...inappropriate statistical methods, omission of some data, etc.  The firestorm that followed implementation of the...condensed into a statistically evaluated set of values.  However, to evaluate the interpretation of the experiment...Instead, selected images are said to be representative or the statistical variation is calculated and placed...overnight revelation, rather it was the result of consultations between researchers and publishers. Nonetheless.... The PLOS policy on data access is a formal statement that is already practiced or required by many ...means that supporting datasets must be logically annotated and arranged, as in an actual publication and ...efficient science. Improvements in our discipline for annotation and archiving of data are likely to improve research...

...astounding number of ways to create chromosomal mutations in bacteria, so many that it may be difficult ...path to take. A quick and easy way to introduce a mutation in the chromosome is to disrupt expression of ...genes. However, there are ways to create scarless mutations, ones that don’t leave any undesired scars in ...technology has also aided in the creation of scarless mutations, both in stand-alone systems (Jiang et al., 2013...plasmid curing steps, and can generate off-target mutations. Modifying bacterial genomes using counter-selectable...is frequently called allelic exchange. Here, a mutated allele introduced from a conjugative plasmid replaces...versatile technique, and is less prone to off-target mutations. Ultimately, successful allelic exchange requires...

...number of limitations that you may run into if you choose to use it. Several of these limitations and possible...protonated and a deprotonated state (Tsien, 1998). The deprotonated state has an absorbance maximum around...protonated state, however, does not absorb light at 488 nm. The ratio between the two states is reflected...encoded probe, but there are limitations. Being aware of the limitations is important for the successful...mEGFP. This variant was made by introducing two mutations (F64L, S65T) in the original jellyfish GFP (AvGFP...with improved brightness (Tsien, 1998). Another mutation (A206K) is necessary to generate the strictly ...autofluorescence is less of a problem when the excitation wavelength is shifted to longer wavelengths. ...

...understand Lowe Syndrome, a devastating genetic disease caused by mutations in the OCRL1 gene that leads...different mutations in a gene called SOX10. To understand the functional role of those mutations, they now...to work to explore the effect of various OCRL1 mutations on cell behavior in greater detail. The goal is...sensitive to sunlight and prone to developing metastatic melanomas and other cancers. Joshua Wang (bottom...CRISPR-Cas9 constructs from Addgene to gene-edit mutations into XP genes and other genes involved in photosensitivity...plasmids to explore the functional differences among mutations responsible for the disease known as Alternating...the brain. McSweeney says they now think that mutations in the gene may prevent neurons from returning...

... mentioned, I also added citations in real time as I wrote, so each statement was referenced even in the...studies that reported mutations in that protein (including how frequently a mutation was found and the size...review Once you start reading, there will be a temptation to include every piece of information that was...review articles Whether submitting a review by invitation or by your own accord,  once you have these rules... write, meaning I use the software to add the citations in real time as I write. Things are going to get...from the beginning. I also recommend using the citation style of (Last name, Year) in the document while...experiments. Later, you can easily convert the citation style to whatever the journal requires. Using ...

...Syndrome research. With a shared passion for facilitating research and discovery, Addgene and RSRT have...approaches. What is Rett Syndrome? Caused by a mutation in the methyl-CpG binding protein 2 (MECP2) gene...Zoghbi's lab discovered the first disease-causing mutations in the MECP2 gene leading to Rett Syndrome (Amir... regulate transcription (Baker et al., 2013). Mutations that affect this interaction to varying degrees...determine the clinical severity of different MECP2 mutations. More recently, the Bird lab found that only a... human MECP2 locus and MECP2 protein, showing mutations corrected by CRISPR/Cas9 in wild-type human iPSCs... exciting and promising results for repairing mutations in models of neurological disease. Klaus Rajewsky...

...primers with your desired mutation, performing PCR to generate the mutation and linearizing your vector... limit to where the mutation can be placed. With other techniques, when mutations are spaced farther apart...multiple synthetic fragments, create multiple mutations in one or multiple fragments, and generate constructs... Generation of constructs with multiple point mutations Cloning sgRNAs Production of Yeast Expression ...Cassettes Generating constructs with multiple point mutations NEBuilder HiFi can simplify multi-position site-directed...assembling multiple fragments containing the desired mutations. This same process can be used simultaneously ...simultaneously for the generation of one or more mutations – it is as easy as obtaining a plasmid with the gene of ...

