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  1. Delivery Methods for Generating iPSCs

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    ...of insertional mutagenesis. Random integration also creates heterogeneous iPSC cell lines, which can complicate...complicate comparisons made between lines. Incomplete silencing of transgenes is a concern as well, and reactivation...reprogramming transgenes and the up-regulation of corresponding endogenous pluripotency genes. Retroviral...to insertional mutagenesis and random integration creates variation between iPSC clones. Retroviruses ...disrupt the expression of tumour suppressor genes and/or oncogenes, potentially leading to the presentation...insertional mutagenesis, the presence of a genetic scar, and incomplete silencing of transgenes. Overall,...Efficient and Stable Genome integration Insertional mutagenesis, transgene reactivation, residual expression ...
  2. Deep Dive: qPCR

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    ...profiles (Dwight, 2011).  Reference Genes  Choosing a set of reference genes deserves more attention than it...want to ensure that your reference genes are suitable for your cell lines and/or tissue types.  Please do...reference genes, plural. Your data will be much improved if you move to using multiple reference genes whenever... multiplex your reference genes to save on plate space. For many cell lines and tissue types, appropriate...and most machines have a protocol that automatically performs the normalization step.  Machines Most general-use...researcher defines log-linear phase Liu and Saint No Raw Data Reference and target genes can have...previously-generated validation data, be aware that different machines, samples, and treatments may affect the assay....
  3. Hassle-free 96-well Format Epitope Tagging Using Cas9 Ribonucleoprotein

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    ... epitope tagging of a large cohort of genes (e.g. tagging genes representing a protein super family). ...generation of clonal knock-in lines that we now use for IP and ChIP assays. Tag 96 genes at a time using Custom...knock-in for 96 different genes in a single go (Figure 3). We were able to tag >30 genes/plate in the first ...Derive clonal lines by single-cell deposition in 96-well plates: Characterize clonal lines by ICC and PCR...designed for ~250 genes, we have had about 30% tagging success, although many of these genes were expressed...be used at high throughput because numerous cell lines can be generated, each with a different tagged protein...ChIP assays. Creating epitope-tagged clonal cell lines remains a challenge as it relies on inefficient ...
  4. Cellosaurus: A Cell Line Information Database

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    ...community – particularly ones that help address ongoing problems, like cells lines. A 2014 study in Science...145,000 cell lines. Cellosaurus Cellosaurus seeks to identify and describe all cell lines used in research...and dog cell lines is included when available, and can be submitted via email for cell lines profiled in...Cellosaurus also identifies problematic cell lines: ones either suspected to be contaminate or easily ...as commonly misidentified lines. Browsing this feature to know if your lines may be especially vulnerable...to help you identify proximal lines you care about. If you have cell lines without a certified origin (...Science found that approximately one-third of cell lines used in scientific research are misidentified! Rigor...
  5. Advancing Biology with Zebrafish: Genetic Tools for Developmental Studies and More

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    ...70% of human genes have a counterpart in zebrafish. Understanding the function of these genes in fish will...Additional mutagenesis projects have since been initiated and today thousands of mutations in genes affecting...zebrafish Random mutagenesis screens provided a major toehold into understanding how genes control biology..., making them ideal for studying vertebrate embryogenesis. To illustrate some of the reasons that zebrafish... is to examine the consequences of manipulating genes. One reason for the success of zebrafish as a model...studies, in which, for example, the activity of all genes in response to an experimental treatment can be ...This can reveal previously unknown functions for genes, and lays the groundwork for understanding the gene...
  6. Fluorescent Proteins 101: Luciferases

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    ...reaction is not fluorescence! Chemiluminescence, which includes all bioluminescence, is the production of light.... Table 1: Properties of luminescence versus fluorescence   Luminescence Fluorescence Source of ...needed — just the luminescent substrate. This approach preserves the advantages of luminescent assays (low ...For most people, the most familiar source of bioluminescence is the firefly. Along with charming nighttime...releasing light. Created with BioRender.com. Bioluminescent reporters require a chemical substrate (and...a laser in fluorescence assays), which means luminescence assays have lower background levels and improved...luciferases Although firefly luciferase was the first bioluminescent reporter to be cloned and remains popular, ...
  7. Plasmids 101: Colony PCR

