We narrowed to 1,042 results for: URE

... view is excited at one time and captured in a single camera exposure. This is much faster than relying...the Harvard Center for Biological Imaging and a Lecturer on Molecular and Cellular Biology at Harvard University...an x-ray, or a biologist imaging the smallest structures of life; the key to a great image is contrast...relatively thicker three dimensional sample (see Figure 1); similar to an MRI or CT scanner. This is accomplished...resolution) limit of a light microscope. Due to the wave nature of light, an infinitely small point of light will...improvement in the resolution of a light microscope (see Figure 1). What microscopy technique should I use for ...live cells with fluorescently labelled, motile structures These samples are thin enough to sit within the...

...proteins with a membrane-impermeable biotin substrate (Figure 1). Biotinylated proteins were isolated, identified...shared proteome of astrocytes and neurons (CS SPAN) featured extracellular matrix proteins, cell adhesion molecules...transporters, ion channels, GPCRs, and more.  Figure 1: Workflow for cell-surface protein labeling and...Huntington's disease model) will be valuable resources for future studies of the molecular bases of astrocyte-neuron...recipient cells from red to green fluorescence (Figure 2). Donor cells express iCre with a mitochondrial...DsRed-STOP to trigger expression of EGFP. Figure 2: Schematic of the MitoTRACER system. NLS = nuclear...The power and potential of mitochondria transfer. Nature, 623(7986), 283–291. https://doi.org/10.1038/s41586...

...perform the IP at 4oC. When choosing the capture antibody for IP, be sure to choose one that recognizes the ...target protein/capture antibody intact. The wash step is repeated several times to ensure non-specific ...complexes, wash away unbound protein, elute and measure the target. However, the two different approaches...process of anchoring an antibody, often called the capture antibody, to agarose or magnetic beads in a way...immunoglobulin, leaving the antigen binding sites free to capture the target protein. The beads can be collected ...Agarose beads are sponge-like and vary in shape and structure. Their porous surface provides a large area for...protein interactions, and limit high throughput procedures. However, agarose beads are often a more cost-effective...

... your culture should always be derived from a single colony to ensure uniformity of the culture. Sequencing...to a shared computer or server. This will ensure that future members of your lab can access and use the...depending on the number of features we need to verify. Determining which features to verify will depend on...important features that differentiate this plasmid from its predecessor. Important features may include...reaction, or about 250 amino acids worth, so make sure the feature you want to verify is within this range. Read...plasmids, such as special growth instructions (temperature, strain, media supplements), suggested sequencing...information in a binder or digital notebook and make sure you note the freezer location of every plasmid in...

...antibodies. Figure 1: Overview of using Sandwich ELISA to quantitatively measure protein concentration...format. Figure 2: Overview of using Competitive ELISA to quantitatively measure protein concentration...the plate. Figure 3: Overview of using Direct ELISA to quantitatively measure protein concentration...proteins. Figure 4: Overview of using Indirect ELISA to quantitatively measure protein concentration...competitive ELISA use antibodies coating the wells to capture antigen from a sample, whereas antigen is bound...coating the wells of a flat bottomed plate with a capture antibody that is specific to the protein you are...that also recognizes the same target protein. The capture antibody and the detection antibody recognize different...

...organism to target large or diffuse biological structures. Of primary interest here are systemic capsids...health. While it’s always helpful to start with a literature search to see what others have done, you’ll need... before using it in an application.     Figure 1: AAV toolkit for targeted gene delivery to the... antibodies developed in response to the first exposure to AAV9. The exception is the X1 capsid for targeting...strains. It is therefore important to review the literature for use of a capsid in your strain of interest...to start selecting and testing systemic capsids! Figure 2 contains a decision tree for selecting a capsid...further highlighted below the table.     Figure 2: This decision tree can help guide your choice...

...elevated temperatures. In both cases, GeoCas9 outperformed SpCas9 at high temperatures. See Figure 1 for ...stearothermophilus grows at temperatures ranging from 30-74 °C, with an optimal growth temperature of 55 °C. For a... longevity. GeoCas9 is active at high temperatures Figure 1: Thermostability of SpCas9 vs GeoCas9... These Cas9 proteins don’t work well at high temperatures, so to use them in thermophiles, bacteria must... to make eSpCas9 and SpCas9-HF1. By mining the treasure trove of naturally occurring Cas9 diversity via...CRAA (R = A or G) Spacer Length 20 nt 22 nt Temperature Range for Optimal Activity 35 - 45 °C 50 - 70...GeoCas9 RNPs were incubated in reaction buffer at temperatures ranging from 25-80 °C. Activity is expressed...