... differences of twofold or greater with good statistical significance (Taylor, 2017). With the right conditions...different efficacies DART-PCR No Raw Data Statistically defined log-linear phase   Table 2: ... them back before reporting the data!   Statistical analysis  Getting your RQ value isn’t the end...your analysis process. You’ll still need to do statistical analysis to determine if there are any significant... Yuan, 2006 has a good overview of different statistical analysis methods that pair well with slightly...step, remember we here at Addgene frown upon statistical laxness in all its forms. Reporting your data...provide you with the highest form of flattery - imitation! Use the MIQE guidelines (Bustin, 2009) to ensure...

...select your state. State Legislatures: To find the website to contact representatives at the state level you...based on our most accurate interpretation of the world, and this interpretation should not effected by claims...contact your representatives in case you would like to talk with them about science: Representatives: To find...contact information for your representative in the House of Representatives all you need to know is your...march in Washington, D.C., the seat of the United States government? Politics and science are intrinsically... you can click on your state in this map. Finally, the march is meant to inspire scientists to be more...Center: The Politics of Climate Change in the United States CNBC: Kellyanne Conway: “I”m not in the job of ...

...frameshift mutation. The majority of cellular repair events will generate these types of mutations, making...recognition sequence is destroyed via mutation. By introducing a mutation in either the PAM or the guide recognition...mishaps in this class of genome edit. Knock-in mutations and gene editing Targeted genome editing events... this is not the case for knock-ins. Knock-in mutations typically require an exact DNA sequence to be ...cells. It is important to know that HR is often mutated in cancer cells, specifically in breast and ovarian...recommended you check your cell lines for HR-related mutations before attempting knock-ins by HDR.   ... with some success (Yu et al., Nat Chem Biol). Mutate the PAM or sgRNA sequences Cas9 likely goes through...

...information regarding immune cell mobility than the static microscopy images of chemically coloured lymphoid...source is mounted above (epi) the specimen and the excitation light passes through the microscope objective... or dyes. 3. Two-photon microscopy Two-photon excitation microscopy is a fluorescence imaging technique...fluorescent molecule (see figure to the right). The excitation generated by these two-photons occurs only at...immunologists the ability to count cells and statistically analyze cell movements. By using cells labelled...diverse tissue environments. These studies provide quantitative measurements of cellular motility, interactions...understand what is going on in the body at steady state or under physio-pathological challenge. However ...

...their leadership status in their current field of expertise augments their authoritative voice. Send a draft...share a common set of criteria such as citizenship status, academic year, and grades that serve as automated...can be found on the Addgene blog.   3. Personal statement brilliance In addition to sending in a cover letter...letter, you are always asked to draft a personal statement, which is the perfect opportunity to paint a comprehensive...devoting some time to writing a solid personal statement will pay dividends. This is the only opportunity...tools that can help you craft a solid personal statement.  4. Letters of recommendation wisdom  Reach out...for the character you painted in your personal statement. Make certain to choose your recommenders based...

...complements the mutation allowing for a functional enzyme. This process is called α-complementation. The system...β-galactosidase enzyme through α-complementation (cell B). As shown on the representative plate to the right, colonies... that deleting a section from the lacZ gene (a mutation called lacZΔM15) creates a non-functional β-galactosidase... inserted it into a plasmid, creating an α-complementation cloning vector. When a cloning reaction goes...will not complement the cell's β-galactosidase mutation. An unsuccessful cloning reaction leaves the α-peptide...initial overnight incubation increases pigment precipitation, enhances the blue color of negative colonies...proper E. coli strain (i.e. contains the lacZΔM15 mutation): XL1-Blue, DH5α, DH10B, JM109, STBL4, JM110, ...

... Validating knockout mutations When a knockout cell line is desired, any mutation that introduces a frameshift...silent mutation in a neighboring nucleotide along with your desired edit. This silent mutation should ...cells were appropriately edited for your desired mutation - insertion, deletion, or site-directed knock-...is. If you are trying to introduce a homozygous mutation, it’s helpful to know how many copies you are ...Secondly, categorize your edit – is it any frameshift mutation? A specific insertion or deletion? A knock-in?...large deletion events.   Validating knock-in mutations You’ve introduced a donor template along with ... editor. What next? When generating a knock-in mutation, the best screening method depends on what your...