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    ...   Saving clones for later culture: At this point, you will want to hang onto your clones for later use...start cultures of your positive clones. If you want to store your clones longer term, just streak the colonies...liquid cultures with the clones you pick and only mini-prep the positive ones. Regardless of which method...larger sized products for positive clones (+) compared to negative clones. Finally, orientation-specific ...identifying a few positive clones, the last step is to mini-prep these clones and submit the plasmids for...type of primer pair is also great for screening clones created with the same backbone but that contain... and back-bone specific primers. Find Empty Backbones at Addgene Each approach has advantages and drawbacks...
  8. Lambda Red: A Homologous Recombination-based Technique for Genetic Engineering

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    ...recombinant clones are generated.  A simple way to do this is to express lambda red genes from a plasmid...the red genes needed for recombineering, but also leads to expression of the int and xis genes which are...generation Expression of lambda red recombination genes. Electroporation of substrate DNA and outgrowth ...bacteria. Selection and confirmation of recombinant clones.    Figure 2: Overview of using Lambda...selectable DNA fragments, such as antibiotic resistance genes, as well as non-selectable DNA fragments, such as...activation Expression of Lambda Red recombination genes There are four ways to express the lambda red recombineering...exist that stably express lambda red recombineering genes due to integration of a defective lambda red phage...
  9. Technical Design of a Western Blot

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    ... common chemiluminescent methods for detection (though the enzymes used for chemiluminescence can be conjugated...classes of reporters: chemiluminescence enzymes and fluorescent proteins. Chemiluminescence enzymes are cheap...Direct westerns are simpler and faster than indirect ones and can be used in highly quantitative assays. On...appropriate for the target(s) and transfer method. Membranes The two membrane options are PVDF and nitrocellulose...the transfer: you’ll need to pre-wet most PVDF membranes before the transfer and allow them to dry afterwards...has higher background noise than nitrocellulose membranes. Pro tip! You can visualize proteins on a PVDF...reprobing, unless you buy specialty nitrocellulose membranes specifically developed to allow stripping. And...
  10. 22 Hot Plasmid Technologies from 2014

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    ...used to generate random mutagenesis libraries or to insert heterologous genes, reporters, or other markers...unprecedentedly-high brightness, bfloGFPa1, and the other with extremely-dim brightness, bfloGFPc1. The plasmids...Updated mini-transposon vector for bacterial mutagenesis or gene targeting Victor de Lorenzo's lab...this vector, called pBAM1, by conducting random mutagenesis in the soil bacterium Pseudomonas putida and ...successfully create GFP fusion proteins with a variety of genes across the genome. Although this tool was published...variety of GFPs with diversity in fluorescence brightness, intensity, excitation and emission spectra. ...-on system (pTRE-Tight-MitoTimer) to show its usefulness in cell culture to report changes in mitochondrial...
  11. Mobile-CRISPRi: Bringing CRISPRi to Diverse Bacteria

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    ...antibiotic resistance genes. Genes that are targets of antibiotics are often essential genes which creates a.... ICEBs1 carries the genes needed for conjugation, but can also carry cargo genes, like Mobile-CRISPRi...essential genes were less represented while bacteria containing guides targeting non-essential genes remained...parts: a plasmid expressing the Tn7 transposition genes (tnsA, tnsB, tnsC, tnsD, and tnsE), and a plasmid...interest following IPTG induction of conjugation genes and bi-parental mating. Following excision from ...components and a plasmid with the Tn7 transposition genes are transferred to a recipient bacteria strain of...colleagues used Mobile-CRISPRi to knockdown individual genes in several bacteria associated with human disease...
  12. Plasmids 101: Multicistronic Vectors

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    ...could replace one of the reporter genes above with your gene or genes of interest. Some of the plasmids...more of the genes replaced.  Additionally, 2A peptides could be PCR-cloned between your genes of interest...Co-expression of multiple genes is valuable in many experimental settings. To achieve this, scientists...useful almost anytime you want to express multiple genes in the same cell. Although it is possible to drive...multiple, individual expression cassettes, having the genes expressed from the same cassette is sometimes advantageous... relative expression levels between two or more genes is important. How do multicistronic vectors work...allow for the efficient translation of multiple genes from a single transcript. The two strategies most...
  13. Technologies Enabled by NanoLuc® Luciferase

