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We narrowed to 876 results for: tra

Showing: 361 - 380 of 876 results

  1. What's Your Organism? Expanding Genomic Tools via the NSF EDGE Program

    Type
    Blog Post
    Published
    May 2, 2019, 12:41 p.m.
    ...species. Discovering ways to culture, propagate, transform, store, and share all of these new organisms continues...organismal systems described at this meeting were extraordinarily diverse. Plans to develop tools to study their...) -  perhaps you’ll choose to study Crepidula atrasolea or Prochlorococcus with your next project. Gymnotiformes...Poison frogs are great for studying parenting strategies and make important ecological indicators since...(which is considered recent). They have diverse traits with good genetic mapping morphology and interesting...mushrooms) but there are over 1,000 species. No transformation techniques are available yet. Polistes (Amy... aspects of cognition. Spiralians - Crepidula atrasolea (Jonathan Henry) This black footed slipper snail...

  2. Tips for Using FRET in Your Experiments

    Type
    Blog Post
    Published
    Nov. 5, 2014, 3:41 p.m.
    ...than the signal generated by the energy transfer. On the contrary, if you choose a pair that are too far...Bioluminescence Resonance Energy Transfer CRET= Chemiluminescence Resonance Energy Transfer    Interesting Articles...FRET, aka Fluorescence (Förster) Resonance Energy Transfer, technique which allows the detection of molecules...distance-dependent physical process by which energy is transferred non-radiatively from an excited molecular fluorophore...absorbed light, at a given wavelength, to the concentration of fluorophore in solution) are two additional...fluorophores with significant overlap in their spectra. The pair CFP-YFP was the first to be used to study...cross-talk but you also don’t have any resonance transfer. You have to find a balance between FRET efficiency...

  3. What Good Citizenship Can Do for Reproducibility in Science

    Type
    Blog Post
    Published
    Nov. 7, 2019, 2:18 p.m.
    ...subtle difference in mouse chow, a different water filtration system, environmental stability in an incubator...is not just a question of being honest and straightforward, it’s an important part of being a “good scientific...differently. Communication comes in many forms—from transparency about data to allow others to see what you actually...communication and sharing fits together to make for a transparent and collaborative research environment. Journals...Currently, most of the burden for pushing for more transparency in science communication falls on the shoulders...developed STAR Methods to improve the structure and transparency of methods sections, including clear information...researchers are not strongly rewarded for being transparent in their communication or making their data and...

  4. Science Career Options

    Type
    Blog Post
    Published
    Feb. 23, 2017, 1:30 p.m.
    ...Technologist/Designer     Fieldwork and traveling Many people are attracted to science because they enjoy spending...job involves traveling, showing that you are a highly organised and experienced traveler by citing specific...skills include: Science Reporter Scientific Illustrator Research and Development Scientific Advisor...Experience in the field or in a position that requires travel can show that you are self organised, reliable,..., including: Livestock Breeder Scientific Illustrator Plant Breeder Zoological Worker Conservationist...writing skills Writing a thesis or dissertation demonstrates that you have advanced writing and formatting...job title actually involves, other than what is portrayed in the media and in films, which can often be ...

  5. Antibodies 101: Flow Cytometry

    Type
    Blog Post
    Published
    July 20, 2021, 1:15 p.m.
    ...target protein expression levels, assessing post-translational modifications, determining cell health, analyzing...a pressurized buffer called sheath fluid and transported through tubes or capillaries to a laser. As the...continues in the same direction as it was initially traveling is called forward scatter (FSC) and provides information...scatters sideways to the path that it was initially traveling is called side scatter (SSC) and provides information...antibodies. It’s also particularly useful for intracellular staining where binding of large immune complexes...antibody thus amplifying the signal.       Intracellular protein targets, measured by fixing and permeabilizing...permeabilizing membranes For intracellular protein targets, users must first fix proteins within the cells...

