... target to specific subcellular regions, laser ablation can damage other cellular structures, and genetic...genetic mutations are not easily reversible. Late last year, the Akhmanova Lab published a new optogenetic...for a wide variety of experiments. Opto-RhoGEFs manipulate cell morphology and adhesion But what if you’... Taking control of a RhoGEF is a great way to stimulate and study these physical processes. Joachim Goedhart...of membrane-recruitment optogenetic tools for manipulating Rho GTPases based on BcLOV4. These single-component...membranes) (Figure 4). The authors used SuperPLD to manipulate phosphatidic acid signaling (such as Hippo, AMPK...minutes of blue light illumination, substantial PA accumulates in the plasma membranes, indicated by the PA ...

... be the hot new way to manipulate gene expression, but other gene manipulation systems remain valuable...To achieve even cell labeling, they generated farnesylated derivatives of the fluorescent proteins, which...trafficked to cell membranes. Membrane trafficking of farnesylated derivatives enables labeling of delicate axonal... default fluorescence due to the addition of translation-blocking STOP cassette immediately following ...woodchuck hepatitis virus post-transcriptional regulatory element (WPRE), commonly used to increase transgene...and Flpbow can be used to label distinct cell populations. To decrease the animal breeding necessary to...

... more open to developing a relationship. The time to develop relationships is before you need them (well...doing interesting things. I call this building relationships because networking has gotten a bad reputation...Scientists enjoy learning new things. Building new relationships is all about learning new things from other ...networking for a job connection with ongoing relationship building through Informational Interviews. Making...is always best to meet in person to develop relationships, but if it is not possible consider a phone ...

...formed 20-40 min later. The CASANOVA system is versatile in that it can be adapted to regulate gene editing...modifications by NHEJ and HDR using split systems Later in 2015, the Sato lab unveiled a photoactivatable...opens intriguing possibilities for optogenetic manipulation of CRISPR-based systems in animal models. Use... prevent DNA binding in the dark. Upon light stimulation, the pdDronpa moieties move apart, allowing DNA...LOV2 has a C-terminal helix that unfolds when stimulated by blue light. When fused to the catalytic site...genome and chromatin architecture, it is useful to regulate the time in which dCas9 binding occurs. Bubeck...Niopek D (2020) Optogenetics and CRISPR: A New Relationship Built to Last. In: Methods in Molecular Biology...

...has the capacity to glycosylate proteins and may recapitulate the post-translational modifications added...requires a substantial amount of properly folded, relatively pure protein, but getting to this stage is often...one’s protein of interest can save a lot of time later. Protein purification specialists recommend doing...the MISTIC (membrane-integrating sequence for translation of integral-membrane protein constructs) protein...

...non-coding regulatory elements. Regulatory DNA function is typically inferred based on correlative biochemical...of the method. One observation was an inverse relationship between deletion size and frequency [3]. There...interested in exploring the function of non-coding regulatory elements in their native chromatin context. An...   Like the video? The Orkin and Bauer lab's related paper describes their methods for CRISPR design...

...asked the individuals behind some of these new platforms what their motivations were for developing these...knowledge that could help fight COVID-19. They’ve also collated a list of useful research resources.  "We realized...Canadian volunteers, and features over 200 COVID-19 related research projects, funding opportunities, and community...community response initiatives. Accelerate the translational impact of research Universities have also been...creating research synergies and accelerating the translational impact of research activities. By streamlining...research in their field including datasets and platforms for discussing new developments, and more. As ...

...organisms and cell lines. Although ChIP-seq is a relatively simple and robust protocol it does have limitations...study how differential access to transcriptional regulatory elements is controlled during development using...fused micrococcal nuclease (MNase) to specifically isolate DNA that is bound by a protein of interest. First...First, nuclei from tissue or cell culture are isolated using lectin-coated magnetic beads. Nuclei are then...MNase requires for its nuclease activity and is chelated from the reaction up until this point. The nuclease...simple lab protocols Browse CRISPR plasmids for isolating a genomic locus Browse FRET plasmids for studying...

...seeds, DNA and other resources for Arabidopsis and related species. Located at The Ohio State University in...member of the Brassicaceae family, Arabidopsis is related to a variety of food crops such as broccoli, cabbage...utility to science, and its well-known edible relatives, it is fair to say that most people do not recognize...teaching community through the TRAINED initiative (Translating Research on Arabidopsis Into a Network of Educational...through TAIR with a new ABRC database and ordering platform soon to be released. For individuals interested...Arabidopsis is small, has a short life cycle, and is relatively easy to grow, it is an ideal organism for teachers...

...balance between positive and negative regulation and can be manipulated with mutations in the replicon. For...produce just a few copies depending on how they are regulated. Generally, control of replication is referred...stringent" depending on whether the ori is positively regulated by RNA or proteins, respectively. A plasmid's ...plasmid copy number  Although the sequence and regulation of the ori dramatically affect the copy number...SB, Furman JL, Xiao H, Schultz PG. A versatile platform for single- and multiple-unnatural amino acid ...

