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We narrowed to 321 results for: POR C

Showing: 1 - 50 of 321 results

  1. Important Considerations in Optogenetics Behavioral Experiments

    Type
    Blog Post
    Published
    Oct. 1, 2015, 2:30 p.m.
    ...response gene c-fos. For example, using Chr2 stimulation should result in robust increases in c-fos expression...after stimulation compared to controls without Chr2. c-Fos is a reliable and widely used molecular marker...proceed with your behavioral experiments. Comparison of c-fos amongst animals that receive different types of...neuronal activation, but it may still be possible to use c-fos expression to get the evidence you need. For example...activation in the novel context as determined by reduced c-fos expression, thus showing successful inhibition... as non-human primates [7, 8], zebrafish [9], and c. elegans [10]. If used properly, optogenetics is sure...but, in today’s post, we’ll discuss some of the important considerations you should think about when developing...

  2. Supporting Rare Disease Research with BeHeard 2017

    Type
    Blog Post
    Published
    July 20, 2017, 2:30 p.m.
    ...future rare disease research funding opportunities. References 1. Jones, C., et al. "PP09. 1–2352: Systematic...disease are unclear. Dr. Di Schiavi plans on using C. elegans as a model to identify SMN1 interacting partners...effects of smn1 disruption. As part of his work in C. elegans, Dr. Di Schiavi will use Addgene plasmids...these genes, CRISPR to disrupt their function, and C. elegans overexpression plasmids to upregulate their... from rare diseases by connecting patients to important resources and promoting research for rare disease...Cancer Alliance Website.  We are proud to provide support to Drs Di Schiavi and Nabavi and will continue ...Blog Previous BeHeard Awardees Other Efforts to Support Rare Disease Research: IFOPA Donating Plasmids ...

  3. CRISPR 101: Any Base Transversion Editors

    Type
    Blog Post
    Published
    April 1, 2025, 1:15 p.m.
    ...Y (T or C), X (any base), or C, respectively. gGBE, gTBE, gCBE Glycosylase-based G, T, or C base editors...transversion editors: CGBEs, or C → G Base Editors. CGBEs first convert a cytosine (C) to uracil (U), just like... a more specific A → C base editor (ACBE), they inserted the deaminase into the C-terminal domain of Cas9...pyrimidines (C ↔ T).   Base transversion Base change from purine (A or G) to pyrimidine (C or T) or vice-versa...type of base editor invented. CGBE C → G Base Editor Converts C → G by fusing a uracil DNA glycosylase..., or C, respectively, to be replaced with another base. References Chen, L., Hong, M., Luan, C., Gao... Zhang, D., Zhang, S., Li, C., Wu, J., Randolph, P. B., Sousa, A. A., Qu, C., Zhu, Y., Guan, Y., Wang,...

  4. CRISPR 101: Cytosine Transversion Editors

    Type
    Blog Post
    Published
    March 25, 2025, 1:15 p.m.
    ...transversions C → TG → A A → GT → C C → G                   C → AG → C                   G → T A → C                   ...Rosser, S. J., Bi, C., & Zhang, X. (2021). Glycosylase base editors enable C-to-A and C-to-G base changes...deaminase could also perform cytidine (C) deamination, converting the C base to uracil (U). This is the same...given the pithier name CGBE1, for “C → G Base Editor 1,” and had a C → G editing efficiency of up to 68%...Beyond UNG: Optimizing C → G editors Now that several labs had shown that preferential C → G editing was possible...pyrimidines (C ↔ T).   Base transversion  Base changes from purine (A or G) to pyrimidine (C or T) or vice-versa...type of base editor invented. CGBE C → G Base Editor Converts C → G; also called a glycosylase base ...

  5. Open Resources and Plasmid Tools For Studying C. elegans

    Type
    Blog Post
    Published
    July 18, 2019, 12:55 p.m.
    ... 22nd International C. elegans meeting, I was again reminded of the extent that C. elegans researchers...and toolkits available at Addgene.  C. elegans open resources The C. elegans Neuronal Gene Expression Map...database specifically for C. elegans. This database provides detailed information about C. elegans 3’UTRs structures...UTRome The 3’UTRs of mRNA are important for post-transcriptional regulation in C. elegans. To study the role...The C. elegans community has always emphasized the need for open science and collaboration. The field...view the anatomy of worm layer by layer, the NeuroML C. elegans connectome, a model of the C.elegans neural...be used to simulate muscle tissue as it applies to C. elegans locomotion. To see the other resources included...

  6. An “elegans” Approach to Better CRISPR/Cas9 Editing Efficiency

    Type
    Blog Post
    Published
    Dec. 17, 2020, 1:30 p.m.
    ...for use in C. elegans. In 2017, the Korswagen lab developed Cas12a (Cpf1) for editing in C. elegans (Ebbing...editing from more sites of the C. elegans genome. Toolkits for editing in C. elegans The development of ...SapTrap-SEC kit for C. elegans genome engineering have also facilitated CRISPR editing in C. elegans. These...2018). To see more CRISPR tools for C. elegans, visit Addgene’s C. elegans CRISPR plasmids page. Future...Ruvkun for their seminal work on micro RNAs in C. elegans. The C. elegans work on small RNAs informed and drove... countless other systems, whereas import of CRISPR technology into C. elegans has been a transformative...possible in a wide range of organisms and cell lines. In C. elegans, one of the model organisms which I use to...

