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We narrowed to 1,030 results for: URE

Showing: 421 - 440 of 1030 results

  1. Hot Plasmids - September 2019 - CRISPR, Auxin Inducible Degradation, MerMAID Channelrhodopsins, and Genome Looping

    Type
    Blog Post
    ...requires an NGG PAM to recognize the target. Osamu Nureki’s lab engineered SpCas9 (SpCas9-NG) with relaxed... with high precision - a valuable optogenetics feature when studying neuronal activity. The researchers...MerMAIDs plasmids at Addgene Opperman J et al., Nature Communications, 2019. PubMed PMID: 31346176. Using... of loops. These loops not only provide a 3-D structure for packing genomic DNA into nuclei, but are also...that heterodimerizes with CIBN upon blue light exposure (see Fig 1*). When the group targeted the enhancer...system promises to be a better model for the dynamic nature of genomic looping due to it’s briefer time scale...scale and its inducible and reversible nature. Find the LADL plasmids at Addgene Kim et al., Nat Methods...

  2. 25 Work From Home Tips for Scientists

    Type
    Blog Post
    ...difficult if your work is based in the lab. If you’re unsure what to do during this period, check out these ... Organize data that you already collected into figures for papers or presentations. Learn a new skill ...novel findings. Most Micropublications contain one figure. If you aren’t there yet, write introductions to...while. Getting started early on introductions and literature reviews could make the months leading up to your...about reproducibility best practices Support your future experiments and other researchers by implementing...Also consider using this framework to design your future experiments.  Use Addgene’s AAV Data Hub. You can...can search the AAV Data Hub for tools to use in future experiments. If you’ve used Addgene’s AAV tools...

  3. Predicting Adverse Reactions to Monoclonal Antibody Drugs

    Type
    Blog Post
    ...Using Existing in silico Algorithm Infrastructure and a Vision for Future Enhancements. Frontiers in drug...immunogenicity score (Mattei et.al., 2022).    Figure 1: Generation of immunogenicity scores by predictive...individually-specific factors, such as previous exposures to that specific antigen, pre-existing conditions...factors that in silico prediction algorithms fail to capture. In vitro evaluation of ‌therapeutic immunogenicity...various components of the immune system. Figure 2: In-vitro models for immunogenicity prediction...and the advancement of precision medicine in the future.   Madhura Acharya is a former co-op and current...

  4. How to Lead a Great Meeting

    Type
    Blog Post
    ...from last meeting. Use some positive peer pressure to make sure everyone completes their assigned items ... on details that do not yet need to be decided. Figure out what you need to accomplish to get to the next...toward a solution. At the end of the meeting, make sure to thank everyone for their participation and offer... are working on. Building this into the agenda ensures that everyone gets a chance to talk and less vocal... so will the length of your group meetings. Make sure to keep them manageable. At Addgene, teams can add...all-company meetings, monthly still works best. Figure out what works for you for each of your meeting...

  5. Plasmids 101: Sequence and Ligation Independent Cloning (SLIC)

    Type
    Blog Post
    ...have stable ssDNA secondary structure — for example, the stem-loop structure of transcriptional terminators...higher temperature at which Gibson assembly takes place may limit formation of secondary structures at the...with 5′ overhangs generated either by annealing a mixture of products or from incomplete PCR — although higher...effective with as little as 3 ng of DNA!) Figure 1: Schematic of SLIC. To start the SLIC cloning...successful, but at a lower efficiency (~20%). Figure 2: Schematic of multicomponent assembly with SLIC...

  6. Fluorescent CRISPR Reporters: SRIRACCHA and GEmCherry2

    Type
    Blog Post
    ... base-pair editing CRISPR reporters in the near future.  SRIRACCHA (stable, but reversible, integrated...reporter into the genome of mammalian cells.  Figure 1: The SRIRACCHA reporter construct. Image from... for assessing CRISPR/Cas9 activity Guide RNA structure and the site in the genome you are trying to target...Thus it is essential to identify the best sgRNA to ensure success in your CRISPR experiments. But how? There... fluorescence and in-frame fluorescence.  Figure 2: The GEmCherry reporter. Image from Højland Knudsen...FACs sorting, confirming yet again that sgRNA structure and genomic recognition sites play a large role... for editing, regulating and targeting genomes. Nature Biotechnology 32:347–355 . https://doi.org/10.1038...

  7. Antibodies 101: Isotypes

    Type
    Blog Post
    ...surface of most immature B cells, its function is unknown. It has a monomer structure with a valency of... region: IgM, IgD, IgG, IgE, and IgA.    Figure 1: Diagram of an antibody labeled with Fc, Fab,...antigen of interest. Isotype controls are used to make sure the staining you see is due to target-specific antibody...region length. Now for some essential isotype nomenclature. Antibody heavy chain proteins as well as the...cells begin by expressing IgM. IgM has a pentamer structure, which means each IgM molecule has a binding capacity... for IgM, IgD, and IgG are deleted.     Figure 2: Isotype switching requires DNA recombination...

