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...enhancer sequences in different chromatin states. Alexander Stark and colleagues at the Research Institute...their position relative to a transcription start site. In STARR-seq, randomly sheared genomic libraries ...(Q3) MARCH 2016Enhancer activity mapping with STARR-seq   Although many technologies have been developed...Pathology have developed an alternative method, called STARR-seq (self-transcribing active regulatory region ...over input levels using next gen sequencing. The STARR-seq backbone is available from Addgene in both human...including but not limited to cell growth and drug resistance. Recently, the Wu Lab at Texas Tech developed...plasmid or as individual plasmids shipped as agar stabs. Iverson, et al. ACS Synth Bio. 2015. PubMed PMID...

...produce substances toxic to themselves? What are toxin-antitoxin systems? These toxic substances are part...these systems is that the toxin is stable while the antitoxin is unstable, meaning that the cells must continually...the pair is more stable than the other. Here, the restriction endonuclease is more stable than the methyltransferase...degraded leaving the cell to be killed by the more stable toxin. Cells only survive if they retain the plasmid... contains the mazF gene and a gene for Zeocin resistance (Figure 2). This MazF-ZeoR cassette is flanked...) contained within it by selecting for Zeocin resistance. Then, counter-selection with methanol medium... unmethylated sites in the chromosome. The more stable endonuclease can then cut the chromosome leading...

...leave. I was really devastated when that happened. I didn't know if I should even stay in science.” ...by choice, but by circumstance. She was working as a research and technical assistant, when her life changed... all of the Meet an Addgenies features on Instagram! Staying true to your values While going through the... major and a Spanish minor, it’s time for me to start considering my future path. Talking to Addgenies... what lies ahead. Thus the “Meet an Addgenie” Instagram interview series was born. Over the six months...who has been in many roles in Addgene since he started, said, “the thing I wanted more of [after undergrad... a few years ago at a CRISPR meeting.Read his Instagram feature here. You also don’t have to go back...

...using biorender.com.   Dye stains Dye stains are non-antibody-based stains that bind DNA or free amines...alongside standard surface labels. Here, I will introduce you to a few useful labeling and staining techniques...techniques beyond standard surface labeling. Pro tip! Many people use 'labeling' and 'staining' interchangeably... it comes to viability and proliferation staining. Dye stains are membrane-permeant or -impermeant and...nucleus, or visualizing DNA instead of proteins. Some stains can diffuse through the cell membrane freely, while...Addgene uses 'labeling' to refer to antibodies and 'staining' to refer to small molecule dyes. Indirect labeling...cross-linking, killing the cell but preserving the cellular state (think of mummification). Permeabilization, as the...

...differentiate between variations in those factors. To understand the principles of gating, you’ll first need to... the magnitude of FSC, SSC, and all fluorescent stains. The cytometer's software will allow you to adjust...specific gates (single cells, live cells, my marker stains of interest). Let’s double-click inside our gate...duplicates can’t be reliably analyzed on their staining signals. For this, you’ll need to gate based on...here, I actually want to gate on my negative, unstained population, which I can clearly differentiate ...positive one (Figure 8). Note that in many cases a stain will not result in clearly distinct positive and...in between. Again, it can depend on the type of stain whether a tighter or looser gate makes sense. Here...

... a small group of scientists including Stanley Falkow, Stanley Cohen, Herbert Boyer, and Charles Brinton...treated a tetracycline resistant plasmid, pSC101, and a newly developed kanamycin resistant plasmid, pSC102,...EPISOME-MEDIATED TRANSFER OF DRUG RESISTANCE IN ENTEROBACTERIACEAE VIII: Six-Drug-Resistance R Factor.” Journal of...the 1940s and 50s, scientists were working to understand genetic cytoplasmic factors that could be transferred...other extrachromosomal particles, particularly Resistance or R-factors. Like F-factors, R-factors could... selected for E. coli transformants that were resistant to both. When this proved successful, pSC101 became...in these cloning experiments. Although plasmids started as a somewhat niche area of research, they are ...

