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...Drew Endy's lab at Stanford develops engineered DNA systems capable of storing data and computing inside...challenge. We have a strategy that organizes how we start the work, and it begins with the central dogma -...beginnings of an operating system for programming life, starting with the central dogma. Addgene: And the BIL gates...these parts be made freely available? Endy: When we start thinking about languages, humans have two types ...into practice? Endy: I think it's important to understand that these platforms, or pieces of a platform...incredible is the bioeconomy is already pretty substantial. It's estimated that genetic engineering as applied... al. "Precise and reliable gene expression via standard transcription and translation initiation." Nature...

...situation is already complex enough that a deep understanding of retroviral biology is necessary in order ...order to use the vectors correctly. A solid understanding of the structure of a wild-type viral particle —...normal, replicative life cycle — can help you understand these seemingly odd choices and lay the foundation...aspects of the viral “life cycle” in order to understand what these vector particles do once they come... thanks to Addgenie Rebecca Hutcheson for her assistance with lentiviral replication.  Resources and ...Gene-Editing Systems Based on CRISPR/Cas: Current State and Perspectives. Viruses, 13(7), 1288. https://... the National Academy of Sciences of the United States of America, 54(1), 137–144. https://doi.org/10.1073...

...libraries performance via the depletion of a gold standard set of genes (1,580 essential and 927 non-essential...effective in a narrow range around the transcription start site (TSS). The Root and Doench lab selected sgRNAs... selected and ranked based on the previously established sgRNA rules and  potential on- and off-target...al. demonstrated that the Calabrese library substantially identified more hits than the SAM library approach... a comparison study screening for vemurafenib resistance in A375 cells. The SAM system (CRISPR/Cas9 Synergistic...reading frame (ORF) overexpression libraries for resistance to MEK inhibition. Although both Calabrese and...allow scientists to conduct genome-wide screens in standard cultured cells as well as more difficult conditions...

... retinal gene therapy. The year was 2001 and I started a job as a technician in a lab using adeno-associated...hemophilia, muscular dystrophy)? AAV gene therapy started in the mid-90's with a lot of work and a little... luck A pioneer in the field, Dr. Jean Bennett started working on ways to deliver genes to correct genetic... another 6 years before the 1st clinical trial started, and 10 more years to obtain FDA approval and make...an ever-growing number of clinical trials for devastating genetic diseases such as hemophilia, muscular... first clinical study combining these tools may start as early as next year. Twenty years after falling...Naldini,L., 2015. Gene Therapy returns to centre stage. Nature Vol 526, p.351. PubMed PMID: 26469046. 6...

...kits. Kit-free alkaline lysis plasmid miniprep Starting material: 2 mL bacterial culture Product: plasmid... DNA gel extraction with glass syringe filters Starting material: bacterial cultures or agarose gel slices...capture up to 150 ug of DNA, and filters can be stacked together in series to increase binding capacity...commercial kits.  DNA gel extraction with glass milk Starting material: agarose gel slices Product: DNA fragments... enzymes.  Cellulose nucleic acid purification Starting material: plant, microbe, blood, or mammalian ...Regeneration of silica columns for DNA purification Starting material: PCR product or agarose gel slices Product... the National Academy of Sciences of the United States of America, 76 2, 615-9 . https://doi.org/10.1073...

...research. Understanding the depth and breadth of this bias, and then using that understanding to intentionally...Studying ancestral group dependencies  Take, for instance, a recent preprint released by the Boehm and Beroukhim... Aaron knew that their study had significant statistical limitations, and expected to find only a few,.... Like any diligent scientist, they sought to understand these strange results by digging deeply into ..., it primarily reflects European ancestry.  Understanding the impact Fig. 3: Histograms indicating...broader swath of human genetic diversity, to better understand how the use of a primarily European reference...

