We narrowed to 954 results for: COMP

...bacterial strains, like NEB Stable. NEB Stable competent cells lack RecA, a protein that aids in the homologous...helps me figure out if I have enough plasmid to complete my experiment. AAV is usually the limiting reagent...produce more virus because I don’t have enough AAV. Compared to the Addgene AAV Production protocol, I take...concentrate the purified virus. This process can be completed in one long day, or the virus can be stored at...set can be used and samples are quantified by comparing to an AAV standard curve, which is generated from... plasmid. This whole process takes ~3 hours to complete: 1 hours hands-on time and 2 hours for the qPCR...

...while also ensuring that my work gets completed? I want my company to pay for me to attend a conference... How can I negotiate my starting date with the company so they know I’m excited while still being able...want to learn more about a different area of the company. How can I negotiate with my manager to gain experience...conference. How can I negotiate to show the company that investing in me is also beneficial to them? I have an...but I need help from another person/team at the company. How do I negotiate with the person/team for help...

...variety of constructs for visualizing cellular components (nucleus, endosomes, lysosome, golgi, ER, inhibitory...inhibitory synapses, and cytoskeleton components) and in a FRET-based biosensor for cAMP dynamics. The ...especially among plant biologists, due to their compact size and ability to generate heritable edits (learn...third of the size of Cas9). Figure 2: Comparison of TnpB (A) and Cas9 (B) genome editors. Effector...mScarlet reporters, so you can choose a color compatible with the other tools in your experiment. These... synapses; however, its modular design allows components to be swapped out, potentially broadening its...

...know that this process only became even more complicated with COVID-19 and standards for hybrid, virtual...without the financial and logistical stress that accompanies traveling for campus visits. This is definitely...where the PhD application cycle becomes much more complex. “How do I reach out to potential mentors?” “Where...very valid questions, and often make an already complicated process even more difficult. I’ve learned that...to be incredibly useful, as it gives a more comprehensive idea of that advisor’s research interests which... for the interview. Having notes close to your computer with things you want to highlight in the interview...

...about a month and a half, without the need for complicated cloning of homology arms. MMEJ: An Introduction...HDR and NHEJ, please see the linked blog posts. Compared to its counterparts NHEJ and HDR, MMEJ doesn’t...strategy looks very similar to HDR, but it is accomplished using much smaller regions of homology, which...strategy looks very similar to HDR, but it is completed using much shorter sequence homologies. Abbreviated...efficiency of PITCh-based genomic insertion would compare to CRISPR sticky-end insertion using the nuclease...Genome-Editing Based Approach for Mapping Multiprotein Complexes in Human Cells.” Cell Rep. 13: 621-633. PMID: ...

...These insights are hard to appreciate without computational support. Indeed, rational sgRNA design is not...experimental applications in CRISPR engineering. When compared to that collective utility, it’s easy to fault...tool unique. The CRISPR Software Matchmaker is composed of these features and enables you to select the... based on their comfort level with operating a computer.  Examples: “offline”, “online”, “CLI”, and “GUI...few offline tools available mostly work on any computer but generally require working knowledge of the... power of each tool they are interested in by comparing their past results to the designs suggested by...pattern at any edit distance. It won’t, however, compute any score other than the edit distance. Added functionality...

...just one or two recombination events, homemade competent cells of 107 CFU/μg are perfectly fine, yet performing...performing multiple modifications will require ultracompetent (109 CFU/μg) cells. Primer design Using specific...insertions, deletions, and point mutagenesis to complex assembly of multiple genes. Primer design for each...the forward primer by adding a short sequence complementary to the 5’ end of the reverse primer. Mutagenesis...efficiency of assembly decreases as the cloning complexity increases. The efficiency of recombination is...increased with greater homology, so performing more complex procedures can be aided by extending homologous...