...publications really the best way to measure impact? As that Nature report also noted, papers detailing...scientific publications. Ventures like Impact Story seek to find ways to capture scholarly work that exists...scientific journals. Of course, no one measure will ever adequately capture a notion as complex as “scientific... you like to measure yours? More Reading Fenner M. "Altmetrics and Other Novel Measures for Scientific...Impact Measures" (2009) PLOS One 4(6): e6022. doi: 10.1371/journal.pone.0006022 Aragon AM. "A measure for...publish in journals with a high “impact factor,” a measure that dates back to 1975 and is based on the average...articles. Of course, a publication in Science or Nature is always nice, but in the wired world we are living...

...packaging as a single payload (Figure 4). Figure 4: ONE-GO biosensors measure the formation of Gα-GTP...uses new combinations of PE protein components (Figure 1), an altered epegRNA delivered with an enhanced...amplification of cargo, and heat treatment.  Figure 1: Left: recombined prime editing tools PE2max-...heritable desired edits in tomato and Arabidopsis. Nature Plants, 10(10), 1502–1513. doi: https://doi.org...N-terminal CLIPf tag and a C-terminal SNAPf tag; see Figure 2), the authors developed a cost-effective expression...solution and when associated with microtubules. Figure 2: CLIP-SNAP fusion proteins for single-molecule... inserted. B) Protein expression and labeling procedure. Adapted from Smith et al. 2024 under a CC-BY ...

...walks through the paper figure by figure. Some follow the same figure by figure organization with a different...adapt the second version (multiple presenter, figure by figure) if the primary purpose is training graduate...enjoy is discussion of current new and exciting literature. As I transitioned out of academia and away from...researchers of all varieties must stay current with literature and emerging technologies to remain competitive...in journal clubs. They also have likely had the pleasure of attending both productive and not so productive...pieces before that first meeting takes place to ensure success. One of the most important is letting people...ready for your first journal club to begin! Figure 1: Discussing next-generation sequencing at the...

...strategies such as the bisarsenical dye (Figure 1a) and FAP systems (Figure 1e) are inherently fluorogenic and...biological environments such as live cells and tissues (Figure 1). These flexible strategies give you the best...peptide tag could be used to label proteins in cells (Figure 1a). Other strategies that have been developed ...substrate ligand motif attached to a fluorophore (Figure 1b). Engineered ligases (e.g., lipoic acid ligase...attachment of a fluorophore ligand to a peptide tag (Figure 1c). Click chemistry (e.g., transcyclooctene–...amino acids can be incorporated into a protein structure and then used with the growing toolbox of bioorthogonal...fluorophore at the specific site of incorporation (Figure 1d). Fluorogen activating proteins (FAPs) – These...

... need to pick a fluorophore for each target and ensure the fluorophores, together, are able to give you...most efficient (i.e., happen most of the time). Figure 1 shows a graph from the BD® Spectrum Viewer, outlining...Fluorescence Resonance Energy Transfer (FRET).   Figure 1: Emission spectra and respective colors of a ... we can recognize a couple of fluorophores from Figure 1. For example, the chart tells us that PE and ...laser. To understand why that is, let's look at Figure 2. The blue laser excites at a wavelength of 488...maximum of PE's excitation spectrum (dotted line, Figure 2). The yellow/green laser, however, excites at...relatively stronger — or brighter — signal.   Figure 2: Excitation and emission spectra for PE. The ...

...transcript by endogenous processing enzymes (Figure 1). To ensure this tRNA processing only occurs on the ...recommends both for use in western blots (Figure 3).      Figure 3: HeLa cells transduced with SARS-...improvements in performance.      Figure 4: Structure of Voltron or Voltron2 conjugated to a JaneliaFluor...reconstituted within the target cells (Figure 6).   Figure 6: Illustration of split fluorophore ...Zeocin®, or nuclear expression of BFP2.     Figure 1: CROPseq-multi uses two sgRNAs with internal ... that incorporates La’s N-terminal domain, PE7 (Figure 2).  PE7 shows enhanced editing efficiencies in...just begun with PE7, it will be exciting to see future studies enabled by this tool as well as additional...