  8. Plasmids 101: Inducible Promoters

    Type
    Blog Post
    ...synthetic) pFZ19 (yellow flame) Temperature inducible promoters Temperature sensitive expression systems ... expression at regular temperatures but can be induced by heat or cold exposure. Examples include the ...Types of inducible promoters Chemical agents, temperature, and light are all examples of factors that can...which a gene of choice is only expressed following exposure to a brief heat shock. In the case of Hsp70, the...since expression can be repressed by glucose. Temperature inducible promoters are also known for their ...

  9. Targeted Mutagenesis with EvolvR

    Type
    Blog Post
    ...PACE) method requires constant turbidity of the culture, so bacteria must be grown in a turbidostat. ...activity degrades the displaced strand.   Figure 1: EvolvR consists of an error-prone polymerase...by 120-fold over background. Due to its modular nature, the Dueber Lab created a few versions of EvolvR... more than one genomic site for mutagenesis, a feature which they used to generate bacteria resistant ...at a user-defined loci in bacteria. Its modular nature provides versatility in defining the mutational...diversification of all nucleotides in a tunable window." Nature 560.7717 (2018): 248. PubMed PMID: 30069054. Sadanand..., Saheli. "EvolvR-ing to targeted mutagenesis." Nature biotechnology 36.9 (2018): 819. Additional resources...

  10. Important Considerations When Using AAVs

    Type
    Blog Post
    ...University of Manitoba. Location, Location, Location! Failure to Plan (for Storage) Is Planning to Fail Patience...Patience Is Bitter but Its Fruit Is Sweet The Future? I knew little about adeno-associated Viral Vectors...sufficient to overcome the transport issues. 2. Failure to plan (for storage) Is planning to fail Freeze...not take much time at all. Much of the previous literature using AAVs for DREADD delivery indicates ~7-21...to use AAV constructs with self-complementing structure (scAAV) (7). As single stranded DNA viruses, AAVs...from ~4.8 kB [8] to ~2.3 kB [9]).     4. The Future What new types of research may be enabled by the...experiments, a group of researchers has identified this feature of AAVs as a new tool for neuroanatomical tracing...

  11. A Practical Guide to Optimizing AAV DIO and FLEx Vector Expression

    Type
    Blog Post
    ...sandwiched between 2 loxp sites and is excised by Cre (Figure 1). This results in one loxp site and one lox2272...Since loxp and lox2272 can not recombine, this ensures that the transgene is no longer able to flip back...the cause of this spurious expression?   Figure 1.  Cre-recombinase binds to either pair of lox...orientation preventing the transgene from reverting. Figure created with BioRender.com   Causes of recombination...to flank the transgenes (non-homologous pairs) (Figure 2.). They found that almost all off-target expression... to exercise caution when using them.    Figure 2. Schematic diagram showing the mechanism of spontaneous...reduced reversion and less off-target expression. Figure created with BioRender.com   Strategies for...

  12. CRISPR 101: Cas9 vs. The Other Cas(s)

    Type
    Blog Post
    ...engineering enzymes, each with their own unique features and quirks. Here, we will review the genome engineering.... Dozens of variants exist with unique cutting features and evolved PAM sites, making Cas9 an adaptable...PAM does not require any G’s or C’s. One curious feature of this Cas is that once it is engaged by its target...target, it will non-specifically cut ssDNA. This feature is shared by other Cas enzymes outlined below as... proteins should not be overlooked. The unique features and targeting abilities of the other Cas family...Janice, et. al. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science, 362(6416): 839-...with the single-protein CRISPR effector Cas7-11. Nature, 597, 720-725 (2021). 10.1038/s41586-021-03886-...

  13. Announcing the Winners of the 2021 Michael Davidson and Roger Tsien Commemorative Conference Awards

    Type
    Blog Post
    ...Glutamate sensing reporters Abhi Aggarwal is a postbaccalaureate research technician in Kaspar Podgorski’s ...expression and trafficking of these biosensors.   Figure 1: Schematic of iGluSnFR3 (left). GluSnFR3 in pMinDisplay... domain), in electroporated in rat hippocampal cultured neurons, imaged 14 days post-transfection, excited...happen inside the cell,” says Pedre Pérez. Figure 2: Micrographs of the biosensor expressed in the...from opioid use disorder,” says Hubbard. Figure 3: 20x confocal image of the periaqueductal gray...response to light touch in mechanical allodynia. Figure 4: While Qiu’s work on the PV neurons is in progress...calcium, and membrane voltage,” says Tian. Figure 5: Citrine-tagged voltage indicator expressed in...