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    ...fluorescent donor for a bioluminescent donor, making BRET probes. Here the bioluminescent donor is unaffected...Fusion Protein, codon-optimized Firefly luciferase genes (e.g., luc2), and NanoLuc® Luciferase are available...deep sea shrimp to a compact powerhouse of bioluminescence, NLuc is 100-fold brighter than our more common...NLuc is bright enough to detect endogenous tagged genes generated through CRISPR/Cas9 knock-in. Finally,...wavelengths should be used. Researchers often use bioluminescence to overcome these issues as traditional luciferases...infeasible for certain experimental setups. The brightness of NLuc has caught the attention of researchers...excites the fluor through a process known as bioluminescent resonance energy transfer (BRET). The fluor...
  14. Uncovering Ancestral Bias in CRISPR Research

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    ...that for approximately 40% of the identified genes, the genes were not expressed at all. This unexpected... and germline sequence variation in cancer cell lines took them down unexpected paths. Though this research...researchers do large-scale CRISPR screens in cancer cell lines, looking to uncover genetic dependencies of individual...if they could identify the ancestry of the cell lines (European, East Asian, Indigenous American, Africa...each ancestry group. Since about 90% of the cell lines used in DepMap CRISPR screens are of either European...for 994 of the Cancer Dependency Map cancer cell lines (left). Heatmap indicating the breakdown of ancestry...groups were differentially dependent on certain genes. This didn’t prove to be correct, either. However...
  15. Antibody Validation for Flow Cytometry

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    ...antibody’s labeling of the cell lines to the -omics data. The cell lines with higher expression of the ...approaches are commonly used to produce KO cell lines, some of which are commercially available. Various... – you’ll need to ensure that the parental cell lines of your chosen KO line are likely to express the...Correlation with RNA or Proteomic data from multiple cell lines/ types with different expression Flow cytometry ...combination with other approaches. If several cell lines express the target at different levels, it is possible...assessed through its ability to separate the cell lines based on expression of the target. In this case,...should have more antibodies labeling them; the cell lines with lower expression should have less antibodies...
  16. Evolution of Brainbow: Using Cre-lox for Multicolor Labeling of Neurons

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    ...directly trafficked to cell membranes. Membrane trafficking of farnesylated derivatives enables labeling...distinct patterns of recombination. In 2007, Joshua Sanes and Jeff Lichtman, both of Harvard’s Department ...Department of Molecular and Cellular Biology, harnessed these attributes of Cre-lox to create the Brainbow mouse...biology towards single-cell resolution imaging. Sanes and Lichtman endeavored to create a map of the brain... deletion, the design of Brainbow-2.1 cleverly combines Cre-mediated deletion and inversion. The Brainbow... prevent constant inversion of the construct. Sanes and Lichtman used pronuclear injection to insert...colors (see table to the right); in various reports, Sanes and Lichtman have observed from 90-160 distinct ...
  17. Illuminating Epigenetics with A FRET Based Biosensor

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    ...play a large role in turning genes ‘off’ and ‘on’, signaling which genes should be ‘read’ by the cellular...with the genes in the compacted region and results in a loss of gene expression. In this way, genes in compacted...the same exact genes, being improperly silenced in both cases. In both diseases, genes from both copies...Epigenetics has recently been hitting the headlines, with sotires like the potential devastation of the...dangerous DNA damage. If the way DNA is wrapped around histones changes, then gene expression can change as well...The more frequently and tightly bound DNA is to histones, the more compacted it becomes. This prevents ...modifications, which can influence the transcription of genes by RNA polymerase II, or by the addition of methyl...
  18. Common Injection Routes in Mice

