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Showing: 21 - 40 of 993 results

  1. QC Sequencing Technologies at Addgene

    Type
    Blog Post
    ...software such as SPAdes, Shovill, apc, and NOVOPlasty. The pipeline contains three de novo assemblers,...manually checks and assembles the raw data.  Addgene’s de novo assembly pipeline usually generates the correct...raw FASTQ reads are used for either guided or new de novo assembly. If a full anticipated sequence is ... doesn’t resolve the assembly issues, we can redo de novo assembly within Geneious.  While this may seem...steps that gave us our initial incorrect assembly, de novo assembly within Geneious gives us additional...

  2. Bricking Science: Portraying Scientific Reality Through LEGO

    Type
    Blog Post
    ...thanks to our guest blogger, Dalila Cunha de Oliveira. Dalila Cunha de Oliveira is a PhD student in Hematology...post was contributed by guest blogger, Dalila Cunha de Oliveira. Bricking Science is an idea built, literally...with my husband, I thought about how the limitless design possibilities of the LEGOs were mirrored by the...made, colorful laboratory. When we started, the hardest part of the process was to embed personality in...

  3. Early Career Researcher Toolbox: Free Tools for Science Writing

    Type
    Blog Post
    ...suggestions, like alternative word suggestions. De-jargonizer The De-jargonizer can identify jargon in your writing...This paper talks more about the development of the De-jargonizer.   Academic Phrasebank  The Academic Phrasebank... of the suggestions Hemmngway makes (it wasn’t designed for technical writing), it’s great at flagging... Just enter the DOI of a paper and select your desired formatting style. This tool is great for generating...library in Microsoft Word. Mendeley has a web and desktop version that works with Windows, Mac, and Linux...easier to work with collaborators. Zotero is a desktop based program that’s compatible with Mac, Windows...

  4. A History of Genome Engineering in Popular Culture

    Type
    Blog Post
    ... Mendel. Comptes Rendus de l’Académie des Sciences - Series III - Sciences de la Vie 323:1053–1060 . https...Mendelian genetics was being revived by the botanist Hugo de Vries (1896).  In 1928, Frederick Griffith used mouse...//doi.org/10.1038/nature17946 Lenay C (2000) Hugo De Vries: from the theory of intracellular pangenesis...domain (FokI). Zinc finger nucleases were first designed in 2005. The DNA-binding domain can be engineered...triplets, the components recognize individual nucleotides. This imparts TALENs more specificity and a broader...editors, new amino acid recognition sites had to be designed each time we wanted to target new genomic sites...chasing an anti-villain geneticist named Zobrist who designs a virus that can potentially kill one-third of ...

  5. A Look at Addgene's QC Process

    Type
    Blog Post
    ...If a depositor provides a sequence for the plasmid, QC scientists will first align the de novo NGS result...are assembled into a circularized plasmid sequence de novo (without the use of a reference sequence) using...sequence, if one was provided. If no reference is given, de novo assembly in Geneious can still provide additional...plasmids in our collection. This standardization provides security for requestors, ensuring that the plasmid...types of data for each of their plasmids, from descriptions of key components of the plasmids to partial...believe may affect the function of the plasmid. This includes point mutations, frame shifts, missing elements...

  6. Adeno Associated Virus (AAV) for Cell and Gene Therapy

    Type
    Blog Post
    ...thanks to our guest blogger, Harshana S De Silva Feelixge. Harshana S De Silva Feelixge is a researcher whose... post was contributed by guest blogger Harshana S De Silva Feelixge. Gene therapy technologies hold ...form, translating gene therapies from conceptual design to clinical trials involve identifying a therapeutic...

  7. CRISPR Protocol for Genomic Deletions in Mammalian Cell Lines [Video]

    Type
    Blog Post
    ...Genome Res. 2010 Jan;20(1):81-89. PubMed. 2. Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, et...11;342(6155):253-257. PubMed. 3. Canver MC, Bauer DE, Dass A, Yien YY, Chung J, Masuda T, et al. Characterization...and Bauer lab's related paper describes their methods for CRISPR design, cloning, and delivery, as well...

  8. FLEx Technology and Optogenetics: Flipping the switch on gene expression with high spatial and temporal resolution

    Type
    Blog Post
    ... rather than aversive stimuli. In a recent paper, de Jong and colleagues used rAAV FLEx-based vectors ...brain regions associated with motivated behaviors (de Jong et al., 2019). FLEx vectors represent, therefore...developmental biology at the École Normale Supérieure de Lyon. Her love for educational science led her to...neuroscience 8.9 (2005): 1263. PubMed PMID: 16116447. de Jong, Johannes W., et al. "A neural circuit mechanism...scientific communication manager at genOway. A few decades ago, the brain remained elusive, not from a lack...Boyden et al., 2005; Deisseroth et al., 2006). Despite its relatively recent development, the history ...Double-floxed Orientation)) is a powerful tool that provides precise temporal and spatial control of gene expression...

  9. Crowdfight, a Platform to Boost Scientific Collaboration During COVID-19 and Beyond

    Type
    Blog Post
    ...postdoctoral researcher at Instituto de Investigación Biomédica de Salamanca (IBSAL) and one of the coordinators... illustrates the power of collaboration, which despite the competitiveness of cutting-edge research, is...physics. Even non-scientists, such as lawyers, designers and other professionals, joined the platform; ...

