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...proteins, which are directly trafficked to cell membranes. Membrane trafficking of farnesylated derivatives... virus post-transcriptional regulatory element (WPRE), commonly used to increase transgene protein levels...has become very useful in lineage tracing; “Zebrabow” was used to trace the development of the corneal epithelium...Brainbow 3.0, 3.1, 3.2 plasmids References: Transgenic strategies for combinatorial expression of fluorescent...2013 May 5. PubMed. Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish... also been applied to cell marking and lineage tracing in other systems, such as zebrafish and Drosophila...This system differs from Brainbow-1.0 in that transient Cre recombination is required to prevent constant...

...different DNA strand comes along, it can attack this covalent bond thus joining the two DNA strands and releasing...planning to transform right away OR you can store the reaction at -20C overnight. 4. Transform TOPO Cloning...end cloning. So how does TOPO cloning work? As illustrated in the Figure below, the “A” overhang on the ...DNA sequence 5´-(C/T)CCTT-3' and digests double stranded DNA at this sequence. The energy from this breakage...stored as a covalent bond between the cleaved 3′ DNA strand and a tyrosyl residue of topoisomerase I (1). If...researcher to perform blue-white screening after transformation - self joining of the vector ends results in... minutes will not significantly improve the transformation efficiency).  5. Select and Analyze 10 White...

...the opposite strand). ABEs make an A to G change (or a T to C change on the opposite strand). Both are ...place on the free strand of DNA and converts a C to U without producing a double strand break. UGI = uracil...Repair CRISPR 101: Cytosine Transversion Editors CRISPR 101: Any Base Transversion Editors Learn about base...repair (HDR), the pathway for resolving DNA double-strand breaks (DSBs) preferred by researchers. Compared...are base transition editors: converting one purine base to the other or one pyrimidine base to the other...other. Figure 1: Base transition editors catalyze purine-to-purine or pyrimidine-to-pyrimidine base... indicate the change introduced to the opposite strand following base editing and DNA repair. Black arrows...

...of DNA, transcription of DNA to make RNA, translation of RNA to make proteins. That's central to everything...Science describing the development of “transcriptors,” transistor-like digital genetic switches that enable...comprised of well-characterized bacterial transcription and translation initiation elements. Open science with.... We have a strategy that organizes how we start the work, and it begins with the central dogma - replication...reliable gene expression via standard transcription and translation initiation." Nature Methods. 10, 354...cellular computing. These logic gates built from transcriptors are available at Addgene as a BIOFAB kit comprised... handle on precise, forward engineering of the central dogma at the genome scale, it's going to be tricky...

...contains 11 β-strands and one central ɑ-helix that can be split into 3 parts: (1) β-strands 1-9 (β1-9) and... and the one ɑ-helix, (2) β-strand 10 (β10), and (3) β-strand 11 (β11). Each part contains components ...developed, such as the Forster resonance energy transfer (FRET)-based executioner caspase reporters. In...GFP (GFP1-9 and GFP10-11) by flipping a single β-strand of GFP, hence the name FlipGFP. FlipGFP increases...from β1-9 they will rapidly recombine with β1-9 strands nearby resulting in fluorescence within tens of...11 are antiparallel. To prevent binding, the β strands in FlipGFP were redesigned so that they are parallel...E5 and K5) that dimerize together and force the strands into a parallel conformation. Between β11 and one...

... of the four strands of the cleaved duplex, while the fourth strand (the released strand in Figure 1 below...discovered that single stranded donor DNA: Complementary to the released strand, 127bp in length, With...single or double stranded donor DNA with other design parameters. Example single stranded donor DNA and ...biological process in detail often suggests new strategies to manipulate that process. We began our research...investigations into the release of DNA post-cut. Using substrate DNA labeled on both sides of the break, we determined...presented in Figure 2. Figure 2: Single-stranded donor DNA interaction with the Cas9-DNA duplex...replacement without cutting Our in vitro results also demonstrated that catalytically inactive dCas9 produced a...

...of scientist training in the US and around the world. There are rumors that we are training too many scientists...few of these trainees are sufficiently prepared during their 6-12+ (!) years of training to get jobs. ...developing transferable skills to enable pursuit of these diverse opportunities after training. One of the... examples of science trainees taking a proactive role in their non-bench training. Grad students at Washington...academic administrators who are finding ways to provide new types of career preparedness training for their...the way we view the graduate school and postdoc training years. There is no doubt that there are too many...academia. Certainly funding for academic research and training is getting tighter and competition is fierce. ...