  7. Of Myc and Men

    Type
    Blog Post
    Published
    Jan. 19, 2023, 2:15 p.m.
    ...bound to the C-terminal peptide. One of these C-terminal antibodies was Myc1-9E10 (aka anti-c-Myc [9E10]...sequences within the middle of the human c-Myc protein or the C-terminus, Evan, et al. isolated six different...that Myc1-9E10 and the other C-terminal antibodies only recognized the human c-Myc protein and did not recognize...experiments? Why Myc? When did the commonly used anti-c-Myc [9E10] antibody come into play? We’ll dive into...This protein had a highly specific antibody to the C-terminal five amino acids, meaning the tag could be...However, substance P has an amide group added to its C-terminus post-translationally, which turned out to.... As such, the peptide could only be added to the C-terminus of proteins of interest and proteins tagged...

  8. Even more elegant: Single injection CRISPR/Cas9 in C. elegans

    Type
    Blog Post
    Published
    July 7, 2015, 3:36 p.m.
    ...genome engineering methods for C. elegans were released, signaling a new era in C. elegans research. Homology...of custom genomic modifications, is very robust in C. elegans, and the methods for HDR-mediated modification...the University of North Carolina has made CRISPR in C. elegans even easier - now, one can generate a fluorescent...-based gene tagging approach Multiple features of C. elegans have made CRISPR/Cas9 so successful in this...previously used a transgene selection strategy for their C. elegans/CRISPR experiments, but this strategy required... make it possible fluorescently label proteins in C. elegans, they inserted the SEC into a synthetic intron...system is both simple to use and highly efficient for C. elegans genome modification. Figure 2: Schematic...

  9. Viral Vectors 101: Inverted Terminal Repeats

    Type
    Blog Post
    Published
    Oct. 19, 2023, 1:15 p.m.
    ... and C-C’) that give the feature its characteristic T-shape. The arrangement of the B-B’ and C-C’ palindromic... Tian, W., Liu, C., Lian, Z., Dong, X., & Wu, X. (2017). Deletion of the B-B’ and C-C’ regions of inverted...contains three palindromic sequences (A-A’, B-B’, and C-C’ regions) and forms a T-shaped structure. The Rep... et al. 2017). For example, deleting the B-B' or C-C' arms can reduce the packaging efficiency but increase...most common variant is an 11 bp deletion in the B or C domain of one ITR. These small deletions are not usually... Conatser, L. M., Lue, V. M., Dobbins, A. L., Li, C., Hirsch, M. L., & Samulski, R. J. (2020). Adeno-Associated...AAV plasmids contain several important elements, but among the most important are the inverted terminal ...

  10. Hot Plasmids - October 2022

    Type
    Blog Post
    Published
    Oct. 6, 2022, 1:15 p.m.
    ...the C-terminal region of the human proto-oncogene c-Myc. Since the generation of the first anti-c-Myc ... on the Anti-c-Myc [9E10] page for more details. Image credit: Addgene.   Find anti-c-Myc antibody...potassium channelrhodopsins Myc-tag antibody anti-c-Myc [9E10] now available! Improved voltage indicator...and tdTomato expressed layer 2/3 neurons in mouse. C) Action potential frequencies with (magenta) and without...10.1101/2021.09.17.460684.)   Myc-tag antibody anti-c-Myc [9E10] now available! by: Ashley Waldron The majority...pulled up over 13,000 plasmids! Our recombinant anti-c-Myc [9E10] (isotype IgG2a) antibody is currently recommended...Isolation of monoclonal antibodies specific for human c-myc proto-oncogene product. Molecular and Cellular...

  11. CRISPR 101: Cytosine and Adenine Base Editors

    Type
    Blog Post
    Published
    Feb. 13, 2025, 2:15 p.m.
    ...fourth-generation base editors, BE4, reduce the undesired C→G or C→A conversions that can happen with BE3s. These...Compared to BE3, BE4 offers a 2.3 fold decrease in C→G and C→A products as well as a 2.3 fold decrease in indel... Hong, M., Zhang, D., Luan, C., Zhang, S., Wu, H., Gao, H., Bai, S., Li, C., Ding, R., Xue, N., Lei, Z... W., Levy, J. M., Yeh, W.-H., Zheng, C., Newby, G. A., Wilson, C., Bhaumik, M., Shubina-Oleinik, O., Holt...) and adenine base editors (ABEs). CBEs mediate a C to T change (or a G to A change on the opposite strand...strand). ABEs make an A to G change (or a T to C change on the opposite strand). Both are base transition...excision repair, which would change the U back to a C base. To increase base editing efficiency, Komor and...

  12. The Advances Behind The World's First Personalized CRISPR Treatment

    Type
    Blog Post
    Published
    Sept. 16, 2025, 1:15 p.m.
    ...Robinson-Garvin, N. A., Small, J. C., McCague, S., Burke, S. M., Wright, C. M., Bick, S., Indurthi, V., Sharma...technology with a fused cytidine deaminase to create C→T base edits at a target locus. A year later, an A...plagued CRISPR editing at the time. KJ was born with a C→T mutation on one allele of his CPS1 gene, which could...necessarily mean researchers can fix any problematic C or A mutations in the genome. Off-target effects, ....1126/science.1231143  Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson... R. (2017). Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature, 551(7681...Liquori, A. J., Murray, R., Packer, M. S., Rinaldi, C., Slaymaker, I. M., Yen, J., Young, L. E., & Ciaramella...

