism in the ...and the one used in Luxturna™, can efficiently transduce various types of retinal neurons. Nowadays a toolbox...engineered AAV serotypes that further expands the range of AAV properties is available. While only natural...

...physiological processes. Re-engineering GFP to increase its range of color and application Almost as soon as its...backbones for constructing fluorescent fusions. Transcription Reporter: Placing GFP under the control of a...promoter in a given cell type. This type of transcription reporting was among the earliest uses of GFP...GFP. Fluorescence resonance energy transfer (FRET): This is used to study the interactions between two ...ion (such as Ca2+) concentrations and pH, using a range of strategies such as FRET, calmodulin, and others... gene of interest, or expressed from the same transcript as the gene of interest, but after an internal...expressing GFP from cells that are not. Developmental/transgenic uses: Because of its stability, GFP can be used...

...conceptualize where the populations are, try drawing a quadrant over the plot that divides it into four, using...different populations by imagining (or drawing) a quadrant over the dot plot. Created with biorender.com....Biorender! While a helpful visualization tool, a quadrant will often be too clean for real-world data. Most...and debris. The side scatter roughly measures granularity, a proxy for nucleic complexity of the cell.  ...these populations, I suggest using the imaginary quadrant to help (Figure 5). Even though this real-world...real-world data is far messier than biorender plots, quadrants can still help me as a reader if I'm struggling...strategy from Barlow-Anacker et al., 2017, with quadrants to help visualize the different populations. Used...

...proteins needed for the virus to replicate,  and the transfer plasmid which contains the viral genome. In today...and cap are expressed from a separate plasmid in trans, freeing up space in the viral genome so that a ...Replication initiates from the AAV genome ITRs on the transfer plasmid, which contain regions of dsDNA. To generate...capsid. Rep proteins are also involved in the transcriptional regulation of the AAV p40 promoter which drives...promoter. Alternative splicing and differing translational start sites generate the three VP proteins. ...Assembly-Activating Protein (AAP) and the recently discovered Membrane Associated Accessory Protein (MAAP) from an alternative...out this blog post to learn more about the AAV transfer plasmid! References: Naso MF, Tomkowicz B, ...

...products are then transformed directly into chemically competent E. coli and transformants selected with ... for further purification before transformation. After transforming cells, you should perform colony ...consisting of digestion, purification, ligation, and transformation. While restriction cloning is still routinely...+ + Gel Purification + - Ligation + - Transformation + + The FastCloning process in brief In ...for this procedure to work properly. Directly transform chemically competent cells with the digested mixture...-cycle PCR leads to the most colonies after transformation. When a 1:1 vector:insert ratio is used in ... and 2 µL of digest product are used in the transformation, >70% of the colonies are correct. Good luck...

...vaccines differed depending on the variants (Garcia-Beltran et al., 2021). Antibodies from individuals who ...and B.1.351 variants tested. Image from Garcia-Beltran et al., 2021 with permission.   The spike variant...represent lineages and variants that are actually transmitting out in the world” says Balazs. “By combining...quantified in terms of luminescence. Image from Garcia-Beltran et al., 2021 with permission.   Mutations ...with various pseudotyped virus. Image from Garcia-Beltran et al., 2021 with permission.   Difference ...https://doi.org/10.1038/s41586-021-03471-w Garcia-Beltran WF, Lam EC, Astudillo MG, Yang D, Miller TE, Feldman...Nitido AD, Murali MR, Alter G, Charles RC, Dighe A, Branda JA, Lennerz JK, Lingwood D, Schmidt AG, Iafrate...

...from one that represses transcription to one that activates transcription.However, this system lacks spatio-temporal...barbara_synbio) May 13, 2021 The original AraC transcriptional regulator Their system is based on the AraC...AraC protein that controls transcription from the PBAD promoter. “AraC is widely used in synthetic biology...It relies on the sugar arabinose to activate transcription by causing conformation changes in the AraC ...domains of the BLADE dimerize and activates transcription. The team created two constructs, among others...your gene of interest, all you have to do is co-transform pBLADEONLY. That way, a previously cloned gene...with AraC,” says Di Ventura. BLADE activates transcription with the flick of a light switch and shuts off...

