...Novophage to Sample 6. To learn more about Novophage's successful transformation into Sample 6 and Dr. ... in food products prior to Sample 6 16:27 - 18:02 : Benefits of the Sample 6 technology and how It works...- 19:56 : Why Sample 6's first test was for Lysteria 19:56 - 24:41 : Who is using Sample 6 and why? 24...Resources Visit the Sample 6 website Check out Dr. Koeris' Website, biotechstart.org Read Sample 6's Paper on...for use in a biotech startup 12:16 - 15:15 : Why Sample 6 began to develop tests for food products as opposed...Directors. We're excited to watch both Addgene and Sample 6 grow with his help! Special thanks to our sound... sample6...

...construction system for multiplex genome engineering. Image from Sakuma at al. (2015). Multiplex genome engineering... construction system for CRISPR/Cas9-mediated multiplex genome engineering is now available thanks to ...new tool in Scientific Reports in June. “The multiplexity is one of the most advantageous properties of...established way of making an all-in-one vector for multiplex genome engineering.” Now, they’ve filled that...Cas9-nickase vectors work successfully to target multiple sites in cultured human cells. While it has not...be applied to efficient viral vector-mediated multiplex genome engineering. The system now provides an...an efficient targeting strategy for multiplex editing of genomes. It will also allow simultaneous activation...

... to implement in practice because FRET depends on a number of hard-to-achieve factors. For example, FRET...Bimolecular Fluorescence Complementation (BiFC). What is bimolecular fluorescence complementation? Bimolecular fluorescence... TK (2006) Design and implementation of bimolecular fluorescence complementation (BiFC) assays for the...often easier said than done. Fortunately, a complementary method exists for visualizing protein-protein... fluorescence complementation is a method for detecting protein-protein interactions that uses split fluorescent...fragments that individually lack fluorescence. When complementary FP fragments are fused to two hypothesized protein...interaction partners (PIPs), the FP fragments form the complete FP because the PIPs they’re tethered to bring ...

...between the glass coverslip and a sample in aqueous buffer it is completely reflected. This reflection occurs...water-like buffer the sample is immersed in. Although the excitation light is completely reflected, energy...microscope to use for a new sample I always start by asking two questions: 1) Is the sample dynamic or static? ...? 2) Is the sample thin (< 15 μm) or thick? These questions will place each sample into one of four categories...capture in these types of samples is their fast movements. Depending on the sample, a temporal resolution... fluorophores higher in the sample. TIRF is also very gentle on the sample as the majority of the laser...sheets of excitation light through multiple focal planes of a sample may also be useful for providing fast...

...more complex experiments. A multiplexed experiment, for example, requires staining with multiple primary...control is generally a sample or group that will have a desired response. For example, if you are studying...to experimental samples (?). B, The inclusion of biological replicates such as multiple mice in each group...control is a sample or group that is not subjected to the experimental condition. In the example above, a ...inhibitors on mice, for example, it would be better to treat and test multiple mice with the drug rather... wild-type and knockout samples. In this test, wild-type and knockout samples are treated with the identical...present in the wild-type samples and absent in the knockout.  If knockout samples are unavailable, try substituting...

...numbers of plasmids. plexWell™ technology overview For any NGS experiment, the DNA sample being sequenced ...costly library prep, as each sample requires an individual library. The plexWell™ workflow is a sequential...carrying sample-specific barcodes. Rather than continuing to process 100s to 1000s of samples individually... of plexWell™’s sequential tagging procedure, the quantities of library molecules for each sample remain... problem in multiplex NGS library preparation. The challenge here is that, as more samples are sequenced...case that individual libraries prepared from multiple samples will then also need to be quantified and re-normalized...in order to be combined with other samples in a single multiplexed pool. The cost of these normalization...

...visualize multiple targets at once. An advantage of multiplexing is that you can ask how multiple proteins... sample type. Sample Preparation This step can involve multiple smaller steps that all help to ensure...and colors makes it easy to perform multiplexed IF. By using multiple primary antibodies made in different... maintains sample morphology with minimal impact to the target epitope. There are multiple methods for...methods you use will depend on target and sample type. Example steps include: permeabilization, antigen...target and sample type. Primary Antibody This is the first antibody applied to your sample, which will... and Imaging Similar to Sample Preparation, this step can involve multiple smaller steps, but the aim...