  13. Design Tips for Prime Editing

    Type
    Blog Post
    Published
    Jan. 23, 2025, 2:15 p.m.
    ... with 40–60% G/C content are most likely to be successful, although sequences with G/C content outside...of the 3′ extension of the pegRNA should not be C. A C base is speculated to base pair with G81 of the..., J., Oyler-Castrillo, P., Ravisankar, P., Ward, C. C., Levesque, S., Jing, Y., Simpson, D., Zhao, A.,...Figure 3: pegRNAs whose 3′ extension begins with a C base can cause unwanted base pairing (left), while... Koblan, L. W., Levy, J. M., Chen, P. J., Wilson, C., Newby, G. A., Raguram, A., & Liu, D. R. (2019). ... Knipping, F., Ravisankar, P., Chen, P.-F., Chen, C., Nelson, J. W., Newby, G. A., Sahin, M., Osborn, ..., Anzalone, A. V., An, M., Newby, G. A., Chen, J. C., Hsu, A., & Liu, D. R. (2022). Engineered pegRNAs...

  14. CRISPR 101: RNA Editing with Cas13

    Type
    Blog Post
    Published
    July 31, 2020, 12:30 p.m.
    ...editing toolkit to allow C to U edits using their RESCUE (RNA Editing for Specific C-to-U Exchange) system...RESCUE-S) offered ~76% on-target C-to-U editing while reducing off-target C-to-U edits by ~45% and off-target...lab published a paper on an RNA editor that allows C to U edits (RESCUE). We’ll walk through how these ...adjusted the structure of the guide RNA by introducing a C opposite the target A to be edited. This change specifies...residues that contact the RNA substrate resulted in 15% C-to-U editing activity. They then performed sixteen...cytidine deaminase activity. While RESCUE can perform C-to-U edits, the authors note that it retains its adenine... that RESCUE is most active in a 30 nt guide when C or U base-flips are present across from the target...

  15. How Dry Ice Affects Viral Vector Sample pH & How to Avoid It

    Type
    Blog Post
    Published
    June 20, 2017, 2:30 p.m.
    ...in fact, permeable to CO2 at low temperatures (-80°C) and once in the tube, the CO2 can alter the pH of...pH indicator phenol red. We froze samples in a -80°C freezer and then moved them to a closed dry ice storage...samples to controls that were only stored in a -80°C freezer and not exposed to CO2/dry ice. All samples...then tested whether returning the tubes to the -80°C freezer after storage on dry ice allowed the CO2 to... (Fig.4). To test this, we froze the tubes at -80°C and then moved them to closed storage on dry ice for...for 48 hours. We then moved the tubes back to a -80°C freezer for various recovery periods between 0 and... samples to controls that were only stored at -80°C. We then thawed the tubes after the indicated incubation...

  16. Four Base Editing Reporters to Monitor and Enrich Editing in Real-time

    Type
    Blog Post
    Published
    July 7, 2020, 1:15 p.m.
    ...expressed to identify successfully transfected cells. C-to-T editing by the APOBEC-Cas9 editosome would restore...codon that is converted to a ‘TAC’ or ‘TAT’ after a C-to-T base editing event. This edit changes the histidine... ATG codon from an ACG codon using a base-editor (C>T conversion) they could induce the translation of...Liu DR (2017) Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551:464... Figure 4: Reporters in Gene On include a mScarlet reporter, luciferase reporter, and neomycin resistance... editing. eGFP reporters for single base editing by APOBEC-Cas9 Though the ACE reporter quantifies APOBEC-Cas9...DSB in their previous reporter, the Harris Lab created a panel of eGFP reporters to quantify the on-target...

  17. Fluorescent Proteins 101: GFP Fusion Proteins - Making the Right Connection

    Type
    Blog Post
    Published
    April 9, 2019, 1:13 p.m.
    ...fluorescent protein is at the C-terminus of the POI or that the POI is at the C-terminus of the fluorescent...dimerization (Shaner et al., 2008 - supplementary figure C). However, these assays are qualitative. The Organized...structural information available, it’s clear that the C-terminus of fluorescent proteins derived from Aequorea...biosensors (yellow cameleon 3.60, EPAC, and Galphai), the C-terminus and N-terminus of the donor fluorescent protein...the FRET efficiency. Creating fusions at the N- and C- termini of your protein of interest The most straightforward...straightforward fusion protein is made by connecting the N- or C-terminus of the fluorescent protein and protein of... the sequence, people often use terminology like “C-terminal fusion,” but I find this very confusing because...

  18. SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas

    Type
    Blog Post
    Published
    May 5, 2020, 1:15 p.m.
    ... Lucia, C., Federico, P.-B., & Alejandra, G. C. (2020). An ultrasensitive, rapid, and portable coronavirus...Time: ~40 minutes Equipment required: 37°C heat block and 62°C heat block Approach: Viral RNA is extracted...range Time: ~1 hour Equipment required: 37°C water bath and 42°C water bath Approach: RNA is extracted from...Valois, E., Solley, S. C., Braig, F., Lach, R. S., Baxter, N. J., Kosik, K. S., Arias, C., Acosta-Alvear, D...incubation  Time: ~90 minutes Equipment needed: 37°C heat block, LED blue light illuminator or UV light... in a range of temperatures varying between 10-50°C. Visit Addgene's COVID-19 Plasmids and Resources ...Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan C-Y, Guevara H, Wadford DA, Chen JS, Chiu CY (2020) ...

  19. Prime Editing: Adding Precision and Flexibility to CRISPR Editing

    Type
    Blog Post
    Published
    Jan. 13, 2025, 9:49 p.m.
    ...j.cell.2021.09.018 Choi, J., Chen, W., Suiter, C. C., Lee, C., Chardon, F. M., Yang, W., Leith, A., Daza,..., J., Oyler-Castrillo, P., Ravisankar, P., Ward, C. C., Levesque, S., Jing, Y., Simpson, D., Zhao, A.,...Leukemia Virus (M-MLV) reverse transcriptase to the C-terminus of Cas9 H840A nickase (PE1). But innovations...pegRNAs (Yan et al., 2024). The team fused La to the C-terminal end of PEmax to produce PE7. PE7 significantly...expression ~ ~ ~ ~ ✓   ✓ SV40 and c-Myc nuclear localization sequences Improve translocation...References Anzalone, A. V., Gao, X. D., Podracky, C. J., Nelson, A. T., Koblan, L. W., Raguram, A., Levy... Koblan, L. W., Levy, J. M., Chen, P. J., Wilson, C., Newby, G. A., Raguram, A., & Liu, D. R. (2019). ...

