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...2020 by Marcy Patrick. CRISPR technology has been widely adopted for genome editing purposes because it'... your next experiment! In this blog post we’ll provide an overview of some CRISPR mammalian expression...and potential delivery methods.   General considerations for planning your CRISPR experiment As with...experiment, there are many factors that need to be considered during the planning process. For CRISPR experiments...choose between them? One of the first steps is to identify what CRISPR components you will need to deliver...deliver a donor plasmid or single-stranded DNA oligonucleotide, so you will need to make sure your expression...are compatible with all your components. Next, consider the best form for those CRISPR components based...

...wasn’t exactly my idea of a dream job, but I knew that I enjoy helping people and decided to compromise and...also explore a range of alternative careers outside of acidemia to have the best chance of finding their ...variety of different organizations, so I tend to provide them with an overview of my experience and how ...about the different positions to enable them to decide for themselves.  Here is my experience looking ...language in Spanish or French, and so they were ideal candidates for these positions.  I had to reassess... to university to study a Masters of Science I decided to apply to study a Master of Science (MSc) in ...research project was hard; I was researching the epidemiology of breast cancer and I loved the practical aspects...

...can also be exciting! Identifying a host institute or lab So, you’ve identified a gap or need in your ...collaborations Transferable Skills Guide: External collaborations Transferable Skills Guide: Teamwork      ...or maybe both, a visiting scientist stint may be ideal for you. Here, we will chat about who might want...visiting role is because the host lab or institute provides something that you can’t obtain at your current...in. Visiting a lab that has this expertise will provide you with guidance and training so that you yourself...new institute and mentor that they may want to consider for future work placements. The chance to learn...your research and decided you want to pursue a visiting position. What now? First, you’ll need to find someone...

...some 1010 oligonucleotides could be screened for their affinity to a wide range of non-nucleotide targets...over the course of the next two decades, these nucleotide-based ligand binders would prove to be highly...their broad range of targets, including proteins, peptides, amino acids, drugs, metal ions, and cells (even...such as a protein. Such flexibility makes aptamers ideal candidates for biosensors. Aptamer biosensors are...several different ways. Researchers have used oligonucleotides in fluorescent visualization techniques for...relatively bulky. One of the advantages of oligonucleotides over proteins is their modularity, which is...- bypassing translation altogether with an oligonucleotide-only sensor could save precious minutes in ...

...'s a good idea to bounce your ideas off of senior faculty members who can help you identify overly ambitious...the central idea. It should be at a high level, broadly understandable to scientists outside your field...least a few times with people that are outside your lab and outside your field. If they can understand and...?" is an open-ended list of proteins. Instead, consider "how do proteins X and Y regulate the Z pathway... or your data favor a different model. Finding evidence for or against a model is a standard scientific...coherent unified story and model can help make your ideas easier to understand and more exciting. Practice...that is easily visible from the back of the room. Consider going beyond the whiteboard. You may wish to create...

...why we decided to do an AMA in the first place and give you some reasons why you should consider using ...hope I was able to provide some good resources to the basic questions and to provide a small bit of support...interested in selling a product than communicating your ideas with people or discussing science, it is a great...users can participate in forum discussions about a wide variety of topics. Individual forums are hosted ...STEM, work-life negotiation, and mentorship, we decided to have her participate in an AMA on these topics...substantial traffic that we thought it would be a good idea. After a bit of research, we realized that the r...You can check out the r/Science AMA Submission Guidelines here, but essentially we just needed to send ...

....  These primers are typically ~70 nucleotides long (20 nucleotides that anneal to the DNA sequence of... Frequency Special Considerations dsDNA Insertion or deletion of >20 nucleotides 1 out of 104 to 105...tube. The donor DNA substrate only requires ~50 nucleotides of homology to the target site for recombination...insertions or deletions greater than approximately 20 nucleotides, while ssDNA substrate is best for point mutations...of interest and 50 nucleotides of homology to regions flanking the target site).  The best applications...out of 104 to 105 colonies. Pro Tip: Use a high-fidelity Taq polymerase with proof-reading ability for ...substrates can be generated by ordering synthetic oligonucleotides or denaturing short PCR products. Either way...