...Sharing data and community concerns AAV vectors are complex biological reagents; many factors, like storage...literature, scientists can use the Data Hub to compare different methods and vectors, and use this data...through word of mouth or old lab notebooks and computer files. If you asked your team members or colleagues...much unpublished AAV data do you have sitting in computers and notebooks right now?, I’m willing to bet the... rat CNS: AAV PHP.EB vector dose–response and comparison to AAV PHP.B. Gene Therapy, 25(5), 392–400. https..., C., & Flotte, T. R. (2015). Stability and compatibility of recombinant adeno-associated virus under ...

...division. These non-plasmid-containing bacteria can compete with and confound the goal of your experiment —...spectinomycin is the more stable and expensive antibiotic compared to streptomycin. Spectinomycin/streptomycin can...option! Otherwise, since it isn’t universally compatible with all bacteria used in research, it isn’t ...express the Tn5 element, but thankfully, most competent cells do not express this factor. Zeocin is handy...host/plasmid DNA during selection if it’s not completely bound up. While this likely occurs at a low rate...Stability Time Saving?  Works for multiple organisms? Compatible with most bacteria? No satellite colonies? ...

...immune system; and reconfiguring of the nuclear compartment, gene expression, and protein translation. Its...producer cells where there is E1 and E3 gene complementation. In target cells that are infected by the vector...virions) are not expressed. Note that replication-competent AdV vectors also exist and are used in certain...topic, which is that natural AdVs, replication-competent viruses with a recombinant genome, and adenoviral...higher than other viral vectors (tens of kilobases; compared to only 4.7 kb for AAV, 9 kb for retroviruses)...Tales: From the Cell Surface to the Nuclear Pore Complex. PLoS Pathog, 11(6), e1004821. https://doi.org/...

...require a single-component nuclease to mediate cleavage rather than the multi-subunit complex employed by ...repair templates should remove the PAM sequence. Comparing Cpf1 and Cas9 on-target and off-target efficiency...lower than that of the widely used SpCas9 and comparable to SaCas9. As seen with Cas9 orthologs, Cpf1 ...sophisticated genome-wide analysis. At many of its computationally predicted off-target sites, Cpf1 does not mediate...sites, according to Kim et al. Kim et al. also compared the ratio of total off-target to on-target modification...

... assortment toxins to claim territory or kill competing microorganisms, but did you know bacteria also...subunit of DNA gyrase and trapping it in the cleaved complex. This results in DNA breakage and cell death. Conversely...toxin-antitoxin roles. Restriction modification systems are composed of restriction endonucleases and methyltransferases...populations to retain more of these plasmids as compared to those without the restriction modification ...described, the hok/sok systems consist of three components: Host killing (hok), a long-living toxin that...K. Burley. "Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition....

...morpholinos. When injected into zygotes, morpholinos complementary to a target mRNA inhibit its translation either...observation unlocked novel research into genetic compensation, a previously unknown mechanism of gene regulation...established body plan including head, eyes, and tail. Compared to the opaque mouse embryo, where similar processes... been tracked using microscopy and advanced computational approaches (Keller et al., 2008). This microscopy-based...generation time and labor-intensive maintenance compared to invertebrate model systems, and their resistance...References El-Brolosy, Mohamed A., et al. "Genetic compensation triggered by mutant mRNA degradation." Nature...

...research proposal will distinguish between competing models. Comparing model A vs. B is more constructive than...about the time and resources required to feasibly accomplish the aims and clarify what type of aim you are...scaffolds with patient stem cells to generate compatible functional livers.” Why are you the best person...exist to solve the problem. What will you have accomplished in 5-10 years? You need to be able to describe...learned and/or now be possible to do? Research accomplishments are remembered for the problem solved, not ...

