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We narrowed to 587 results for: des.1

Showing: 141 - 160 of 587 results

  1. Plasmids 101: Modular Cloning

    Type
    Blog Post
    Published
    March 12, 2024, 1:15 p.m.
    .... Level 1: Assembly of multiple Level 0 parts into TUs. Level 2: Assembly of multiple Level 1 TUs into...: promoter, gene, and terminator.     Fig 1. MoClo enables individual parts to be assembled into... peptide can easily be tested by generating Level 1 TUs with unique promoters, and the ideal phosphatase...cloning, or MoClo, is a systematic cloning strategy designed by synthetic biologists to perform large scale...specifically refers to the organizational schema described above, and not any particular cloning technique...example of an individual part, this category also includes promoters, UTRs, terminators, etc. Once selected...behave in a cell. For unpredictable cases, MoClo provides two answers: first, sets of parts with characterized...

  2. Viral Vectors 101: Parts of the AAV Packaging Plasmid

    Type
    Blog Post
    Published
    Dec. 3, 2020, 2:15 p.m.
    ... The three VP proteins assemble into capsid at a 1:1:10 ratio (VP1:VP2:VP3). There are eleven naturally...closer look at the rep and cap genes. Figure 1. The RepCap plasmid and its products. Created with...plasmid The packaging plasmid aka the RepCap plasmid encodes two genes: the replication (rep) gene and the capsid....com   Replication (rep) gene The rep gene encodes four proteins that are required for viral genome...cross-packaging.  Capsid (cap) gene The cap gene encodes three AAV viral capsid proteins VP1, VP2, and VP3...type tropism. Introducing changes and/or short peptides sequences into these variable loops is one method...method for changing a capsid’s tropism.  cap also encodes the Assembly-Activating Protein (AAP) and the recently...

  3. Cancer and the Immune System: Deciphering the Relationship

    Type
    Blog Post
    Published
    March 14, 2017, 2:30 p.m.
    ...such as IL-8, IFNγ, and colony stimulating factor 1 (CSF-1). Additionally, tumor cells recruit regulatory...introduced the “Three Es of Immunoediting” nomenclature. 1. Eliminate - Latent tumors are recognized by effector...the tumor, activates hypoxia inducing factor (HIF-1), which promotes the production of VEGF to increase...This study used CRISPR gene editing to knockout PD-1 on immune cells harvested from patients and thereby...exploring new avenues in healthcare.   References 1. Vinay, Dass S., et al. "Immune evasion in cancer:...lymphoblastic leukaemia in children and young adults: a phase 1 dose-escalation trial." The Lancet 385.9967 (2015)... recognition are a few methods by which tumors sidestep immune surveillance: Suppressing Function Antigen...

  4. Plasmids 101: Broad Host Range Plasmids

    Type
    Blog Post
    Published
    April 11, 2024, 1:15 p.m.
    ...Table 1 has a detailed list of the bacterial species these plasmids are compatible with.  Table 1: Non-...reduced metabolic load (Meyer 2009). Figure 1: Idealized examples of a narrow host range plasmid...for DNA cloning in Gram-negative bacteria. Gene, 70(1), 191–197. https://doi.org/10.1016/0378-1119(88)90117... N.J.), 765, 327–343. https://doi.org/10.1007/978-1-61779-197-0_19  Meyer, R. (2009). Replication and ... meliloti, Rhodobacter sphaeroides, R. capsulatus, Rhodopseudomonas spheroides, Salmonella spp., Serratia...Brevibacterium methylicum, Caulobacter crescentus, Desulfovibrio vulgaris, Erwinia carotovora, E. chrysanthemi...meliloti, R. leguminosarum by. viciae, Rhodobacter sphaeroides, Salmonella typhimurium, Vibrio cholerae, Xanthomonas...

  5. Three Key Considerations for Precise Neuronal Targeting Using AAV Technologies

    Type
    Blog Post
    Published
    Nov. 27, 2019, 2:03 p.m.
    ...main takeaways from the paper for designing experiments with AAV: 1. Getting your viral vector into your... administration routes for neuroscience see Table 1 from the paper. 2. Manipulate your cell of interest...information from a region. In the example shown in Figure 1, injected retrograde AAVs at one location result in...AAV from our viral service can share experimental design and data. With these different approaches to open...