...detect or analyze complex edits, such as those generated by multiplexed delivery of multiple sgRNAs. Since...For a multiplex sample, ICE includes visual representations of all detected edit types in the sample. The...with each sample. Successfully analyzed samples will display the following parameters: Sample - The unique...indel.   For a complete guide to ICE analysis, including detailed explanation and examples, read the paper...the ICE software has two analysis formats: sample by sample analysis, which can compare up to five editing...results and a list of the analyzed samples (see below).   If the sample run had no issues, the analysis ...perform more in-depth analyses on each sample by clicking on the sample name or on its corresponding bar graph...

...emulsion droplet technology that fractions the PCR reaction sample into approximately 20,000 droplets. Each... our blog post “Droplet Digital PCR for AAV Quantification.”   Multiplex PCR Multiplex PCR, as the name...utilize multiplex qPCR to quantify the concentrations of multiple starting DNA templates in one sample. It...target DNA levels Multiplex PCR Amplify multiple targets from one sample Disease or pathogen identification... molecular diagnostics.  Digital droplet PCR, ddPCR  Digital droplet PCR or ddPCR is a method that provides...analyzed by a droplet reader, which measures the fluorescence amplitude of each droplet. The fraction ...method in which multiple targets can be amplified in a single PCR experiment using multiple primers all in...

...detecting specific populations of cells in a complex tissue or sample (1). When combined with cell sorters, ...information about the cell’s complexity. A cell with a high degree of internal complexity such as extensive membranes... of cells. During FACS, the sample stream oscillates to generate droplets that are charged as they pass...plate. Each droplet contains a single cell that is assessed for the desired parameter. A droplet containing...rule out dead cells and debris. For example, a whole blood sample will contain a mix of cells including...differences in their size and complexity, cells from a whole blood sample will separate into distinct populations...ensure that samples are single cell suspensions. For cells that tend to aggregate, pass the sample through...

...can test three or more groups (two samples and a control, for example) simultaneously, with up to two independent...differences exist between. For example, if an ANOVA analysis on a five-sample data set yields statistical...appropriate to use if all sample comparison is needed, without a high number of samples (~5). Tukey’s test ...positives. Control vs. all samples Oftentimes there exists a control group and multiple experimental groups,...test assumes your data follows. Fig. 1: Examples of comparable groups with and without equal levels... variance among data.     Fig. 2: Examples of data distribution profiles.   Parametric...They are classic parametric tests and one of the simplest statistical tests available. Tailed t-tests If...

...molecule in an unknown sample. To do this, you serially dilute a control sample of known concentration...extrapolate the concentration of an unknown sample. For example, a BCA assay uses a serial dilution of a ...concentration of the unknown sample based on its measured response. An example of this is shown in Figure...their bicinchoninic acid assay (BCA) to normalize samples before running a western blot. Standard curves ...control protein, incubated alongside an unknown sample with the BCA reagent. The absorbance of both is...you to determine the concentration of the unknown sample.  How do I make the standards for a standard curve...standard curve by serially diluting a known control sample, called a standard. The ideal standard curve has...

... the sample to that of a standard curve to extrapolate the concentration of antigen in the sample. A variety...coated with a competing antigen (green).  The sample (purple) is preincubated with a reporter enzyme labeled...-containing sample with their conjugated primary antibody. Users next incubate the sample with the multiwell...control, include a sample that is known to contain the target antigen. Some examples could be an endogenous...used to quantify the level of target antigen in a sample. While Engvall et al. originally developed the ... proteins and small molecules from a variety of sample types (Engvall 1971). Scientists value ELISAs for...capture antibody that binds to the antigen in a sample and then a second detection antibody binds. The...