...editing is the potential for off-target effects. To compare the off-target effects of SpCas9 and SaCas9, Zhang...normal and liver injury markers were not increased compared to a control AAV-GFP. Not only did the AAV-SaCas9...had modest editing rates in HEK-293T cells when compared to the full-length SpCas9. In 2016, Chew et al...cleavage of HBB and CCR5 genes in human cells using compact expression cassettes. Sci Rep 5: . https://doi....Desmarais J, Nogales E, Doudna JA (2019) CasX enzymes comprise a distinct family of RNA-guided genome editors..., Nureki O (2014) Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell 156:935–949...

... and/or are too expensive, time-consuming, and complex to use outside of standard laboratories. In the...step allowing for greater quantitation without compromising sensitivity. To detect multiple targets in ...signal of a single target. Csm6 can cleave ssRNA complementary to a crRNA of interest (Niewoehner and Jinek...with high sensitivity and specificity without compromising speed, ease of use, and portability. This method...molecular and clinical diagnostic applications. The company Mammoth Biosciences has been started based on DETECTR...ES, Koonin EV, Zhang F (2016) C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector...

...find a comparable library if it’s gone stale or we will need to update our code to be compatible with the...parts to our software, which has grown with the company. It would be easy to assign each developer to a.... Third party libraries are reusable software components that can be incorporated into software. You can...or they make significant changes that make it incompatible with our software. When this happens, we need...took us a total of two years, from planning to completion, to do this upgrade while continuing to add new...

...proteins. lon protease: Strains where this is completely deleted (designated lon or Δlon) similary reduce... and a p15A origin of replication, making it incompatible with other p15A plasmids. pLys comes in two ...measures that can help get you back on track: Compatibility: Double-check your plasmid backbone and expression...expression strain to make sure they are compatible. An arabinose-inducible plasmid will not express in an...strain for example, nor will a p15 plasmid be compatible with a pLys strain. Your strain may require additional...better at 30°C or room-temperature, which is accomplished by growing your culture to the desired density...

...across the entire blot. So how can you accurately compare different lanes? In relative quantification, the... conclusions, and it’s also problematic for computational quantification. Outside the linear detection...individual protein. This ensures you are truly comparing the abundance of your POI as a fraction of the...detection ranges of multiple targets. Convenient! Comparison of loading control approaches Cartoons are nice...all, but we’ll leave you with this real-world comparison of different loading control approaches from ...different methods of quantifying total protein are compared. While a higher slope indicates higher sensitivity...

...metabolites. Biotin acts as a carboxyl carrier from one compound to the other. These biotin dependent enzymes are...discovered in the 1960s, strepavidin. The Biotin-avidin complex can then be used and/or manipulated for a scientist...immunoprecipitation experiments. Biotinylated proteins or complexes can be easily purified using columns or beads ... sample. Any free biotin-binding sites on this complex can bind to your biotinylated antibody. This creates...creates a large meshwork of biotin-avidin complexes bound to your protein of interest leading to amplification...This strategy is referred to as the Avidin-Biotin Complex (ABC) immunohistochemistry (IHC). For more information...

... different universities are trying to compile more comprehensive demographic information about the postdoc...Postdoc: An Institutional Perspective. This lack of complete information does not, however, prevent us from...from the career panel was that there are many companies and organizations (including Addgene), that need...scientifically minded, and able to communicate complex information - all traits you are likely to find...others within their labs - as a sort of over-compensation, these mentors can treat the underrepresented...

...bacterial CRISPR engineering One common way of accomplishing bacterial genome engineering is done with recombineering...transposition. INTEGRATE consists of four major components including (1) a CRISPR RNA, (2) four proteins...transcription by physically blocking the elongation complex from binding the DNA or extending the transcript...transcription factors, phage proteins, and RNAP components (Dong et al., 2018). They found a transcription...transcription factor called SoxS for CRISPRa. Adding complexity, they found that they could also include a CRISPRi...systems is base editing. This process is generally accomplished by fusing an enzyme capable of converting one... targeting approach is then used to direct the complex to a specific locus. This approach provides a more...

