.... The team at the Victoria Makerspace is composed of computer scientists, engineers, and biologists working... elegans as a computer model. When I first heard about it, I got excited from a computer scientist perspective...defects above 25 degrees. Computer scientists and biologists work together to compare the predictions about...interests in biology and computing. In 2009, he founded a team at UVic to compete in iGem, an MIT-sponsored... really epitomizes what the makerspace is. The computer scientists can get involved in modelling, the ...Developing these skills relies upon biologists and computer scientists learning and communicating with one...coding the molecular biology of the worm into a computer model that recapitulates how molecular biology...

...of oxidation (dehydrogenation). MitoTimers are composed of a Timer protein fused to the mitochondrial ...upregulate an alternative pathway or induce other compensatory mechanisms. How can protein function be dissected...’s lab, acutely depleted proteins from their compartment of action via sequestration. The strategy relies...outer mitochondrial membrane. Sequestration is accomplished by knocking down your endogenous protein of ...May 1;126(Pt 9):2102-13. Assemble multiple component plasmids from building blocks via Golden GATEway...GATEway Cloning Frustrated by the complexity of assembling recombination of transgenesis constructs? A new...cloning kit simplifies the cloning process for complex DNA constructs, particular for those involving ...

... pre-mRNA splicing in a compound screen. Their reporter system is comprised of two plasmids: Luc (intronless... Vacuolar Compartment mCherry-Rab5 BFP-Rab5 GFP-Rab5B Vacuolar & Budding Compartment GFP-Rab4B ...insights into the make-up of multiprotein complexes like the EPC1 complex.. Going one step further, they also...about it! Split Cas9 system The Cas9 protein is composed of an n-terminal DNA recognition domain and a ...sequencing or other readout. Cellular memory is accomplished by the use of sequence-specific enzymes (e.g...calculated (the BRET ratio), which allows for compensation of varying fusion protein expression levels....more powerful LID, the authors recently used computational protein design, phage display and high throughput...

...important that the digest go until completion. The time required for complete digestion varies for different...want to use electro-competent cells instead of the more common chemically-competent cells. You should perform...fragment of DNA (insert) that has been cut by compatible restriction enzymes. An enzyme, DNA ligase, then...plasmid to the new fragment thereby generating a complete, circular plasmid that can be easily maintained... are cut with restriction enzymes to generate compatible overhangs that allow them to bind. Ligase is ...your backbone and insert - these both must have compatible cut sites for restriction enzymes that allow ...    Alternatively, this whole process can be completed using a single enzyme if your insert is flanked...

... work for biotechnology companies and help other researchers use the company’s products successfully. ...guidance, and resolve complaints about products. As you might expect, different companies produce different... duties. Bigger companies have dedicated technical support teams, sometimes comprised of several layers...cells (manufactured by one of the larger biotech companies), and as far as I remember, it was the first time...time that I was absolutely convinced it was the company’s fault. I contacted them to express my concerns...rather painful to get there: I had to send the company detailed documentation of my results, answer loads...takes some time (several years) to build up comprehensive lab experience. With this valuable training ...

... to accommodate high protein levels including:  ompT: Strains harboring this mutation are deficient in...proteins. lon protease: Strains where this is completely deleted (designated lon or Δlon) similary reduce...IPTG-inducible strain containing T7 RNAP (DE3) F- ompT lon hsdSB (rB- mB-) gal dcm (DE3) General protein...vector cannot have p15A origin of replication F- ompT lon hsdSB (rB- mB-) gal dcm (DE3) pLysS (CamR) ...vector cannot have p15A origin of replication F- ompT lon hsdSB (rB- mB-) gal dcm (DE3) pLysE (CamR) ...which results in longer transcript half-life F- ompT lon hsdSB (rB- mB-) gal dcm rne131 (DE3) General...RNAP; IPTG may still be required for expression F- ompT lon hsdSB (rB- mB-) gal dcm araB::T7RNAP-tetA General...

