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We narrowed to 1,025 results for: URE

Showing: 421 - 450 of 1025 results

  1. 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...

  2. 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 ...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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-...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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/...

  14. 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,...

  15. 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...

  16. Quickest Way to Deposit Plasmids: The Deposit Spreadsheet

    Type
    Blog Post
    ...office or other authorized office directly to make sure the deposit agreement/MTA is taken care of and, ...Deposit” and “Download Deposit Spreadsheet” (see Figure 1). Please read our “How to Deposit Your Plasmids...thorough guide to our online data entry process. Figure 1: Begin the deposit process by clicking “Submit...Required columns are shown in red in the spreadsheet (Figure 2) and are described in Table 1. Some cells have...Growth Temp Choose from 30 °C, 37 °C, or room temperature. Growth Strain Please indicate which growth...Filling out and sending the deposit spreadsheet Figure 2: Example of the deposit spreadsheet showing the...update the spreadsheet every so often and this ensures you are using our most up-to-date version! We hope...

  17. Pathways Over Time Plasmids Engage Students in Functional Genomics Research

    Type
    Blog Post
    ...Met protein complementation. In the procedure diagrammed in Figure 3, students first transform the S. ...available (6). Methionine synthesis in S. cerevisiae (Figure 1) occurs through a well-characterized pathway ... the deletion). Find the Plasmids Here Plasmid features enable multiple student experiments We used TOPO...coding sequences for ten different MET/Met genes (Figure 1) from the two yeast species into the pYES2.1/... controlled by the GAL1 promoter. The cloning procedure adds both V5 and His6 epitope tags to the C-termini...expression by western blotting in other experiments (Figure 2).   Complementation reveals conservation of function...

  18. 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...

  19. CRISPR in the Clinic

    Type
    Blog Post
    ...focus was on editing animal models of disease and cultured cells. For example, in 2013, Jinsong Li and colleagues...When all was said and done, the researchers had cured 24 mice of their disease. Meanwhile, Hans Clevers...significant progress in clinical trials.     Figure 1: Types of delivery and editing strategies for...success rate in clearing misfolded protein levels as measured in the blood. More information is expected soon...blindness, and diabetes. Directions and obstacles for future CRISPR therapies CRISPR technology is rapidly evolving...strides since we first wrote this blog post. The future success of CRISPR in the clinical will rely on ...MA, Berkhout B, Herrera-Carrillo E. A CRISPR-Cas Cure for HIV/AIDS. Int J Mol Sci. 2023 Jan 13;24(2):1563...

  20. The AAVantages of AAV in CRISPR Screens

    Type
    Blog Post
    ...sequencing (NGS) to identify genes of interest. Figure 1: Overview of in vitro AAV CRISPR screens. Created... capsids, or serotypes, have been identified in nature, while many more have been engineered in labs. ...improve infection rates in your experiment. Figure 2: Visual representation of common AAV serotypes...smaller Cas9 ortholog like SaCas9. You could even venture away from the comfort of Cas9, and opt for a completely...design and execution of CRISPR in vivo screens. Nature Protocols, 17(9), 1903–1925. https://doi.org/10.1038...vector integration into CRISPR-induced DNA breaks. Nature Communications, 10(1). https://doi.org/10.1038/... linkage analysis with in vivo AAV-Perturb-seq. Nature, 622(7982), 367–375. https://doi.org/10.1038/s41586...

  21. xCas9: Engineering a CRISPR Variant with PAM Flexibility

    Type
    Blog Post
    ...compatibility and high DNA specificity." Nature (2018) doi: 10.1038/nature26155 PubMed PMID: 29512652 Plasmids...loci or genomes. Cas9s from other species, like S. aureus and N. meningitidis require different PAM sites...first restored catalytic residues D10 and H840. To ensure that the clones were capable of cleavage, they ...fused to third generation cytidine base editor architecture (BE3) slightly improves NGG PAM editing efficiency...efficiencies (edit frequency in cell population measured with NGS) are shown as percentages, with fold ...lot we still don’t know about xCas9. “I’m not 100% sure xCas9 is going to be flat out better than SpCas9...

  22. Adenoviral Delivery of CRISPR/Cas9 Aims to Expand Genome Editing to Primary Cells

    Type
    Blog Post
    ...the CRISPR/Cas9 system. Nature 516:423–427 . https://doi.org/10.1038/nature13902 Maggio I, Holkers M, Liu... the target cells (Beatty et al., 2012). These features make AdV an attractive candidate for in vivo delivery...genome editing machinery such as CRISPR-Cas. Figure 1: Schematic of targeted gene knock-out (left) ...Gonçalves' lab found in a second paper published in Nature Methods the same year that delivering RNA-guided...double-stranded AdV genomes. Such protein-DNA structures presumably reduce the likelihood that donor DNA... that advantages of AdVs include their episomal nature and very efficient introduction of DNA into therapeutically...

  23. Viral Vectors 101: Voltage Indicators

    Type
    Blog Post
    ...electrical potential. Thankfully, there is a tool to measure these electrical events! Voltage indicators are...They can be targeted to the plasma membrane to measure membrane potential and can also be directed to ...applications such as in vivo tissue imaging.   Figure 1: Ace-mScarlet is a fusion between the voltage-sensitive...depending on your experimental system.   Figure 2: General overview of chemigenetic tools. A genetically...vitro and a small molecule is added exogenously to measure a phenotypic response in the form of fluorescence...Indicators As previously mentioned, cellular voltage is measured at the cell membrane, and this voltage is particularly...has you covered. Happy voltage sensing!   Figure 3: Components of the types of voltage indicators...

