...immortalized cells (see Weinberg Lab page for resistance variants) Weinberg 1773 pBABE-hygro-hTERT MoMLV Expression...expression; also expresses GFP. Also see pMIG-w , a variant that has WRE, a post-transcriptional regulatory...

...individual variants found in tumors are exceedingly rare. As a result, how most of these “variants of unknown...cancer clinical sequencing report includes rare variants that haven’t been characterized? Some have developed...approach this challenge, using attributes of cancer variants such as evolutionary conservation, or predicted...hope researchers can use to characterize these variants in a high-throughput manner and therefore push...precision medicine a reality. Challenges for cancer variant characterization For many years, we’ve hoped that...laboratory-based functional experiments that classify which variants are likely gain-of-function, loss-of-function ...these experiments could find correlations between variants in a gene of poorly classified function and a ...

...four novel SpCas9 variants with altered PAM binding specificity: SpCas9 variant Mutations (relative...SpCas9) PAM sequence D1135E variant D1135E NGG VQR variant D1135V, R1335Q and T1337R NGAN...NGAN or NGNG EQR variant D1135E, R1335Q and T1337R NGAG VRER variant D1135V, G1218R, R1335E...the VQR and VRER variants is similar to wild-type SpCas9, indicating that the variants are likely just ...reported the development of near-PAMless Cas9 variants. These variants, named SpG and SpRY, can target NGN PAMs...limitation: 1) the use of novel S. pyogenes Cas9 variants with varying PAM sequences, 2) the use of Cas9...R1335E and T1337R NGCG The D1135E variant is far more selective for the canonical S. pyogenes PAM...

...try developing a variant with an enhanced response. Evolution of a new variant Maria and the team set ...suggest she deprioritize the project, Maria’s screens of AsLOV2 variants showed some significant gains! After...several other labs. Andrew and Maria expect that further-improved variants of MagLOV will be possible with...applications that don’t even exist yet? Andrew York, Maria Ingaramo, and their team at Calico Life Sciences...right through our tissues unimpeded. Andrew and Maria dreamed about the possibilities of a magnetoresponsive...appears to be weak — if they exist at all. Andrew and Maria were encouraged by previous reports that described...developing useful tools. A lucky start As Andrew and Maria explained, “to our surprise and delight,” the very...

...Clover Green Mammalian Expresses Clover (a GFP variant) commonly used with mRuby2 pLSSmOrange-N1 Orange...LSSmOrange mRuby2 Red Mammalian Expresses mRuby2 (a RFP variant) commonly used with Clover pGWF1 Cyan & Yellow ...

...Campbell’s lab added two new mCherry variants to the repository. These variants can be used as tools to learn... Podcast Segment The impact of KLF4 N-terminal variants on iPSC generation Deriving iPSCs (induced pluripotent...polycistronic cassette. However, it was unknown whether variations in gene expression from these polycistronic cassettes...transposons, the Woltjen Lab compared different variants of the polycistronic cassettes and discovered ...which they traced to a 9 amino acid N-terminal variation in the Klf4 isoform (KLF4s or KLF4L). Polycistronic...discovered that monocistronic expression of either variation of Klf4 did not lead to the observed reprogramming... developed a synthetic red fluorescent protein variant they call mScarlet. Bindels et al used a combination...

...green (v857) variants differing in kinetics, affinity, and ∆F/F0. Introduce the two variants in three different...for sfGFP to create SF-iGluSnFR. This improved variant has higher expression levels in bacteria and produces...models. Furthermore, they created three affinity variants – A184S (increased affinity for glutamate), S72A...Kaspar Podgorski’s lab have recently made iGluSnFR3 variants that are more sensitive and better localized for...predecessors. The detailed characterization of the new variants is available here. Upgrades to iGluSnFR3 To improve...Improved photophysical properties The improved variants of iGluSnFR3 have higher expression levels and...   Increased versatility through two different variants The yellow (v82) and lime green (v857) versions...

...' TTTV AsCpf1 RR variant 5' TYCV LbCpf1 RR variant 5' TYCV AsCpf1 RVR variant 5' TATV Campylobacter... PAM sequence. Cas9 Species/Variants and PAM Sequences Species/Variant of Cas9 PAM Sequence ...NGG SpCas9 D1135E variant 3' NGG (reduced NAG binding) SpCas9 VRER variant 3' NGCG SpCas9...SpCas9 EQR variant 3' NGAG SpCas9 VQR variant  3' NGAN or NGNG  xCas9 3' NG, GAA, or GAT SpCas9...general overview of CRISPR components, new Cas9 variants are being discovered all the time and the requirements...different systems can vary (for example, xCas9 is a variant with increased PAM flexibiliy and eSpCas9/SpCas9...protein required is the Cas9 endonuclease or a variant thereof. This individual protein has all the components...

...AAV6 Vectors: Strategies for Overcoming Donor-Variation and Implications in Genome Editing. Sci Rep . ...

...controls are invariably inconclusive and unreliable. Proper controls provide the constant variables that enable...independent variable. Referring back to the experiment associated with Figure 1, the independent variable is the...interpretation of the effect of the independent variable you are testing. Importantly, they demonstrate...is specifically associated with the independent variable you are testing and not some other unintended ...to minimize any effects of the non-independent variables.  To illustrate the importance of control plasmids...to minimize the effects of the non-independent variables within an experiment, both the design and selection...experiment and the interrogation of the independent variable. Replicate controls: technical and biological ...

...combination of gene variation and lifestyle or environmental factors. For example, variations of Apolipoprotein...

