...one another, and a value of “1” indicating those markers are identical and completely indistinguishable... tumors, and moreso than other methods, the identification and isolation of rare cell types. In recent...relies on “unmixing.” Unmixing uses a complex mathematical algorithm and single stained reference controls...spectral flow experiment and panel, there are a few critical factors to keep in mind in order to get the best...autofluorescence across various tissue types varies, it is critical to include an unstained sample for each tissue...complexity index ranges from 0-1, with a value of “0” indicating those markers are completely distinct from one...samples. If you are using conjugated dyes, it is critical that your controls and your sample antibodies ...

...in normal biological processes and disease states. While LITE plasmids have clear application to anyone...effectors (TALEs) as anchors for genome engineering applications was still very new. Now, Konermann and her colleagues.... All of this requires genes to be regulated dynamically.” To understand how that works in memory formation...they could package LITEs in viral vectors and genetically target them to specific cell populations. They... the brains of living mice both quickly and significantly. Genes under LITE control showed a rise in transcription...prove the causal role of specific epigenetic modifications in the genome,” Zhang said in MIT’s press release...with LITE? Reference: Silvana Konermann et al. "Optical control of mammalian endogenous transcription and...

...? The available filtering options now change dynamically based on the type of material and specific search...articles. From paper to plasmid Authors regularly indicate that their plasmids are available from Addgene...papers. Maybe they started their deposit prior to publication and were able to include specific plasmid ID ...terms we can use to find materials from this publication. Searching for the title of a paper works You...filters Not every plasmid search will start from a publication. You may have an idea for a plasmid that would...guide RNA / shRNA inserts Resistance Marker: This indicates the selectable marker used in your model system...Requests: Only see plasmids with more than the indicated number of requests Availability to Industry: Restrict...

...retroviruses ” (Cullen, 1992) because of their more complicated genomes. Here, we will mostly use the gamma-retroviruses...(Prussin et al., 2015), only a small fraction typically cause disease. The gamma-retroviruses have their...wild-type viral particle — and of the normal, replicative life cycle — can help you understand these seemingly...of a non-living viral particle, and how we as dedicated researchers can exploit it. This blog was written...Hutcheson for her assistance with lentiviral replication.  Resources and References More resources on...101: Types of Viruses Viral Vectors 101: Viral Applications Resources on addgene.org Addgene's Lentiviral... proteins encoded by complex retroviruses. Microbiological Reviews, 56(3), 375–394. https://doi.org/10.1128...

...MCC develops and makes freely available technical and pedagogical resources, offers mentoring for instructors...best teachers and mentors pass on more than just technical knowledge, shaping their trainees’ very way of...citrate synthase and presented their findings at the American Society for Biochemistry and Molecular Biology...their research capabilities and laboratory and critical thinking skills (Knutson et al., 2010a,b). Classroom-based...implementation. Funded by the NSF (with Co-PIs Jessica Bell, Lisa Gentile, Ellis Bell, and Amy Springer...Einstein: A Life. Chapter 17, Einstein Discovers America. New York./  Callahan, K., Peterson, C., et al....biochemistry laboratory: Part I – guided inquiry – purification and characterization of a fusion protein: Histidine...

...candidate in the Sternberg Lab at Columbia University Medical Center. DNA transposons are ubiquitous genetic ... and have been adapted for a wide variety of applications - as mutagenesis tools for genetic studies (... The process also creates a 5-bp target-site duplication (TSD), a hallmark characteristic of the Tn7-family...a multi-spacer CRISPR array. Workflow and technical considerations Making insertions in bacterial ...into cells and plate overnight Screen colonies phenotypically or by PCR/sequencing While CRISPR-transposons...few important details. For transposons to be specifically recognized during transposition, genetic cargos...Leveraging a unique marriage between distinct biological elements, CRISPR-transposons excel at programmable...

... can often be accounted for using appropriate replicates and controls (see Tips below), and by validating...two-hybrid screening Minimizing false positives: Run replicates of the experiment to reduce the likelihood of...expression and correct folding, post-translational modification, protein degradation, access to the nucleus ...organisms, including bacteria, alternative fungi (C. albicans, pC2HB) (7) and mammalian cells. If the problem...co-expression of the enzyme responsible for the modification in the assay host strain can help. In order...that the configuration of your fusion proteins physically blocks the binding sites for the protein partner...Tachihara, K., Umezawa, Y.l. Split luciferase as an optical probe for detecting protein-protein interactions...

