...JS, Legube G, Miller KM Genes Dev. 2015 Jan 15;29(2):197-211. DNA Cross-Bridging Shapes a Single Nucleus...Single Nucleus from a Set of Mitotic Chromosomes. Samwer M, Schneider MWG, Hoefler R, Schmalhorst PS, Jude...Nucleus from a Set of Mitotic Chromosomes. Samwer M, Schneider MWG, Hoefler R, Schmalhorst PS, Jude JG, Zuber...

..., but at a lower efficiency (~20%). Figure 2: Schematic of multicomponent assembly with SLIC. Multiple...allows both insert and vector to be digested in the same tube. Alternatively, SLIC can also work directly...using multiple fragments that share homology in the same reaction. In these cases, the use of another cloning...

...with abundance whenever possible.      Fig 2: Try to inversely pair fluorophore strength with protein... the antibodies time-sensitive, using precious samples, or being compared to other data in a manner that...signaling molecule, that all need to be detected in the same assay. This is one of the most complex subjects ...

... would release them into the cytosol. Fig. 2: Endogenous sources of duplexed RNA DNA:RNA hybrids...systems can lead to local dsRNA production. In the same vein, genotoxic stress, such as chemotherapy treatment...dsRNA finds its way outside of the mitochondria, the same inflammatory response can activate. These types ...

...interferon gamma (IFNγ) - and eliminate cancer cells. 2. Equilibrium - In a process analogous to the development... 35. Academic Press, 2015. PubMed PMID: 25818339. 2. Curiel, Tyler J., et al. "Specific recruitment of...multiple immunotherapy targets can be utilized at the same time. A combination of tolerance marker blockade...

...take care when using this method.      Fig 2:  A, The polyhistidine tag is a string of histidine...metal ions are immobilized on a bead or resin and a sample containing the protein of interest flowed through...interest and the metal ions.      Fig. 1: A sample containing a polyhistidine tagged protein of interest...tags are also recommended if you need a very pure sample. Because binding strength is proportional to the...

...protocols 4.4 (2009): 495-505. PubMed PMID: 19300443. 2. Geraerts, Martine, et al. "Comparison of lentiviral...titers measure the amount of viral particles in a sample and are usually based on the presence of a viral...however, is that a p24 ELISA measures all p24 in the sample regardless of whether or not it is incorporated...lentiviral prep may be significantly higher than the same prep that has been stored in the freezer. If you...

.... Find Plasmids from the publication at Addgene 2. Green, Alexander A., et al. "Toehold switches: de-novo-designed...high and above what would be expected in patient samples (e.g.: blood, urine). Adapting toehold switches...pathogen’s genome as unique barcodes to identify samples containing the virus. Of the 48 sensors, targeting... diagnostic results.  Our approach now detects samples at clinically relevant concentrations (1-3 fM; ... look at viral load in patient blood and urine samples; we showed that we can detect the virus directly...Interview with Previous Collin's Lab Member and Sample 6 Cofounder Michael Koeris Learn How Minigenomes...

...Reports 9: https://doi.org/10.1038/s41598-019-41088-2 Magnus C, Lee P, Bonaventura J, Zemla R, Gomez J, ... results (Goutaudier et al., 2019). Using PSAMs PSAMs PSAMs, or pharmacologically selective actuator modules...interactions and still set off the same pathways, giving rise to the same cellular responses. The cellular...working with PSAM receptors, your impact on the cell is determined by what IPD your PSAM is combined with... will promote hyperpolarization. PSAM ligands The advantage of PSAMs lies in their ability to be specifically...manipulate. It is important to consider that the same receptor can elicit different responses depending...currently used in chemogenetics are DREADDs and PSAMs. Using DREADDs DREADDs DREADDS, or designer receptors...

...beginning Let’s take a quick flash back to 2004. “Shrek 2” was the most popular movie in theaters, the Razr ...Because we have a resource like Addgene to all get the same virus.” — Grad student visiting Addgene’s booth ...quality reagents, and we realized we could use the same principles to provide recombinant antibodies, another...

... enrich the microvesicles containing AAVs (Figure 2). Since the development of the exo-AAV isolation protocol... have a higher transduction efficiency, i.e. the same number of AAV particles is able to infect more cells...