... received his PhD in Computer Science from MIT. His research focused on computer systems and networks.... 4 - Developing Addgene as a modern e-commerce company and establishing credibility Chapter 5 - Realizing...Kenneth received his Bachelor of Science degree in Computer Engineering from Tufts University and his Master...and a Masters in Engineering from MIT, both in Computer Science.   Special thanks to our sound engineer...

...Drs. Koeris and Lu founded the biotech startup company, Novophage. As you'll hear Dr. Koeris explain however...Ventures, Koeris helped change Novophage's focus. The company went from developing therapeutics to developing...pathogens in food products. Along the way, the company changed its name from Novophage to Sample 6. To...using Sample 6 and why? 24:41 - 29:00 : Dr. Koeris compares and contrasts being a graduate student with being...personally take on the risk of founding a startup company? 32:20 - 34:37 : Whose responsibility is it to ...

...reporters Difficult to Multiplex: FRET reporters are comprised of two fluorescent proteins with very specific...encoded fluorescent kinase reporters. A KTR is comprised of a fluorescently-tagged substrate for a kinase...for kinase activity.  Advantages of KTRs When compared to FRET reporters for measuring kinase activity...of KTRs KTRs also have some disadvantages when compared to FRET reporters. First, KTRs monitor global ...measure kinase activity in specific subcellular compartments. Second, because KTRs shuttle between the nucleus...

...possibilities in the engineering of complex gene networks. A comparable system for targeting specific sequences... of RNA is highly desirable for extending the complexity of genetic circuits, allowing for tighter spatio-temporal... protein that binds an alternate sequence. By comparison, Abil explained, the specificity of other RNA..., designer PUF proteins can be fused to other components to lend them many other functions for use in ...

...markers. These are especially useful in protein complex studies where tagging of multiple protein products...for easy capture and detection of proteins and complexes, without the artifacts sometimes associated with...Formosa, at the University of Utah, has built a complete collection of yeast tagging modules with each ...ideal for tandem affinity purification of protein complexes. John Pringle and Jürg Bähler have deposited a...GST, or GFP). Longtine et al.(3) describe a complimentary set of plasmids for use in S. cerevisiae, with...

...The application process When I first saw the comprehensive job description for this co-op, I was immediately...description of the tasks I would be responsible for, in comparison to the other positions listed with a much less...training, I was gradually introduced to Addgene as a company and given more details on what my position entailed...they do and how it relates to other teams at the company. This provides new (and old) employees with information...Northwestern University. She is one of several students completing their co-op at Addgene. This is her second contribution...

...without the exo/polymerase generation of annealed complementary regions. Why use a high fidelity ligase? Numerous...the Ligase Detection Reaction (LDR), probes complementary to the sequence of interest are annealed to ...separate pools were prepared, each with a different complement strand covering all 16 possible NN pairs in the... system for direct identification of allelic composition of mutated DNA in a mixed population of excess...JS, et al. "A high-throughput assay for the comprehensive profiling of DNA ligase fidelity." Nucleic acids.... Pascal, John M., et al. "Human DNA ligase I completely encircles and partially unwinds nicked DNA." ...

...Development Manager at eScience Labs, an educational company that creates hands-on science lab kits and digital...from.” Working at eScience Labs, an educational company that creates hands-on science lab kits and digital... editing.” It was for Cactus Communications, a company that provides scientific editing services. “I was... stumbled upon eScience by luck, by chance, by complete happenstance. It was on Indeed or one of the job...what it’s like to work for a science education company. And make sure to subscribe to the Career Channel...

...Visualize components of individual cells Separation/identification of fluorescently-labeled components Fluorescence-activated...process or detect a given molecule. The sensor component is usually a protein that undergoes a conformational...biosensors can be targeted to a particular cellular compartment such as the nucleus, mitochondria, endoplasmic... biosensor: which fluorescent protein is most compatible with your lab and experimental setup? Consider...