...While the importance of understanding these complex processes can’t be overstated, we can also learn a lot...solutions to transmitting forces over long distances. For instance, how much force can be generated by conformational... a structured material over a long distance? And can we understand such a structure well enough to engineer...dynamically rearranging into different polymerization states. Instead, R body monomers respond to pH changes...

...guarantee 100% transfection efficiency. Stable transfection A stable transfection is used to create a population...genetic material directly into the genome to form a stable transfection. Unlike bacterial transformation, ...described below, are typically employed when creating stable cell lines and are not used for general plasmid...this ever-versatile fluorophore in a later post, so stay tuned! Transient transfection and the elusive "mammalian...expression in yeast and bacteria, plasmids used for stable transfections rarely contain an ORI since the integrated... subsequently pass it on to future generations. Stably transfected cells may be considered an entirely...Positive selection in mammalian cells To achieve stable transfection, there should be a selective pressure...

...functional antibiotic resistance. Colonies with an insert in pUCXKT will therefore have resistance to both kanamycin...the genome and to determine, for instance, the intra-nuclear distance between loci on different chromosomes...many paths. Understanding how a protein traffics through these pathways is key to understanding, and potentially...ingenious two-state assay based on the reversible interaction between a hook protein stably localized in...and monitor individual living cells in order to understand how they work. Light activation allows scientists...This leads to 2048 (211) possible combinations of states. Each of the integrases is supplied on its own ....1038/nmeth.3147. Bioluminescent pH sensor Understanding intracellular pH regulation is important as ...

...your ideas are not well received, understand that people can be resistant to change. Ask your peers or your...: creativity. I’ve heard quite a few scientists state that they’re not creative, usually saying that they...creative problem-solving process?  You may want to start by carving out time to tackle it. It’s easy to get...Another strategy for your brainstorm session is to start with something completely unrelated to the issue...Originals by Adam Grant, a creativity expert at Stanford conducted an experiment in which people were asked...were instructed to use the three-ring binder as a starting point, the ideas generated were hardly novel. .... When told to use a roller skate as a starting point, their ideas scored 37% higher in originality. It...

...worrying about the status of your RNA. gRNAs modifications are even going beyond stability, adding color and...modified) for optimal stability and efficacy.    Base modifications What is more stable than RNA? DNA! One...their precious RNA samples. RNA is inherently less stable than most macromolecules used in scientific research...or protein. It comes as no surprise then that stability of the RNA used in CRISPR-Cas9 experiments – the... and even on-off switches. Stabilizing gRNA modifications  Sugar phosphate backbone modifications The...phosphate molecules of the RNA backbone to increase stability.  Nature has evolved ways to prevent degradation... protect it from nucleolytic attack. Another stabilizing sugar modification, found at the same site, is...

...not yet have a comprehensive understanding of how cancers become resistant, an emerging theme is that they...involved in drug resistance Wood wanted to find out which particular pathways drive resistance to specific ...relatively short amount of time, cancers become resistant to drugs, particularly targeted therapies,” said...David Sabatini at the Whitehead Institute and MIT, started with a list of 17 signaling pathways that are frequently... a time, you could identify those that confer resistance to drugs,” in a rapid, straightforward, and scalable...Wood says, and it took them about six months from start to finish. They cloned all the cDNAs into a single... for use in screening for pathways that drive resistance to drugs in vitro, and they’ve shown that it ...

...such as Golgi staining, injection of diffusible labels, or electron microscopy of stained sections, were...characteristics (low aggregation, high photostability, and high stability after fixation.) From the seven resulting...transient Cre recombination is required to prevent constant inversion of the construct. Sanes and Lichtman...intensity, caused partially by fluorophore photoinstability, as well as the tendency of fluorophores to...Second, the system did not permit analysis by immunostaining. Although the fluorophores used are fluorescently...Brainbow-1 and Brainbow-2 each contained a “default” state; for example, Brainbow-1.0 expresses RFP when the...construct has not undergone recombination. This default state was disproportionately expressed by a majority of...