  6. Plasmids 101: Knockout/Knock-In Plasmids

    Type
    Blog Post
    Published
    Dec. 1, 2016, 3:30 p.m.
    ... the example shown in Figure 1, large sequences corresponding to exons 1 and 3 of the targeted gene have...through an experiment designed to knock out exon 2 of a given gene.   Figure 1: A knockout targeting... the Neomycin resistance (NeoR) gene between exon 1 and 3 of the targeted gene. Upon recombination, the...often use the Cre/Lox system described earlier. In this case, you design your targeting vector such that...replacing it or disrupting it with an piece of DNA designed in the lab. Specially constructed plasmids can...template with the endogenous gene. Here, we'll describe the techniques and the plasmids used to inactivate...inactivate specific genes in mammalian cells. Despite the popularity of CRISPR-based knockout/knock-in systems...

  7. Finding and Joining Your Dream Lab

    Type
    Blog Post
    Published
    April 8, 2014, 2:50 p.m.
    ...choosing direction of a project. If you expect more 1:1 time with the advisor, you should choose accordingly...potential hire visits the lab for a full day, gives a 1 hour talk about his or her interests, and spends one-on-one...that supports both paths – you won't know in year 1 what you will want in year 6. Have lab alumni taken... a Good Mentor for Scientists". This post also includes a useful list of questions for a candidate to ...

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

    Type
    Blog Post
    Published
    Jan. 24, 2023, 2:15 p.m.
    ...under a wide range of inducer concentrations (0.1-1% L-arabinose) without signs of toxicity or burden ...bacteria have colonized (Fig. 1c).     Fig. 1: Expressing bARGSer in E. coli. (a) Plasmid diagram...ultrasound contrast. In all the cell lines we tested, 1 µg/mL doxycycline was sufficient to saturate expression...engineering a cell line, cotransfect the mARG cassettes 2:1 (A:N-V) with PiggyBac transposase and outgrow the ... tumors and tumor-homing bacteria. Nat Biotechnol 1–13 (2023) doi:10.1038/s41587-022-01581-y  ...to distinguish from background tissue unless destructive ultrasound imaging was used. We set out to develop...acoustic properties of these gas vesicles made non-destructive specific imaging in tissue difficult. The first-generation...

  9. RNA Interference in Plant Biology: New Tools for an Old Favorite

    Type
    Blog Post
    Published
    Oct. 27, 2020, 1:15 p.m.
    ...applications. Figure 1: Schematic of an RNAi-inducing transgene. Typically, the desired target of RNAi is...dsRNA via an RNase III enzyme named Dicer (Figure 1). The plant kingdom has expanded its repertoire of...in the biogenesis of different small RNAs (Figure 1). These siRNAs can exert their gene silencing effect...modifications of complementary gene sequences (Figure 1). As a result, gene silencing can be easily induced...complementary to your gene target as inverted repeats (Figure 1). With this technique, multiple genes can be simultaneously...selection of plants undergoing RNAi, and LIIbeta F 1-2 RNAi, which allows assembly of intron-spliced hpRNAs...eukaryotic process where approximately 20-30 nucleotides of double-stranded RNA (dsRNA) results in downregulation...

  10. Antibodies 101: Antibody Engineering and Directed Evolution

    Type
    Blog Post
    Published
    Aug. 5, 2025, 1:15 p.m.
    ...versatility of the basic antibody structure (Figure 1). Antibodies can be broken up into smaller parts, ...antibodies for a specific purpose. Figure 1: Overview of antibody engineering methods. (A) Basic...,"rgb":"rgb(0, 82, 169)","rgba":"rgba(0, 82, 169, 1)"},"button_font":{"size":19,"styles":{"font-family...:"rgb(255, 255, 255)","rgba":"rgba(255, 255, 255, 1)"}}{% endraw %}{% end_module_attribute %}{% module_attribute...Molecular Biology, 29–62. https://doi.org/10.1007/978-1-0716-2285-8_2 McMahon, C., Baier, A. S., Pascolutti...by PCR. Current Protocols in Molecular Biology, 51(1). https://doi.org/10.1002/0471142727.mb0803s51 Additional... antibody sequences, degenerate primers can be designed to selectively mutate specific regions of your...