... 293HEK Inhibits termination step of translation 2-10 ug/mL G418/Geneticin neo HeLa, NIH3T3, CHO, 293HEK... for cells that have taken up the plasmid in the same way. Selection methods, described below, are typically...

...contain the expected plasmid features.  Figure 2. Addgene’s basic QC process. Created with BioRender.com...ensure the entire team is using the same rubric and making the same decisions when analyzing the wide variety... that is provided, each deposit goes through the same QC process to ensure all plasmids pass our high-...

...improve the brightness of previous Nano-lanterns by 2-4 fold and permit five-color fluorescent imaging! ...external light source. Therefore, especially thick samples may not be appropriate for use with Nano-lantern...

...aspects of the work you presented may also be unclear. 2. Make the audience your primary focus When writing...suggests a change to a slide, think about whether the same principle applies to other slides in your deck.  ...

...to visualize multiprotein complexes.  Fig. 2. Multiplex immunolabeling with subclass-switched recombinant...detect multiple targets with different mAbs in the same experiment. The Trimmer Lab found that they could...

...promising monoclonal antibody with high specificity. (2) Narrow down the specific epitope that your antibody...between endogenous and exogenous versions of the same target. In the 1980s, Munro and Pelham set out to... ideal.  Unexpected connections Right around the same time that Munro and Pelham were devising their tagging...from this year.  But are we all really using the same antibody developed almost 40 years ago? Well…kinda...distributing monoclonal antibodies derived from the same hybridoma developed by Evans, et al. In other cases...

...al (Nature. 1988 Jul 28;334(6180):320-5.) PubMed. 2. A segment of the 5' nontranslated region of encephalomyocarditis...simultaneously express two or more separate proteins from the same mRNA. We've discussed promoters before so in this...expressing your gene as they are both derived from the same transcript. Of course multicistronic vectors do ...anytime you want to express multiple genes in the same cell. Although it is possible to drive co-expression...expression cassettes, having the genes expressed from the same cassette is sometimes advantageous, particularly...produce equimolar levels of mulitple genes from the same mRNA. The term "self-cleaving" is not entirely accurate...successfully utilized 2A and IRES elements within the same multicistronic vector, effectively making a construct...

...rate of 10-55% - the PASTE system.     Fig. 2: Schematic of programmable gene insertion with PASTE...lab often tests samples of new bacteria from anywhere they can find, whether the samples are from a rain...was safe to say the sample had their attention! They isolated DNA from the sample, amplified the CRISPR...range of mammalian cell lines. However, in those same comparisons, the AbuGoot lab reported no detectable...thousands of different mutations, all found in the same gene. If we only have small, directed editing abilities...

...divided by the off-target activity. Figure 2: Specificity is the measure of off-target activity...NGG, NGAN, NGNG, NGAG, and NGCG). Since then, the Osamu Nureki Lab described a rationally engineered Cas9...

...Era of Personalized Medicine. Genes Dis. 2017 Jun;4(2):43-63. DOI: 10.1016/j.gendis.2017.04.001 Maetzig...low immunogenicity, meaning it does not induce the same high immune response as retroviruses. This virus...

...PubMed PMID: 8491198. PubMed Central PMCID: PMC413431. 2. Bukrinsky MI, et al. “Active nuclear import of human...designed to make you sick…well, you feel it. But the same features that make these familiar viruses such a...

... high-priced commercial devices.     Fig. 2: Workflow for open software (left) vs. open hardware...very difficult to adapt the device to one's own samples and limits the use of microscopy in open science...

...and are considered “high copy”. A fragment from the 2 micron circle (a natural yeast plasmid) allows for...modify proteins yet they still share many of the same technical advantages that come with working with...

...PMID: 20543841. PubMed Central PMCID: PMC2920597. 2. Nathans, Daniel. "Puromycin inhibition of protein... suspected to interact, are added to a cellular sample. Both antibodies have a short antibody specific...

