...out for help so you can get the support you need. 2) Prepare an agenda for every meeting Supervisors are...familiar with the minute details of your work. Describe the problem by stating the facts and explain how...

...You’ve probably heard that only 2% of our genome is made of protein-coding genes, and you might be wondering...non-coding RNAs (lncRNA). lncRNAs are over 200 nucleotides in length and lack an open reading frame, so ...transcription machinery of a target gene or DNA that codes for ncRNA. CRISPRa, on the other hand, recruits ...which targets RNA instead of DNA and selectively degrades RNA molecules. This system is often used to knock...

... already have an end product in mind, steps 1 and 2 will generally be straightforward. Likewise for step...components into mammalian cell lines is quite broad and includes several different methods, so we've summarized...

... Werner S, Marillonnet S. PLoS One. 2011 Feb 18;6(2):e16765. doi: 10.1371/journal.pone.0016765. PubMed...resistant to disease. They also devise biosensors designed to elucidate the molecular interactions that go...things for day-to-day life in a plant lab, so it includes everyone’s favorite promoters, plus a few new ...

...al (Nature. 1988 Jul 28;334(6180):320-5.) PubMed. 2. A segment of the 5' nontranslated region of encephalomyocarditis...adapted "self-cleaving" 2A peptides into their muliticistronic vectors. These peptides, first discovered in ...plasmids) are designed to have one or more of the genes replaced.  Additionally, 2A peptides could be PCR-cloned...PDF that you can save on your desktop. The Plasmids 101 eBook is designed to educate all levels of scientists...incorporated into plasmids for research purposes are described below. IRES Elements Translation in eukaryotes...the specific genes cloned into the vector.3  2A Peptides To overcome some of the disadvantages of the IRES...self-cleaving" is not entirely accurate, as these peptides are thought to function by making the ribosome...

...overhang twice; (2) avoid palindromes; (3) no overhangs with the same three nucleotides in a row; (4) no...rules of thumb for designing your overhang sets. But are those rules the best way to design GGA overhang sets...data-optimized assembly design (DAD) to build out three tools to help researchers design high-fidelity Golden... no more than two nucleotides in the same position; (5) avoid overhangs with either 0% or 100% GC.) In...the traditional rules of thumb for overhang set design allowed for high-fidelity assembly for sets of ... overhangs that violate some of the traditional design rules) for successful high-complexity Golden Gate...with a high potential for mismatches, so you can redesign individual pieces as needed to improve fidelity...

...Central PMCID: MC4262738. 2. Doench, John G., et al. "Optimized sgRNA design to maximize activity and ...These libraries utilize optimized sgRNAs that were designed based on the rules identified in Doench et al....1,000 non-coding control sgRNAs. This library was designed to improve on-target activity while reducing off-target...with 6 sgRNAS, highlighting the benefit of sgRNA design in CRISPR libraries. Thus, the Brunello library... that if an essential gene plays a role in the desired screening phenotype, it may be missed because it's... the sgRNA metrics, confirming again that sgRNA design plays a significant role in library efficiency....CRISPRa, sgRNAs were targeted between 150-75 nucleotides upstream of the TSS. Similar to the Brunello ...

...Henrietta Lacks. New York: Crown Publishers, 2010. 2. Gold, Michael. "A conspiracy of cells." State University...contamination and match their original description. The oldest, largest, and most diverse of these repositories...culture in the present day Cell culture is a widespread tool used in the fields of oncology, virology...problems surrounding cell culture over the last few decades some pharmacologists have tended to avoid cell ...International Cell Line Authentication Committee includes a database listing all cross contaminated or misidentified...comparable studies to be performed on a cell line even decades after it is initially isolated. Regrettably this...Master and Working stocks to work from. The future Attitudes are changing but yet more is needed to convince...

...split at 175 Arabidopsis homolog of the yeast TREX-2 mRNA export complex: components and anchoring nucleoporin...Have no fear, Addgene is here to help!  General Design Figure 1: Two proteins are fused to the ...from the associated paper:   Color Base FP Description Article PI Blue EBFP2 EBFP2(1-10) and Capri...contains both fragments of split mVenus (aa 155), includes I152L in N-terminal fragment An enhanced recombinant... Dan Mulvihill mVenus Split mVenus (aa 155), includes I152L in N-terminal fragment Constant rate of ...reversible complementation. TagBiFC (split HaloTag) provides maximum flexibility in color labeling with exogenous...single-molecule tracking in live cells.  Controls  When designing experiments, it’s important to include proper ...

... vivo and in vitro applications.   Figure 2: Modular features of DIRECTED particles where the ...unstructured templates and significantly reduced undesired edits (indels, etc.), while PE6c and PE6d were...Delivery to Intended REcipient Cells Through Envelope Design). This modular approach combines an interchangeable...Cell type-specific delivery by modular envelope design. Nature Communications, 14(1), 5141. https://doi.org...LOV-Turbo plasmids here! Next, Qin and Cheah et al. described TransitID, where two proximity labeling enzymes...that had been trafficked from the “source” to “destination”. Images adapted from Lee and Cheah et al. 2023...Figure 4: Time-resolved protein ticker tape. A) Design of iPAK4 protein ticker tape recording. B) HEK ...

