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...involved “plates,” and our scientists and lab technicians always knew from context what a “plate” was. Our...these plates now” to a fellow team member. But, at Addgene, we use seven different types of “plates” (Fig...barcode for your plate, you will get in trouble if you don’t qualify what kind of “plate” you mean. Without...to know what kind of plate they were talking about during the meetings. And “plate” certainly wasn’t the...our engineers (Fig. 2). Creating this guide was relatively easy. I took a picture of virtually every container...information Prescribing an official name to all of our plates, tubes, and racks meant we had fewer errors in ...important documentation, including SOPs or project-related documents, we define new and potentially ambiguous...

...proteins that promote RNA decay and their upregulation is correlated with poor survival in breast cancer patients.... BirA* requires 16-18 hours to sufficiently biotinylate interacting proteins, which results in poor spatiotemporal...interactions with RaPID RaPID is similar to the BioID platform for identifying protein-protein interactions, ...promiscuous E. coli biotin ligase, BirA*, to biotinylate proteins that are within ~10 nm of the bait, ... also tweaked BirA* to increase its rate of biotinylation. The improved enzyme, called BASU, is derived...one to study RNAs expressed from their native regulatory elements. Controls for RaPID experiments RaPID...Affinity Purification (CRAPome), to identify highly biotinylated background proteins reported by other research...

...engineering projects in a very big way. In one of his latest papers, published in Molecular Systems Biology ...CRISPR/Cas genetic circuits are linked to the regulatory networks within E. coli host cells. ...in building genetic circuits is getting enough regulatory proteins that don’t interfere with each other...programmable that you can make a very large number of regulators. That basically means larger genetic circuits...that could conceivably be as large as natural regulatory networks. Addgene: What kinds of things could... pattern, shape. All of that is controlled by regulatory networks in the plant. If we want to access that...biology can do - it’s good to be able to build regulation thats as sophisticated as a natural network. ...

...protein’s post-translational modifications such as phosphorylation, acetylation, methylation and ubiquitination...proteins are being up- or downregulated in a system, detect post-translational modifications, quantify ...quantify protein levels relative to standards, detect the cellular location of proteins, and can be a readout...submerged in a tank filled with a transfer buffer formulated to conduct the electric current. The wet transfer...thickness of the band provides information about the relative abundance of the protein in the sample. More protein...immunosorbent assay (ELISA) (Aydin et al., 2015). Post-translational modifications In addition to protein abundance...ubiquitination. For example, to test if a protein is phosphorylated following a specific experimental condition...

...colonies on the backbone alone plate and many colonies on the backbone + insert plate (or at least more colonies...backbone alone plate). Unsuccessful ligations will usually result in few colonies on both plates (unsuccessful...), in a vector alone plate with many more colonies than the vector + insert plate (unsuccessful 2), or... each plate (unsuccessful 3).     If you have a high number of colonies on your backbone plate (greater... Follow the manufacturer’s instructions.   2. Isolate Your Insert and Vector by Gel Purification     ...throw the digestion mixtures together. You need to isolate your insert and backbone from the enzymes used ...base pairs for each varies, it is difficult to calculate this based on DNA concentration alone. One method...

...Elements Translation in eukaryotes usually begins at the 5’ cap so that only a single translation event ...plasmid is packaged for viral delivery, or the relative expression levels between two or more genes is...single-stranded RNA viruses to allow for the efficient translation of multiple genes from a single transcript. The...Entry Site (IRES) to allow for initiation of translation from an internal region of the mRNA. In the ...discovered in poliovirus RNA, where it promotes translation of the viral genome in eukaryotic cells.1,2 Since...they all have in common is the ability to spark translation initiation independent of the 5’ cap.  IRES elements...bicistronic expression; however, many could be easily manipulated to express more than two genes. Plasmid Name...

... via acetylation or demethylation. Casilio DNA Methylation Editing (Casilio-ME) is a methylation editing...human pluripotent stem cells CRISPR-based DNA demethylation Optogenetic repressors of gene expression ...50–90% of average on-target DNA-editing levels relative to BE4max.  Read the paper in Nature Biotechnology...Michael Laub’s lab developed a CRISPRi system to downregulate expression of specific Caulobacter genes using...ctrA, a gene encoding an essential cell cycle regulator. The lab expressed both dCas9 and the ctrA sgRNA... demonstrated the system can also be used to downregulate multiple genes at once. Read the paper in mBio...Find the plasmids Enhanced CRISPR-based DNA demethylation Figure 2: The components of Casilio-ME1...