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    ... you wait for the anesthetized mice to breathe in the liquid. Restraint: anesthesia Location: nose Gauge...Intradermal Anesthesia Between skin layers 26 < 0.05 mL Advanced Intrathecal Anesthesia Spinal cord ...Intratracheal Anesthesia Trachea 20–23 (tubing) < 0.07 mL Advanced Intranasal Anesthesia Nose n/a < 0.05...be less stressful, because the mice are under anesthesia, but they are not recommended for tumorigenic... required. Restraint: mechanical restraint or anesthesia Location: tail vein or retro-orbitally Gauge:... the muscle. Common uses include administering vaccines, pain meds, or other drugs. Identifying the proper...sciatic nerve. Mice likely experience some muscle soreness after injection, like you might after getting ...
  19. Addgene's Cancer Collection Pages Connect the Research Community

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    ...roles of proto-oncogenes, tumor suppressors, and their protein products. Proto-oncogenes consist of a group...specific genes involved. Downregulation of tumor suppressors and upregulation of proto-oncogenes ­­­can ... group of genes/proteins that, when expressed, normally encourage cell survival, growth and proliferation...of control. One may compare the roles of proto-oncogenes and tumor suppressors to the accelerator and brake... the health of an organism that both classes of genes function normally to maintain balance – encouraging...lining the digestive system, causing discomfort and illness. Further, depending on the specific type of cancer...-Ras, and N-Ras) encoded by a family of proto-oncogenes. Ras proteins are special because they are known...
  20. The Challenges of Cell Culture

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    ...mantra being “you can’t trust those whacky cell lines”. This may certainly have been a valid concern for...quality work in cell culture. The problems with cell lines Simply put, the majority of cell line problems come... for authentication and contamination) and cell lines can become cross contaminated and are invariably...Stanley Gartler reported that most of the 18 cell lines he had studied (the majority in those days) were...line. He proved this by examining whether the cell lines had isoenzymes and genetic polymorphisms specific...problem today. It is now known that nearly 500 cell lines suffer from contamination with HeLa being the most...listing all cross contaminated or misidentified cell lines. The solution Fortunately it has never been easier...
  21. Mycoplasma Contamination: Where Does It Come From and How to Prevent It

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    ...reusing pipettes for multiple cell lines rather than using disposable ones or reusing gloves. The serum is... technique, PCR primers specific to the 16s RNA genes of various commonly infecting mycoplasmas are used...sensitivity but low specificity (Degeling, 2012). Bioluminescence assay kits are available from different biotech...which trigger cellular mechanisms that generate luminescence. This can then be detected by a luminometer.... for cell culturing and maintenance of the cell lines. Providing such an environment for the lab facility...Wear a clean lab coat and mask while handling cell lines. Avoid discussion with other lab members, sneezing...wearing PPE. Photo by Kate Harten DeMaio. Cell lines and reagents Examine your cell line stock for mycoplasma...
  22. Viral Vectors 101: Integrase-Deficient Lentiviral Vectors

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    ... to insertional mutagenesis (Howe et al., 2008). 2. Transient expression of transgenes/shRNAs If you want.... Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene...of research purposes, like creating stable cell lines, delivering CRISPR/Cas9 to cells for genome editing...packaging plasmid contains Gag, Pol, Rev, and Tat genes. Specifically for our knowledge here, the Pol gene...transcriptase), and IN (integrase). These viral packaging genes are required for the production of lentiviral particles...portion does not contain any of the viral packaging genes, the natural cycle of the lentiviral vector ends...process and episomal forms of non-integrating transgenes. Created with BioRender.com; adapted from Banasik...
  23. Antibodies 101: Designing Your First Flow Panel

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    ...important to know the brightness of individual fluorophores. Table 1 describes the brightness of a few commonly...fluorophore brightness levels, these differences are much more subtle (think of brightness levels on your...there are fixable dye stains that react with free amines on and inside the cells and are thus typically ...en-us/resources/bd-spectrum-viewer.       Brightness Apart from the excitation and emission wavelengths...commonly used fluorophores. A fluorophore's brightness refers to the signal strength of the emitted photons...fluorophores have a stronger signal. Table 1: Degrees of brightness for a few commonly used fluorophores in relation...emea.bd.com/panel-design/en/flow-cytometry-fluochrome-brightness-spillover Excitation Laser Color Very Bright...
  24. CRISPR 101: Targeting Non-Coding RNAs with CRISPR/Cas9