... at Sanofi Pharmaceuticals. This post highlights a rare disease, Fibrodysplasia ossificans progressiva...surpassed 60,000 views for the month of September! Historically we do better in September than in the summer...or you can’t quite remember the hazards of that chemical in your obscure growth medium, these apps can ...Binding Proteins," was contributed by guest blogger Jessica Sacher from the University of Alberta and describes...the post for the full details and many thanks to Jessica for all of her hard work and attention to detail...can find the rest of our September posts in chronological order here: Four Things I Learned at the 10... a Lab and a Project That’s it for now. As I indicated in the opening paragraph, I’m currently on my ...

...cancer. These later stages of a cancer diagnosis indicate, for Stage 3, that the cancer is large in size...size and may have spread while Stage 4 indicates that the cancer has spread from where it originated to ...asbestiform minerals such as erionite, are the only scientifically proven causes of the disease. There is no question... question on this point within the medical and scientific communities, and the link between asbestos and.... New techniques are currently being tested in clinical trials to detect mesothelioma earlier than ever...earlier, thus improving the patient’s prognosis significantly, but also to monitor those who may be at greater... working to fight the cancer.  Beyond early modifications to standard treatments and early detection, ...

...are subject to excision and ssDNA cleavage by canonical base excision repair enzymes. At the same time...2019). TREE is a real-time, fluorescent based identification system for the isolation of base-edited cell...targeted by a cytidine deaminase base DNA editor. Specifically the BFP mutant (BFPH66) contains a histidine...GFP positive cells isolated with TREE have a significantly higher frequency of genomic base pair edits ...GFP positive cells can be sorted and have a significantly higher frequency of base edits of interest than...robust induction of GFP fluorescence confirming the efficacy of GO as a base-editing reporter. As the initiation...markers, and other enzymes such as Cre-recombinase drastically expanding the base-editing reporter toolbox. ...

...were less significant than when non-targeting guides are used as controls. Less significant p-values lead... approach for identifying genes involved in a biological process. These screens provide an alternative...highly effective, are affected by low on-target efficacy, non-specific toxicity, and off-target effects...calling a gene a hit when really it’s not). In practical terms, this means that using safe-targeting guides...guides and may more accurately determine the significance of hits in non-growth screens. Off-target cutting...of on-target activity. However, there was no significant difference in depletion of ricin sensitizer genes...and do not have a major reduction in on-target efficacy. Results from Morgens et al. show that genome-...

...Addgene ID number, your publication will be listed on our website as a “Publication Citing this Plasmid” ...upon other researchers being able to find their publications in the first place. As a curator of the thousands...make it easier for you to find the plasmids and publications relevant to your research interests. We do this... this by promoting citation, supporting sophisticated search, and curating plasmid collections. Addgene's...number as well as the reference for its original publication. To help facilitate this process, we explain ...fruits of your labor and won’t have to repeat the modification. This will save both time and money. A quick...whether the plasmid has been used in your system. Sophisticated search You can search for specific plasmids ...

...any DNA editing functionality Collecting preclinical and clinical data about a disease or therapeutic Side-by-side... ReFigure. Reading and exploration including replications and experiments resulting in “negative data”...small selection of data found in full-length publications. As early career researchers, we wondered how...performance as in this antibody ReFigure Analyzing replications as in this ReFigure about whether Natronobacterium...reagent performs well, or you might publish a replication experiment that you conducted as part of setting...papers as they are not included in traditional publications. By submitting your data to a repository (Figshare...-registration, preprints, data, software, micropublications) in grant proposals. ReFigures are one such...

...If you use a kit for DNA purification or if you use a DIY purification protocol, you might have noticed... mutations in single stranded DNA undergoing replication.   DNase on the other hand can digest and degrade...degradation during plasmid DNA extraction and purification from E. coli is the presence of the protein ...most common E. coli strains used for plasmid amplification are endA negative, meaning the gene has been...chelating agents that can be introduced in the purification protocol to remove endonucleases activity. For...directly use your DNA preparation in any downstream application involving enzymatic reactions, a valid alternative...temperature for a short period, and there are indications that Tris buffer is better than water in these...

...The biomedical field is often concerned with understanding the cause of diseases and how to treat those...optimization is performed to take the drug to the pre-clinical and human trial phases.   So how does CRISPR factor...put into them in those later stages. Target identification Not all diseases are fully characterized or...simple pathology. In these cases, preliminary identification of potential targets by CRISPR can accelerate...enables researchers to select and generate physiologically relevant models. In complex diseases, it can...patient mutations which are variants of unknown significance – mutations with unclear effects on disease ...standard is to test the drug on models which are genetically proficient and deficient for the target. CRISPR...