  20. Bringing Sustainable Practices to the Lab: Easy Action Items

    Type
    Blog Post
    Published
    April 22, 2019, 12:26 p.m.
    ...institute. Set your -80 °C freezer to -70 °C and teach other labs to do the same. -70 °C is cold enough to keep...years. In fact, some scientists speculate the -80 °C setting might have been a marketing campaign! MIT ...biological samples that are stored long term at -70 °C. My Green Lab also has resources and even a freezer... list some easy but effective habits you can incorporate to reduce your lab consumption and increase your...in your daily habits can feel ineffective or unimportant. With so many big contributors to the sustainability...

  21. Viral Vectors 101: Systemic Capsids

    Type
    Blog Post
    Published
    Oct. 12, 2023, 1:15 p.m.
    ...Tobey, I. G., Moncada-Reid, C., Eid, F.-E., Walkey, C. J., Ljungberg, M. C., Lagor, W. R., Heaney, J. ...Ravindra Kumar, S., Adams, C. D., Yang, D., Wang, T., Wolfe, D. A., Arokiaraj, C. M., Ngo, V., Campos, L....Gong, Y., Ng, C., Nammour, J., Maiz, D., Dujardin, S., Ramirez, S. H., Hudry, E., & Maguire, C. A. (2019)... Poterba, T., Boutros, C. L., Balazs, A. B., Daneman, R., Bloom, J. M., Seed, C., & Deverman, B. E. (2019...expression control. (c) Viral delivery methods include focused ultrasound (FUS), intracorporeal (IC), intracerebroventricular...to the brain. The AAV (a) capsid, (b) cargo, and (c) delivery method determine cell type- or region-specific...Challis, R.C., Ravindra Kumar, S., Chan, K.Y., Challis, C., Beadle, K., Jang, M.J., Kim, H.M., Rajendran, P....

  22. Hot Plasmids: Fall 2024

    Type
    Blog Post
    Published
    Nov. 21, 2024, 1:30 p.m.
    ...imaging in C. elegans CRISPR/Cas9 for gene disruption in M. abscessus  Bioluminescent reporter of mechanical...tagging proteins, as it can be fused to the N- or C-terminus (or even in the middle of proteins) and performs.... E., Young, D. F., Goswami, K. K., & Russell, W. C. (1987). Isolation and characterization of monoclonal...39406745. Optimizing mScarlet tags for live imaging in C. elegans By Alyssa Neuhaus Red fluorescent proteins...maturation rate limits its use in systems like the C. elegans embryo, where developmental processes happen...recently generated new constructs specifically for C. elegans (Cao et al., 2024). The team designed coding...mScarlet3 and mScarlet-I3 that were codon-optimized for C. elegans and included artificial introns to improve...

  23. An Introduction to Adenovirus

    Type
    Blog Post
    Published
    Oct. 3, 2023, 1:15 p.m.
    ...., Pan, C. Y., Rizzo, K., Bertumen, J. B., Morales, C., Oluniyi, P. E., Nguyen, J., … Chiu, C. Y. (2023...36996871. Tatsis, N., Fitzgerald, J. C., Reyes-Sandoval, A., Harris-McCoy, K. C., Hensley, S. E., Zhou, D., Lin..., Iparraguirre, A., Lopez-Camacho, C., Wherry, E. J., & Ertl, H. C. J. (2007). Adenoviral vectors persist...Borkenhagen, L. K., Fieldhouse, J. K., Seto, D., & Gray, G. C. (2019). Are adenoviruses zoonotic? A systematic review....org/10.1016/B978-0-12-801238-3.02523-X. Hofmann, C., Löser, P., Cichon, G., Arnold, W., Both, G. W., ...toward saying that host-virus interactions are an important part of the biology of adenoviruses (AdVs). AdVs... Although host-virus interactions likely seem important for any virus, we will see that they are very ...

  24. Viral Vectors 101: AAV Serotypes and Tissue Tropism

    Type
    Blog Post
    Published
    Jan. 16, 2025, 2:15 p.m.
    ...Vitale, J., Wong, A. C. H., Gokal, D., Feng, Y., Tabar, M. S., Metierre, C., Parsania, C., Song, X., Wang,...Michael, S., Kuleshova, E., Ojala, D., Huang, C.-C., Gerfen, C. R., Schiller, J., Dudman, J. T., Hantman,...Wang, G., Su, X.-D., Bailey, C. G., & Rasko, J. E. J. (2025). An alternate receptor for adeno-associated ...https://doi.org/10.1016/j.cell.2025.06.026 Halbert, C. L., Allen, J. M., & Miller, A. D. (2001). Adeno-Associated...Peng, S., Xu, Z., Zhang, W., Qiu, Y., Wu, Y., Ye, C., Lin, K., & Xu, F. (2023). AAV11 enables efficient...Butler-Browne, G., Mouly, V., Negroni, E., & Trollet, C. (2020). Transduction Efficiency of Adeno-Associated...Ishikawa, Y., Jae, L. T., Wosen, J. E., Nagamine, C. M., Chapman, M. S., & Carette, J. E. (2016). An essential...