  6. A Primer on Optogenetics: Introduction and Opsin Delivery

    Type
    Blog Post
    Published
    Sept. 10, 2015, 2:30 p.m.
    ...injections can be found here [5, 6]. Opsin transgenic mice Transgenic mouse lines have also been engineered...vectors for anterograde axonal tracing with fluorescent proteins in nontransgenic and cre driver mice. Current...and versatility, the technique is remarkably straightforward to learn and relatively cheap (compared to ...Director of the National Institutes of Drug Abuse Intramural Research Program (NIH-NIDA IRP), with the stated...specific brain region can result in a particular neurotransmitter release or post-synaptic current. Fortunately...available, instructions for obtaining a material transfer agreement, and list of vendors (such as the vector...to express. For example, if you inject into the ventral tegmental area (VTA) but wish to stimulate VTA ...

  7. CasPEDIA: A Functional Classification of Cas Enzymes

    Type
    Blog Post
    Published
    Jan. 25, 2024, 2:15 p.m.
    ...cleaves ssDNA in trans. In sum, CasPEDIA documents the target substrate (DNA/RNA and strandedness) along with...Cas enzymes) cleaves both strands of its dsDNA target in cis and has no trans activity. AsCas12a, on the...Cas enzyme: Nuclease properties (CasID): Cis/trans activity, PAM requirement, gRNA, and multiplex ability...features: CasID CasPEDIA will display both the cis and trans activity of each entry. For example, SpyCas9a (one...with its action on the substrate (nick, bind, cleave, mixed). This information represents the ‘big picture...required? CasPEDIA provides information on crRNA and tracrRNA requirements, along with any other required non-CRISPR-associated...common applications of an enzyme for your non-traditional experiment. Perhaps you are a structure junky...

  8. Viral Vectors 101: Biosensors

    Type
    Blog Post
    Published
    July 6, 2023, 1 p.m.
    ...cell!)—ATP. There are biosensors for intracellular, extracellular, and even the ADP:ATP ratio. Most of... or animal system. This ‘thing’ could be a neurotransmitter, such as norepinephrine, or an electrolyte...last component of the biosensor is the signal transducer which will quantitatively give a readout for ...bio-recognition event is (fluorescence, pH, etc.). The transducer will generate a numerical value which represents...activated GFP expression (receptor), then the transducer could be a microscope, plate reader, or any other...sensors developed for it. Calcium triggers muscle contraction, and calcium channels are activated for neuronal...—keep reading to find out how!   Neurotransmitters Many canonical fluorescent as well as FRET-based...

  9. CRISPR 101: Non-Homologous End Joining

    Type
    Blog Post
    Published
    April 16, 2015, 3:45 p.m.
    ... single strand break; when two such breaks are introduced near each other, in opposite strands. This “...Cas9 can be easily programmed to make a DNA double strand break (DSB) in the genome wherever the user chooses...Aprataxin, Tdp2) that function to make ends better substrates for ligation. Although we do not describe these...introduced. Repair of Cas9-induced breaks by NHEJ As illustrated below, NHEJ-mediated repair of Cas9-generated... the deletion can be less heterogeneous when constrained by sequence identities in flanking sequence (... “double nickase” strategy vastly reduces breaks and mutations at off-target sites. Christina Mork contributed....org/10.1371/journal.pgen.1000683 Bétermier M, Bertrand P, Lopez BS (2014) Is Non-Homologous End-Joining...

  10. Enabling Precision Functional Genomics with the Target Accelerator Plasmid Collection

    Type
    Blog Post
    Published
    May 11, 2017, 2:30 p.m.
    ...Cancer Colleciton Pages Use the ClonTracer Library for Lineage Tracing Learn About Cancer Immunotherapies... with vulnerabilities) to design a therapeutic strategy that works. But, those darn cancers have revealed...patients still don’t benefit from this approach. One central bottleneck is that most recurrently mutated cancer...are likely gain-of-function, loss-of-function or neutral, as compared to wild type, would be extremely helpful...the cancer plasmid collections listed above to demonstrate how gene expression profiling, systematic tumorigenesis...morphological profiling can be used as generalizable strategies to map the function of rare cancer variants and...MH, Elife, 2017. PubMed PMID: 28315521. PubMed Central PMCID: PMC5386591.  The genetic pathway reference...

