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We narrowed to 811 results for: lars

Showing: 141 - 160 of 811 results

  1. Quick Guide to Near-Infrared Fluorescent Proteins

    Type
    Blog Post
    Published
    Oct. 5, 2021, 1:15 p.m.
    ...miRFPnanos9 do not yield to (m)iRFPs in cellular and molecular brightness (Table 1).  NIR reporters and...). Modern state-of-the-art NIR FPs can be used similar to GFP-like probes by supplying a single gene to...brightness of NIR FPs in cells, in addition to their molecular brightness (a product of the fluorescence quantum...biosensors can be imaged at spatial scales from sub-cellular to whole-body in small animals, such as mice (...phytochrome (BphPs) photoreceptors have higher apparent cellular brightness than previously reported widely used...and biosensors NIR reporters can tell us about cellular events via  fluorescence changes occurring due...FP Ex, nm Em, nm ECa, M-1cm-1 QYb, %   Molecular brightness vs. iRFP713, % Oligomeric state Photo-stabilityc...

  2. Antibodies 101: Single Chain Fragment Variables (scFvs)

    Type
    Blog Post
    Published
    June 3, 2021, 1:15 p.m.
    ...disulfide bonds, made by molecular evolution 1 1Edited by I. A. Wilson. Journal of Molecular Biology 275:245–253...sequences of hybridomas, but phage display is a popular way to generate scFvs.  For phage display, a pooled...oxidizing cytoplasm. expression in the presence of molecular chaperones that help scFvs fold properly in the...blocks for engineered proteins. This flexibility is largely due to scFvs being smaller than antibodies. scFvs...cells to a tumor site. ScFvs can also be fused to cellular toxins, radioisotopes, cytokines, and enzymes ...also used for eye diseases, such as age-related macular degeneration (AMD) since direction injection to...expressed on T cells to make CAR T cells. The extracellular scFv portion of the receptors recognizes an ...

  3. The CRISPR Software Matchmaker: A New Tool for Choosing the Best CRISPR Software for Your Needs

    Type
    Blog Post
    Published
    Nov. 3, 2015, 3:30 p.m.
    ... have a large impact on downstream results. Examples: “HTML”, “visual track”, “plot”, “tabular”, “interactive...Pasteur, Paris) that changed genome editing in the malaria community for the better (Nat. Biotechnol., 2014...Plasmodium falciparum (the parasite that causes malaria). I attribute their success to technical expertise...audience blindly receiving them; it results in highly similar content and the absence of iterative design; it...The third, WGE (published 15 Sep 2015), is more similar to EENdb than CrisprGE, but is also a good example...interactive”, and “save”. Trends: Most tools provide tabular HTML formatted output. Surprisingly only 2 tools... agnostic”, “model organisms”, “small genome”, “large genome”, and “organism biased scoring”. Trends: ...

  4. Targeted Mutagenesis with EvolvR

    Type
    Blog Post
    Published
    Feb. 21, 2019, 1:15 p.m.
    ...Mutagenesis is a tool that both evolution and molecular biologists use to tinker with DNA. Making changes...phenotypes, and forward genetics harnesses this at a large scale by screening diverse libraries of genetic ...must be grown in a turbidostat. Only mutate particular types of nucleotides. Both the Bassik Lab and...PolI3M that’s fused to a nicking Cas9 (nCas9). Similar to mutagenesis with error prone PCR, EvolvR uses...However, by using nCas9 to direct PolI3m to a particular genomic loci, EvolvR allows for targeted mutagenesis...replication by 120-fold over background. Due to its modular nature, the Dueber Lab created a few versions of...increasing the editing window of EvolvR to ~56 bp. A larger editing window also increased the likelihood that...