...gene at once. Therefore, applications that require simultaneous modification of all alleles of a gene,...frequency three orders of magnitude higher than identical targeting vectors delivered through transfection... recommends designing homology arms with the modification of interest, ordering them from a gene synthesis...with a homologous repair template. It is this application - the creation of sequence-specific knockins ...clones, making it unsuitable for most in vivo applications.  Third, even in the most optimized tissue-culture...tissue culture based approaches that require modification of only a single allele of a gene, such as the...efficiently deliver large repair templates for applications that require large gene fusions. The current...

...where you can start to identify which items aren’t critical to your research success. If you can get away ... most start-up P.I.’s. It doesn’t have to be complicated, or difficult to create this list. Start BEFORE...resources to keep, and which ones to abandon. It’s critical to make these decisions in the following order... budget can help you compare the monetary and empirical value that helps you determine whether or not ...know how to decide which components are the most critical to your research, negotiations can be much easier...negotiating finances, instead of solely discussing numerical values, try to keep conversations focused on research...discounts, collaborations, access to internal award applications, etc. If this is the institute that can help...

...structural characterization and applications in fluorescence imaging." Biochemical Journal 400.3 (2006): 531...fluorescent protein: identification of the molecular determinants of color and applications in fluorescence... be used as a fusion tag for a wide range of applications from traditional imaging to FRET and stochastic...492 nm, respectively), they gave this a teal classification rather than cyan and named the protein mTFP1...FRET reporters. mTFP1 is also insensitive to physiologically relevant changes in pH. Find mTFP1 plasmids...excitation maximum 399 nm) because it does not significantly excite at 400 nm while EGFP does. Find mWasabi...

... or pharmacological manipulations on cells, and has potential use for a wide range of applications in ...platform at Addgene. Braselmann E, et al. Nature Chemical Biology. 2018 PubMed PMID: 30061719. New tools...expression vector (pRSETB). Fabritius A, et al. Cell Chemical Biology 2018. PubMed: PMID 30220597. ACE system...versatile in vivo fluorescent reporter for rapid quantification of base-editing and Cas9 cleavage activity ...plasmid that allows for rapid fluorescence-based quantification of base editors that utilize dCas9 fused to... The reporter constitutively expresses eGFP to indicate reporter abundance, and mCherry fluorescence is...frame-shift mutation within the mCherry reporter. Quantification of editing efficiencies simply involves tracking...

...tolerates occasional mismatches or indels. Empirical tests indicated that a reasonable rule is to require at... While there were software tools available to biomedical researchers manipulating DNA sequences on a daily...features such as antibiotic resistance markers and replication origins, but there is extensive heterogeneity...different microbial strains. It proved to be impractical to catalog every variant of a feature. Instead...that have different properties. To prevent misidentification, we augment the database with new fluorescent...protein variants. The future of DNA feature identification What’s next for common features? We plan to...Genetics and Cell Biology at the University of Chicago. He was an early depositor at Addgene, and conceived...

...Storytelling is a crucial part of interpersonal communication, which makes honing your ability to tell stories...calmed the situation down by opening a dialogue specifically about the project and contributions, rather ...wherever it makes sense to start and try to be as chronological as possible — if you find yourself jumping backwards.... Your story should be too. Use drama Use any rhetorical technique you have in your arsenal to make sure...start point and it needs a good end point. One thematically pleasing option is to end at the present — ‘...other options. Choose something with emotional significance that is likely to be memorable. Work out what...Addgene Blog Check out our blog posts on science communication Find interviews scientists in SciComm careers...

...type; however, their usage has been limited by technical problems. For instance, it’s much more difficult...protein-only transduction method and its potential applications to CRISPR/Cas9 genome editing.   Protein-only...that components in the buffer used for protein purification must be helping the untagged protein enter cells...Diego D'Astolfo. CRISPR/Cas9: a potential application of iTOP Having tested iTOP using Cre-lox recombination...showed up to 70% resistance to diphtheria toxin, indicating a 70% frequency of biallelic mutations. Importantly...Importantly, hESCs retained their stemness, indicating that iTOP may be valuable for CRISPR/Cas9 stem cell...potential for off-target effects. Third, protein purification (once a protocol has been established) may be...