  11. Screening for Successful Genome Editing with Digital PCR

    Type
    Blog Post
    Published
    March 30, 2017, 2:30 p.m.
    ...for mutation validation, we found these assays frustrating to work with, time consuming, and minimally informative...performed to amplify the target using PCR. Instead of tracking the reaction progress as in real time PCR, each...edit. Since exploitation of NHEJ to generate translational reading frame-altering indels for “functional... an unedited site distal tothe predicted double strand break, and a NHEJ/ “drop-off” probe designed to...to bind directly at the predicted double strand break site (Figure 2A). The single molecule resolution... 291–293 (2014). PubMed PMID: 24509632. PubMed Central PMCID: PMC4063274. 2. Findlay, S. D., Vincent, ...PubMed PMID: 26914317. 4. Mock, U. et al. mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates...

  12. Antibodies 101: Normalization and Loading Controls for Western Blots

    Type
    Blog Post
    Published
    April 8, 2025, 1:15 p.m.
    ...quantity of your POI, but simply whether its concentration changes in response to experimental parameters...errors like uneven pipetting or irregular membrane transfer. Figure 1: A loading control is a type ...type of positive control necessary to demonstrate a POI’s absence. It also helps confirm that lanes are loaded.... No pipetter is perfect, and proteins may not transfer precisely evenly across the entire blot. So how... Figure 3: In a perfect world, protein concentration in your sample would directly correlate to protein... in the loading control are due to loading and transfer errors — not to any factors from before the proteins...you’ll need to conduct a control experiment to demonstrate that expression of your reference protein does...

  13. CRISPR 101: Validating Your Genome Edit

    Type
    Blog Post
    Published
    Nov. 3, 2022, 12:15 p.m.
    ... look like (the 3rd sequencing trace). While it requires a little extra wet lab work, this is still a ...your edit of interest. For all of the screening strategies outlined below, the technique can be used as ...do. A popular screening method for knockouts is Tracking of Indels by Decomposition (TIDE) (Brinkman et...et al., NAR). This technique uses the trace file generated in Sanger sequencing and a simple algorithm...Fig. 1: Overview of TIDE. The input is sequencing trace files of WT and edited cell lines. Then decomposition...and your Cas9-targeted cells. Simply upload both trace files to the TIDE tool online along with your sgRNA...design phase of your experiment for a screening strategy. Restriction enzyme screening is sensitive to ...

  14. Plasmids 101: Gibson Assembly and Other Long-Homology Based Cloning Methods

    Type
    Blog Post
    Published
    March 1, 2016, 3:30 p.m.
    ...MODAL) strategy." Nucleic acids research 42.1 (2014): e7-e7. PubMed PMID: 24153110. PubMed Central PMCID... reason. They offer many advantages over the traditional restriction enzyme cloning we once relied exclusively...generating long overhangs which allows the single stranded regions with homology to anneal a polymerase, ...hour or so, the sample is immediately ready to transform into competent cells. The master mix of enzymes...regions of homology. This video gives a helpful demonstration of how to use Snapgene’s program to design primers...Gibson assembly master mix for 1 hour, and then transform into competent cells. The success rate of this...if the ends of the fragments have stable single stranded DNA secondary structure, such as a hairpin or ...

  15. Tagging Optogenetics and Chemogenetics Receptors: Fluorescent Proteins and Other Options

    Type
    Blog Post
    Published
    May 11, 2021, 1:15 p.m.
    ...expression of the transgene of interest. In our studies, mCherry interfered with the transport to the membrane...versatile method to identify the expression of transgenes of interest. Furthermore, fluorophore variants...between them, could affect the properties or trafficking of the fusion protein (Kimple et al., 2013). ...different tag fused to the hM4Di might improve the transport of this DREADD to the plasma membrane. The haemagglutinin... important influence on the expression of the transgene of interest and its localization in the membrane... (Kimple et al., 2013) could help improve the transport of protein of interest the membrane.   ...Figure 1: Electron microscope images showing ultrastructural localization of hM4Di in monkeys. The pre-embedding...