  25. Tips for Using FRET in Your Experiments

    Type
    Blog Post
    Published
    Nov. 5, 2014, 3:41 p.m.
    ...CyPet with C-terminal His tag SCFP3A Cyan Mammalian Express a gene of interest fused to the C-terminus...YPet with C-terminal His tag SYFP2 Yellow Mammalian Express a gene of interest fused to the C-terminus...Mammalian Express a gene of interest fused to the C-terminus of monomeric Cerulean mTurquoise2 Cyan ...Mammalian Express a gene of interest fused to the C-terminus of Amber mVenus N1 Yellow Mammalian Express...Mammalian Express a gene of interest fused to the C-terminus of monomeric Venus pCEP4YPet-MAMM Yellow...Mammalian Express a gene of interest fused to the C-terminus of LSSmOrange mRuby2 Red Mammalian Expresses... theory, is an easy technique, but it is very important to follow some simple rules to avoid common pitfalls...

  26. Reflections and Looking Ahead

    Type
    Blog Post
    Published
    Feb. 25, 2025, 2:15 p.m.
    ... D. W., Kumaran, R., Rego, M., Schofield, C., … Laflamme, C. (2024). A consensus platform for antibody... H., Laflamme, C., Houston, D. W., Polinski, N. K., Meijers, R., Levey, A. I., Saper, C. B., Errington...Ayoubi, R., Ryan, J., Gonzalez Bolivar, S., Alende, C., Ruiz Moleon, V., Fotouhi, M., Alqazzaz, M., Southern...We continue to expand our educational content supporting the tools in our collection, such as blogs describing...viral vector serotypes, or hundreds of Data Hub reports detailing antibody experimental results. We also...exactly what you need, faster. We’re also building a portal to easily share sequences and characterization ...

  27. Hot Plasmids June 2018 - Reverse transcriptase, nanobody, and protein-DNA interaction tools

    Type
    Blog Post
    Published
    June 27, 2018, 1:16 p.m.
    ...specific genomic locus: C-BERST Article contributed by Klaus Wanisch  Listen to the C-BERST podcast segment...Zhao C, et al. RNA. 2018 PubMed PMID:29109157. Nanobody toolkit to monitor retrograde transport at the...Sontheimer lab used this technology, which they call C-BERST (dCas9–APEX2 biotinylation at genomic elements...in future studies of other genomic loci. Find the C-BERST plasmids here. Gao at al. Nature Methods (... RNA templates to DNA but suffer from several important shortcomings including low processivity (ie. the...functionalized nanobodies to study retrograde transport from the cell surface. Their toolkit includes ...

  28. Save Time with Transient Plant Leaf Transformations

    Type
    Blog Post
    Published
    July 25, 2019, 12:03 p.m.
    ....   C. roseus is not a model organism such as Arabidopsis or tobacco. Studying gene function in C. roseus...De Ruijter, N. C. A., et al. "Evaluation and comparison of the GUS, LUC and GFP reporter system for gene...in tissue culture. This method is commonly used in C. roseus, but processes specific to photosynthetic ...Unver and Budak, 2009). This method works well in C. roseus. A common method for overexpressing genes ...of interest is transferred into the cells. But for C. roseus, Agrobacterium infiltration into leaves does...infiltrate. We have recently overcome this problem in C. roseus by working with young seedlings and optimizing... transformation. Choose good reporter genes There are many great reporter genes available and which one...

  29. Five Popular Model Organisms

    Type
    Blog Post
    Published
    April 11, 2019, 12:39 p.m.
    ...an ortholog in C. elegans making it ideal to study basic molecular biology processes. C. elegans are also...PMCID: PMC5525645. Mello, Craig C., et al. "Efficient gene transfer in C. elegans: extrachromosomal maintenance...lab to study neuronal development (Brenner, 1973). C. elegans are small, transparent worms that have a ...life cycle and large brood sizes. The majority of C. elegans are also self-fertile hermaphrodites making... Nobel Prize in 2006. One of  major advantages of C. elegans is that they are transparent throughout their...GCaMP6 (Nguyen et al., 2015). If you are interested in C. elegans plasmids and resources check out Addgene’...cerevisiae to human: The important gene co‑expression modules." Biomedical Reports 7.2 (2017): 153-158. PubMed...

  30. Plasmids 101: Expressing shRNAs for RNA Interference

    Type
    Blog Post
    Published
    June 17, 2025, 1:15 p.m.
    ...Carlisle, A. J., Daub, C. O., Detmar, M., Deviatiiarov, R., Fort, A., Gebhard, C., Goldowitz, D., Guhl,...Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998). Potent and specific genetic interference...10.1038/sj.emboj.7600385 McIntyre, G. J., & Fanning, G. C. (2006). Design and cloning strategies for constructing...6750-6-1 O’Brien, J., Hayder, H., Zayed, Y., & Peng, C. (2018). Overview of MicroRNA biogenesis, mechanisms....1080/15476286.2023.2288741 Taxman, D. J., Moore, C. B., Guthrie, E. H., & Huang, M. T. (2010). Short ....org/10.1007/978-1-60761-657-3_10 Vergani-Junior, C. A., Tonon-Da-Silva, G., Inan, M. D., & Mori, M. A... out of fashion but is still useful and most importantly, effective. In the research world, there is a...

  31. Three Tips for Preventing Viral Plasmid Recombination in Your Samples

    Type
    Blog Post
    Published
    Sept. 14, 2021, 1:15 p.m.
    ..., it is important to not overgrow the plasmid at 37°C. Some researchers find that using a 30°C incubation...pnas.77.8.4847 Trepotec Z, Geiger J, Plank C, Aneja MK, Rudolph C (2019) Segmented poly(A) tails significantly...https://doi.org/10.2144/000112585   Ding T, Huang C, Liang Z, Ma X, Wang N, Huo Y-X (2020) Reversed paired-gRNA...Working on the scientific support team at Addgene, I get to see everything that can go wrong with a plasmid...