...storage and distribution at Addgene are DH5α, NEB stable, ccdb survival, and Pir1. The majority of plasmids...plasmids contain either an ampicillin or kanamycin resistance gene. Every step along the way involves good ...and prepare fresh media with antibiotics at each stage. The barcodes and LIMS help us track each sample...detail-oriented lab team that works carefully to catch mistakes. Each sample that is transformed is plated onto... way that can be easily traced. If you’re just starting a lab, or are looking for a way to organize samples...necessary.   Tips for barcoding and tracking samples 1. Start with the tube - Barcoded tubes come in many forms...with a barcode reader and an Excel spreadsheet. Start by scanning the sample barcodes into the cells in...

...purification of recombinant proteins. Tags for stability and solubility What are some of the hurdles to...protect against proteolysis. That’s one form of instability. Prokaryotes can also have a hard time folding...s not folded correctly, there’s no point in crystallizing it or testing its function. Small ubiquitin-...ubiquitin-related modifier (SUMO) can help with folding and stabilization, as can maltose-binding protein (MBP). Overexpression... site GST Large Protein 26 Purification and Stability Good for purification with glutathione; protects... detection SUMO ~100 amino acid protein  12 Stability At N-terminus, promotes folding and structural..., with various mutations used to increase its stability activity, can be readily purified using plasmids...

...the signal intensity of the sample to that of a standard curve to extrapolate the concentration of antigen...chromogenic substrates since they can be read on a standard plate reader as opposed to chemifluorescent, and...sample and is calculated by extrapolating from the standard curve. Because the primary antibody is directly...ELISAs generally have higher levels of background staining. Antigen-containing samples often include undesirable...non-specifically to assay components and increase background staining. Direct ELISAs also lack the signal amplification...sample and is calculated by extrapolating from the standard curve. Scientists often opt for sandwich ELISAs...cross-reactivity Higher level of background stainingLess sensitivityLess specificityLimited availability...

... will stall at regions calling for low abundance, poorly charged tRNAs. When the ribosome stalls, this...may be preferentially charged during amino acid starvation thus resulting in higher production of amino ... a gene of interest from the human genome, for instance, it may not express at all in E. coli (you can...translating these codons, the ribosome may therefore stall at inappropriate locations or fail to make it through...charging of tRNA isoacceptors induced by amino‐acid starvation." EMBO reports 6.2 (2005): 151-157. PubMed PMID... 2265611. PubMed Central PMCID: PMC552224. 4. Gustafsson, Claes, Sridhar Govindarajan, and Jeremy Minshull...

... these tips might help to get you started. Once you have established a well working protocol in your lab...Agrobacterium rhizogenes can be used to develop stable hairy root lines in tissue culture. This method...transient transformation” usual means that neither a stable cell line or plant is regenerated from the transformed... gene (β-glucuronidase) with histochemical GUS-staining is a very useful visual reporter (Figure 2). The...precipitate. GUS is usually the first choice for establishing a new transformation protocol as it can easily...Leibniz Universität Hannover (Germany), before starting his work in the Lee-Parsons Lab.     References...

...incompatibility with antibiotic-resistance plasmids, scientists have expelled antibiotic resistant plasmids from Enterobacteriaceae...happens, how it might affect your work, and how understanding it can be used for good.  First, why are plasmids...same replicon and/or partitioning system. Let’s start with the replicon- the part of the plasmid that ...it may seem like plasmid incompatibility may be standing in your way to bacterial cloning glory, scientists...plasmid incompatibility to combat antimicrobial resistance. Using novel plasmids based partly on plasmid...2017) Plasmid interference for curing antibiotic resistance plasmids in vivo. PLOS ONE 12:e0172913 . https...

...Is Required for Acquisition of Anoikis Resistance and Metastatic Potential in Adenoid Cystic Carcinoma,...cross-contaminated cells have been known about since 1966 when Stanley Gartler reported that most of the 18 cell lines...Publishing Group recently reiterated its strict stance on the matter. Funding bodies such as the Biotechnology...reliable. With this two-pronged approach, the many mistakes of the past can be prevented and we can progress...pharmaceutical topics. The LGC Group also provides standards and has laboratories to carry our independent ...2010. 2. Gold, Michael. "A conspiracy of cells." State University of New York Press, Albany (1986). 3. ...