  24. Anatomy of a Plasmid Page at Addgene

    Type
    Blog Post
    ... to quickly check out the plasmid's structural features and see if I can easily clone my gene into it?...plasmid map based off of the plasmid sequence and feature information given by our depositors. Many depositors...plasmids are sent as bacterial stabs at room temperature. Core of the plasmid page - Core of the plasmid...), antibiotic resistance, and optimal growth temperature are listed, as well as the name of the strain... Citing this Plasmid: This is a relatively new feature of our plasmid pages, and provides a list of publications...our blog post) for more information about this feature!).  This means you can see which labs have already...the Addgene Blog Read about Our New Citations Feature Check out Our Walkthrough of the Deposit Process...

  25. CRISPR 101: Mammalian Expression Systems and Delivery Methods

    Type
    Blog Post
    ...exclusively to in vitro cell culture. The user should review the current literature about their preferred model...single-stranded DNA oligonucleotide, so you will need to make sure your expression system and delivery methods are ...system, a good first step would be to consult the literature to see if anyone has published a protocol that...in in vitro transcription reactions to generate mature Cas9 mRNA and gRNA. RNA is delivered to target ...different methods, so we've summarized some key features of common  delivery methods below: Chemical transfection...Resources on the Addgene Blog Check out our CRISPR Featured Topic Page Learn about CRISPR Delivery Using Ribonucleoproteins...

  26. Genome-wide Screening Using CRISPR

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    Blog Post
    .... Figure 1: Like this jar of jellybeans, a pooled CRISPR library is a complex mixture. Pooled libraries...experimental system are absolutely necessary to ensure that you select the correct CRISPR library. Choosing...concentration that is sufficient to generate lentivirus. Be sure to use next-generation sequencing to check the quality...cells gain resistance to drugs and can identify future therapeutic targets for diseases causing uncontrolled...uncontrolled cell growth, such as cancer. Figure 2: The CRISPR library must be amplified (A) to be ...the screen should be independently validated to ensure that the desired modification produces the phenotype...

  27. An Introduction to Adenovirus

    Type
    Blog Post
    ...causing a lack of exposure, a lack of immunity, and then finally a synchronized exposure under these conditions...conditions once the measures were lifted (Servellita et al., 2023).  This anecdote goes toward saying that...certain contexts (Bauzon et al., 2003).        Figure 1: The adenovirus life cycle. Image reused from...31749409. Harrach, B. (2014). Adenoviruses: General Features. In Reference Module in Biomedical Sciences. Elsevier... Undergoing Spontaneous Degeneration in Tissue Culture. Proc Soc Exp Biol Med. 84(3), 570–573. https:/...type 2 in US children with acute severe hepatitis. Nature, 617(7961), 574–580. https://doi.org/10.1038/s41586...

  28. Don’t FRET: Bimolecular Fluorescence Complementation Makes Visualizing Protein-Protein Interactions Easy

    Type
    Blog Post
    ...re tethered to bring them into close proximity (Figure 1). Formation of the complete FP results in a fluorescent...can be detected by fluorescence microscopy. Figure 1: How BiFC works. A split FP (e.g., yellow fluorescent...localization of the studied PIPs. The straightforward nature of BiFC also makes it easier to generate a large...fragments and, preferably, some information about the structures of the tested PIPs. Many split FPs have been ...BiFC experiments only require that you image and measure the fluorescence of a single FP. Your control construct...one another — which means it cannot be used to measure the dissociation of PIPs. Thus, whereas BiFC is...fluorescence complementation (BiFC): A 5-year update and future perspectives. Biotech 53. https://doi.org/10.2144...

  29. Fluorescent Proteins 101: Green Fluorescent Protein (GFP)

    Type
    Blog Post
    ...center of the structure, shielded from quenching by aqueous solvent. This tightly-packed structure explains...Fluorescent Protein (GFP) has likely existed in creatures such as jellyfish for millions of years; however...while still maintaining fluorescence. The protein structure, first reported in 1996, is an eleven β-sheet-...yield for BFP Y145A and H148D Stabilizes the structure of Cerulean derivatives F99S, M153T, V163A Improves...Optogenetics: Scientists can use light to detect, measure, and control molecular signals, cells, and groups...This is a type of flow cytometry that separates mixtures of cells into distinct populations based on fluorescent...

  30. Podcast: A Malawian Professor's Path to Biotech Research

    Type
    Blog Post
    ...Kwapata now works as a lecturer in molecular genetics and biotechnology for Horticulture and Forest Crops at... at the Lilongwe University of Agriculture and Natural Resources. He recently received an award from nonprofit...Kingdom ended up working in the life sciences and agriculture 5:47-9:35 : Kingdom's biotechnology research ...transition back to Malawi and Lilongwe University of Agriculture and Natural Resources 10:30-11:41 : Kingdom on...Seeding Lab's Work with Lilongwe Univeristy of Agriculture and Natural Resources Watch Dr. Kwapata's Speech...
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