...constructs to visualize cell cycle dynamics, titrate inducible transgene expression, or a variety of other clever...throughput cloning strategies There are several high-throughput cloning strategies available for assembling...PubMed PMID: 25909630. PubMed Central PMCID: PMC4409215. 7. Swartz MN, Trautner TA, Kornberg A. Enzymatic ...incorporate each element into the final construct. This strategy can be used to build vectors with diverse functions...containing a unique fluorescent protein with minimal spectral overlap between them (Table 1). In each construct...expression) and a polyA signal (to terminate transcription) and the four constructs were then combined ...suited for particular downstream applications. The tradeoffs between various cloning methods are listed in ...

...detect a variety of intracellular conditions, including ion (such as Ca2+) concentrations and pH, using a ...Developmental/transgenic uses: Because of its stability, GFP can be used in lineage tracking capacities ...reporter for DNA double strand break repair, and to label pathogenic intracellular microbes to visualize...spontaneously and without additional co-factors, substrates, or enzymatic activity – it only requires the...folding at 37C, reduces aggregation at high concentrations T203Y Red-shifts the wavelength (yellow derivatives...K26R, Q80R, N146H, H231L, (and probably others) Neutral mutations    A multitude of applications Due...backbones for constructing fluorescent fusions. Transcription Reporter: Placing GFP under the control of a...

...control than is achieved by traditional pharmacologic methods. A number of strategies have been developed for... in the extracellular domain which activates the native signaling cascade of the intracellular part of...and Ca++ to passively enter the cell with the concentration gradient to depolarize it (Nagel et al., 2003...pumps that pass ions (Cl-, H+, Na+) against the concentration gradient and hyperpolarize the cell (Mattis ...activation by light showing ions flowing with the concentration gradient, and of activation inhibitory (ArCH...ArCH) proton pump passing ions against the concentration gradient. Created with BioRender.com.   Opto-G-protein...GPCR) regulate cellular function through multiple intra-cellular signaling cascades. Optical methods for...

...size, multimers may exhibit reduced transformation and transfection efficiency compared to the monomeric...1981). E. coli strains such as DH5α, HB101, NEB Stable, Stbl3, etc., are recA- mutant strains, and therefore... You can then gel extract the linearized band, ligate the plasmid, and re-transform the ligated plasmid... Elfinger M, Hartl D, Rudolph C. Transgene expression of transfected supercoiled plasmid DNA concatemers...multimeric forms (e.g. concatemers, dimers, trimers, tetramers). Since then, multimerization has been observed...the repeated plasmid sequence, giving greater concentration of cut DNA without changing the size. As a result...   Grow plasmids in recombinase-deficient strains Since plasmid multimerization is caused by homologous...

...RNA cargo into their targets makes them attractive and tractable tools for genome engineering. Scientists... Packaging Capacity (>8kb) High Transduction Efficiency Transient Gene Expression High Immunogenecity...alternatives? Well, for one they have a high transduction efficiency and can effectively infect a wide...of cell types that are typically ‘difficult to transfect’, such as primary cells. They can also be directly...organisms. Finally, viral delivery is typically straightforward across applications, while electroporation ...derived from viruses that infect people in nature, extra safety measures, like replication incompetent viral...through nuclear localization signals which can traffic their viral particles inside the nucleus, without...

...fluor. Transcribing and translating a protein fluorophore also takes time - bypassing translation altogether...expression strategies.” Chem Biol. 2015 May 21;22(5):649-60. PubMed PMID: 26000751. PubMed Central PMCID: ... PubMed Central PMCID: PMC3279232. 10. Song, Shiping, et al. “Aptamer-based biosensors.” TrAC Trends in...have used antibodies for diagnostics know how frustrating it can be to get a “bad batch”); Customizable...help reduce such background, thereby improving traditional visualization techniques. In addition, their ...biosensors. Aptabeacons Fluorescence resonance energy transfer (FRET) technology has been studied and used in...fluorescence-activated cell sorting (FACS) of E. coli transformed with aptamer libraries, the Jaffrey group selected...