... resistance genes so that you can specifically isolate bacteria containing your constructs of interest...bacteria as a way to produce more of the plasmid, isolate individual plasmids, or express a gene contained...goal of your experiment — to grow, express, or isolate plasmids. The presence of an antibiotic resistance...shaking at 37 degrees) can be shortened since the plated cells will have time to produce beta-lactamase ...to produce satellite colonies when used on agar plates due to the fact that beta-lactamase is excreted...Cons: Prone to satellite colony formation on agar plates, less stable at high temperatures and in acidic... and is less susceptible to degradation in agar plates. This prevents satellite colonies from forming ...

...highlighted below. Preparing template: Pick a single colony with a sterile flat toothpick or pipette tip ... clones for later culture: At this point, you will want to hang onto your clones for later use. There ..., just streak the colonies on an LB plate. You can use this plate to start liquid cultures. Lastly, you...polymerase) using the supernatant of lysed bacteria as template; and 3) run your PCR product on a gel to analyze... to preparing a standard PCR reaction: combine template, primers, polymerase, and dNTPs and then incubate...released from the bacteria in order to serve as PCR template. Dealing with this and a few other colony PCR ...background colonies on your no ligation control plate. The more background, the more colonies you will...

... vs. the factor that is being experimentally manipulated. Below are several core factors of statistics...t-tests Samples that come from the same subject or population - before and after a treatment, for example -.... Samples arising from different subjects or populations (a treatment group vs. a control group), on the...analysis, must be performed. These will be discussed later. One and two-way ANOVAs ANOVA tests can compare...Quantifying and controlling for any covariance between manipulated independent variables allows for a more accurate...how independent variables you are not directly manipulating affect an outcome (age, demographic, diet, etc...to know every pairwise comparison within your population? Sometimes this can’t be avoided, but if it can...

...furimazine. Right: Demonstration of PILATeS. Cell adhesion to a PILATeS-functionalized coverslip creates ...reversible, making PILATeS suitable for live imaging with a time resolution of minutes.  Find PILATeS plasmids ... F., Goswami, K. K., & Russell, W. C. (1987). Isolation and characterization of monoclonal antibodies ...antigenic differences between human, canine and simian isolates. J Gen Virol., 68 (Pt 11), 2769–2780. https://... happen within a few hours. In order to use the latest mScarlet tags, mScarlet3 and mScarlet-I3, Oliver...for CRISPR/Cas9 in M. abscessus here! Neo D, Clatworthy A, and Hung, D. (2024). A dual-plasmid CRISPR...Bioluminescent reporting of mechanical forces with PILATeS By Emily P. Bentley Time to get flexible! Alex ...

... learned, and ask questions later – maybe even the next day. In the latter case, you can say “I usually...planning you can do to build a bench mentor-mentee relationship and bring your best self to the training experience...plenty of articles on building successful mentor relationships, asking for mentor support, and choosing your...the research group). The bench mentor-mentee relationship is extremely important – without a good set ...mentor than your scientific mentor. Thus, this relationship will probably define your experience in the ...Luckily, you can do a lot to contribute to the relationship dynamic and set yourself up for success! Getting...ll probably forget and end up asking your mentor later if you don’t write it down. And don’t be afraid ...

...chemiluminescence, precipitate the protein out of solution, or isolate cells expressing this protein. Read on to learn...antibodies against the injected protein. Several weeks later, blood from the animal is drawn and the antibodies... hand, monoclonal antibodies are a homogenous population of antibodies that all recognize the same epitope...dilution, which produces an immortalized, clonal population of cells that produce a single variant of antibody...antibodies, recombinant antibodies are a homogeneous population. However, unlike monoclonal antibodies, which.... Western blots are frequently used to compare relative levels of protein expression between cell types... present. The reaction takes place in a 96-well plate, where primary and secondary antibodies are used...