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    ...protein-coding genes thanks to systems like CRISPR/Cas9 that allow them to manipulate full genes and observe...nearby genes and its role in gene expression, though this may still unexpectedly affect nearby genes (Figure...DA, Weissman JS. Fitness effects of CRISPR/Cas9-targeting of long non-coding RNA genes. Nature biotechnology...only 2% of our genome is made of protein-coding genes, and you might be wondering what the rest of our...manipulate and study in comparison to protein-coding genes (Rinn and Chang 2012). Scientists have determined...knock-out, or permanently disable, protein-coding genes by generating insertions or deletions in the DNA...multiple gRNAs poses the risk of disrupting adjacent genes, especially those regulated by or overlapping with...
  25. Save Time with Transient Plant Leaf Transformations

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    ...Infection with Agrobacterium rhizogenes can be used to develop stable hairy root lines in tissue culture. This...transformation. Choose good reporter genes There are many great reporter genes available and which one you choose...process. While developing transgenic hairy root lines in tissue cultures takes half a year, and generating...transcription factor candidates and the regulation of genes in the biosynthetic pathway. Why plant scientists...interest in the plant. A common method for silencing genes Virus induced gene silencing (VIGS) is a transient...plant's post-transcriptional machinery to silence genes of interest (Unver and Budak, 2009). This method...in C. roseus. A common method for overexpressing genes In plants like Arabidopsis and tobacco, Agrobacterium...
  26. Quick Guide to Working with Drosophila Part 3: Genome Engineering in Flies

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    ...different fly lines. Also, if there is a chance you need to combine multiple transgenes in one fly, having...having the transgenes in different loci allows for genetic recombination so that the transgenes can be inherited...comparisons between lines expressing different variants of YFG because the transgenes are found in the same... same locus across fly lines (i.e. there won’t be positioning effects). When designing experiments where...where you want to express multiple transgenes, remember that you’ll need to integrate them all at different...accomplished with a few matings to balancer chromosome lines but is not necessary with targeted insertions (here...the white gene, which restores eye color to fly lines where the endogenous white gene is knocked out. ...
  27. Enabling Precision Functional Genomics with the Target Accelerator Plasmid Collection

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    ...bottleneck is that most recurrently mutated cancer genes are rare and most of the individual variants found...as evolutionary conservation, or predicted deleteriousness of the amino acid change based on maps of protein...scale, broadly available collection of mutant cDNA clones corresponding to cancer variants found in genome...genome sequencing studies (as well as reference cDNA clones mapping to well-annotated cellular pathways). It...These include 634 sequence confirmed mutant cDNA clones corresponding to cancer variants derived from analysis...collaborators to aggregate a sequence-confirmed series of clones corresponding to known cellular signaling pathways...Pathway Reference Set. These Gateway-compatible entry clones are the product of many years of work and we’re...
  28. Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens

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    ...technology has changed how scientists edit and control genes, but according to the Broad Institute's Silvana ...technical leap from mutating and deactivating a gene or genes to selectively activating them with the CRISPR system...Konermann said. “If you want to activate all 20,000 genes, it is not possible to test each one and make sure...you are really confident about working for most genes and individual targeting modules. Those two things...for the transcriptional activation of endogenous genes and it consists of three components: 1. A nucleolytically...colleagues demonstrated the new system by screening for genes that, when turned on, make melanoma cells resistant...for each transcription start site in 15,977 human genes. The transcriptional repressor (CRISPRi) library...
  29. X-CHIME: Context Dependent Germline Knockout in Immune Cells

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    ...combination with different genes. Having CRISPR systems for assessing genes in defined contexts would ...Annotation of genes in immune cells typically involves the creation of germline knockout mice, which ...the constitutive, ubiquitous knockout of single genes in immune cells in vivo (LaFleur et al., 2019a and...knockouts in their immune systems. However, many genes have different functions in different cell types...Mouse Strain C-CHIME Knocks out a pair of genes pXPR_219 Violet-excited GFP (vex) Rosa26-Cas9...; Rosa26-Cas9 S-CHIME Knocks out pairs of genes sequentially pXPR_220 Violet-excited GFP (vex...These systems were benchmarked on positive control genes in CD4+ and CD8+ T cells. To demonstrate the power...
  30. CRISPR Activators: A Comparison Between dCas9-VP64, SAM, SunTag, VPR, and More!