...72 hours post-transformation/transfection in a transient assay. For stable transformation, regenerated ...Agrobacterium-mediated transformation. We also constructed smaller vectors suitable for transient assays using ...double-stranded DNA cleavage." Nature 533.7603 (2016): 420. PubMed PMID: 27096365. PubMed Central PMCID...creates a nick in the DNA by cutting only a single strand, dramatically reducing the likelihood of detrimental...of the desired T-A base pair. Figure 1: Transition mutation (C>T, G>A, A>G, and T>C) installation...deaminases (ecTadA), fused it with dCas9, and transformed it into E. coli harboring the defective CamR ...TadA*) that satisfactorily accepts DNA as its substrate (see figure 2).          The artificially evolved...

...reporter of transfection, which only report the efficiency of plasmid delivery to a cell. In contrast, TREE ... affecting protein translation of different reporter proteins. Protein translation requires the start ...compared to CRISPR/Cas9 edits that rely on double strand DNA breaks. Due to this inefficiency it is crucial...At the same time Cas9n cleaves the opposing DNA strain which results in two DSBs that can be repaired ...constitutively expressed to identify successfully transfected cells. C-to-T editing by the APOBEC-Cas9 editosome...that results in the restoration of fluorescence. Transient reporter for editing enrichment (TREE) The Wang...Wang and Brafman lab developed a transient reporter for editing enrichment (TREE) to purify single base...

...RNA polymerase III transcript, the sgRNAs were encoded on the lentiviral minus strand in the 3’ LTR. These... Figure 6: Illustration of split fluorophore assay to test reconstitution via mRNA trans-splicing. A ... with tRNAs, which are cleaved out of the RNA transcript by endogenous processing enzymes (Figure 1). ...including modifications to the Cas9 or reverse transcriptase enzymes, inhibition of host cell proteins, and...(Figure 3).      Figure 3: HeLa cells transduced with SARS-CoV-2 nucleocapsid protein (Plasmid...modification of microglial immune cells is critical for central nervous system research; however, microglia are...are notoriously resistant to viral transduction. Through in vivo screening of human promoters, the Zhang...

...examples I’m personally interested in include: intracranial self-stimulation (ICSS) and place preference... a behavioral experiment in which an animal is trained to “freeze” upon anticipation of a mild electric...(viral expression, efficiency of laser light transmission to the target neurons, appropriate stimulation...mistakes. The easiest way to learn optogenetics is straight through the source - find a lab within your own...optogenetics is performed in this species. However, transgenic rat technology is improving and may one day reach... reach the sophistication of mouse transgenics. Everything that has been described is intended for the...References 1. Stuber, Garret D., et al. "Excitatory transmission from the amygdala to nucleus accumbens facilitates...

...increases when target DNA strand separation is stabilized (2,3). Stable strand separation is maintained...and therefore destabilize basal strand separation. This decreased strand separation combined with the weak... Figure 1: Strand separation and target DNA binding to the Cas9 nuclease. Stable strand separation is...the non-target strand and the HNH/RuvC groove, and interactions between the target strand and the gRNA....interactions : 1. Interactions between the non-target strand and a positively charged groove formed by the Cas9...nuclease domains 2. Interactions between the target strand and the gRNA (see figure below) Because off-target...by a technique for detecting genome-wide double strand breaks (BLESS), revealed that these mutants do ...

... cell types. Specific transgene expression can be also achieved in nontransgenic animals by using cis ...population.  Combinatorial strategies can also be used for retrograde tracing: visualizing neurons that...delivery by increasing transgene cargo capacity, enhancing anterograde transport efficiency, and engineering...and Development workshop aimed at brainstorming strategies for using combinations of AAV-based molecular... cell of interest: AAV tropism and route of administration AAV tropism is defined by the viral capsid ...proteins that determine the AAV serotype. During transduction, the viral capsid proteins bind to the target...serotype used for a specific cell type. Find some transduction characteristics of select AAV serotypes in Table...

...STPF) at the Veterans Health Administration, I could never get one straight answer about what science policy...early demonstrates not only your interest to future positions, but will also make your transition from ...Technology Policy Fellow at the Veterans Health Administration. “But, seriously, what even is science policy...first few decades of my life following a very straightforward conveyor belt from high school to college to...professionals that entered the field from a more traditional policy background, learning the science part ... or LinkedIn to learn more about their career trajectory. If there’s one thing everyone loves, it’s talking...through convening activities, formal lobbying, or strategy setting.  The “little p” policy is non-governmental...