...the late 1980s, scientists even created a codon adaptation index (CAI) that is based on the codon usage ...codon bias. The idea is that scientists can make mutations throughout a gene of interest based on an organisms...) to name a few. This could affect synonymous mutations which have even been linked to some diseases. ...human genes contain a region where a synonymous mutation can be harmful (Sauna and Kimchi-Sarfaty, 2011...tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Research 28:292... Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet 12:683–691. https...10.1038/nrg3051 Sharp PM, Li W-H (1987) The codon adaptation index-a measure of directional synonymous codon...

...template to create mutations HDR donors can contain insertable sequences or specific mutations, along with homologous...sequence at the DSB, or it can introduce specific mutations into the damaged DNA if these modifications exist...HDR efficiency for more details on how "Cut-to-Mutation distance" affects editing efficiency. One important... cutting and repairing your target DNA until a mutation is introduced disrupting one or both of these ...sequences. To prevent re-cutting and the resulting mutations after an HDR event, ensure the gRNA or PAM site...off-target effects. A technique that pushes the size limitations of ssODNs is Easi-CRISPR (Quadros et al., 2017...

...fluorescence that is generated allows for qualitative and quantitative measurement of processes including RNA...photobleaches, DFHBI can only be used for qualitative, but not quantitative, studies. Additionally, Spinach, the... In the search for something more stable for quantitative imaging, Ming Hammond’s group created Spinach2...photostable than Spinach and Broccoli, and useful for quantitative studies. Specifically, Corn was developed to... and both TO1-biotin and TO3-biotin contain an acetate modification that reduces nonspecific binding with...

...biotin ligase, BirA*, with a site mutation (R11G). This site mutation destabilizes the ligase, allowing...the E. coli version. It also contains a single mutation (R40G) in a conserved residue in the biotin catalytic...ascorbate peroxidase for proximity labeling A major limitation of APEX was its low sensitivity. Sensitivity ... two mutants, the 35 kD TurboID, which has 15 mutations compared to BirA and the 28kD miniTurbo, which...which has the N-terminus domain deleted and 13 mutations compared to wild type BirA. TurboID and miniTurbo...interactions Split-BioID combines a protein fragment complementation (PCA) technique with proximity labelling to...

... introduce naturally occurring cancer-causing mutations into the endogenous allele of the STAG2 tumor ... introducing non-sequence specific frameshift mutations through aberrant double strand break repair, it...knockins, it is not always ideal. Because of these limitations, the AAV approach is best suited for tissue culture...epitope tags, or the introduction of dominant mutations of a gene into the endogenous allele in cultured...template to mouse zygotes and thereby correct a mutation that causes Hemophilia B. Unfortunately, work ...applications that require large gene fusions. The current state-of-the-art in combining the AAV and CRISPR-based...segregation in human cells harboring tumor-derived mutations in STAG2." PLoS genetics 12.2 (2016): e1005865...

...within this kit contain a variety of promoters to facilitate gene expression in bacteria, yeast, mammalian...His, Avi, and GFP) as well as protease sites to facilitate protein purification. We hope this kit will allow...important microalgae: intrinsic suicide switch implementation in cyanobacterium Synechocystis sp. PCC 6803...Furthermore, some plasmids contain peptides to facilitate protein folding and/or protease sites to remove...The gene set was carefully chosen to perform statistically relevant benchmarking of cell-free expression...By counting DNA sequence reads, FREQ-Seq can quantitatively determine allele frequencies across timepoints...selective pressures: Miller, Corwin, et al. "Adaptation of Enterococcus faecalis to daptomycin reveals...

...purified GFP could be imaged in the green state after excitation at 488 nm, photoconverted with 405 nm light... light, and then captured in the red state after excitation at 561 nm. This imaging process worked well...S65T GFP, and no red color was observed after excitation at 488 nm, indicating that spontaneous conversion...al., Sci Rep. 2015 CC BY 4.0 Applications and limitations of GFP photoconversion One concern with photoconverting...

...knock-ins of patient mutations which are variants of unknown significance – mutations with unclear effects...with defined, straightforward causes (a specific mutation in a known gene = disease onset) may be best served...accessible, fast, and easy. In cases where the mutational basis of a disease is known – repeat expansion... can aid in generation of multiple edits or implementation of expression systems to accurately mimic a...CRISPR could even be used to generate patient mutations and then test both individual and combinatorial...

...detect proteins in different states. For example, in immunoprecipitation (IP) the antibody interacts with... for protein interaction studies such as immunoprecipitation and pull-down assays.  Westerns are divided... with a protein in its native state while a western blot detects denatured polypeptide chains. The protein...epitopes, differ between a protein in its native state versus the polypeptide chain. Consequently, antibodies... way to gauge protein abundance they provide qualitative measurements. If you require precise quantification...determine protein interactions following immunoprecipitation and are a common readout for subcellular ...

... H161Y, P163T, I175Q, C176T and N177F mutations). Its excitation maximum is reported as 603 nm, while ...aptamers and MS2-binding fluorescent proteins were the state of the art in RNA imaging in vivo. These new “Riboglow...et al. PLoS One, 2016) and tested a series of mutations. Through this process mCarmine was developed (...several cell types is the lack of a rapid and quantitative editing assay. To help accelerate the expansion...-UGI-mediated activity edits out a frame-shift mutation within the mCherry reporter. Quantification of...