...polyA  The polyadenylation or polyA signal aids in the nuclear export of RNA and RNA translation, and promotes...plasmid. Parts shown in grey are optional cis-regulatory elements.   Key elements of an AAV plasmid...plasmid harbors non-coding sequences. Other cis-regulatory elements Next let’s talk about some of the elements...Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE) forms a tertiary structure when...Technologies and Methods for Targeted Neuronal Manipulation. Front Neuroanat 13: . https://doi.org/10.3389...

...viral preps   Improved cell-free transcription/translation system to examine biosynthetic pathways  By Gabrielle...Gabrielle Clouse Recently, cell-free transcription/translation systems (also referred to as TX-TL systems) have...In summary, this cell free system allows for a relatively simple, controlled “one-pot” reaction capable...plasmids that helps identify base edited cell populations without end-point sequencing assays. These plasmids..., or XMAS-TREE, to identify base edited cell populations without end-point sequencing assays.  This tool...different vectors and flow cytometry is used to sort populations by mCherry and GFP expression to check for ABE...

...DNA, a cDNA library, or by RT-PCR. Isolate the PCR product Isolate your PCR product from the rest of the...function in the same buffer, as this will save time later In our example, we will use EcoRI and NotI to ...TGGCATATCTCGAAGTACTGAGCGGCCGCTAAGCA-3’) into this calculator we get a final Reverse Primer sequence of 5’-...If you are amplifying from a plasmid or simple template, there is very little chance for mis-priming, ...now ready for restriction digestion. As such, the later steps in this process are the same as those discussed...

...of interest as well as sequences necessary to encapsulate that insert into a viral particle (the packaging...lentiviral vector system is the tetracycline (Tet)-regulated system. You can choose either the Tet-off system...rtTA (FUW-M2rtTA). In this kind of approach, a population of cells might express only the tTA or your transgene...proto-oncogenes or oncogenes for instance should be manipulated with care. See the NIH’s biosafety guidelines...viral capsid antigen p24, the FACS dosing method correlates viral titre to the number of cells transduced...order to aid viral binding. This method, called spinoculation, has been found very effective for T cells transduction...Yasutsugu Suzuki and Youichi Suzuki (2011). Gene Regulatable Lentiviral Vector System, Viral Gene Therapy,...

...Stable Cell Lines with Lentivirus Isolating a Monoclonal Cell Population by Limiting Dilution Lentivirus...high Cas9 MOI considering that A549 cells are relatively easy to transduce. I ended up with too many Cas9...be uniform editing across all the cells in the population, so some of the cells will still appear green...efficiently editing, don’t expect a 100% knockout population. BRAF gRNA delivery  Overview: In practice you...on genomic DNA. The surveyor assay itself was relatively easy. Figure 4: Detection of edited BRAF...get an idea of the percentage of cells in the population that have an edit. I didn’t do this, but to do...

...BG) (Keppler et al., 2003). This engineered hAGT later became known as SNAP-tag. There is also a fast-reacting...demonstrated in 2005 that proteins fused with E. coli dihydrofolate reductase (eDHFR) could be labeled with fluorescent...Although this tight interaction is not covalent, later work showed that introducing a Leu28Cys mutation...SNAP-OMP25 with Atto590-BG (green), imaged with stimulated emission depletion (STED) nanoscopy. Scale bar...different ligands to the same sample to label sub-populations of your protein of interest. For example, the...-molecule tracking of actin filament assembly-regulating proteins in vitro reveals complex events. a) ...Gaska, I., & Shekhar, S. (2023). Multicomponent regulation of actin barbed end assembly by twinfilin, formin...

...genetic manipulation more hands on While teaching courses about gene therapy and genetic manipulation, I and...on genetic manipulation of human stem cells when students are not even allowed to manipulate prokaryotic...transfer plasmid that could be used to genetically manipulate human stem cells. Then they had 10 minutes to...explain why they selected a certain target cell population. Who is the winner? Ultimately, society should...

...Kurt Thorn (UCSF at the time) began an effort to collate some of the current “best” FPs, and I collaborated...using simple web forms) while also maintaining a relatively strict database design (schema).  Registered ...allows for visual comparison of FPs and how they relate to one another. .  In addition, the FPbase Fluorescence...feature filter spectra and collection efficiency calculations.  With ~80 FP spectra (and rapidly growing, ... page with all the information in the database relating to that specific protein (for instance: EGFP)....retrieve all of the information in the database relating to that set of proteins.  For computer-savvy users...

...technology (Yesbolatova et al., 2019). Find the mAID tagging toolkit at Addgene Yesbolatova et al., Methods...ubiquitin ligase, the Kanemaki lab was able to translate AID to yeast, as well as mammalian and human cell...tagging of proteins with mAID and other tags (Yesbolatova et al., 2019) using CRISPR. This toolkit makes...thought to play a key role in the transcriptional regulation of many genes. A number of groups have designed...synthetic looping factors developed thus far for these latter experiments, such as transcription factors tethered...

...might not have to do the calculation yourself as many fluorometers will calculate your sample concentration...than 1.5. Then, using the A260 reading, you can calculate the DNA concentration. Generally, A260 of 1.0 ... start by pouring your gel containing a DNA intercalating dye (ex: ethidium bromide) and choosing a DNA...quantify based on band intensities of your DNA relative to the intensity in the ladder. It’s best to compare...quantified over time using a fluorescent dye that intercalates into the DNA such that smaller fragments are...