...don’t use the same overhang twice; (2) avoid palindromes; (3) no overhangs with the same three nucleotides...in a row; (4) no more than two nucleotides in the same position; (5) avoid overhangs with either 0% or ...71% (Pryor et al., 2020). And in 2022, using the same tools, they successfully assembled a 40 kb T7 phage...

...GUS-staining is a very useful visual reporter (Figure 2). The GUS enzyme cleaves a substrate, which will then...thanks to our guest blogger Samuel Mortensen from Northeastern University. Samuel Mortensen is a PhD candidate...This post was contributed by Samuel Mortensen, a PhD candidate at Northeastern University. Working with...19457242. PubMed Central PMCID: PMC2693113. Mortensen, Samuel, et al. "EASI transformation: An efficient transient...

... 2008 Dec; 18(6): 617–623. Pubmed PMID 19349161.  2. Deshpande A, Bergami M, Ghanem A, Conzelmann KK, ...necessary and sufficient for retrograde transmission (Etessami et al., 2000, Wickersham et al., 2007). Thus, ...Mar 19;110(12):E1152-61 Pubmed PMID 23487772. 3. Etessami R, Conzelmann KK, Fadai-Ghotbi B, Natelson B, ...

...work. Nobody wins, and you need to make a change. #2 Thou shalt sometimes put work ahead of life Sometimes...whatever works for you, but most days go home at the same time. Use time management tools and tactics to plan...need to match up exactly when you fold them. The same with sheets – wash them and put them right back ...family by forming a social circle of people in the same situation. Go to church, join a club, meet the neighbors...

...PMID: 24901218. PubMed Central PMCID: PMC4047077. 2. Pagliara, Patrizia, et al. "Ostreopsis cf. ovata ... this purpose.Learn about the effects of CO2 on sample pH Cell morphology: Shape and size matter You should...contaminated.Learn how Addgene uses barcodes to track samples Keep track of passage numbers Keep an eye on the...

...) 12 (>100) xCas9(3.7)-ABE 69 (1.4) 43 (2) 21 (3) Not examined 16 (>100) Average percent...mammalian cells, finding xCas9 3.7 displayed about the same editing rate as SpCas9 at an NGG PAM. When they ...Adenine base editor xCas9 3.7-ABE also follows the same pattern, with improved editing at an NGG PAM (69...

...PMID: 25538079. PubMed Central PMCID: PMC4353587. 2. Stephen, Andrew G., et al. "Dragging ras back in ...brake pedal that does not work. Both cases yield the same result – uncontrolled movement of the vehicle or...transcript most commonly found across all TCGA tumor samples is represented, making the results of any such ...

... the Cas machinery where to cut.      Fig. 2: Heatmap indicating loci where SNPs reside on sgRNA...sequences of guides across 8 CRISPR libraries. Samples are divided into those of African ancestry(orange... on these and any other CRISPR screens using the same reference genomes and libraries. Further complicating...

... replication competent virus [usually HIV-1]; and 2) the potential for oncogenesis through insertional...often: Q1: Are retroviruses and lentiviruses the same thing? Can I package lentivirus with retroviral ...both lentiviruses and gamma-retroviruses use the same genes for packaging (that's gag, pol, and env), ...

...this year. Designing the donor plasmid Figure 2: Donor plasmid design strategy. A donor plasmid contains... For an N-terminally tagged protein, we used the same strategy, inserting the tag and the linker preceding...

...strain (which will be covered in more detail in part 2 of this blog series) controls the cell types in which...repair is a random process, zygotes edited using the same nuclease may not result in genetically identical...

...replicate, then purify the DNA.     Figure 2: A pooled library page with protocols boxed in red...plasmids, all of which need to be represented in the same proportion after amplification as they were prior...visualization) that confirm diversity of the library sample, and any other information or scripts provided ...

...Hoogsten base pairs and wobble pairs.  Figure 2: (A) The codon wheel depicts the 64 codons that encodes...amino acids and three stop codons, meaning that the same amino acid can be encoded by more than one codon...organisms. There are several codons that encode the same amino acid. Each organism, however, may preferentially...

...Henrietta Lacks. New York: Crown Publishers, 2010. 2. Gold, Michael. "A conspiracy of cells." State University...materials available from commercial repositories and the same cell line from a colleague?”. The main difference...) profiling can be used to ID the cell line. The same test is so good that it is used as a forensic technique...

