We narrowed to 702 results for: BASE;

...the content of our paper, “Synthetic recombinase-based state machines in living cells” (1), into a more...how to adapt our engineered devices, recombinase-based state machines for your own experimental needs. ...the order or timing of these factors. Recombinase-based state machines (RSMs), which take on a particular...particular DNA-sequence configuration (state) based on the identity and order of a particular set of inputs, ...Sanger sequencing, qPCR, and fluorescent reporter-based) each come with their advantages and disadvantages... the predominant state of registers in a sample based on a similarity metric that we defined in our paper...convenient strategy is the fluorescent reporter based method since it lends itself to cheap, quick, and...

...instrument changes. Base-calling software can then identify the nucleotide that passed through based on these characteristic... relies on “sequencing-by-synthesis,” where each base is recognized and recorded as a DNA strand is synthesized... reactions, where a fraction of one of the four bases (A, C, T, or G) is supplied as a dideoxyribonucleoside...sequencing results are deconvoluted to identify the bases (and, if necessary, separate different samples),...and Sanger sequencing are limited to hundreds of base pairs, long-read sequencing can read sequence lengths...lengths in the thousands or even millions of base pairs. Several companies have worked on this technology...Nanopore sequencing deviates from the synthesis-based sequencing methods (Figure 3). It uses (aptly named...

...Here’s what you’ll find in this article: CRISPR-based editing in organoid Biosensors for detecting strigolactones...ready-to-use viral preps New toolkit for CRISPR-based genome editing in organoids By Ashley Waldron Organoids...organoid users have recently begun to develop CRISPR-based approaches for studying gene function in these systems...other tissue-types. By bringing together CRISPR-based approaches and organoid models, toolkits like this... SLs. The authors also showed that the receptor-based fluorescent biosensor has a high sensitivity (50...and validate a ratiometric fluorescent biosensor based on the parasitic Striga hermonthica SL receptor ... Design and mechanism of action of the receptor-based SL fluorescent biosensor. Image from Chesterfield...

...MXS-chaining is repeatable, restriction-enzyme based (chaining-based) cloning. The modules (Figure 2) are contained...BioBricks, Bglbricks, etc. Chaining-based methods (restriction enzyme-based). Well suited for the modular ...methods are listed in Table 2. For example,  chaining-based cloning methods require that the separate modules...2008; Anderson et al., 2010 Among the chaining-based methods, the specific restriction enzymes used affect...specific restriction enzymes used in various chaining-based cloning methods are listed in Table 3. The goal ...emailing us at [email protected]. Table 3: Chaining Based Cloning Methods Method Restriction Enzymes ...deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. The Journal ...

....  Here's what you'll find in this post: Yeast-based protein evolution Fluorescent tools for mammalian...the viral service Faster catalysis after yeast-based protein evolution By Joanne Kamens Mateo Sanchez...optimize another. The authors have created a yeast-based directed evolution approach with some notable improvements...antiviral CRISPR in human cells) is a CRISPR-Cas13 based antiviral method to degrade RNA from SARS-CoV-2 ... 95 plasmids consisting of CRISPR/Cas nucleases, base editors, gRNA backbones, and promoters for expression... the plasmids at Addgene! A new dual-deaminase base editor enables concurrent adenine and cytosine editing...control gene expression. This includes a CRISPRi-based synthetic oscillator, bistable network, stripe pattern-forming...

...restrictions, anything within 5 base pairs should work well, and up to 10 base pairs away (especially 3’ of...introduce you to a simpler, yet more effective, CRISPR-based epigenetic approach (spoiler alert: it’s dCas9… ...When I started to work on building a CRISPR/dCas9-based tool for DNA demethylation in 2015, none existed...that oxidize 5-methylcytosine to create rare DNA bases that are recognized by distinct proteins and result...Kaas et al. 2013). Figure 2: CRISPR TET-based epigenetic editing. In reality, editing your target...system to balance these needs is the lentiviral-based expression of floxed dCas9 so that it may later ...at McGill University, working to develop CRISPR-based tools for epigenetic editing.   References and resources...

... et al, 2014). The second was an in vitro paper-based platform that allowed gene circuits to be deployed... of these combined technologies, we built paper-based synthetic gene networks for the detection of antibiotic...work was exciting because it enabled gene circuit-based sensors to be used outside of the laboratory. The...the lab had been working on advancing the paper-based platform toward a more field-ready format when the...that, given the critical need for low-cost, field-based diagnostics, our approach could make an impact. ...paper when we say the timeline to develop our paper-based platform into clinically relevant diagnostics for...week (Pardee et al, 2016). Using toehold switch-based RNA sensors, our approach uses portions of the pathogen...

...termed a mixed site. One can also use a nucleotide-based molecular insert (inosine) instead of a regular ... have the following properties: Length of 18-24 bases 40-60% G/C content Start and end with 1-2 G/C pairs...site at the 5’ end of your primer, note that a 3-6 base pair "clamp" should be added upstream in order for...

...as the Forster resonance energy transfer (FRET)-based executioner caspase reporters. In these reporters...in fluorescence emission. FRET and fluorescence based reporters however have several limitations. First...also designed a red fluorogenic protease reporter based on superfolder Cherry (sfCherry). Like FlipGFP, ...used to cleave proteins. This protease reporter based on sfCherry however did not initially fluoresce ...). Studying apoptosis in vivo using the FlipGFP-based caspase reporter The Shu Lab successfully used FlipGFP...Lastly, the Shu Lab demonstrated that the FlipGFP-based caspase reporter can be used to visualize apoptosis...et al. "A new protein-protein interaction sensor based on tripartite split-GFP association." Scientific...

...determines ideal shipping conditions for each order based on the total items in the order, ensuring each item...