... grad school to a startup and back to academia. Chapter 1: How working at a startup prepared Tom for an...synthetic biology, synthetic chromosomes, and obstacles to becoming an academic researcher. Listen to...to the UK with foundational research, training, startups, and real applications of SynBio. Chapter 3: Synthetic...of biology at the level of DNA using modular, standardized, disciplined, and open techniques. Chapter 4...Golden Gate Cloning Learn About Working at a SynBio Startup in Our Interview with Michael Koeris Resources...

...as transformed bacteria in stab culture format. Our lab team creates stabs for each plasmid being shipped...information in our lab software, labeling stabs with barcodes as they go. Stabs are organized by shipment and moved...their boxes with shipping labels and paperwork. Our stacks of Addgene boxes are now ready to be sent around...depicts where plasmids have been shipped to. Plasmids start out at our Cambridge office – previously at 1 Kendall...

...only in their skeletal muscle show resistance to stressful circumstances – including unpredictable loud noises...mck-PGC-1a1 mice, and those who exercise, show resistance to depression. For the researchers led by Dr...hypothesis was that trained muscle would produce a substance with beneficial effects on the brain,” Ruas said...produces an enzyme that purges the body of harmful substances. So in this context the muscle's function is ...your own lab, you’ve come to the right place. Get started with PGC-1 plasmids from Addgene. References: ...

...fused to the puromycin resistance gene through a 2A peptide. The puromycin resistance gene enables selection...uninitiated, contains much of the information needed to understand how to use it. TLDR: This is a versatile mammalian...ribosome to translate Cas9-2A and the Puromycin resistance gene as separate peptides. PX459 This is the ..., which had a point mutation in the puromycin resistance gene that made it less effective in certain cell...nickase), which nicks DNA rather than creating double stand breaks and may better facilitate homology directed...

...String assembly gRNA cloning (STAgR) String assembly gRNA cloning (STAgR), developed by Stefan Stricker...developed another AAV toolkit - this time using the Staphylococcus aureus Cas9 (SaCas9). This AAV-based genome...high numbers of gRNAs in one overnight reaction. STAgR is highly customizable as vector backbones, and ...chosen. Read the paper in PLoS One Find the STAgR cloning plasmids Mobile-CRISPRi allows CRISPRi...from various environments. It has the advantage of stable genomic integration and is easily transferred via...

...Lentiviral vectors have been a staple in molecular biology for over three decades. Widely used across...for a variety of research purposes, like creating stable cell lines, delivering CRISPR/Cas9 to cells for... isn’t so great. In this post, we’ll cover how standard lentiviral vectors work with regards to integration... risks associated with prolonged expression. 3. Stable expression in non-dividing cells IDLVs can also...insertional mutagenesis while still allowing for stable expression of the transgene. This makes IDLVs an...integrase-deficient packaging plasmid instead of the standard packaging plasmid. For more details on how to ...., Adams, S., Thornhill, S. I., Parsley, K. L., Staal, F. J., Gale, R. E., Linch, D. C., Bayford, J., ...

...voltage response, brightness, and photostability. It enables sustained deep-tissue imaging in vivo. Image... and increased brightness, sensitivity, and photostability under two-photon illumination than previous...pAAV-EF1a-DIO-JEDI-2P-Kv-WPRE   Liu Z, et al. Sustained deep-tissue voltage recording using a fast indicator...ZAP70 (ZtSH2) which binds only the phosphorylated state of an immunoreceptor tyrosinase-based activation...options for potassium biosensors and are a promising starting point for further engineering. Figure 5: Structure-guided...lifetime imaging. B) LiLac responses are highly resistant to pH changes. Image adapted from Koveal et al...