...science policy even is! In this article, I hope to provide a brief explainer of the who, what, where, when...The folks who work in science policy come from a wide variety of backgrounds with technical expertise ...creatively connect seemingly disparate individuals and ideas toward solving one problem. It often requires thinking...the field.  Read the CCST Science Policy Career Guide to learn more about science policy as a profession...in DC, is that so much policy actually happens outside of the government itself. You can work to influence...communities. Think a university system who develops evidence-based university policy to combat sexual harassment...harassment in academia or a large company who decides how they are going pursue regulatory approval for a...

...easily and precisely identifies plasmid features that differ by only a few nucleotides, such as the fluorescent... BLAST to verify plasmids. Analyzer guide A quick guide to all of the tabs listed above and their...Feature Library - SnapGene’s software seamlessly identifies a variety of common plasmid features such as ... Enzymes, and Primers - The new maps have the identities of most features labeled directly on them making...making them much easier to quickly identify. Improved Restriction Enzyme Handling - SnapGene’s software..., & downloadable .gb & .dna files Once you’ve identified a plasmid that you want to learn more about, ...your sequence viewer of choice. If the depositor provided a custom annotated GenBank file, this can be found...

... Other useful backbone modifications to consider include amide linkages, unlocked nucleic acids, and a...to simply swap out several of the ribonucleotides for deoxynucleotides. A partially DNA gRNA is surprisingly...perfect guide; now check out our blog posts on choosing the best Cas9 enzyme to pair with your guide and ...larger CRISPR RNA (crRNA). In addition to the 20 bp guide sequence, the crRNA also contains a ~20 bp repeat... a constrained ethyl.  Can’t decide which RNA backbone modification is best? Studies suggest coupling ...use in applications like siRNA and antisense oligonucleotides. Some of these synthetic modifications, specifically...photoactivatable and photocleavable gRNAs. Photocleavable guides are generated by introduction of a single photocleavable...

...Fab Fragment? Consider the classic IgG antibody (Figure 1): it is composed of four peptide chains (two ...two identical heavy chains and two identical light chains) each with a constant region and a variable region...chains are covalently linked to one another by disulfide bonds between the two heavy chains and between...four chains make a Y-shaped protein that can be divided into the Fragment Crystallizable region (or the... means that it is relatively easy to physically divide up the different regions, both through genetic ...proteolytic digestion that retains an antibody’s disulfide bonds within the hinge region. The resulting product...')2 fragments, which reduces the hinge region disulfide bonds, resulting in two independent Fab fragments...

...amino acids or peptide tags. 5) Strong protein-protein interactions with other peptides. Created with ...Addgene’s antibodies are provided in a buffer with the antimicrobial agent sodium azide, which can interfere...spectral properties of the fluorophores you are considering to make sure that they’ll be compatible with ...antibody conjugates (especially if you start to consider clinical applications). But there are a few other...we would be remiss not to at least mention. Oligonucleotides allow for sensitive detection of low abundance...multiplexing potential. You will find antibody-oligonucleotide conjugates used in assays like proximity ligation...strong protein-protein interactions with other peptides, like an Fc-binding domain (Figure 1).  ...

...in the face of evidence” (4). Frustration among scientists has been rising as evidence of climate change...not in the job of having evidence”, scientists want to make sure having evidence is the job of everyone ...marching for every cause. The references provided also only provide a snapshot into the opinions or research...Health endanger scientists’ ability to uphold their side of the bargain and do the research required to inform...while alienating the other While scientists do identify as Democrats more often than Republicans, the ...Republicans (16). This is a Pro-Science and Pro-Evidence march. Who is marching and why? Who? All sorts...include science in decision making, it will be considered a success. Below are resources for the march ...

...mutagenesis of Spinach. In doing so, they identified the nucleotides that contribute to the instability of...describes the enrichment process used to evaluate oligonucleotides for binding affinity to a specific target,...molecule derivative of GFP called 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). DFHBI is membrane ...studies. Additionally, Spinach, the first aptamer identified to bind DFHBI, is highly unstable in vivo due...Spinach. It was developed in a study of artificial guide RNAs that can be used to simultaneously target cellular...Broccoli, the other green fluorescent aptamer, was identified through directed evolution. First, a pool of ... that activate the fluorescence of DFHBI were identified using systematic evolution of ligands by exponential...