  11. Plasmids 101: Using Transposons in the Lab

    Type
    Blog Post
    Published
    July 6, 2021, 1:28 p.m.
    ...Transposons: The jumping genes. Nature Education 1(1):204. https://www.nature.com/scitable/topicpage/transposons-the-jumping-genes...poly(A). ORF2 encodes endonuclease and reverse transcriptase activities.    Figure 1: Overview of...cholerae that encodes a Type I-F CRISPR-Cas system. This system has four major components: 1) a CRISPR RNA... They transpose by a ‘copy-paste’ mechanism (Fig. 1). They first copy themselves as RNA transcripts and...their host’s genome.   There are two types of Class 1 TEs: those with long terminal repeats (LTRs) and those... sequence that moves around. This DNA sequence encodes the proteins the transposon needs for transposition...contain two genes: gag and pol. The pol polyprotein encodes the reverse transcriptase and integrase enzymes...

  12. Educational Planarian Tools for Teaching Developmental Biology Techniques

    Type
    Blog Post
    Published
    May 24, 2018, 1:20 p.m.
    ...experiments. A recent publication [1] from the Sánchez lab describes the plasmids and protocols required...available through the deposit) are described in the Sánchez lab publication [1] so that the students performing...can easily investigate in planarians. References 1. Alice Accorsi, Monique M. Williams, Eric J. Ross,...Proceedings of the National Academy of Sciences 100.suppl 1 (2003): 11861-11865. PubMed PMID: 12917490. PubMed...companion resource called “cutting class” which provides more detailed materials and protocol resources...synthetically made RNA (riboprobes) with modified nucleotides (for example, Digoxigenin-labelled Uracil) that... molecular cloning to insert the cDNA into the desired plasmid backbone. The Sánchez lab plasmids allow...

  13. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    Published
    June 4, 2024, 1:15 p.m.
    ...2017). Within an interior cavity, Cas9 grips nucleotides 1-10 of the guide RNA, prearranged for base pairing... basic parts of the Cas9 enzyme.   Figure 1: A cartoon depiction of Cas9’s two major lobes, REC...the CRISPR system (Nishimasu et al., 2014). Table 1. Summary of Cas9 domains, the lobe each domain belongs...state (PDB ID 4CMP) with domains colored as in Figure 1. HNH, red; RuvC, orange; CTD, yellow; REC lobe, light... on itself at the bottom of the image. Stem loops 1 and 2 extend horizontally across both lobes. The guide...outside of the protein, spanning both lobes. Stem loop 1, nestled between the REC and CTD domains, is required...343–347. https://doi.org/10.1038/s41586-022-04470-1 Cofsky, J. C., Soczek, K. M., Knott, G. J., Nogales...

  14. Fluorescent Proteins 101: Photoactivatable Fluorescent Proteins

    Type
    Blog Post
    Published
    April 25, 2017, 2:30 p.m.
    ...discovered such as Kaede and PS-CFP2 (see Table 1). Table 1: Properties of Selected Irreversible Photoactivatable...preserve cellular structures (0.5-1% osmium tetroxide). These conditions destroy most PA-FPs, but, in 2015, ...) by mutating Threonine 203 to Histidine (T203H) (1). wtGFP normally contains a mixed population of neutral...in fluorescence when illuminated with blue light (1). Similar to PA-GFP, scientists later developed red...with extraordinary molecular detail.   References 1.Patterson, George H., and Jennifer Lippincott-Schwartz...is believing." Annu. Rev. Biomed. Eng. 10 (2008): 1-38. PubMed PMID:18647110. Additional Resources on ...to green). For example, mEosFP (named after the goddess of dawn in Greek mythology) switches from green...

  15. Fluorescent Proteins 101: Introduction to FRET

    Type
    Blog Post
    Published
    June 27, 2017, 1:03 p.m.
    ...acceptor fluorophore. The typical steps in FRET are: 1. Donor fluorophore excitation by absorption of a photon... overlap, the fluorophores must be located within 1-10nm of each other and be oriented appropriately for... from various papers to make the decision easier. 1. Müller, Sara M., et al. "Quantification of Förster...diseases and even assist in drug discovery. References 1. Baird, Geoffrey S., et al. "Circular permutation ...Resonance Energy Transfer (FRET) was originally described by Theodor Förster in 1948 as a variation of the... observed light emission by fluorescence. The widespread use of FRET with fluorescent molecules, including...FRET probe, try searching PubMed for articles describing the FRET tool that you are looking for and check...