...one of the most inclusive databases of post-translational modifications, identifies a staggering ~250,... enabled researchers to create an orthogonal translation system (OTS) for the incorporation of phosphoserine...system defined three components required for translation (Figure 1): A tRNA that recognizes a specific...elongation factor that allows proper extension and translation of the pSer-incorporated polypeptide. These ...Sep-OTS, contains the components required for the translation of pSer-incorporated proteins on a single plasmid...factor that accepts Sep-charged tRNAs during translation. Many ‘flavors’ of Sep-OTS plasmids are available...bacterial strain would result in read-through translation of many stop codons and detrimental effects on...

...remote collaborations Transferable Skills Guide: External collaborations Transferable Skills Guide: Teamwork...to explore this role, how to seek out such an arrangement, and how to operate once in that position. What... plan as well. Making logistical and funding arrangements Visiting scientist positions take commitment...structured visiting program, you will have to make arrangements on your own. This will include, but is not limited... limited to temporary housing, transportation, living expenses, and necessary reagents. Your primary lab...these expenses, or you may need to seek out travel grants available from third parties or your home institute...generate data that will contribute to a publication? A grant? A patent? It is never too early to discuss authorship...

... Wenning Qin. Single-stranded DNA repair templates Short single-stranded DNA templates have been shown...perform in vitro transcription, and use the IVT product as a template for reverse transcription to create your...order to insert two loxP sites. Since two double-strand breaks are made, it is common to see deletions ...traditionally been difficult to produce long single-stranded DNA, but Miura et al. (2015) developed the ivTRT...structure. Today, multiple companies offer long single-stranded DNA production services or kits, including the...microinjection and electroporation methods using in mouse transgenics. Designing an Easi-CRISPR knock-in allele To ...used guides targeting the same or complementary strands, as well as guides facing towards or away from ...

...are not always easy to track at the transcriptional or translational level. However, several genetic tools...slightly slower scale.  All living cells with a membrane possess an electrical state. This state, known...is maintained by ion channels and pumps in the membrane. An emerging interdisciplinary field of biology...features increased brightness and improved plasma membrane specificity. Stable Step Function Opsin - A stabilized...Use of genetically encoded, light-gated ion translocators to control tumorigenesis." Oncotarget 7.15 (...PMID: 29684787. Oviedo, Néstor J., et al. "Long-range neural and gap junction protein-mediated cues control...PMCID: PMC2823934. Pai, Vaibhav P., et al. "Transmembrane voltage potential controls embryonic eye patterning...

... from Abhi Aggarwal.   Brandán Pedre Pérez: Redox biosensors Brandán Pedre Pérez is a postdoc at... enable multiplexed imaging of neurotransmitter, calcium, and membrane voltage,” says Tian. Figure...Congratulations to the five winners! Abhi Aggarwal Brandán Pedre Pérez Elizabeth Hubbard Haoyi Qiu He Tian...hippocampal cultured neurons, imaged 14 days post-transfection, excited at 505 nm (right). Scalebar represents...hydropersulfide-propagating enzymes 3-mercaptopyruvate sulfurtransferase (MPST) which catalyzes the desulfuration of...an enzyme-bound hydropersulfide that is then transferred to thiol-containing acceptors. These hydropersulfides...redox modification, the MPST hydrosulfide can be transferred to the roGFP2 cysteine thiols and change its ...

...the co-transduction by two viruses would lower editing efficiency, the split editors transduced at levels...capacity of 4-5 kb limits the delivery of larger transgenes, such as base editors which have a gene size ...base editor is split into two plasmids and co-transfected into cells for reconstitution. Image from Levy...-opsin GEVIs. With an increase in the neuron’s membrane potential, Ace absorbance increases and results...promoters, CRISPRi parts, selectable markers, transformation acceptor vectors, and sequences for genomic...plasmids using the Cyanogate Kit and subsequent transformation into cyanobacteria. Image from Vasudevan et... evaluated CreLite for cell tracing using the transgenic zebrafish model, ubi:zebrabow. In this system...

... integration of a novel gene randomly into their genome, some transgenic strains are difficult to breed...expression level of the transgene. In existing strains of mice, the transgene can be maintained on a hemizygous...are many types of genetically engineered mice: transgenic mice, knockin and knockout mice, and conditional...that only one chromosome needs to contain the transgene in order to see an effect. Hemizygous mice can...breed. Some problems with transgenic mice that can impact reproduction include embryonic lethality, a short...expression level, and site of integration of the transgene. These problems can be mitigated in different ...different ways. Prior to engineering a transgenic strain, the promoter being used should be tested in cell lines...