  32. Viral Vectors 101: Producing Your rAAV

    Type
    Blog Post
    Published
    July 16, 2024, 1:15 p.m.
    ...S., Croft, C. L., Futch, H. S., Ryu, D., Ceballos-Diaz, C., Liu, X., Paterno, G., Mejia, C., Deng, D.,...References  Aurnhammer, C., Haase, M., Muether, N., Hausl, M., Rauschhuber, C., Huber, I., Nitschko, H...Esbin, M. N., Whitney, O., Walther, N., & Maurer, A. C. (2023). Transgene Expression in Cultured Cells Using...., Chtarto, A., Clark, K. R., Conlon, T., Darmon, C., Doria, M., Douar, A., Flotte, T. R., Francis, J....different titers are measured. A TCID50 measurement reports an infectious titer, meaning the concentration ...

  33. Easi-CRISPR: Generating Knock-In and Conditional Mouse Models

    Type
    Blog Post
    Published
    April 5, 2018, 12:42 p.m.
    ...terminal); 2xNLS (C terminal) 47327 pET-28b-Cas9-His 6xHis (C terminal); NLS (C terminal) 62933...6xHis 6xHis (C terminal); NLS (C terminal) 62934 pET-NLS-Cas9-6xHis 6xHis (C terminal); NLS ...also made targeted insertions relatively simple in C. elegans and bacteria. But CRISPRing typical mouse...the stop codon!  Figure 3: How to design a C-terminal insertion with Easi-CRISPR. Potential guide... homology arms and a selection marker, then electroporate it into mouse embryonic stem cells. After selecting...compatible with standard microinjection and electroporation methods using in mouse transgenics. Designing...between the ampulla and infundibulum. In vivo electroporation is performed immediately after injection. Image...

  34. 5 Tips for Troubleshooting Viral Transductions

    Type
    Blog Post
    Published
    Aug. 11, 2016, 2:23 p.m.
    ... standard strain, like DH5α, grown at 30 °C instead of 37 °C. If you’re unsure about the integrity of ...freshly harvested virus at 4 °C instead of storing it briefly at -80 °C. If troubleshooting, the safest...ultracentrifugation (75,000 - 225,000 g for 1.5 – 4 hours at 4 °C). After ultracentrifugation, virus may appear as a...freeze-thaw cycles on hepatitis B virus DNA and hepatitis C virus RNA quantification as measured with branched-DNA...that infect bacteria), many of which are doing important work in our microbiomes. Given that viruses are... and the type of virus, there have been varied reports of titer losses from 5% to 50% per freeze thaw ...vector: optimization of conditions for storage, transport and delivery." Japanese journal of cancer research...

  35. Hot Plasmids: Summer 2024

    Type
    Blog Post
    Published
    Aug. 27, 2024, 1:15 p.m.
    .... K., Chen, J., Pommier, G. C., Cogan, J. Z., Replogle, J. M., Adriaens, C., Ramadoss, G. N., Shi, Q.,... module (SpyTag-GFP nanobody) assembled on beads. C) Micrograph of H1.8-GFP nucleosomes collected with...Protein samples protected from AWI by helical LEAs. C-E) cryo-EM single-particle analysis of PRC2 with RvLEAMshort...glutaraldehyde crosslinking: representative micrograph (C), particle orientation distribution and Fourier-shell...tardigrades!  Find RvLEAMshort here!    Abe, K. M., & Lim, C. J. (2024). Small LEA proteins as an effective air-water...-02078-y.  Anzalone, A. V., Gao, X. D., Podracky, C. J., Nelson, A. T., Koblan, L. W., Raguram, A., Levy...Serack, F., Harvey, J. W., Brauer, P. P., Pirtle, C. P., Coffey, A., Howard, M., Kamath, N., … & Weissman...

  36. New Acoustic Reporter Genes: Ultrasound Imaging of Gene Expression

    Type
    Blog Post
    Published
    Jan. 24, 2023, 2:15 p.m.
    ...110, 073704 (2017). Hurt, R. C. et al. Genomically mined acoustic reporter genes for real-time in vivo ...visible in cells via TEM, and purified GVs under TEM. (c) Ultrasound imaging of tumor colonization by bARGSer-expressing...general method to create your own mARGAna cell line. (c) Z-projected phase contrast images of GV expressing...What are Acoustic Reporter Genes (ARGs)? Fluorescent and bioluminescent reporter genes are widely used... to study gene expression in cells. But these reporters have limited use in vivo because they are based... penetration depth as well as high spatial and temporal resolution, making it ideal for visualizing gene...expression in vivo.  But what ultrasound lacked was reporter genes that could produce ultrasound contrast. ...

  37. Developing a cold tolerant E. coli using specialized chaperones

    Type
    Blog Post
    Published
    Jan. 28, 2020, 2:35 p.m.
    ...defined between a fairly nippy 20°C to a decidedly uncomfortable 45°C). Their more adventurous cousins ...of growth, say around 37°C, is a far cry from their native conditions of ~0°C, which drastically affects... But what about placing the mesophilic hosts at 0°C? That won’t work out either - most mesophilic systems...severely cold conditions. To understand their unique importance, let’s begin with a few basics.  Mesophiles vs...understanding and appreciating their biology. The importance of psychrophilic enzymes From an industrial perspective...decided to create a hybrid system where we could incorporate cold-tolerance inducing genes within a regular...scientist from Addgene. The talk highlighted the importance of reagent repositories and the myriad facilities...