...will cover: Miniature CRISPR-Cas systems SEND plasmids Prime editing improvements Miniature CRISPR-Cas...problem. A miniature CRISPR-Cas system for mammalian use Stanley Qi’s lab has developed a miniature Cas system...paper in Nature Biotechnology Find the Cas12f-GE plasmids Programmed genome editing by a miniature CRISPR-Cas12f... guide RNAs Yong-Sam Kim’s lab also created a miniature yet active Cas system starting with the same Un1Cas12f1...nuclease Quanjiang Ji’s lab describes an effective miniature Cas system that utilizes a Cas12f from a different...ribonucleoprotein, and AAV.  Read the paper in Nature Chemical Biology Find the AsCas12f1 plasmids   ...paper in Science Find the SEND plasmids    Figure 1: SEND combines an endogenous Gag homolog, cargo...

...and, when they mature, fluoresce red. The ratio of the mature color (red) to the immature color (green ...determination of expression time The ratio of mature to immature fluorescence from the FP timer is dependent...their knowledge of protein structure and saturation mutagenesis. mK-GO matures from green to red, and the...they predominantly fluoresce one color but slowly mature until they predominantly fluoresce a second color...580 nm) over the course of 18 hours in vitro (see figure 1B in Terskikh et al.) and even displays predictable...linear window for the theoretical timer shown in Figure 1B, you can use the equation fit to this linear... system composed of two separate FPs (one that matures quickly and the other slowly, see Verkhusha et ...

... from a heterogeneous mixture - for example, cell lysate or media from cultured cells. ELISA can be used...cell subsets of interest from among the mixture and to measure the relative amount of your protein of ...antigen the antibody recognizes and binds to.   Figure 1: Labeled diagram of an antibody including Fc,...). Single-chain variable fragment (ScFv) Figure 2: Comparison between the IgG antibody and scFv...Chain Fragment Variables (scFvs). Nanobodies Figure 3: Comparison of the Hcab and nanobody. Nanobodies...can be used for qualitative and quantitative measurement of protein expression in cell lysates, whole ...presence of proteins from samples containing a mixture of proteins. The proteins are separated based on...

... IF instead (Figure 1B). To label all your targets in one step, you simply use a mixture of primary antibodies...puncta in each cell. When making figures for a paper or presentation, make sure the images are accessible to...as immunocytochemistry (ICC) when the sample is cultured cells or immunohistochemistry (IHC) with tissues... you can perform simultaneous detection with a mixture of primary antibodies and appropriate secondary...(Im et al., 2019; McLaughlin, 2019).    Figure 1: Schematic of multiplex immunofluorescence approaches.... Sequential IF For a sequential IF experiment (Figure 1A), you’ll block, add primary antibody to bind...antibodies, wash, add a mixture of secondary antibodies, and image all the different colors in one session...

...is consistent with the result in Figure 1 could look like this: Figure 2: Expression of Plasmid B (as internal...effect, which is green fluorescent cells (Figure 3).   Figure 3: Expression of Plasmid B (as positive control...control plasmids? Generally, control plasmids help to ensure that the observed phenomenon in your experiment...of Gene X using shRNA expressed from a plasmid   Figure 1: Expression Level of Gene X The results shown...vector and internal control A transfection control measures transfection efficiency and enables observation...Referring back to the experiment associated with Figure 1, the independent variable is the shRNA. Therefore...transfection control is an internal control vector, which measures transfection efficiency. An internal control may...

...the full plasmid and confirm features you annotate on this page. Figure 7: Enter information about the... (for emailed submission) in the Deposit menu: Figure 1: Begin the deposit process by clicking "Submit...are two options to begin your plasmid deposit. Figure 2: Choose to submit plasmid(s) online or by using...deposits of 10 or more plasmids.     Figure 3: If submitting plasmid(s) online (left), choose...will become your article title.       Figure 4: Add plasmids to the article by clicking “Add...begin entering the specifics of your plasmids. Figure 5: Click the "Enter Data" button to add your plasmid...Continue to Next Step" (blue button at the bottom of Figure 6) or you can click the "Save" button and jump ...