  5. Sharing is Caring: But How to Distribute Open Hardware?

    Type
    Blog Post
    Published
    Feb. 28, 2023, 2:15 p.m.
    ... that actively engage with the community are particularly successful. Machine-learning denoising of raw...segmentation of imaging data (ILASTIK), or the popular plugin-based image process framework FIJI are just...such as the OpenFlexure microscope or open-source modular optical toolbox openUC2 are trying to overcome ...rely on such tools has allowed the community to regularly replicate designs worldwide. Distributing hardware...facilitates the reproduction of the structure in a similar way to the biological protocol, and assembly designs...Nevertheless, there are still many open questions to be clarified, especially with regard to licensing models. Direct...is a great example of how sharing of data and molecular tools can lead to faster and more efficient science...

  6. GPCRs: How Do They Work and How Do We Study Them?

    Type
    Blog Post
    Published
    Feb. 11, 2021, 2:15 p.m.
    ...on the intracellular side of the cell membrane. Heterotrimeric G proteins are important molecular switches...induce or inhibit intracellular signaling cascades as a response to the extracellular stimuli. Ligand dissociation...to the seven alpha helices that transverse the cellular membrane. The receptor recognizes the appropriate...signaling is initiated when a ligand binds to the extracellular surface of the GPCR. This results in a conformational...response in a certain cell type. Chemogenetics is similar to optogenetics but instead of light, these genetically...activate or inhibit neuronal firing. As GPCRs are the largest class of signal transducing receptors in the brain...

  7. REPLACR Mutagenesis: Replacing In Vitro Recombination Methods

    Type
    Blog Post
    Published
    Feb. 10, 2016, 3:30 p.m.
    ...key tools researchers use to prove causation in molecular biology and genetics. It can be used to characterize...are available for making small point mutations, large deletions/insertions require complicated, often ...possible to use the same technique just using a large primer known as a megaprimer. Piecing together multiple...methods can be expensive because they require particular enzymes, some of which are proprietary. These...have secondary structure or too much sequence similarity. REPLACR-mutagenesis: Letting bacteria do the...then joins the linear PCR products into stable circular plasmids - no nick repair is needed. Since the...L-arabinose. These cells can be made and frozen in large batches suitable for many experiments. When REPLACR-mutagenesis...

  8. 3 Challenges in Plant Synthetic Biology

    Type
    Blog Post
    Published
    July 22, 2014, 5:46 p.m.
    ...another challenge associated with molecular plant parts, particularly for applied projects intended for...challenging to engineer a specific function in these multicellular organisms. However, the rewards are great if...biotechnology and provide a much needed boost to basic molecular plant research, more initiatives are needed to...associated with plant synthetic biology. Plant molecular biology has traditionally relied on overexpression...processes. Often the tools developed for plant molecular biology are specific to a given project, and like...pieces developed over the years were generated by large agricultural companies and carry associated intellectual...and the ocean. After receiving her bachelors in Molecular Biophysics and Biochemistry from the Illinois ...

  9. The Breast Cancer Microenvironment: A Tumor’s Backstage Team

    Type
    Blog Post
    Published
    Jan. 31, 2019, 1:32 p.m.
    ... tumor’s backstage team. Microenvironments are cellular regions with specialized structures. Tumors are...neuroendocrine, adipose, immune, inflammatory, angiogenic vascular, endothelial, and stromal cells - a rich soup ...promoting proteins, such as human growth factor, vascular endothelial growth factor, and interleukin-6 (...2009). Then, scientists began focusing on the extracellular matrix and fibroblasts. With each cell mechanism...Centro Ciência Viva" in Aveiro, Portugal. She is particularly interested in science journalism and writing...BrbaraPinho6.      References Allinen, Minna, et al. "Molecular characterization of the tumor microenvironment...PMCID: PMC4788391. Kogure, Takayuki, et al. "Intercellular nanovesicle‐mediated microRNA transfer: A mechanism...

  10. Giving gRNAs a Facelift - Synthetic and Beyond

    Type
    Blog Post
    Published
    Oct. 20, 2022, 1:15 p.m.
    ...targeting is led by a ~20 bp gRNA which is part of the larger CRISPR RNA (crRNA). In addition to the 20 bp guide...evolved ways to prevent degradation of important cellular RNA molecules with post translational modifications... Moving one position over in the sugar ring, a popular stabilizing modification is 3’ phosphorothioate...resulting in less off-target events. While both have similar advantages, bridged nucleic acids with N-methyl...et al., Frontiers in Genome Editing). This is particularly important in experiments in which viability ...transfection efficiency and even track localization in cellular experiments. There are many suitable dyes to choose...References and Resources References Hendel, A., Bak, R., Clark, J. et al. Chemically modified guide RNAs enhance...