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    ...choose from when looking to activate genes across diverse cell lines.   dCas9-VP64 Description CRISPR activation...loci across Drosophila cell lines (Sajwan et al., 2019). SPH SPH combines components of SAM and SunTag...variant lacking its endonuclease ability, to bind to genes without editing the genome (Qi et al., 2013). To...exhibits modest levels of gene activation, with some genes experiencing around 2-fold activation levels. Although...HS1 and p65). Performance When targeting single genes, SAM consistently shows the highest levels of gene... multiplex gene regulation (activating multiple genes at once), however, SAM exhibits activation levels...design (SAM) or peptide design (SunTag). This streamlines its delivery, making it a common choice for CRISPR...
  31. Story of a SynBio Startup: RevBio's Epiphany (or Lack Thereof)

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    ... own money at this business and started things up for real: bank account, business cards, incorporation...issues about continuing with the business. We ended up applying to a business accelerator freely stating that...how to run a business. SynBio Axlr8r thought color-changing flowers was a great business idea as well,...social media comments were more often along the lines of “I hate GMOs, but what you are doing makes sense...GMOs that result in a new utility, was there a business opportunity out there for us? After about a month...research and another $30,000 in mentorship and business training. The money is a drop in the bucket against...to develop the technology we will need, and the business training to make the most of it. It has also allowed...
  32. Your Lentiviral Plasmid FAQs Answered

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    ...transgene but also that of adjacent cellular genes. Q7: Which genes are deleted or modified to result in replication...1]; and 2) the potential for oncogenesis through insertional mutagenesis. These risks are largely based...lentiviruses and gamma-retroviruses use the same genes for packaging (that's gag, pol, and env), the isoforms...specifically for transient expression (find some useful backbones here) or from viral transduction. While not ideal...cell line is used; several common laboratory cell lines including 293 were immortalized with adenoviral ...3rd-generation transfer vectors apart? A3: Addgene defines 2nd- or 3rd-generation transfer vectors based on...expression of lentiviral vectors in producer cell lines. Identifying less toxic envelope proteins or envelope...
  33. Controlling for Off-target Effects with a New Genome-wide CRISPR Screen Design

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    ... identified ricin toxicity genes. The screen also discovered several genes previously not associated with...-throughput systematic approach for identifying genes involved in a biological process. These screens ...per gene and targets all ~20,500 protein-coding genes. Unique, non-overlapping sites in the genome were... pooled library via a lentiviral vector to cell lines that either stably expressed Cas9 or that had been...toxicity screen since essential and non-essential genes for both pathways had previously been identified...identifying >88% of previously identified essential genes while previous Cas9 and shRNA library screens only...only identified  60% of the essential genes. The ricin toxicity screen had a 10% false discovery rate ...
  34. Quick Guide to Working with Drosophila Part 2: Controlling Gene Expression in Flies with Gal4/UAS

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    ...multiple genes with Gal4/UAS system One can also use Gal4 to drive expression of multiple genes under the... Drosophila geneticist’s main workhorse to turn genes on or off. Gal4 is a transcriptional activator that...machinery to the site to induce gene expression. Thus, genes and siRNA encoded downstream of the UAS sequence...promoter, and Bloomington’s Stock Center has fly lines expressing Gal4 under a variety of promoters resulting...quickly mate your UAS-YFG line with a variety of Gal4 lines and study gene expression in many different tissue...sequences. For example, if you discovered five new genes and wanted to express them within a specific neuronal...dosage effects. For example, overexpression of two genes by one Gal4 driver will produce roughly half as ...
  35. Five Popular Model Organisms

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    ... They share about 70% of their genes with humans and 85% of human genes associated with a disease have...Zuber, Johannes, et al. "Mouse models of human AML accurately predict chemotherapy response." Genes & development...researchers around the globe. These organisms share many genes with humans, are easily maintained in the lab, and...manipulated with tools like CRISPR to make transgenic lines. The fruit fly (Drosophila melanogaster) Another... of Drosophila research. Morgan discovered that genes were found within chromosomes using the fruit fly... as it is estimated that 75% of disease causing genes in humans have a functional homolog in the fly (...packaged into chromosomes and about 23% of yeast genes have a counterpart in humans (Liu et al., 2017) ...
  36. Plasmids 101: The Wide World of Natural Plasmids