...mazF gene and a gene for Zeocin resistance (Figure 2). This MazF-ZeoR cassette is flanked by two direct...than plasmids without this DNA. They eventually designated this fragment as the ccdB region (for “coupled... serves as a counterselectable marker in the destination vector. Successful cloning occurs when the ccdB...restriction endonucleases in plasmid addition was first described by studies of EcoRI and Bsp6I in Escherichia coli...systems. As with the other toxin-antitoxin systems described above, one part of the pair is more stable than...toxin-antitoxin system discovered. Unlike the systems just described, the hok/sok systems consist of three components...long-term experiments. They’ve also helped researchers design and optimize cloning methodologies using counterselection...

...the necessary steps to perform:      Fig. 2: Quick-stepping to a FASTA file   With our outline...of data. In this two-part blog series, we will describe the importance of bioinformatics at Addgene and...each week. Our internal software was originally designed to help us work in large formats, such as 96-well...Thanks to the flexibility inherent in Nextflow’s design, we were free to use multiple programming languages...alone! The benefits of containers are they are designed to ‘contain,’ in a complete package, all of the... who or which computer ran the process. Another design choice we appreciated about Nextflow was how effortless...small with a print statement and tested that the desired data was available so we felt confident we were...

...PMID: 18478103. PubMed Central PMCID: PMC2364656. 2. Dittmar, Kimberly A., et al. "Selective charging ...features to consider when designing a full gene. A non-exhaustive list includes: Codon abundance relative...that their codons are more appropriate for the desired expression host. This is known as “codon optimization...as easy as it sounds. Even for relatively short peptides, there can be many possible ways to encode them...every amino acid I’d like to encode,” but, as described above, not every region of a protein should necessarily...PubMed Central PMCID: PMC4794256. This review provides a great overview of codon usage bias 8. Tuller...

...based antiviral method to degrade RNA from SARS-CoV-2 sequences and live influenza A virus. It was demonstrated...their BioRxiv post, the authors generated and described several improved genetically encoded fluorescent...Takayuki Iwaki, Kimiko Hara, and Kazuo Umemura have described a simple method which alleviates the inclusion...contains the signal peptide of MBP, followed by the desired nanobody (NB) sequence, an AviTAG, and 6xHis tag...expression can vary significantly depending on transgene design and delivery. To overcome these variations in human...Addgene The MoClo CRISPR/Cas Toolkit for plants includes 95 plasmids consisting of CRISPR/Cas nucleases... uses CRISPRi to control gene expression. This includes a CRISPRi-based synthetic oscillator, bistable...

...transposase systems utilize with type I-F Cascades. Figure 2: Cascade complex from CRISPR type I-E....Cas11. Type I-E Cascades contains all five of these Cas proteins, while type I-C Cascades do not contain... 1: Schematic of Class 1 CRISPR types. Class 1 includes type I with a Cas3 effector, type III with a Cas10...maximum efficiency of the process. Various labs have designed all-in-one Cascade plasmids — such as the Tomoji...

...rate of 10-55% - the PASTE system.     Fig. 2: Schematic of programmable gene insertion with PASTE...The hardest part of any revolutionary discovery, including CRISPR, is turning potential into impact. ...two pieces: a single protein, computationally described as a fusion of four Cas7 proteins and a putative...RNA editing methods — streamlining experimental design and its potential for clinical applications. Specifically...high-fidelity rate. Both Cas7-11 and PASTE open up multitudes of possibilities at the bench and potentially...

...that view (Callahan et al., 2022).     Fig. 2: Students in an MDH CURE replaced select residues ...semester one and then proceed to use those skills to design and carry out their own novel experiments in semester...resources, offers mentoring for instructors, and provides opportunities for students to exchange ideas and...results in student learning gains and positive STEM attitudes in CUREs. CBE Life Sciences Education. 21(4):ar74...

...would help them grasp some of the key concepts (Fig. 2). One thing I will likely change for next time is ... can teach  5-10 year olds in a single evening. Grades K-5 cover a broad range of attention spans, skill...CRISPR work? This section was essentially background slides getting everyone on the same page in terms of the... by running it by the teachers and sharing some slides on Twitter, where I was able to get some great ...

...replicate, then purify the DNA.     Figure 2: A pooled library page with protocols boxed in red... If not, our protocol on Lentivirus Production provides a general approach for producing lentivirus in...excellent protocol paper by the Feng Zhang lab describing construction, lentiviral production, transduction...the Broad Institute- A variety of protocols and guides regarding pooled libraries, from cloning a pooled...

...pairs.  Figure 2: (A) The codon wheel depicts the 64 codons that encodes the 20 amino acids and...Usage Tabulated from GenBank database (CUTG), that provides an electronic dataset for codon-usage of 257,468...Codon Optimization  ATUM DNA2.0  IDT Synthetic gene design made easy GenScript- GenSmart Codon Optimization...