...lead to comparable experimental results. Using PiggyBac transposons, the Woltjen Lab compared different...robust engineering. These components are provided in Golden Gate compatible backbones that can be combined...latest hot plasmid updates!     Tol2 Gateway-compatiable toolbox for studying the nervous system The... Cole lab recently deposited the Tol2 Gateway-Compatible Toolobox, which will allow scientists to quickly... neuorodgenerative diseases. The Tol2 Gateway-Compatible Toolbox is based on the original Tol2kit generated...vectors that have standard cloning sites or gateway compatible cloning sites for easy cloning of your genes ...adds new neuronal tools to the expanding gateway compatible vectors currently shared amongst the zebrafish...

...with increasingly complex experimental conditions. The ability to construct more complex, multi-fragment...fragments in a single “one-pot” reaction to form complex, multi-insert modular assemblies that enable biosynthetic...as enzyme efficiency, stability, and buffer compatibility have placed practical limits on single- or two-step...enzyme cutting results in 5’ four base overhangs complementary to the overhangs of the assembled inserts. After...assembly Intermediate 5- or 12-fragment assembly More complex 24-fragment assembly Single insert cloning efficiencies...Sequencing of blue colonies showed the expected complete sequence for the lacI/lacZ genes (1), while sequencing...setting up assembly reactions in which a single component was purposefully omitted. Since any assembly is...

... Nextflow script. With our completed pipeline, we could adjust the compute resources when needed, for ... number of deposited plasmids increased, the accompanying sequencing data collection and analysis eventually...needed to transform the raw sequencing data into a complete plasmid sequence that would be ready for our QC...data pipeline is to perform several sequential computational tasks for which existing script(s) have been...containers are they are designed to ‘contain,’ in a complete package, all of the pieces of software that depend...is sequestered from other programs running on a computer, so it safely operates in isolation, and can be... be easily shared with others without any complicated setup. We created, tested, and debugged each of ...

...before vitrification, they can be completely denaturated (left) or complexes may dissociate  (right). B) Protein...determine structures at comparable or higher resolution than using more complex protective methods or detergents...evolved optimizations for prime editing CHARM: A compact epigenetic silencer Recombinant antibodies for ...for low-abundance targets or natively isolated complexes. To address these limitations, the Funabiki Lab...linker histone H1.8 in Xenopus nucleosomes and in complex with its chaperone NPM2, but the technique should...tardigrade LEA, RvLEAMshort, protected samples and was compatible with the buffer additive MgCl2 and the crosslinking...other viral delivery methods, allowing all the PE components to be delivered in a single package. In a recent...

...tasks that can be accomplished quickly and things that will take longer. Completing the quick and useful...project they’re a part of, completing them will give me some sense of accomplishment. I will prioritize which...its utility) How much time it will take you to complete the task When picking which tasks to actually...will swiftly give you the wonderful feeling of accomplishment while the longer tasks will give you larger...larger payoffs later. Don’t be afraid to accomplish some quick but moderately useful tasks at the expense ...the long and highly useful tasks. The quick accomplishments will likely energize you. For example, let'...experiment. The first way, it will take you 3 days to complete the entire experiment, but you’ll have to spend...

...user to compare the emission spectra between all of the markers in the panel. This complexity index ranges...choice for overlapping markers. Compensation/reference control(s) Compensation or “reference” controls are...detector for PE. In order to correct for this, compensation has to be applied to “subtract” this spillover...up a small portion of that spectra to use for compensation.     Figure 1: The emission spectra... discern one marker from another. Instead of compensation, which relies on user adjustment, spectral flow...cytometry relies on “unmixing.” Unmixing uses a complex mathematical algorithm and single stained reference...series of histograms flipped onto its side and compressed into a heat map. BV421 peaks in V1, with secondary...

... were used to express the necessary components in E. coli (Klompe et al., 2019). Recently, the lab introduced... Sternberg and Zhang labs (Peters et al., 2017; Klompe et al., 2019; Strecker et al., 2019), which direct... a Type I-F CRISPR-Cas system. The four major components required for RNA-guided DNA integration are (... (Fig. 1A, top):  A CRISPR RNA (crRNA) comprising a 32 nt spacer sequence specifying the target site....sequences (R and L ends).  Figure 1: (A) Components involved in each type of CRISPR-Transposon system...multiple Cas proteins to form the Cascade targeting complex is a hallmark of Type I CRISPR-Cas systems, in ...nuclease activity. Instead, it forms a novel co-complex with the transposition protein TniQ for targeting...