... designed to insert a resistance gene. The vector contains a neomycin resistance gene (NeoR) flanked by...insert and later remove a resistance gene. In this construct, the neomycin resistance gene is floxed so that...into the vector on either side of an antibiotic resistance gene. To avoid selecting for cells in which the...perform a positive selection for the antibiotic resistance gene and then a counter selection for the negative...removed from the chromosome and and replaced by the resistance gene.The gene is thus disrupted, or knocked out...occurred. Neomycin, puromycin, and hygromycin resistance genes are commonly used for positive selection...positive selection marker. Since an antibiotic resistance gene can affect a cell's phenotype, researchers...

...By stitching together a stable scaffold and HA-binding regions, the Stasevich lab created a versatile ...Part stable scaffold, part epitope binding region, all fused to a fluorescent protein. “Frankenbody,”...the issues with these antibody based probes the Stasevich lab used an alternative strategy to develop a ...et al., 2019).  To develop HA frankenbody, the Stasevich lab tested several scFvs scaffolds previously ... scFv hybrid provides the probe structure and stability from the scaffold as well as specificity towards...cells.  In their proof of concept experiment the Stasevich lab observed colocalization of GFP tagged HA frankenbody... the HA frankenbody tool-kit at Addgene to get started with your experiments! What else can you do with...

...orientation. For instance, if you were cloning a gene into an expression vector, you would want the start of the...gel (this table is not inclusive of all gel stains):  Stain Pre or Post Run? Visualization Sensitivity...these stains see the Bitesize Bio Blog and their associated manufacturers websites. These stains require...require you to either stain your gel after you run your samples or add the stain as the gel is being made...promoter, you can add an EcoRI site just 5’ of the start of the gene and a HindIII site just 3’ of the end...purification step, it is important to digest plenty of starting material. We recommend 1.5-2μg of insert and 1μg... recommended) UV or Green (~500nm) Light 0.1 Crystal Violet Pre and Post Visible Light 100 Methylene...

...with three coordinates: chromosome, start, and stop. For instance (chr3, 1, 10) indicates a stretch of...first generated a multi-fasta file of the hg19 genome using Bedtools getFasta. These regions and their...find all coffee shops near your house, excluding Starbucks. Taking a nerdy perspective, you might denote ...your search as follows: (my_house + coffee) - starbucks See how the notation works? The + operator denotes...regions of DNA that demonstrate “spooky action at a distance.” Through the marvel of DNA compaction, an enhancer...above formula to a real-world experiment. We’ll start with ChIP-seq data from the ENCODE project, find... final step is to conduct our CRISPR screen. We start by infecting millions of embryonic stem cells (ESCs...

...searching. Start your career planning early, start now Don't wait until the day you defend to start thinking... job asks for experience in “statistical analysis”, mention “statistical analysis” (word by word) in your...thinking about your next step. Start thinking now. Start browsing job postings and look at the jobs you are... debating whether to stay in academia or not, it is even more important to start early. Think about your...during graduate school into your resume? How can you stand out among all the candidates applying for the position...handled large data sets and are familiar with statistical analysis. If you have done fluorescent imaging... which case talk about your research, as an understanding of the topic will give you some advantage over...

... improve solubility and stability (Figure 2).      Figure 2: Crystal structures of CRBNmidi alone...resource for advancing our understanding of its biology, pathogenicity, and resistance mechanisms.     ...version is a fusion of mouse variable and rabbit constant domains and is recommended for use in western ...produce your own antibody or want to swap out the constant domains, the plasmids for the heavy chain and ...Kroupova et al., 2024). They were able to study and crystallize CRBNmidi on its own, with drug ligands, and in... in ternary complexes with other proteins, establishing CRBNmidi as a promising tool for future structure-guided...(2024). Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders...

...consultants advise pharmaceutical companies, biotech start-ups, health insurance companies, and governments...these teams develop communication strategies, or understand, and publish on the health and economic benefits...senior leadership and members of their consulting staff. Who would enjoy healthcare consulting? One of the...situations might be especially challenging. For instance, the client might need to get a large amount of...decision determines whether the client invests substantial monetary and human resources towards the development...communicating ideas in a content-rich, easy-to-understand set of PowerPoint slides. What are some of the...These mechanisms include efforts like flexible staffing on case teams, where case managers are encouraged...