  16. Multiplexed Capture of Promoter-enhancer 3D Chromatin Structures Using CRISPR

    Type
    Blog Post
    Published
    July 2, 2020, 12:40 p.m.
    ...by PCR or next-generation sequencing. Figure 1: Overview of the key steps of the CAPTURE method. ...ligases Expression system Stable cell line expressing 1) FLAG-biotin-tagged dCas9, 2) BirA, and 3) one or ...or more gRNAs Two separate lentiviruses delivering 1) a BioTAP-tagged dCas9 and an eGFP tag, and 2) gRNAs...(s) Cell lines Cell lines, primary cells Table 1: Key differences between original CAPTURE and CAPTURE...The Xu lab presented three ways to use CAPTURE 2.0: 1. Multiplex capture of chromatin interactions The Xu...Variant for Your Next Experiment Learn More About Designing gRNAs Against Your Favorite CREs Here Additional...

  17. Magnetic Control of Proteins: More than a Dream

    Type
    Blog Post
    Published
    Sept. 24, 2024, 1:15 p.m.
    ...the sample (by less than 1%) and recovered after the magnet was removed (Figure 1). At first, Andrew and...since the initial report in 2023.)     Figure 1: Fluorescence intensity of EGFP-FlavinTag in E. coli...that could be expressed and purified. Although a ~1% change in signal might not make a very powerful tool...Hayward et al. 2024 under CC-BY license.   Video 1: Fluorescence movie of E. coli expressing MagLOV while...Maria were encouraged by previous reports that described magnetic responses of cryptochrome proteins or...

  18. Generating Mouse Models Using CRISPR/Cas9

    Type
    Blog Post
    Published
    July 12, 2016, 2:30 p.m.
    ...Sullender M, Ebert BL, Xavier RJ, Root DE (2014) Rational design of highly active sgRNAs for CRISPR-Cas9...Last updated on Oct 1, 2020 by Aliyah Weinstein. This post was contributed by guest bloggers, Wenning...process check out our Mouse Modeling blog posts: Part 1: Genetically Engineered Mice and Part 2: Breeding ...LO, Morgan JL, Juan WC, Roca X, Ong ST, Bergstrom DE (2018) Viable Mice with Extensive Gene Humanization... mouse genome is made up of 3 x 109 nucleotides (nt), and encodes 23,000 or so genes. It would be great...guide you in gRNA design. We have been using Benchling, but there are many other gRNA design tools available...for cells that had successfully incorporated the desired mutation, and then derive mice from these engineered...

  19. Antibodies 101: Affinity Tags

    Type
    Blog Post
    Published
    Sept. 19, 2023, 1 p.m.
    ...118). Humana Press. https://doi.org/10.1385/1-59259-301-1:99 Resources on Addgene.org Addgene antibodies...antibody detection is desired… and yes, we have an antibody for that!   Fig. 1 - Diagram of His-tagged...You’ve designed the perfect experiment – controls, conditions, and everything in between – now all you...This is where affinity tags come in – they are peptides which do not naturally exist in most expression...protein for downstream applications Below, we describe a few of the most common tags available. Maltose...antibody is an alternative to amylose resin and also provides a visual detection mechanism via applications ...

  20. RUBY-Red Siliques

    Type
    Blog Post
    Published
    March 1, 2022, 2:15 p.m.
    ...collected from heterozygous individuals. Only 1/4 of the descendants of the heterozygous plants, therefore, ...in all other plants, anthocyanins.   Figure 1: An adult plant expressing RUBY. Photos by Andrew ... (2020). https://doi.org/10.1038/s41438-020-00390-1 Additional resources on the Addgene blog  CRISPR 101... Antibiotic selection would only then kill the desired plants! PCR or fluorescent markers are currently... have similar drawbacks, often requiring the destruction of plants or tissue for GUS staining or are not...from these plants will be green, containing the desired mutation but lacking both RUBY and the construct...compared to other markers lends itself well to nondestructive selection. If RUBY was integrated into a CRISPR...
Showing: 141 - 160 of 587 results