... contain similar features and it allows you to more quickly identify the same feature in other plasmids...our new Snapgene generated maps provide improved feature detection with an easy to use interface. We regularly...quality control process because of its expansive feature library and useful tools. In this blog, we’ll walk... a plasmid and we’ll highlight some of the new features available on our website through our Snapgene ...quality control are: To identify important plasmid features To align NGS sequencing results with reference...further plasmid verification Identifying plasmid features While our quality control process for incoming...Snapgene to visualize the sequence and look for features. The first thing that the Snapgene software will...

...nanometers of each other, or measure the tension in the helical structure of spider silk, or the activity...that you want to measure (overexpressing a gene or protein after transfection). Future of FRET The first...in a synapse. What kinds of tools enable us to measure these properties, and what fascinating experiments...dipole-dipole interaction. The efficiency of FRET can be measured for a given donor-acceptor pair and a change in...fluorophores and serves as a small-scale ruler to measure distances that are too miniscule for conventional...improved dynamic range for fluorescence lifetime measurements." PloS one 10.8 (2015): e0134436. PubMed PMID...proteins can contribute additional noise to the measurement. If the distance or orientation of the donor ...

...processing (Figure 1). The shRNA sequence is transcribed to produce hairpin shRNA structures that are processed...Dicer chops off the loop of hairpin structures to create a mature siRNA duplex. Fun fact! Endogenous miRNA...upstream and downstream genomic sequences (Figure 2B).   Figure 2: A comparison of an shRNA plasmid sequence...mRNA or recruits other silencing proteins. Figure 1: Comparison of shRNA and miRNA processing and...Choosing the plasmid backbone Choosing the promoter Mature siRNAs typically range from 19–22 nucleotides and...target sequence. However, you can’t just use the mature sequence in a plasmid and call it a day. You need...complementary RNA duplex and the hairpin loop sequence (Figure 2A). Since you don’t need additional flanking sequences...

... and how will you ensure this?). You should also consider if there are any features of the library backbone... estimate transformation efficiency (Figure 2).    Figure 2: Example of a serial dilution to estimate...might be more difficult to transform.    Figure 1: Factors to consider when creating a pooled library...estimate transformation efficiency. Figure used with permission from the Mark Dawson lab Re-transformation...generally electroporated into electrocompetent cells to ensure the highest possible transformation efficiency....Using Stbl4 or other ultra-high efficiency cells ensures that plasmid diversity in the library is maintained.... The specifics of this can be based on the manufacturer’s protocol for transformation and expected transformation...

... In Figure 1, you can see cumulative numbers of CRISPR plasmid distribution and deposits (Figures 1A and...although we used different categories (Figure 2C). Note that in Figure 2, the numbers on the X axis refer ...new tools, illustrated in Figure 2, and the longevity of tools seen in Figure 3, indicates that the usefulness...the top ten countries for each group (Figure 4).    Figure 4: Addgene deposits and distribution ...number of labs who have deposited CRISPR plasmids (Figure 1C), and the cumulative number of CRISPR libraries... 100 new CRISPR depositors each year.    Figure 1: Addgene CRISPR distribution and deposits. (A...300,000 CRISPR plasmids and 12,000 CRISPR libraries (Figure 1D). That’s a lot of editing!  CRISPR functions...

...autofluorescence extraction feature. Although autofluorescence extraction is an optional feature of spectral flow...that have distinct spectral signatures and a low similarity index. In figure 3, we can see that PerCP and... detector for that fluorophore. For example, in figure 1, the FITC signal is spilling over into the primary...that spectra to use for compensation.     Figure 1: The emission spectra and filters for FITC and...flow since the machine uses the full spectral signature, not just a narrow band, to discern one marker...fluorophore from another within a fully stained sample. Figure 2 is an example of the emission spectra for two...another during spectral unmixing.     Figure 2: The full emission spectra for BV421 and BV711...

... through a structured material over a long distance? And can we understand such a structure well enough...that contain an R body-like structure. As the bacteria develop, the structure extends to rip the bacteria...’t be overstated, we can also learn a lot from Nature’s simpler solutions to transmitting forces over ...contract in response to changing pH, and they can rupture E. coli spheroplasts to release encapsulated proteins...inside cells, and these constructs may be useful to future scientists who would like to further study R body...