  38. Negative Can Be Positive: Open AAV Data with Addgene

    Type
    Blog Post
    Published
    Sept. 6, 2022, 1:15 p.m.
    ...into the A2 noradrenergic area of the caudal NST. (A-C) Low-magnification images showing viral spread. (D-F...Backer, M. W. A., Brans, M. A. D., Luijendijk, M. C., Garner, K. M., & Adan, R. A. H. (2010). Optimization...Gruntman, A. M., Su, L., Su, Q., Gao, G., Mueller, C., & Flotte, T. R. (2015). Stability and compatibility...data free. Nature, 5–7. O’Connor, D. M., Lutomski, C., Jarrold, M. F., Boulis, N. M., & Donsante, A. (2019...Malaker, S. A., Poweleit, N., Maynard, L. H., Adams, C. M., Leib, R. D., Cirolia, G., Thomas, D., Stamnes...doi.org/10.1016/j.ymthe.2005.02.021 Zuk, P., Sanchez, C. E., Kostick, K., Torgerson, L., Muñoz, K. A., Hsu...experiments didn’t provide any information on other important factors such as what is the best promoter to use...

  39. Hot Plasmids December 2018 - C. elegans RNAi, TurboID, Detecting Viral Outbreaks, and Protein Binding Specificity Tools

    Type
    Blog Post
    Published
    Dec. 6, 2018, 1:34 p.m.
    ...construct for C. elegans gene knockdown Article contributed by Alyssa Cecchetelli  Listen to the C. elegans...segment RNA interference (RNAi) is extensively used in C. elegans research to study gene function. RNAi is ...commonly achieved by feeding E. coli expressing dsRNA to C. elegans. These dsRNAs target specific mRNA transcripts...previously not an option, including Drosophila and C. elegans.   Find the TurboID plasmids here! Branon...producing long unspecific RNA fragments that are incorporated into the dsRNA necessary for RNAi. The Vellai...adjacent to the T7 promoters to prevent the incorporation of non-specific nucleotides into the dsRNA leading...enzyme and a small-molecule substrate to map the spatiotemporal distribution and interaction networks of specific...

  40. Degrading DNA with Cascade-Cas3

    Type
    Blog Post
    Published
    Feb. 11, 2025, 2:15 p.m.
    ..., Banh, L. M., Williams, C., Toh, M. S., Irby, M. J., Edwards, L. S., Lin, C., Owen, A. L. G., Künne, ...contains all five of these Cas proteins, while type I-C Cascades do not contain Cas6. Regardless of the subtype...Resources References Loeff, L., Brouns, S. J., & Joo, C. (2018). Repetitive DNA reeling by the Cascade-Cas3...Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular Cell, 83(5), 746-758.e5....Coons, M. M., Klompe, S. E., Lied, A. M., Smith, S. C., Vidal, B., Donohoue, P. D., Rotstein, T., Kohrs,....com.   The Cascade complex Cascade is an important component of the CRISPR Cas3 system. Most Cascade... appears to be conserved. This DNA degradation portion can be bypassed by leaving out Cas3 — a tactic ...

  41. Hot Plasmids: Winter 2025

    Type
    Blog Post
    Published
    March 11, 2025, 1:15 p.m.
    ...Park, J. C., Zhao, J., Luebbers, A., Green, E., Philibert, C. E., Zhang, H., Layne, M. D., Wu, J. C., & Garcia-Marcos...including "CLAP", combining an N-terminal CLIPf tag and a C-terminal SNAPf tag; see Figure 2), the authors developed...human stem cell-derived neurons expressing ASAP5-Kv. C) Cultured rat hippocampal neuron expressing pan-membrane...the soma. The initiation site identified in panel (C) is indicated; red line is exponential fit. Adapted...all the components of the biosensor in optimal proportions from a vector backbone that allows lentiviral...Waldron We recently added two antibodies against important targets for neurodegeneration research: Anti-MAPT...6E10-A5] in Immunohistochemistry (Human). Addgene Report, doi: https://doi.org/10.57733/addgene.6ncijt.  ...

  42. Fluorescent Tagging of Endogenous Genes with SapTrap

    Type
    Blog Post
    Published
    Oct. 12, 2017, 2:26 p.m.
    ...PCR or by evaluating visual phenotypes. Improving C. elegans fluorescent protein tagging with SapTrap ...called SapTrap to improve CRISPR genomic tagging in C. elegans. SapTrap offers scientists a convenient one...protein tagging systems For those who do not work with C. elegans, several groups have designed modular toolkits...by the Hornung Lab, allows users to easily create C-terminal tag fusions of endogenous genes in human ...plasmid containing the homology arms and an N- or C-terminal tag. The two PCR reactions are then mixed...line stably expressing Cas9. This PCR toolkit offers C- and N-terminal tagging vectors (eg GFP, Flag, YFP... mitosis, mitochondrial fission/fusion, nuclear import, and neuronal trafficking. Although FPs have enabled...

  43. Viral Vectors 101: Integrase-Deficient Lentiviral Vectors

    Type
    Blog Post
    Published
    May 13, 2025, 1:15 p.m.
    ...Gilmour, K. C., Adams, S., Thornhill, S. I., Parsley, K. L., Staal, F. J., Gale, R. E., Linch, D. C., Bayford...L., Quaye, M., Kinnon, C., Ancliff, P., Webb, D. K., Schmidt, M., von Kalle, C., Gaspar, H. B., Thrasher... PMCID: PMC7120651 Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander... Mansour, M. R., Schwarzwaelder, K., Bartholomae, C., Hubank, M., Kempski, H., Brugman, M. H., Pike-Overzet...PMC189872 Schröder, A. R., Shinn, P., Chen, H., Berry, C., Ecker, J. R., & Bushman, F. (2002). HIV-1 integration...sequences, which facilitate integration of this portion into the host genome. The packaging plasmid contains...more detailed description). Since the integrated portion does not contain any of the viral packaging genes...