...in Figure 3. Though Cas9 is not a static molecule in any binding state, RNA loading stabilizes the closed...pyogenes Cas9 in the apo state (PDB ID 4CMP, top) compared to the guide RNA-bound state (PDB ID 4ZT0, bottom...Crystal structure of S. pyogenes Cas9 in the apo state (PDB ID 4CMP) with domains colored as in Figure ..., 2018), but it’s most often shown in an “open” state, with the NUC and REC lobes laying open like a book... that recognizes the PAM is so flexible in this state that it doesn’t appear in the crystal structure ...very weakly, most likely through unstructured electrostatic interactions. It also can’t recognize PAMs, ...region of the CTD, which is disordered in the apo state and absent from that structure. HNH, red; RuvC, ...

...unfavorable donor-acceptor orientation limiting FRET efficiency, circular permutation (Baird et al., 1999) ...Resonance Energy Transfer. Unlike the typical excitation and emission of an excited fluorophore, FRET ...typical steps in FRET are: 1. Donor fluorophore excitation by absorption of a photon 2. Energy transfer ... of the acceptor fluorophore back to its ground state by emission of a photon with wavelength specific...spectrum of the donor fluorophore overlaps with the excitation spectrum of the acceptor fluorophore. Otherwise...correlates with a change in the distance and/or orientation of the FRET pair. Since many biological processes...noise to the measurement. If the distance or orientation of the donor and acceptor proteins is not optimal...

...rely on that clone not having any confounding mutations, the risk is high. You are generating a gene therapy...patients and the diseases associated with an elevated mutation burden. The CRISPR platform must be optimized ...off-target sites. For example, if there are 10 putative off-target locations you can 1) determine if editing...hardly any flexibility in gRNA placement (e.g., mutating a specific amino acid or introducing a specified...evoCas9 are a few spCas9s which have been evolved or mutated to be more specific for exact gRNA matches (Rabinowitz...occurs. 2 gRNA approach Off-targets that come from mutations arise from base/prime editing or Cas cleavage....cleavage. In the case of Cas cleavage, off-target mutations can be mitigated by using two gRNAs in close proximity...

...balanced against the limitations of the assay.      Fig. 1: A schematic representation of Sybr Green ...PCR-based applications (qPCR and ddPCR.) qPCR Quantitative/real-time PCR (qPCR) has been used for copy ...amplicons under 100 bp (Ma, 2015.) A schematic representation of the Taqman reaction can be seen to the left...each reaction, math happens (this time, Poisson statistics), and the readout gives an absolute value of ....  Whichever method you choose, resist the temptation to over interpret your results: Sybr cannot be...product on a gel. And only ddPCR provides absolute quantitative data, instead of relative quantification.  Even...Arya N, Patel HR. Basic principles of real-time quantitative PCR. Expert Rev Mol Diagn. 2005 Mar;5(2):209...

...outlined below (or emission wavelenght range).  By mutating GFP, the variants blue FP (BFP), cyan FP (CFP)...breakdown of GFP, it's variants, and their relevant mutations, check out Marcy's post from last week on GFP....switch their color when activated by a specific excitation wavelength. This means that the emission wavelength...wavelength can change. In a few cases, the initial state of the protein is non-fluorescent, thus allowing...George G. Stokes) is the shift in wavelength from excitation to emission. For most FPs, Stokes shift is less.... Fluorescent Sensors: These FPs change their excitation/emission behavior upon environmental changes ...also is also called Bimolecular Fluorescence Complementation (BiFC). 8 points to keep in mind when choosing...

...CamR) by introducing a point mutation (H193Y). The reversion of this mutation by an adenine base editor ... Fulbright Visiting Scholar at the Pennsylvania State University. Imagine you are dealing with a defective...relies on the efficient delivery of donor DNA to facilitate repair. Since the development of CRISPR-mediated... of different basic BE technologies and their adaptation for plant genome editing. Cytosine base editors...desired T-A base pair. Figure 1: Transition mutation (C>T, G>A, A>G, and T>C) installation by base ...systems. Thus, the Yang Lab at The Pennsylvania State University (PSU) is adapting and improving base ...base editor (ABE) vectors to install A>G or T>C mutations in the plant genome. We constructed three versions...