...studies used SMRT sequencing, TA-based ligation and tagmentation-based methods for AAV genome sequencing...only works for self-complementary AAVs and the TA-based ligation and tagmentation preparation approaches...because the AAV genome is single-stranded and both TA-based ligation and tagmentation require a double-stranded...Berns, 1972). Using qPCR and restriction enzyme based methods, we showed that the DNA extract is a heterogeneous... serve as effective substrates for tagmentation-based library preparation procedures. This finding eliminates...data. Unlike previously described thermodynamics-based methods of serotype confirmation, this method does...

...ABE’s. b) Quantification of base-editing efficiency using XMAS-TREE-based methods at various genomic loci...enrichment of ABE-targeted cells By Ellie Adams Single base modifications through ABE or CBE's have the potential... deposited a set of plasmids that helps identify base edited cell populations without end-point sequencing...for editing enrichment”, or XMAS-TREE, to identify base edited cell populations without end-point sequencing...library targets E-boxes genome-wide. It was designed based on MYC-ChIP-seq data from several MYC-dependent .... The BARBEKO sgRNA library uses CRISPR cytosine base editors to disrupt gene function by targeting start...

...publication: http://www.freebase.com/base/aptamer Cruz-Toledo, J. et al. Aptamer base: a collaborative ...collaborative knowledge base to describe aptamers and SELEX experiments. Database, bas006 (2012). PubMed. For a ...biofactories by demonstrating the use of CRISPR-based RNA scaffolds to mimic natural transcriptional programs... RNA scaffolds follows the rules of Watson-Crick base pairing, allowing for rational, straightforward ...straightforward design. Since the technique relies on base pairing, it has promise to be host-independent, beyond the...the University of Western Ontario studying plant-based recombinant pharmaceuticals. Follow him on Twitter...

...utility of cytidine and adenine base editors that enable C-to-T and A-to-G base substitutions respectively.... were first discovered in bacteria, most CRISPR-based genome engineering has taken place in other organisms...CRMAGE system combines CRISPR and recombineering-based MAGE The Nielsen lab’s CRMAGE system is a fast, ... method that combines CRISPR and recombineering-based MAGE (Multiplex Automated Genome Engineering) technology...Bikard et al., 2013), the Qi lab employed a gRNA-based design more familiar to those using CRISPR in eukaryotes...catalytically dead Cas9 enzyme allows reversible repression based on the presence of the inducer, in this case anhydro-tetracycline...RNAP-Omega-dCas9 fusions. Here’s some others. SoxS based CRISPRa In the search for a CRISPR activation method...

...IDT estimates that there is an NGG PAM every 42 bases in the human genome. SpCas9 targeting should be ...difficult if there’s no PAM near your insertion site. Base editing, another method to create point mutations...Employing xCas9 for transcriptional regulation and base editing Hu et al. also engineered transcriptional...NGG PAM, confirming the flexibility of xCas9 3.7. Base editor variants with xCas9 are similarly flexible...nuclease, xCas9 3.7 fused to third generation cytidine base editor architecture (BE3) slightly improves NGG ...efficiency over that of SpCas9-BE3 (37 vs 28%). Cytidine base editing at NGT, NGC, GAA, and GAT PAMs is improved... with a smaller increase in NGA editing. Adenine base editor xCas9 3.7-ABE also follows the same pattern...

...IBEX Knowledge-Base, with every contributor listed as an author.  The IBEX Knowledge-Base is an invaluable...amplified staining methods, and oligonucleotide-based staining. Of course, if you’re interested in using... Ziv Yaniv, PhD, have created the IBEX Knowledge-Base, a community repository and resource for spatial...open-software community when designing the IBEX Knowledge-Base, seeking to create an iterative process that is .... Everyone who contributes to the IBEX Knowledge-Base is named on the Zenodo release in keeping with their...components of building both the community and the database. They particularly encourage people to upload ...

...plasmids Cytosine base editors with minimized off-target DNA editing The original cytosine base editor, BE3,...research! This time: Optogenetic repression in yeast Base editing CRISPRi in Caulobacter crescentus Multiplexed...Multiplexed gRNA for human pluripotent stem cells CRISPR-based DNA demethylation Optogenetic repressors of gene... Read the paper in Nature Biotechnology Find the base editor plasmids CRISPRi in Caulobacter crescentus...Scientific Reports Find the plasmids Enhanced CRISPR-based DNA demethylation Figure 2: The components...

...that cover some of the hottest CRISPR tools. Base Edit: Base editing plasmids allow you to make precise ...causing double-strand breaks. Our new page shows you base editing plasmids for mammalian systems, bacteria...bacteria, plants, and yeast. Popular cytosine base editor pCMV-BE3 has been requested nearly 400 times, and ... has already earned a blue flame for its adenine base editing capabilities. Epigenetics: CRISPR has made...for Gene Editing Day 9: Precision editing: Single Base Editing with CRISPR and Enhancing CRISPR Targeting...

... on base editing from the first generation of base editors to the eighth generation (and dual base editors...Addgene gave to me: SHERLOCK and DETECTR, two CRISPR-based methods to detect nucleic acids.  On the third day...

... Course-based Undergraduate Research Experience (CURE). Having incorporated a discovery-based lab on planarian...and research-based learning in a year-long biochemistry laboratory : Part II – research-based laboratory...thinking skills (Knutson et al., 2010a,b). Classroom-based research projects have also been proposed as a mechanism...References Bangera, G., Brownell, S. 2014. Course-based undergraduate research experiences can make scientific... E., Kowalko, J., Keene, A. et al. 2022. Course-based undergraduate research experiences (CUREs) as a ...research to students; Using inquiry and research-based learning in a year-long biochemistry laboratory:...Implementation of a collaborative series of classroom-based undergraduate research experiences spanning chemical...