...researcher and science communicator.  Update (7/17/2018): Check out Fatima's recent publication on her HMO work...protein-protein interactions. Beyond these common applications, researchers are finding new ways to apply fluorescent...Zhou and Fatima Enam. There were many excellent applicants but Xin and Fatima stood out for their creativity...utility of these FLiPs in a variety of research applications and particularly notes their ability to be precisely...known to bind to the HMO of interest. Fatima specifically proposes using this sensor to detect HMOs found...endeavors, Fatima hopes to practice her science communication skills throughout her training and wants to ...work in Cell Chemical Biology! Additional Resources on the Addgene Blog Learn More about Photosactivatable...

...Harvard Medical School and the University of Toronto. He is an author of 20+ scientific publications and ...quick turn-around time of Sanger sequencing have historically matched the needs of most molecular biology ...smaller fragments that are then barcoded for identification. This mixture of barcoded fragments is known... a collection of 96 plasmids on a plate) will typically have a wide range of input quantities. This variation...samples. As mentioned above, one of the primary technical benefits of plexWell™ is that normalized libraries... proprietary chemistry). This turns out to be critically important for getting adequate sequencing depth...computational biologist with a passion for solving critical sequencing problems. He received his PhD in Bioinformatics...

...these proteins are FDA-approved or in clinical trials or preclinical studies already. We are following up...expand to other cell types, including more physiologically-relevant systems, to catch all the important... we found in our map have an impact on virus replication. While we and our collaborators are starting ... Nsp3 and Nsp16, and includes an additional catalytically dead version of the viral protease, Nsp5. Our... 2xStrep-tag for easy detection and affinity purification. All but one are in a pLVX vector background...coronavirus, one FedEx package at a time Since the publication of our paper, our group has been inundated with...Eckhardt and Melanie Brewer are on the Science Communications Team at QBI UCSF. They are particularly interested...

...ll be talking about the ins and outs of this classification system, including its history, biology, and...repeatable phenomenon, Gram began using it as a classification system. Eventually, any bacteria that retained...gramstain.html Smith, A. & Hussey, M. Gram Stain Protocols. American Society for Microbiology (2005). https://asm.org... or pink. Purpose Gram staining can be used in medical settings to determine the general type of bacteria...permeable to different classes of antibiotics. The classification system is also useful in a laboratory setting...bacteria type. The gram positive and negative classification system is incredibly helpful in visualizing...stepping into a lab.   Anna Kamens is a science communication summer intern at Addgene and a rising third-...

...Technology and its Application in Genetic Diseases: A Review.” Current pharmaceutical biotechnology. https...2020.  “CRISPR Gene Therapy: Applications, Limitations, and Implications for the Future.” Front. Oncol...several treatments are currently being tested in clinical trials. It is speeding the process of the discovery...the technology in different labs for different applications.” Li’s team noted that CRISPR/Cas9 has been ...cleavage sites are repaired.” Those insights will be critical for scientists’ ability to influence editing efficiency...with size limitations. In addition, non-viral applications are also possible through the use of nanoparticles...

...mentor (if you have one) to communicate your plan as well. Making logistical and funding arrangements Visiting...the host university does not hire or pay them (typically). A visiting scientist is distinct from equipment...the scientist to the new institute where their typical workdays will be carried out until the end of the...equipment! Preparing for your visit   Design and communicate a research plan Your time at the new research... and you are set up for success. If you are communicating with a professor or institute, ask if you will...expect to generate data that will contribute to a publication? A grant? A patent? It is never too early to ...Resources Resources on the Addgene blog Fostering communication in remote collaborations Transferable Skills...

... and 15/17 morphologically aligned. Documentation of the network that initiates biological reprogramming...unique barcodes for each TF help streamline identification. While the Zhang lab controlled their multiplicity...single TF was delivered to each cell, future applications could deliver multiple TFs to each cell, allowing...processes. For help with library transformation and amplification, refer to the Zhang lab’s previously published...published protocol and its relevant modifications on the pooled library webpage. Disease models Good disease...generate, in part because of difficulty with replicating the specific dysregulation in the disease. For...Addgene.org Plasmid Pooled Libraries Pooled library amplification Zhang Lab CRISPR Plasmids The Human TFome Library...

...agreement on the transfer of biological materials in 1995: the UBMTA. Because biological materials are widely ...many different flavors of MTAs, but the Uniform Biological Material Transfer Agreement (UBMTA) is one of...MTA for that plasmid facilitated by Addgene — basically, instead of having to sign individual MTAs for...things being organized, tracked, and clearly communicated. And that’s where MTAs, and similar agreements...agreements allow for centralized tracking when biological reagents are shared — both at what time and with... options for the terms you want to share your biological materials under! While most plasmids at Addgene...portal automates a lot of the process, from notifications and emails to generating the UBMTA link for ...