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    ...carrying genes for bacterial toxins like colicin typically also carry the necessary resistance genes to help...cell to another). Bacteria need special fertility genes to be capable of conjugation, and these are encoded...organisms to thrive in competitive environments. The genes encoding these functions form the basis of many ... Resistance (R) plasmids: microbial defense Genes allowing bacteria to survive toxins are the clearest...Nevertheless, the transfer of plasmids carrying these genes between bacteria can also have serious implications...: microbial infection Virulence plasmids encode genes that allow the host to infect other organisms. If...difference is virulence plasmids! This category includes genes that help bacteria invade hosts, including attaching...
  37. A New Generation of Adenine Base Editors Improves Editing in Primary Human Cells

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    ...replaced S. pyogenes Cas9 in the ABE complex with PAM-variant Cas9 proteins: the S. pyogenes NG-Cas9 (PAM...While editing single genes is very useful, sometimes, you need to modify multiple genes to generate a cellular...adenine base editors with improved editing in cell lines Nicole Gaudelli, the Associate Director and Head...ABE8 constructs using a catalytically “dead” S. pyogenes Cas9 (dC9-ABE8.x-m/d). The dC9-ABE8.x-m/d constructs...adenine base editors The most commonly used S. pyogenes Cas9 requires the target site in the genomic DNA...(“N” can be any nucleotide base, followed by 2 guanines). This limits the use of ABEs as DNA sites that...In addition to stem cells the authors targeted 6 genes in primary human T cells using 8 selected ABE8s ...
  38. A Needle in a Base-Stack: Cas9 Structural Biology

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    ...from Streptococcus pyogenes.   Figure 2:  Crystal structure of S. pyogenes Cas9 in the apo state... we can see why: two arginines make base-specific hydrogen bonds to the guanines, but the N (a thymine...    Figure 3: Crystal structure of S. pyogenes Cas9 bound to guide RNA (PDB ID 4ZT0), shown opaque...the protein, spanning both lobes. Stem loop 1, nestled between the REC and CTD domains, is required for...protein portion of the CTD, ready to check for PAM sequencines. This helps explain why Cas9 can’t locate PAM...sequence isn’t in place yet.     Figure 4: S. pyogenes Cas9 in the apo state (PDB ID 4CMP, top) compared... residues in the CTD can get cozy with DNA. S. pyogenes Cas9 recognizes the PAM sequence 5’-NGG-3’, where...
  39. Genome-wide Screening Using CRISPR

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    ...This post was updated on Aug 20, 2020. What genes are important in your phenotype of interest? Many scientists... cause is not entirely known. Identifying which genes are important for a phenotype can lead to a wealth...experiments investigating the role of individual genes or entire pathways in a particular disease process... can also be used to activate or repress target genes without permanently modifying the genome. If you'd... is to use Cas9 and a pool of gRNAs to identify genes that are essential for a given phenotype. Image ...screen a population of mutant cells to identify genes involved in a particular phenotype. CRISPR can be...created to knock out, activate or repress target genes by combining a gRNA library with the aforementioned...
  40. Supporting Rare Disease Research with BeHeard 2017

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    ...with other genes. He will use fluorescent proteins to monitor the localization of these genes, CRISPR to...to identify candidate genes as drivers of peritoneal mesothelioma tumorigenesis. They plan to use CRISPR...derived peritoneal mesothelioma cells lines and assess their tumorigenesis. These experiments will serve to...validate these candidate genes and allow Nabavi and colleagues to prioritize which genes they will use to develop... Di Schiavi will be able to better choose which genes and pathways to target in future small molecule ...molecules targeting SMN1 and its partners in mouse cell lines. Dr. Di Schiavi hopes that these studies will accelerate... research funding opportunities. References 1. Jones, C., et al. "PP09. 1–2352: Systematic review of ...
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