  14. Hot Plasmids - March 2020 - base editors, GEVI, MoClo, and optogenetics

    Type
    Blog Post
    ... a native peptide bond at the split site. Figure 1: The base editor is split into two plasmids and...the split base editors at Addgene. Levy et al., Nature Biomedical Engineering, 2020. PubMed PMID: 31937940...in higher quenching of mScarlet emission. Figure 2: Ace-mScarlet is a fusion between the voltage-sensitive...synthetic biology tools for cyanobacteria. Figure 3: Assembly of plasmids using the Cyanogate Kit...reducing Cre toxicity in long-term experiments.  Figure 4: The C-terminus of Cre (CreC) and the N-terminus...(PCB), is required for PhyBΔ to be functional. Exposure to red light induces PhyBΔ and PIF6APB binding...This novel tool is practical in cell and organ culture, as well as cell lineage studies. Eisenhoffer and...

  15. Gendered Innovations: Why Does Sex of the Cell Matter?

    Type
    Blog Post
    ...the analysis did find 263,000 more osteoporotic fractures. The overall economic savings to the US healthcare... Unfortunately, it also meant that, by the very nature of the way the experiments were performed, they...and cell research. Using cells from both sexes ensures that the diagnostics and therapeutic interventions...recent years, and you can see a summary of this literature in our health and medicine checklist. A common...not analyzed) may harm humans or contribute to failures in drug development – costs far greater than those...doing the research correctly from the get go. The future of sex and gender in research There is much work...Blog Learn How Scientists Are Trying to Shape the Future of Research Learn How Notions of Scientific Impact...

  16. Plasmids 101: Modular Cloning Applications and Kits

    Type
    Blog Post
    ...individual parts are reusable, saving time and money on future assemblies. If you are new to MoClo, give our MoClo...synthesis of these molecules. To make large amounts of pure product in an affordable way, researchers test many...your yeast experimental goals are more general in nature, or you aren’t planning on using K. phaffii, then...proteins within the mitochondrial matrix.     Figure 1: A chart with MoClo kit recommendations for different...2023). The Plant Parts II kit has a focus on infrastructure with shuttle vectors, several delivery systems...targets or multiple sgRNAs against the same target to ensure efficient cutting. Beyond sgRNAs, MoClo can also...convolute the results of these experiments. The modular nature of the Fragmid system allows for direct comparisons...

  17. A Primer on Optogenetics: Introduction and Opsin Delivery

    Type
    Blog Post
    ...Behavioral experimentation I’ll discuss some of the key features of each of these steps. Today we’ll discuss selection...relies on identification of the bregma and lambda sutures and subsequent determination of the proper coordinates... your brain region of interest (as shown in the figure below). Since most of the precision of optogenetics...circuits underlying brain disease in animal models. Nature reviews Neuroscience. 2012;13(4):251-66. doi: 10.1038...of neuroscience. 2011;34:389-412. doi: 10.1146/annurev-neuro-061010-113817. PMID: 21692661.  3. Bernstein...direct comparative analysis of microbial opsins. Nature methods. 2012;9(2):159-72. doi: 10.1038/nmeth.1808...mice for light-induced activation and silencing. Nature neuroscience. 2012;15(5):793-802. doi: 10.1038/...

  18. Plasmids 101: The Wide World of Natural Plasmids

    Type
    Blog Post
    ...we’re really borrowing these tools from Mother Nature’s toolbox. Natural plasmids, also called environmental...the basis of many molecular biology tools! Figure 1: Common functions of natural plasmids. Created... to survive where others can’t. This ability to endure a harsh environment is distinct from the benefit...new types of plasmids without clear analogues in nature. For example, helper plasmids were developed to... To learn more about some other common plasmid features, such as origins of replication and promoters,... blog as scientists continue to explore Mother Nature’s toolbox for new and exciting molecular technologies...Resources References Demanèche, S., Bertolla, F., Buret, F., Nalin, R., Sailland, A., Auriol, P., Vogel,...

  19. Making CRISPR Plasmids Using Fragmid

    Type
    Blog Post
    ...Did you say… easier? Fragmid’s modular assembly structure takes a lot of the design work out of the plasmid...Fragmid components on the Fragmid website.   Figure 1: (Top) Schematic overview and timeline of the...schematized. Sizes of fragments are not to scale. Figure and caption from McGee et al., 2024, used under...designing a CRISPR vector the Fragmid way!    Figure 1: Selecting your vector type on the Fragmid website...website.   In step one, you’ll select the features of your vector, which are: Organism (Mammalian...mechanism (KO, CRISPRa, CRISPRi, editing)   Figure 2: Selecting module fragments on the Fragmid website...want? You can make your own Fragmid components! Ensure your backbone and genes contain only the Bbsl cut...

  20. Adenoviral Vector Production and Troubleshooting

    Type
    Blog Post
    ...(ITR) present at both ends.   Figure 1: A) The structure of an adenovirus: the virion is ~ 100nm...genomes/mL) can be measured by: Optical density: particle concentration is measured by looking at absorbance... construct from step #1 and allowed to stay in culture for up to 20 additional days at which time the ...recombinant adenoviruses using the AdEasy system." Nature protocols 2.5 (2007): 1236. PubMed PMID: 17546019...production of high-capacity adenoviral vectors." Nature protocols 4.4 (2009): 547. PubMed PMID: 19373227...
Showing: 421 - 440 of 1030 results