...biologist tool box” for its common use in plasmid manipulation and genetics research. Plasmids are ideal tools...studying genetic modification for their ease of manipulation and their ability to be replicated. Because ...processes naturally found in E. coli have been manipulated for use in molecular biology studies. For example...BSL-1 status, E. coli can be used as a model to relate these processes in more pathogenic bacteria (Blount...rat, is another popular model organism. A close relative to the mouse, both are great mammalian models ...limiting attributes of rats is their difficult to manipulate genome and limited genetic data. To bridge this...biological processes and signaling pathways that regulate regeneration and wound healing are conserved across...

... overall inflation of USD has gone up 19.8% in the same time period. For ease of calculations*, let’s ...well (or 384-well) plate! How much do repositories help?   Designing precise calculations for any of the ...Debate of ’18, Blue Flame depositor John Doench calculated the time to make a plasmid. Doench’s lab in the...long does it take in total? While much harder to calculate, in both our 2018 and 2023 poll, most people said...much does it cost to make a plasmid? Doench also calculated the cost of consumable reagents used to make ...2018 numbers, and the intervening five years, inflation has occurred. Here at Addgene, the consumables...s split the difference and put scientific inflation at… roughly 34.9%, which means that the same plasmid...

...immunogen, then isolating and purifying the antibodies produced from its serum several weeks later. Created ...as KLH or Freund’s adjuvant is injected, which stimulates the overall immune response. Once the initial... antibody response starts to wane about a month later, the animal is given additional booster immunizations...contains the antibodies - is further processed to isolate the antibodies. Most commonly, antibodies of the...the IgG isotype are used for research purposes. Isolating polyclonal antibodies from the serum There are...are a few different ways the antibodies can be isolated from the serum. Protein A/G purification Protein...different type of purification can be performed to isolate antibodies only recognizing your protein of interest...

...reporter lines for more sophisticated experimental manipulations, saving the time and money needed to develop...control gene expression, he could then selectively manipulate only GFP-labeled cells. Once Tang and Cepko found...but specific system. T-DDOGs also successfully regulated expression of channelrhodopsin-2, commonly used...for optogenetics experiments in specific cell populations. Listen to Our Podcast Interview with Connie ...-DOGs The T-DDOG results showed that GFP could regulate transcription in a cell-type specific manner, ...Cepko were eager to see if they could apply GFP regulation to other types of proteins. They started with...system may make optogenetics in specific cell populations even easier. Advantages and other possibilities...

...specific genes involved. Downregulation of tumor suppressors and upregulation of proto-oncogenes ­­­can...while simultaneously stimulating growth and division. The combined effect is unregulated proliferation. Another...cases arise and millions of people die from cancer-related complications each year. Despite these grim statistics...cells still need to successfully infiltrate the circulatory or lymph systems to spread, or metastasize. Many...Many cancerous cells will die trying, as the circulatory and lymph systems are not ideal environments ...Ras researchers, one of the most exciting and relatively new resources is the RAS Pathway Clone Collection...set of vectors for use with the Gateway Cloning Platform (Life Technologies, Carlsbad, CA) that represents...

...knock-out. The goal of a knock-out is to disrupt DNA translation by generating a frameshift mutation. The majority...like to introduce the edit. Finally, you must stipulate what sequence to introduce, which is done through... will guide the cell to use the donor DNA as a template for repair, which will result in the incorporation... knock-in! So how does the donor get used as a template for repair? Read on to find out! Homology-directed...is recommended you check your cell lines for HR-related mutations before attempting knock-ins by HDR. ...basis of the HDR pathway relies on repair from a template molecule, which is usually an endogenously available...and uses the ends of the ssDNA to find a repair template. The highest HDR efficiency is observed when inserts...

...enzyme specifically cuts methylated DNA, so it will selectively destroy the template, but not newly synthesized...-55 °C for the homologous region (calculated using Oligo Calculator). Insertions - To insert short sequences...confirm primer design.  Use minimal template DNA Use 1 ng of PCR template DNA to minimize false positive colonies...for example for subcloning genes from different templates. All PCRs are run as an 18 cycle, 25 μl single-tube...Primers consist of two regions: the 3’ end binds template DNA for PCR amplification, while modifications...sequences are encoded at the 5’ end. First design the template binding region, with a melting temperature (Tm... bp, such as epitope tags, design primers with template binding regions to amplify away from the insertion...