...run as long as the protocol remains the same.    Figure 2: Microscopy-based antibody experiments... replicates are repeated measurements of the same sample and are included to assess variability in the... the tau western blot several times with the same samples and compare the results across runs. If the ... 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...interactions between the sample and the secondary antibody. C, a label control treats the sample to the full protocol...interpretation of results. A positive control is generally a sample or group that will have a desired response. For...

...C-terminus of human codon-optimized  cryptochrome 2 (CRY2) from Arabidopsis thaliana. When exposed to ...living biosensor for measuring caffeine content in samples. The Barrick lab and the UT Austin undergraduate...

...more tips on using social media as a scientist here. 2) Public engagement - Participate in science festivals...requires lots of data. Get your community involved in sampling or bioinformatics analysis or upload your data...

...systems to defend against both DNA and RNA viruses - 2 cas systems regulate at the DNA level and 1 at the...from my talk below). Largely organized by Dmitry Samarsky, and a very welcoming team from China’s Ribobio...

...backbone, which expresses the gRNA from a Drosophila U6:2 promoter and Cas9 from the actin 5C promoter. Addgene...backbones for lentivirus LV 1-5 and retrovirus RV 2-5 were constructed. The authors then used GMAP assembly...engineering (MAGE) (1). MAGE uses recombineering (2) to simultaneously incorporate multiple single-strand...number of tandemly expressed gRNAs respectively) and 2) the size of the deletion. Smaller deletions generally...population within a given tissue rather than a mixed sample. TRIBE was developed in Drosophila, and further...

... Werner S, Marillonnet S. PLoS One. 2011 Feb 18;6(2):e16765. doi: 10.1371/journal.pone.0016765. PubMed... with a knockout and expression construct on the same piece of DNA. We do a lot of protein-protein interaction...

...Nature 339 (1989). 487–488. PubMed PMID: 2725683. 2. Miller, C.J., Kassem H.S., Pepper S.D., Hey Y., Ward.... Know your target cells Labs tend to follow the same general procedure for lentiviral infections, produce...but also between different lots of serum from the same source. Labs that routinely produce lentivirus may...

...  Figure 2: Examples of simultaneous multiplex IF labeling of rat brain samples from the James ...presence of several biomarkers together in the same tissue sample predicts a certain cancer and want to look...you will need to start with a fixed sample. Depending on the sample type, this might be frozen or formalin-fixed...al, 2022 for a sample protocol.)  Simultaneous IF Depending on your needs, your sample, and targets, you...known to be abundant in your samples (with a primary antibody that has the same species and isotype as the...set of samples where you label only one target in each. Compare these individually-labeled samples with ...referred to as immunocytochemistry (ICC) when the sample is cultured cells or immunohistochemistry (IHC)...

...of 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO), a fluorophore modified from DsRed. DFHO...orange fluorescent aptamers Corn was described in the same study as Red Broccoli and Orange Broccoli, two more...PMC5679246. Strack, Rita L., Matthew D. Disney, and Samie R. Jaffrey. "A superfolding Spinach2 reveals the...

..., can protect cryo-EM samples from damage (Abe & Lim, 2024).    Figure 2: A) When proteins (blue...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 ...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...beads for scarce macromolecules in heterogeneous samples. bioRxiv 2024.01.21.576499; doi: https://doi.org...

...start selecting and testing systemic capsids! Figure 2 contains a decision tree for selecting a capsid, while... highlighted below the table.     Figure 2: This decision tree can help guide your choice on ...transfer to the adult brain. Nature Biotechnology, 34(2), 204–209. https://doi.org/10.1038/nbt.3440 Goertsen...function like your average AAVs — and have many of the same restrictions, like limited cargo space (~4.7 kb)...systems, which use two or more AAVs to transduce the same cell, can accommodate larger, modular genetic payloads...efficient AAV-PHP.eB, developed and deposited by the same lab. AAV-PHP.eB is the most commonly requested systemic...off-target organs. AAV.CAP-B22 was developed through the same process as AAV.CAP-B10 and shows high transduction...