...protein:DNA complexes with antibodies specific to your protein(s) of interest. Once the complex is captured... Once you have your sample, the first step is to ensure your protein:DNA complexes will remain bound to...you’re working with a tissue sample, you’ll need to homogenize your sample before moving on to the next...the protein:DNA complexes. Once you’ve finished fragmenting the DNA, spin down the samples to remove cell...protein:DNA complexes and finally (5) isolated the DNA from your antibody:protein:DNA complexes. Your DNA...Homogenization for a tissue sample can also need significant optimization for the sample type and size.) It can...process is very similar for both, though tissue samples do require an extra homogenization step. For this...

...structure of the complementary heteroduplex. Base mismatches cause bulges in the duplex that may not fit...helix, purple; sgRNA, dark blue.   The REC lobe binds tightly to the repeat:anti-repeat duplex of the...This cap is where the DNA:RNA heteroduplex transitions back to DNA duplex, and it’s the reason guide sequences... A RuvC loop caps the heteroduplex and marks the transition back to a DNA duplex. sgRNA, dark blue; target...structurally resemble any other known proteins; they are completely unique to the CRISPR system (Nishimasu et al....CTD, yellow; REC lobe, light blue; bridge helix, purple.   Apo Cas9 changes conformation frequently... these regions, even if they are present in the sample. Other techniques, like electron microscopy and...

...If your plasmid can be classified in multiple categories, please check all of the appropriate categories... a collection that is greater than 75 plasmids, please let us know by contacting [email protected]. ...plasmid can be added on subsequent pages. Type - please choose from one of the following descriptions for...used to knockdown expression of mRNAs with complementarity to the shRNA sequence. Empty backbone A plasmid...through cloning. *Note — If you will be depositing multiple plasmids and would prefer to send us your plasmid...e-mail us at  [email protected] Special cases Please contact us at [email protected] or +1 (617)-ADDGENE...must be verified by next-generation sequencing. Please see the help center article, "Can I deposit a pooled...

...across the board. If the samples or sample conditions change, the multiplexed protocol may have to be ... If there are multiple amplicons, or primer dimers forming, the curve will show multiple peaks.    ...optimizing for LightCycler machines.) Multiplexing It is possible to multiplex qPCR when using fluorescent probe-based...individually run sample when developing the protocol and optimized until the multiplexed and individual ... With the right conditions and parameters, some people find it can detect even smaller differences, and... can be the more optimal choices at times. For example, chemistries that rely on hairpin design of probes...the Lightcycler while being relatively easy to multiplex (Thellwell, 2000). See Table 1 for a comparison...

... worked with people outside the department to accomplish a variety of goals. For example, I worked with...experts that complement your (scientific) skill set and is therefore very useful for complex projects. It...met interesting people at conferences and you have successfully reached out to people outside your organization...Meeting people outside your organization just to have a quick chat can be rather tricky (think people based...Addgene I work with people from various organizations in science and beyond. For example, I help organize...collaborations are becoming increasingly important as more complex approaches to scientific questions become popular...mutual benefit.  Our partnership with SnapGene, for example, allows us to display high-quality maps and annotations...

... can be completely denaturated (left) or complexes may dissociate  (right). B) Protein samples protected...protect fragile samples during cryo-EM grid plunge freezing By Rachel Leeson Cryo-EM samples can be damaged...and structure determination LEA proteins protect samples during cryo-EM grid freezing Engineered and evolved...antibodies for marking astrocytes MagIC-Cryo-EM for sample enrichment and structure determination By Mike ...for low-abundance targets or natively isolated complexes. To address these limitations, the Funabiki Lab...enrichment streamlines the purification and minimizes sample loss while also supporting imaging, making it easy...cryo-EM grid.     Figure 1: MagIC-cryo-EM for sample enrichment and structure determination. A) Schematic...

...cells or tissues contain a complex mix of proteins seen as green squares, purple circles and blue triangles... adjusted depending on the sample. It is important to remember that sample lysates will also contain proteases...capture antibody. This will deplete the nonspecific proteins from the sample prior to beginning the IP....proteins are completely removed. Wash steps should be performed even with a pre-cleared sample.  Eluting ...parallel with both a sample known to express the protein of interest, such as a sample transiently transfected...immunoglobulins, to isolate a specific protein out of a complex mix. Using this technique, users can look for the...the antibody or antibody-target protein immune complexes, wash away unbound protein, elute and measure ...