  10. Visualizing Protein Turnover In Situ

    Type
    Blog Post
    ...unpublished, that allowed the visualization of specific de novo synthesized proteins in situ. I was privileged..., 2010) and allows the visualization of the whole de novo synthesized proteome. However, FUNCAT alone ...radioactive materials is highly regulated, requires designated work areas and come with health risks. Importantly...synthesized endogenous proteins in situ. Now FUNCAT-PLA provides both quantitative and spatio-temporal information...

  11. Celebrating the 2024 Nobel Prize in Chemistry

    Type
    Blog Post
    ...protein design goals, both from the Baker Lab and others. The introduction of de novo designed proteins...concept that this kind of protein design is possible. Although Top7 was designed simply to be stable and novel...Hassabis and John Jumper! The Baker Lab focuses on designing entirely new proteins, improving our understanding...team was the first to develop and publish a human-designed protein that was not based on any existing protein...least that we’ve seen so far!). They started by designing a novel topology, then iteratively generated 3D...got closer and closer to achieving it. Once they designed the protein computationally, the researchers expressed...demonstrating “the structure is strikingly similar to the design model at atomic resolution” (Kuhlman and Dantas...

  12. CRISPR Plasmids - Cascade-Cas3

    Type
    Collection
    ...Cascade ( C RISPR- as sociated c omplex for a ntiviral de fense) complex, comprised of a combination of Cas5... CRISPR Guide Viral Preps CRISPR Protocols gRNA Design Tools CRISPR Blogs CasPEDIA Content last reviewed...

  13. CRISPR Plasmids - CRISPR Transposases (CAST)

    Type
    Collection
    ...Cascade ( C RISPR- as sociated c omplex for a ntiviral de fense), and four transposase components (TnsA, TnsB... CRISPR Guide Viral Preps CRISPR Protocols gRNA Design Tools CRISPR Blogs CasPEDIA Content last reviewed...

  14. Save Time with Transient Plant Leaf Transformations

    Type
    Blog Post
    ... which one you choose depends on your experiment (de Ruijter et al., 2003). For example, we did our initial...Humana Press, 2009. 41-50. PubMed PMID: 19183892. De Ruijter, N. C. A., et al. "Evaluation and comparison...and a vacuum is applied with a vacuum bell or desiccator. Successful infiltration can often be seen by...

  15. PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs

    Type
    Blog Post
    ...References Akhtar, W., De Jong, J., Pindyurin, A. V., Pagie, L., Meuleman, W., De Ridder, J., Berns, A....this means we could design hundreds to thousands of different pegRNAs for each desired edit, it simply becomes...via GitHub (which includes prediction in batch mode). To predict the best pegRNA design for a specific edit...or offline via GitHub. The model provides users with different designs of pegRNAs, ranked by their PRIDICT...and a reverse transcription template (RTT). The design of the pegRNA has been shown to play a critical...find a way to predict the efficiencies of pegRNA designs based on patterns observed from high-throughput...experiments, where we can evaluate tens of thousands of designs in parallel. To do this, we performed high-throughput...

  18. Rett Syndrome: A History of Research and Therapeutic Outlooks

    Type
    Blog Post
    ...in transcriptional repression, activity dependent de-repression, chromatin remodeling, gene activation...Tillotson R, Selfridge J, Koerner MV, Gadalla KKE, Guy J, De Sousa D, Hector RD, Cobb SR, Bird A (2017) Radically...that MECP2 binds to methylated CpG dinucleotides and CAC trinucleotides during neuronal maturation (Tillotson...If you’re new to Rett Syndrome, this blog post describes the history of Rett Syndrome research, the role...MECP2 in Rett Syndrome Rett Syndrome was first described in 1966 by Austrian physician, Andreas Rett, who... his observations in a German medical journal. Decades later and after years of painstaking work trying...

  19. Plasmids 101: Expressing shRNAs for RNA Interference

    Type
    Blog Post
    ...297. https://doi.org/10.1016/s0092-8674(04)00045-5 De Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner...Gebhard, C., Goldowitz, D., Guhl, S., Ha, T. J., . . . De Hoon, M. J. L. (2017). An integrated expression atlas...using plasmids The design of shRNA plasmids requires three important steps: Designing the shRNA sequence...shRNA plasmids are being designed using RNA polymerase II promoters. The design of these plasmids is meant...promoter Mature siRNAs typically range from 19–22 nucleotides and are 100% complementary to their target sequence...plasmid and call it a day. You need to include both sides of the complementary RNA duplex and the hairpin ... and just needs to be taken into account when designing experiments.   {% module_block module "widget_...

  20. Generating Mouse Models Using CRISPR/Cas9

    Type
    Blog Post
    ...Sullender M, Ebert BL, Xavier RJ, Root DE (2014) Rational design of highly active sgRNAs for CRISPR-Cas9...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...NHEJ), this will leave behind a “scar”, with nucleotides missing or added at the broken ends and, as such...CRISPR is much more efficient at generating the desired mutant offspring, with 85% success compared to ...
Showing: 21 - 40 of 993 results