  16. Lighting Up Cell Signaling with Photoswitchable Kinases

    Type
    Blog Post
    Published
    July 25, 2017, 1:20 p.m.
    ...Signal transduction pathways are a lot like cell phone networks. Protein kinases deliver messages to ..., and how long their signals last all impact transduction of the message. To study signaling pathways,... game of telephone, often the signal must be transmitted by intermediate messengers. Optical control of...prone to aggregation in cells compared to the tetrameric Dronpa it was derived from. What are photoswitchable...photoswitchable kinases.  Below are a few examples demonstrated in Zhou et al. 1. Testing kinase inhibitors ...signaling by using psMEK1 and an ERK kinase translocation reporter with a mRuby2 fluorescent reporter ...feedback loops are a common feature of signal transduction pathways, but are often hard to decipher because...

  17. Visualizing Protein Turnover In Situ

    Type
    Blog Post
    Published
    Jan. 16, 2018, 3:20 p.m.
    ...regulating its translatability." Science 343.6169 (2014): 419-422. PubMed PMID: 24458642. PubMed Central PMCID:... has recently published techniques to follow translation in living single cells. However, before CRISPR-Cas9...Both antibodies have a short antibody specific DNA strand added to them. Only if the proteins of interest...are in close proximity to each other can the DNA strands take part in rolling circle DNA amplification. ...When Eugenia is not by the microscope she likes to travel, discover new restaurants, go to concerts and bake...(2010): 897-905. PubMed PMID: 20543841. PubMed Central PMCID: PMC2920597. 2. Nathans, Daniel. "Puromycin...(1964): 585-592. PubMed PMID: 14166766. PubMed Central PMCID: PMC300121. 3. Söderberg, Ola, et al. "Direct...

  18. How to Design Your gRNA for CRISPR Genome Editing

    Type
    Blog Post
    Published
    Sept. 24, 2020, 1:15 p.m.
    ... efficacious to target the coding or non-coding strand of DNA. As a rule of thumb, we avoid target sites...for HDR, the choice of target site is far more constrained by the desired location of edit; efficiency decreases...HDR for introducing edits. The same locational constraints are even more exquisite for the so-called base..., 2020). is not limited to single nucleotide transitions but still requires a nearby PAM, although these... modulating gene expression at the level of transcription – CRISPRa (activation) and CRISPRi (inhibition...most-efficacious to target a ~100nt window upstream of the transcription start site (TSS), while for CRISPRi, a ~100nt...of producing the guide (synthetic, in vitro transcription, or lentiviral delivery) can affect the accuracy...

  19. Let There Be LITE Plasmids

    Type
    Blog Post
    Published
    Nov. 21, 2013, 3:56 p.m.
    ...dinucleotide and methyltetrahydrofolate, which are universally abundant. Second, induction of transcription occurs...of customizable DNA-binding domains based on transcription-activator-like effectors (TALEs) as anchors ... thaliana. The results are light-inducible transcriptional effectors (LITEs) designed to bind specific...target them to specific cell populations. They demonstrated use of the LITEs to control gene expression .... Genes under LITE control showed a rise in transcription in as little as 30 minutes after light stimulation...light dose and is fully reversible after light retraction. Finally, because light can be applied non-invasively...really flexible and modular,” Konermann said. “Transcriptional activators are easy to expand or combine with...

  20. PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs

    Type
    Blog Post
    Published
    June 25, 2024, 1:15 p.m.
    ...efficiencies, we could train our prediction model PRIDICT (Mathis & Allam et al., 2023). We trained our models in..., and deletions) without introducing DNA double-strand breaks (Anzalone et al., 2019; Chen & Liu, 2023...typically a Cas9 H840A nickase fused to a reverse transcriptase) together with a prime editing guide RNA (pegRNA...containing a primer binding site and a reverse transcription template (RTT). The design of the pegRNA has...learning-wizard colleague Ahmed Allam. Continued training led to the recent development of PRIDICT2.0 (Mathis...al., 2024). The additional datasets used in the training of PRIDICT2.0 make this model more suited for ...nicking gRNAs (used for PE3 and PE5 prime editing strategies) based on a DeepSpCas9 score ranking (Kim et ...
Showing: 361 - 380 of 876 results