... job asks for experience in “statistical analysis”, mention “statistical analysis” (word by word) in your...general format of a resume and the different presentation styles. Wikipedia does a good job summarizing...handled large data sets and are familiar with statistical analysis. If you have done fluorescent imaging...publishing or patent application processes? How about facilitating a collaboration between research groups? Perhaps...universities make their job postings and salary expectations public, so start by looking at these university...

... that cluttered our old plasmid maps. Clearly Annotated Features, Enzymes, and Primers - The new maps ...SnapGene’s software positions restriction enzyme annotations throughout the map at locations better aligned...map, you also have the ability to to download the static image file (PNG, see above) for your own reference...sequencing results: On this page you can download an annotated GenBank File or a SnapGene file for the sequences...of choice. If the depositor provided a custom annotated GenBank file, this can be found on the main plasmid...hosted here retain all the features shown in the static maps discussed above, but also have interactive...

...incorporation of a desired mutation into your plasmid of interest by PCR generates mutated plasmids with no methylation...only the non-mutated and methylated template is destroyed leaving behind a pool of mutated plasmids which...dam-/dcm- strains may have an increased rate of mutation (as these would also be deficient in mis-match...Your Sequencing Results Use REPLACR Mutagenesis to Mutate Your Plasmids Resources on Addgene.org Check ...

...the immune mechanisms of the host. The cause, manifestation, diagnosis, recurrence, and treatment of cancer...molecular targets under research include TIM-3, LAG-3, STAT-3, EGFR, CD20 and CD73 on specific solid as well..., tumor penetration, inadequate concentration, mutation of cell surface targets by tumor cells, are a ...currently the only FDA-approved DC therapy for prostate cancer and is aimed at increasing life expectancy...radiotherapies have caused increased death receptor presentation on tumor cells thus making these cells more ...differ in practically every facet starting from manifestation to their specific interactions with different...the most important: How will cancers evolve and mutate based on the immunotherapeutics we use on them?...

...cartoon of the protein.) In the middle of my presentation, lost in a sea of data, my mind went completely...taught me an incredibly valuable lesson: Your presentation will be better if you take time when you need...need it, rather than trying to push through a state of panic. Now, if I feel myself getting too nervous...sense. As tempting as option two was in my panicked state, only option one would let me accomplish my goal...often as needed until you get to the end of the presentation, at which point you will have achieved your ...gig. Being able to give a clear, informative presentation, speak at conferences, or even just provide ...

...light-sensitive protein QuasAr2 and systematically mutated it. Using a robotic picking approach to select ...2015) or ratiometric Bimolecular Fluorescence Complementation (rBiFC, Grefen and Blatt, 2012). The 2in1 Plasmid...vectors with all possible combinations of tag orientation (NN, NC, CN, and CC). The 4 kits also contain...proteins that bind to either the light- and dark- states of the photoswitchable cPYP, which changes in conformation... partners that bind to only the light- or dark- state of the photoswitchable proteins offers a powerful...binders (which bind to either the light- or dark- state of the photoswitchable proteins) fused to mVenus...

...dominant negative mutation in MLH1 (PE4 = PE2+MLH1dn and PE5 = PE3+MLH1dn). Silent mutations added near the...the Cas12f scaffold gRNA and making strategic mutations in the DNA binding cavity of Cas12f. The CasMINI...  and base editing, whereas a different set of mutations (the “V3.1” version) works best for genome editing...protein PEG10 specifically binds its own mRNA to facilitate its packaging into virus-like particles. Feng...boosts the efficiency of prime editing to correct mutations in a variety of target genes and cell types. Their...

...-invasive gene delivery and optogenetic excitation. Excitation of neurons deeper in the brain may still...makes them light-responsive. When light shines on excitatory channelrhodopsin-expressing neurons, the channelrhodopsins...action potential (Figure 1). This light-induced excitation can take place in a tissue culture dish but can...high-intensity light for activation which requires implantation of fiber-optic cables into the brain. ...still require fiber-optic cannula implantation, but altering ChRgers so they can be activated with tissue-penetrating...

...articles. Then just start reading and following citations through the literature until you have all of the...they mean. Could there be any other possible interpretation of the results? Then think deeper about the...Is the data of sufficient quality (error bars, statistics, clarity in images etc)? Did they perform all...doesn’t mean that there are no mistakes or misinterpretations. After all, the science was performed, written... brim with reprints and papers with scribbled notations in the margins. If you prefer, printing and hand-writing... Department of Biological Sciences at Louisiana State University. She is a fan of photosynthesis and writes...

...elegans. To study the role of 3’UTRs, the Arizona State University (ASU) Biodesign institute developed a...polyadenylation for all protein coding mRNAs, and annotations extracted from other databases (Mangone et al...Dynamics Database (WDDD) The WDDD aims to acquire quantitative data on all the cell divisions of the C. elegans...methods provides unique opportunities to develop computational methods to better understand animal development...additional SapTrap plasmids used for introducing point mutations that was published in a microPublication (Schwartz... E. M. "SapTrap vectors for introducing point mutations with unc- 119 + selection." MicroPublication 1...