...previously induced gene knockout. Besides amine- and DNA-binding dyes, nucleoside analogs like bromodeoxyuridine... useful for classifying and sorting cells by identifying lineage markers, like many of the cluster of ...one or several of those techniques can be used alongside standard surface labels. Here, I will introduce...streptavidin conjugates are commercially available for a wide range of fluorophores, allowing for great flexibility... you to include further (non-lineage) markers alongside, e.g., for cellular activation. In addition, FACS...interest is not located on the cell membrane but inside the cell. Due to their chemical nature, antibodies...antibodies to enter the cell (Figure 3). A useful side effect of the fixing/permeabilization (fix/perm)...

...attribution: Zetsche, Bernd, et al. "Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system." Cell... cleaves in a staggered fashion, creating a 5 nucleotide 5’ overhang 18-23 bases away from the PAM. Cpf1...through homology-directed repair. Both Cpf1 and its guide RNAs are smaller than their SpCas9 counterparts,...smaller than any of these options (2.7 kb with 24 nt guides), so it has the potential to eclipse any of the... al. and Kleinstiver et al. characterized genome-wide editing efficiency of two Cpf1 orthologs known to...orthologs was only slightly lower than that of the widely used SpCas9 and comparable to SaCas9. As seen with... with Cas9 orthologs, Cpf1 efficiency varies widely with gRNA sequence. Both groups used multiple methods...

...they can’t be avoided. What are off-target effects? The CRISPR-Cas system is an RNA-guided nuclease that... gene expression by various mechanisms. The RNA guide is typically 20 nts and the genomic locus must often... concern, or nothing to worry about all. Let’s consider several scenarios below for a CRISPR experiment...An off-target rate of 5% is far too high when considering human patients and the diseases associated with...off-target measurements at those sites to get an idea of how high the off-target frequency is (more on...many more. While such software typically only considers DNA sequence and doesn’t take into account chromatin...the genome to reduce off-targets, it is time to consider your Cas enzyme. Even if there are similar sequences...

...donor oligonucleotide can be electroporated into the mouse zygote (Qin et al., 2015).  When inside the ...However, if repair material is provided (in the form of an oligonucleotide or plasmid), precise changes ...genome, the mouse genome is made up of 3 x 109 nucleotides (nt), and encodes 23,000 or so genes. It would...for genome editing in eukaryotes, with the most widely used CRISPR genome editing system derived from ... CRISPR/Cas system makes use of 3 components, a guide RNA (gRNA) of about 125 nt that specifies the target...break (DSB) at the target site, and a donor oligonucleotide or plasmid as the repair material if needed...create a mouse model, the gRNA, Cas9, and donor oligonucleotide or plasmid components are brought together ...

...and are inconsistent between universities!) This guide tells you how to use online platforms, such as Zoom...recognizing the importance and benefit of remote and video communication. But first, take a deep breath; at...navigate a global pandemic can also be the thing that provides a new perspective that helps to clarify the harder...before selecting an advisor, it is always a good idea to introduce yourself to a few members of your desired...incredibly useful, as it gives a more comprehensive idea of that advisor’s research interests which can be...further discuss aspects of the lab, research, and provide them with a CV or transcripts if requested Thank...Thank them, and eagerly await a reply. It’s a good idea to email around three professors per program. Most...

... dedicated summary page with PubMed identifiers and links provided, in addition to a list of individual...read-outs other than cell viability. The following video provides an in-depth walk through of how to use ORCS...and other species. By accurately compiling genome-wide datasets, which are often obscured in large supplementary...different datasets that might otherwise be hard to identify. Figure 2: Users can cross-interrogate ...linked to the original publication via its PubMed identifier, which can also be used to search the entire ...as the original quantitative gene-level scores provided by authors rather than sgRNA-level sequence read...tables available with the publication are also provided for the user. This approach serves to maintain...