...which can compare up to five editing experiments at a time, and batch analysis, which compares hundreds...edits performed over multiple experiments and comparing the robustness, accuracy, and speed with existing...the accuracy of ICE analysis results was highly comparable (within r2=0.96) to that of NGS data. Advantages... functional KO of the targeted gene.   Analyze Complex Edits   Traditional Sanger sequencing-based analysis...analysis tools are unable to detect or analyze complex edits, such as those generated by multiplexed delivery... How ICE works   Following delivery of CRISPR components into target cells, genomic DNA from both edited...populations is PCR-amplified and Sanger sequenced. ICE compares these sequence traces to give a detailed analysis...

... the “damage” and producing a complete plasmid. Besides being compatible with any vector, the SLIC protocol...overhangs perfectly match up. They just need enough complementary ssDNA to hold the plasmid together, even if ...if there are gaps or flaps remaining. This incomplete plasmid looks like a homologous recombination intermediate...either by annealing a mixture of products or from incomplete PCR — although higher DNA concentrations are ... separate PCR products (middle branch); or by incomplete PCR, which skips the final extension step to ...single-stranded overhangs (right branch). The mixed PCR and incomplete PCR methods yield a minority of usable product...the linearized vector by T4 digestion; then the components are combined and annealed. The resulting recombination...

...tissue and compare the IHC results to both NeuroMab and the Allen Brain Atlas. The comparison with two ...what you’re comparing your sample to. For example, we use our negative control to compare exposure times...cannot be reproduced and projects that cannot be completed. A 2015 review analyzing and explaining the antibody...reliable (wouldn’t perform differently over time), compatible with the desired applications (such as immunohistochemistry...techniques on rodent brains and is expanding to more complex brain systems such as non-human primates and humans...polyclonal antibodies because of their immunoglobin component that can be produced in large “copies.” This homogeneity...monoclonal antibodies; Addgene collaborates with these companies to create and provide general availability of ...

...is mediated via individual neurons. Neurons are composed of a cell body, with dendrites receiving incoming...tracing experiments, brain tissue is injected with compounds that intracellularly spread away from the site...distant brain areas. It is desirable for tracing compounds to outline neurons in the direction of information...proteins facilitate transport of neuronal tracing compounds and this is an area that requires further study... neuronal tracing methods Traditional tracing compounds either produce a colorimetric product or are fluorescent...health. Another limitation of traditional tracing compounds is that their diffusion across the synaptic cleft... These methods are less neurotoxic and better compatible with other neuroscience methods such as electrophysiological...

...more about the company’s program. Once you’ve found a few positions to apply for, compare and contrast ...eventually work at the company at which you’re doing your postdoc? Some companies, such as AstraZeneca,... open up. Other companies, such as Genentech, will not. The point is that each company has a unique approach...people involved is staggering. The process is complicated. If you’re interested in the drug discovery process... publish, but this can vary depending on which company you choose. If publishing is important to you, ...that your project will not involve proprietary compounds or information. Where publication is expected,...meetings. How do I get an industry postdoc? Many companies have industry postdoc positions, including AstraZeneca...

...these components are necessary to efficiently reconstitute a functional viral polymerase complex and utilize...proteins are provided in trans (see Other Important Components of EBOV Minigenome System). However, minigenomes...RNA viruses (reviewed in 2, 3). Other important components of the Zaire ebola virus minigenome system Similar...with the viral polymerase, which is formed by a complex of two proteins: the large (L) catalytic protein...-stranded RNA minigenome. The viral polymerase complex then recognizes the encapsidated minigenome as ... genes in this plasmid would be more difficult compared to if each gene were encoded in separate (and ...particular observation can be easily studied as each component can be examined independently. In addition, experiments...

...antibody can be used. In a competitive ELISA a multiwell plate is coated with a competing antigen (green).  The...antibodies are used.  Competitive ELISAs Scientists typically use a competitive or inhibition ELISA when...converts into a detectable product. Scientists compare the signal intensity of the sample to that of a... of ELISA are direct, indirect, sandwich and competitive. In a direct ELISA a reporter enzyme conjugated...sample, the less antibody available to bind to the competing antigen. In direct, indirect and sandwich ELISA... level of antigen in the sample whereas in a competitive ELISA the reporter signal is inversely proportional...molecules that may bind non-specifically to assay components and increase background staining. Direct ELISAs...