  11. The Future of Research Symposium Boston 2015

    Type
    Blog Post
    Published
    Oct. 20, 2015, 2:30 p.m.
    ...Research Symposium organizer, David T. Riglar PhD. Here, Dr. Riglar discusses one of the six panel discussions...Many thanks to our guest blogger David T. Riglar! David T Riglar is a postdoc at Harvard Medical School.... problems that were identified last year.  In particular, at the symposium we will discuss where better...Jonathan Dinman, Chair of the Cell Biology and Molecular Genetics Department at University of Maryland ...collection about the scientific workforce, in particular about postdocs. Among other involvements, he ...science and public policy. Follow David on Twitter @driglar.     References 1. Alberts, Bruce, et al. "Rescuing...

  12. Writing Scientific Manuscripts: Literature Searching, Reading, & Organizing

    Type
    Blog Post
    Published
    May 5, 2015, 3:54 p.m.
    ...sign up for Google Scholar alerts. Based on keywords that you provide, Google Scholar will send you daily...Johnna's New Under The Sun Blog and is part of her larger tutorial series, A Beginner’s Guide to Writing ...useful to make literature searching and reading a regular part of your routine. Set a goal to read a certain...engines for finding scientific literature are Google Scholar and PubMed. You can search keywords, titles, authors...given research area. Unless you are looking for a particular protocol or are trying to replicate an experiment...possibilities until the results focus in on a particular conclusion. Many papers aren’t always written...of sufficient quality (error bars, statistics, clarity in images etc)? Did they perform all of the appropriate...

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

    Type
    Blog Post
    Published
    Oct. 27, 2020, 1:15 p.m.
    ...) is conceptually similar to the microRNA precursor mentioned above and is a popular RNAi trigger in the...exquisitely and robustly self-organize at the cellular and multicellular scale.     References Bezanilla M, Perroud...is fair to say that CRISPR has revolutionized molecular biology and has enabled functional studies in ...micro RNAs (amiRNAs) are frequently used. Although similar, amiRNAs are engineered from endogenous precursors...silencing plants. Non-destructive methods, most popularly with a fluorescent reporter, directly couple silencing...Institute where he investigated how plants achieve polarized cell growth in the lab of Luis Vidali. For his...10.1242/dev.186452 Wilson RC, Doudna JA (2013) Molecular Mechanisms of RNA Interference. Annu Rev Biophys...

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

    Type
    Blog Post
    Published
    Dec. 15, 2016, 3:57 p.m.
    ...Restriction enzyme cloning is the workhorse of molecular cloning; however, one of its biggest limitations...The best applications for dsDNA inserts include: large insertions or deletions, including selectable DNA... sure to read the associated papers for their particular uses - *note* not all linked strains contain ...is to use mini-λ, a defective non-replicating, circular piece of phage DNA, that when introduced into ...generation of bacteriophage, which is not a common molecular biology technique. However, an advantage of this...Medicine at the University of Washington. She is particularly interested in science communication and in vitro...PubMed Central PMCID: PMC307639. 2. Daiguan Yu, Hilary M. Ellis, E-Chiang Lee, Nancy A. Jenkins, Neal ...

  15. CRISPR Activators: A Comparison Between dCas9-VP64, SAM, SunTag, VPR, and More!

    Type
    Blog Post
    Published
    Oct. 6, 2020, 1:15 p.m.
    ...improved CRISPRa, expanding its practicality and popularity in research (Tanenbaum et al., 2014, Konermann...Konermann et al., 2015, Chavez et al., 2015). Most popular methods for CRISPR activation CRISPR activation ...compared to other CRISPR activators, making it a popular method for gene activation experiments. In cases...exhibits activation levels comparable to other popular activation methods (VPR and SunTag) (Chavez et ...relies on antibody chains, which are relatively large and are not expressed consistently throughout cells...compared to the SAM system. Its activation levels are similar to that of SunTag. An advantage to this method ...While SAM, SunTag, and VPR have become the most popular methods for CRISPR activation, research in the ...