  44. What's the Best Way to Elute and Store Your Plasmid DNA?

    Type
    Blog Post
    Published
    June 4, 2020, 1:22 p.m.
    ...common solution is to keep your plasmid at -20°C or even at -80°C, in this case your preparation can be eluted...periods of time, especially at room temperature or at 4°C. Storing DNA: temperature and longevity You should... stable for years. Plasmid DNA can be stable at 4°C or even room temperature for a short period, and there...preventing the activity of DNase. While this is very important to preserve the stability of your DNA, it will...

  45. Lambda Red: A Homologous Recombination-based Technique for Genetic Engineering

    Type
    Blog Post
    Published
    Dec. 15, 2016, 3:57 p.m.
    ...MMR activation.  The first way is to introduce a C/C mismatch at or within 6 base pairs of the edit site...-50% when activation of MMR is avoided Introduce C/C mismatches or silent changes in wobble codons to ...recombination genes at low temperatures (30-34˚C).  Shifting bacteria to 42˚C for 15 minutes quickly inactivates ...required for maintenance. A temperature shift to 42˚C not only allows for activation of the red genes needed...PubMed Central PMCID: PMC2790811. 5. Thomason, L. C., Sawitzke, J. A., Li, X., Costantino, N. and Court...system to modify your target DNA, you first electroporate a linear donor DNA substrate (either dsDNA or...Expression of lambda red recombination genes. Electroporation of substrate DNA and outgrowth of bacteria....

  46. Lighting Up Cell Signaling with Photoswitchable Kinases

    Type
    Blog Post
    Published
    July 25, 2017, 1:20 p.m.
    ...with C. elegans. Researchers commonly use rectal bacterial infection to induce tail swelling in C. elegans...also used a photoswitchable CDK5 in C. elegans. See figures 4B and C in Zhou et al for details on these...-ERK signaling in the hypodermis and gut cells of C. elegans causes the same phenotype. Activation of ... an ERK kinase translocation reporter with a mRuby2 fluorescent reporter (ERK KTR-mRuby2). The ERK KTR...control of kinase activity can provide greater spatiotemporal resolution than pharmacological or genetic ...everything downstream of MEK1), bypassing the upstream portion of the pathway and focusing on the downstream steps...protein of interest. If you plan to try this, it’s important to check that the function of the protein and ...

  47. Antibody Validation for Flow Cytometry

    Type
    Blog Post
    Published
    Sept. 10, 2024, 1:15 p.m.
    ...Biddle, M. S., Alende, C., Fotouhi, M., Jones, C., Ayoubi, R., Southern, K., Laflamme, C., Virk, H., NeuroSGC...T. M., Brown, C., Bandrowski, A., Virk, H., Edwards, A. M., McPherson, P., & Laflamme, C. (2023). Scaling....154034.1 Laflamme, C., McKeever, P. M., Kumar, R., Schwartz, J., Kolahdouzan, M., Chen, C. X., You, Z., Benaliouad..., H. S., Biddle, M. S., Smallwood, D. T., Weston, C. A., Castells, E., Bowman, V. W., McCarthy, J., Amrani...Biddle, M. S., Wright, A. K. A., Sousa, J., Weston, C. A., Chachi, L., Roach, K. M., & Bradding, P. (2019... monoclonal antibodies. It is also important to seek out supportive data on candidate antibodies from ...t always indicate the presence of supportive data. To be supportive, the data must show that the antigen...

  48. Plasmids for Endogenous Gene Tagging in Human Cells

    Type
    Blog Post
    Published
    April 6, 2017, 1:02 p.m.
    ...example gene targeted for tagging with GFP at the C terminus, resulting in one edited allele, or gene ... gene of interest and decide which terminus, N or C, to tag and which short amino acid linker to use. ...study the protein or structure of interest. For a C-terminal tag, as shown in the example above, we inserted...precisely where we need it, in this example, at the C-terminus of the gene of interest. To get the molecular...tagging mammalian cell lines, Drosophila cells, and C. elegans. In addition to generating fluorescent protein...lines can be found in the Cell Catalog on our data portal. The plasmids should be functional in many different...and the donor plasmid into the cells we use electroporation, a technique that briefly destabilizes the ...

  49. Experimenting in an Open Source lab: from CRISPR to Cats

    Type
    Blog Post
    Published
    July 23, 2015, 2:30 p.m.
    ...recent models of C. elegans molecular biology are based on the standard worm genome. While C. elegans are ...list of active spaces near you.   Learning about C. elegans with the OpenWorm Project One such space ...project. The main goal of OpenWorm is to simulate C. elegans as a computer model. When I first heard about...deconstruct and understand this complexity using existing C. elegans mutants. For instance, we use a mutant known... funded by someone else (KittyBiome has been incorporated as a non-profit entity and so far most of their...

  50. What's New in CRISPR - Spring 2019

    Type
    Blog Post
    Published
    March 21, 2019, 12:47 p.m.
    ... (AacCas12b) exhibits optimal DNA cleavage at 48 °C, a temperature incompatible to genome editing in human...Bacillus hisashii, BhCas12b that is functional at 37 °C but preferentially nicks the non-target DNA strand...nicking Cas9. This base editor can be used for A•T to G•C edits in protoplasts or plants of rice and wheat. ...containing these base editors Spatially and temporally regulated AAV-based genome editing In 2016, Jonathan...AAV-based genome editing system is regulated not only temporally with doxycycline, but it can also be regulated...
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