...CAST systems rely on the Cascade complex minus its nuclease component, Cas3, while Type V-K CAST systems...CAST activity allowed certain mutated phages to outcompete their brethren, and the researchers isolated ...evolved and engineered adjustments to the other components. It drove 19% integration in HEK293T cells (more...that kind of gene treatment. The researchers also compared evoCAST to the Liu lab’s own PASSIGE (Prime-Editing-Assisted...

...give you the reverse sequence, complement sequence, or reverse and complement sequence.  Filter DNA tool:...well as those deposited with Addgene. NCBI BLAST: Compares nucleotide or protein sequences to sequences in... tools help with that.  DNA sequence reverse complement tool: Enter a DNA sequence and the program will...DAD): This tool designs overhang sets for high complexity Golden Gate Reactions Cloning ligation reaction...

...Palindromic Repeats. That contrast of simplicity and complexity is reflected in the biology, too. CRISPR is an...proteins, and a CRISPR array. The CRISPR array is composed of identical repeat sequences and variable spacer..., and the spacer sequence is used to target complementary DNA sequences. In laboratory settings, an sgRNA...whose sequence is not checked. Assuming full complementarity, its sequence matches the guide sequence. PAM...either crRNA or sgRNA). Cas9 requires perfect complementarity in this region between the guide and target...

...response to a viral infection a) antibody-dependent complement deposition (ADCD) b) antibody-dependent cellular... Erp, et al., 2019.    Antibody-dependent complement deposition (ADCD) Antibodies can bind to a pathogen... known as opsonization. In antibody-dependent complement deposition (ADCD), opsonization of IgG and IgM...pathogen activates the immune system's classical complement pathway, starting a cascade of events that results.... PMID: 10742152. Dunkelberger, J., Song, WC. Complement and its role in innate and adaptive immune responses...

...hand. Records of plasmid construction were often incomplete or nonexistent. In the 21st century, many molecular...molecular biologists didn’t know the complete sequences or properties of the DNA molecules they were using...has been thoroughly answered by experts in human-computer interaction (HCI), and we have adhered rigorously...what the user wants to do and make the path to accomplishing their goals as intuitive and painless as possible...who uses SnapGene or the free SnapGene Viewer companion product. If you don’t use SnapGene yet, you can...

...30678704. Sparse cell labeling using recombinase competition Article contributed by Aliyah Weinstein Sparse...Sparse Predictive Activity through Recombinase Competition (SPARC) is a fully genetic tool for labeling just...heat-shocking the organism. The SPARC system uses competitive recombination sites to selectively remove a stop...microscopy, they also show that this method is compatible with dead cell staining using propidium iodine...purification of tTALE-eGFP and tTALE-mCherry. In comparison to intercalating fluorescent dyes which can cause...

...build and grow the gene therapy division of the company.  Ultragenyx’s goal is to develop novel products...manufacturing and quality, especially with regard to compliance with health authority regulations,” Baradaran...Belgium. “That’s where I not only got incredibly compelled by wet bench molecular research, but also became...grants, or setting up commercial and nonprofit companies. His lab focuses on gene therapy work for genetic...these inefficiencies is pretty remarkable. I was compelled to be part of that.” He’s deposited AAV constructs...

...between two opposing forces or (2) the result of competing desires or (3) the presence of obstacles that ...until you don't, of trying to understand your completely unexpected findings, or understanding why your...thrice-failed experiment, this paper was actually from a completely unexpected finding in a different experiment,...your conflict, you’ll need two other things to complete your story: an introduction, and a resolution....conflict to get your audience invested in the more complex story, and then build on that in your resolution...

...when Neil Thompson, a research scientist at MIT’s Computer Science and Artificial Intelligence Lab and a ...properties (GC content or rare codon percentage) and comparative properties (percent sequence identity and percent...query coverage) that could be determined through comparisons with a reference sequence database. Through a...content between many organisms and DNA synthesis companies often work within a narrow range for GC content...synthetic vs. natural gene are essential and complementary tools in a time where biological engineering...