  16. Overcoming the Challenges of Lentiviral Production

    Type
    Blog Post
    Published
    Aug. 7, 2018, 12:31 p.m.
    ...is often the case with large genes. This is due to inefficient packaging of large inserts; a study by Kumar... While lentiviral vectors are popular gene delivery tools, producing lentivirus, can pose certain challenges... deciding what packaging system is best for a particular experiment. The newer generation lentiviral packaging... guides) while a single 72h harvest is best for larger genes such as Cas9. See figure 1 for an example...dishes or increasing the vessel size. Opting for a larger vessel, such as a 3 or 5-layer flask will require...calculating the ratio of the surface area of the larger vessel to the 10 cm2 dish and adjusting the cell...start. If you don’t anticipate that you will need large volumes of lentivirus routinely, you may opt for...

  17. A Guide to Designing a Scientific Poster: Content, Layout, and More

    Type
    Blog Post
    Published
    Oct. 22, 2019, 12:20 p.m.
    ...vertical.  Large central box. Another commonly used and effective style is one employing a large central ... figures fit nicely into circular shapes rather than a square or rectangular boxes. Background and color...poster together, be aware that there are some particular styles recognized to work well. It is important...is written across the center of the poster in a large font. Hence, spectators can read the text from many...written and graphical information are inserted into larger circles or ovals, that are arranged in some logical...these colors so that your text is easily read. Similarly, be cognizant of audience members that are color-blind...

  18. High Complexity Golden Gate Assembly with NEB’s DAD

    Type
    Blog Post
    Published
    Aug. 1, 2023, 1:15 p.m.
    ... and circular assemblies. While Golden Gate Assembly worked for all the assembly types, circular assemblies... 52-piece circular assembly of the T7 genome had lower efficiency than the 10-piece circular assembly,...rules the best way to design GGA overhang sets, particularly for high-complexity reactions? The researchers...outlined below, allow for researchers to select large sets (with overhangs that violate some of the traditional... use to identify fusion sequences for either a circular or linear assembly. If you aren’t constricted ...fairly easy cloning technique (which may be of particular interest to MoClo users!). If you’re interested...

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

    Type
    Blog Post
    Published
    July 2, 2020, 12:40 p.m.
    ... are particularly good models for building chromatin interaction networks since they are a large cluster...biotinylated by BirA. From here, the CAPTURE method is similar to other 3C methods: crosslinking captures chromatin...Additionally, CAPTURE 3C-based sequencing requires a large number of cells (~5x107). Together, these two requirements...well-characterized beta globin locus. The two methods had similar rates of specificity for the DNA sequence targeted...interactions identified with the multiplexed CAPTURE 2.0 largely replicated interactions previously identified with..., like those that occur during development and cellular differentiation. Using a cell line model, the ... for spatial genome organization deciphering. Molecular Cytogenetics, 11. https://doi.org/10.1186/s13039...

  20. Degrading DNA with Cascade-Cas3

    Type
    Blog Post
    Published
    Feb. 11, 2025, 2:15 p.m.
    ...single base pairs, to chromosomal inversions and large deletions. Many of these methods rely on Cas9 or...Although seemingly ubiquitous in nature, they are largely underutilized in research settings — mostly a consequence...is not as well understood but likely occurs in similar regions. This combination of chewing up one stand...stand and cutting the template strand causes large deletions of up to hundreds or even thousands of base...proteins naturally bound to the DNA. Cas3 or Cas9? Large genomic deletions can be achieved using Cas9, but...but Cas3 may be a better option. To get large deletions using Cas9, two or more gRNAs must be used along...Cascade-Cas3 complex in nucleotide unwinding steps. Molecular Cell, 70(3), 385-394.e3. https://doi.org/10.1016...
Showing: 141 - 160 of 811 results