...library of AAV9 variants (Chuapoco et al., 2023). They found the best-performing variant, CAP-Mac, was ...genome editing for primary cells Monomeric StayGold variants AAV.CAP-Mac for systemic gene transfer in primate... Breaking up is hard to do: Monomeric StayGold variants By Mike Lacy In 2022, Atsushi Miyawaki and colleagues...stability. Here’s a quick overview of these new variants:   Figure 2: Inner mitochondrial membranes...QC2-6 FIQ or mStayGold (Ando et al., 2023). This variant has similar photostability and brightness compared...Ivorra-Molla et al., 2023). They also named their variant mStayGold. It is worth mentioning that Kiryl Piatkevich...colleagues generated yet another monomeric StayGold variant (Piatkevich et al., 2023). Check out their preprint...

...nervous system function. While there is wide variability in symptoms even within patients with the same...algorithms for data analysis to calculate heart rate variability (Link opens in a new window) Protocols.io - protocol...

...downstream of the variable region gene in this order: μ, δ, γ, ε, and α. An antibody variable gene is initially...heavy chain, light chain, constant region, and variable region.   Why are antibody isotypes important... heavy chain constant domain it pairs with its variable chain domain. B cells start by co-expressing IgM...antibodies, but later in an immune response, the variable region of an antibody is paired with any of the...intervening DNA sequence is deleted, which places the variable region next to a different constant domain gene...heavy-chain constant domain genes, placing the variable domain genes next to a different constant domain...the B cell expressing an antibody with the same variable domain but a different heavy-chain constant domain...

...Kim et al., 2017 SaBE3, BE3 PAM variants, BE3 editing window variants   Greatly expands the number of ...upstream of the PAM.  David Liu’s lab generated BE3 variants with other deaminases: AID, CDA1, and APOBEC3G... Liu lab also used natural and engineered Cas9 variants to develop five new base editors with distinct...HF-BE3, a base editor containing high fidelity Cas9 variant HF-Cas9 (Rees et al., 2017). HF-BE3 showed 37-fold...Gaudelli evolved the base editor into 40 new ABE8 variants (Gaudelli et al., 2020). Compared to ABE7.10, ...-fold higher editing efficiency at non-NGG PAM variants compared to ABE7.10. ABE8s have an improved base...genome. So the development of near-PAMless Cas9 variants significantly expands the library of accessible...

...regions are completed with the Ig light chains. The variable region of the heavy and light chain determine ...Fab, heavy chain, light chain, constant region, variable region   The constant region of the heavy chain...antibody depends partially on its isotype. The variable region of an antibody does not recognize the entirety...antibodies against different protein epitopes and so variability between lots is a big concern. You can find more...clonal population of cells that produce a single variant of antibody. Monoclonal antibodies are less likely...an antibody (Ayyar et al., 2017). Single-chain variable fragment (ScFv) Figure 2: Comparison between...molecule is not necessary for antigen binding, the variable regions alone can be generated as a fusion protein...

...measure the frequency of each variant during the selection process. Each variant is assigned a functional ...of a plasmid library that expresses all desired variants of a protein. Applying a selective pressure winnows...winnows the pool down to plasmids expressing variants with optimal function. High-throughput DNA sequencing...mutational scanning Hundreds of thousands of protein variants can be tested in one experiment. There are many...experiments, libraries of DNA fragments that contain variable bases (NNN) at any given codon site of interest...opposite wild-type DNA strand is nicked by the BbvCI variant not used in step 1. Then this strand is degraded... and cost. You need at least 100-200 reads per variant, so the more codons you test in one library, the...

... released a new variant of jGCaMP7 (keep reading) and will be releasing more variants in the next few ...few months (see “coming soon”). The 7b variant (pGP-AAV-syn-FLEX-jGCaMP7b-WPRE) exhibits the brightest resting...processes like dendrites and axons. Find the 7b variant of jGCaMP7 in AAV1 at Addgene! See all calcium ...membrane localization and brightness. The F102G variant (pAAV.hSyn-FLEX.iGABASnFR.F102G) is noticeably ...responses to GABA. Find the iGABASnFR and its F102G variant in AAV1 at Addgene! Archon1, a voltage sensor AAV...neurons. 105321  AAV1  pGP-AAV-syn-jGCaMP7c variant 1513-WPRE 7c exhibits high contrast between peak...reduced. 105322  AAV1  pGP-AAV-syn-FLEX-jGCaMP7c variant 1513-WPRE7c exhibits high contrast between peak...

...are numerous GFP variants. Here I use the name ‘GFP’, which refers to mEGFP. This variant was made by introducing... generate the strictly monomeric EGFP variant, mEGFP (Zacharias et al., 2002). GFP needs oxygen Chromophore...jellyfish GFP (AvGFP) to create enhanced GFP (EGFP), a variant with improved brightness (Tsien, 1998). Another...Cranfill et al., 2016 and FPbase.org). A number of variants remain fluorescent under acidic conditions, with...although it still is worthwhile to generate several variants and check the functionality of the fusion (Mastop...on twitter: @joachimgoedhart.   References 1. Zacharias, David A., et al. "Partitioning of lipid-modified...

...should be 60-65°C For qPCR, the important primer variable is the annealing temperature, not the melting ...reference genes have shown to have as much as sixfold variation in expression levels reported (Biassoni, 2014)...negative error on the other will introduce unwanted variation into your data. Try different types of pipettes... within each set of triplicates to understand variation due to technical error.  Plate readouts can be...type or tubes, sealing method, and other small variations in consumables. Track and record these details...Reference Dyes Whatever your pipetting method, some variation will occur. A passive reference dye, such as ROX...they are, however, affected by bubbles in wells, variations in volume, or machine surge errors and allow ...