...undue pressure, impossible deadlines, unnecessary disruptions Destabilization – including failure to acknowledge...choose and it will make a huge difference for your future career and life. You might see a lab head as choosing...can give open, revealing information about the culture and lab head. While it’s good to talk to new lab...head. Former lab members can give you a fuller picture. Consider talking to people in the lab across the...frequently cancelled? Choosing a role model Make sure the mentors you choose are teaching the stuff you...stay around? Is it too long or do they leave prematurely? Do lab alumni stay in the same field taking...bullying. Even with the rise of movements such as the Future of Research Symposium and #MeTooSTEM, academic ...

... users coat a multiwell plate with a capture reagent. The capture reagent may be an antigen or an antibody...et al. originally developed the ELISA assay to measure antibody levels, scientists have since adapted ...on how the assay is set up. Then they block the capture reagent to prevent non-specific interactions. Next...consider alternative detection methods.      Figure 1: The four types of ELISA are direct, indirect...ELISA the multiwell plate is first coated with a capture antibody that binds to the antigen in a sample ...proportional to the level of antigen in the sample. This figure was created with BioRender.com  Direct ELISAs...cross-react with samples, eliminating them from the procedure removes one potential source of cross-reactivity...

...give a quick overview of each CasPEDIA feature. Activity features: CasID CasPEDIA will display both the...mixed). This information represents the ‘big picture’ features of the enzymes documented that should narrow...design, etc.). With this feature, you can compare different Cas enzymes to make sure you are getting the desired...resource for the scientific community. What are the features? CasPEDIA has collected relevant information on...Experimental guidelines and applications Protein structure and properties Links to relevant resources The...designed, if that’s your end goal. CasPEDIA also features useful links to Addgene resources throughout the...packaging limitations. Maybe you want to read literature on the less common applications of an enzyme ...

...without DNA cleavage. Nature, 551(7681), 464–471. https://doi.org/10.1038/nature24644 Gaudelli, N. M., Lam...double-stranded DNA cleavage. Nature, 533(7603), 420–424. https://doi.org/10.1038/nature17946 Komor, A. C., Zhao,...other or one pyrimidine base to the other. Figure 1: Base transition editors catalyze purine-to-purine...strand as a template, copying the base edit. Figure 2: Cytidine deamination takes place on the free...base editing efficiency for mammalian edits is to ensure the editors make it into the nucleus and that they...and specific CRISPR-based cytosine base editing. Nature Biotechnology, 41(5), 663–672. https://doi.org/...increased activity and therapeutic application. Nature Biotechnology, 38(7), 892–900. https://doi.org/...

... photostability measurement of various cyan fluorescent proteins is depicted in figure 1. Of note, the... noted that the photostability measurements reported in the literature are performed in different ways...photostability, an experiment is performed that measures fluorescence intensity over time. In order to ...with low excitation power. By repeating these measurements for different fluorescent proteins and by comparing...protein distribution. Therefore, photostability measurements can be performed with soluble fluorescent proteins... the experimental designs used to make these measurements and hope this information can help guide your... The second issue is that, in experiments that measure photostability, high excitation powers are often...

...et al., Nature Chemical Biology additionally provides detailed information on cloning procedures used to...at doses as high as 20 µM (see Figures 3 and 5 in Nabet et al., Nature Chemical Biology for examples).... cereblon, leading to rapid target degradation (Figure 1). Plasmids: We generated a series of plasmids...molecules will be commercially available in the near future, and we will provide an update with vendor and ...FKBP12F36V tag without disrupting protein function. A literature search can help determine which terminus is favorable...molecules in your biological assay of choice to ensure that there are no toxicities at the doses used ... roles in Multiple Myeloma), it is important to ensure lack of degradation in your context. Immunoblotting...

...candidate antibodies from the manufacturer and/or in the published literature. Note that the antibody being...candidate cell line (e.g. DepMap) – you’ll need to ensure that the parental cell lines of your chosen KO ...specific antibody:target combination of interest (Figure 1). It can therefore be helpful to try all three...looking to label an intracellular target.   Figure 1: HCT 116 WT and SYT1 KO cells were labelled with...monoclonal antibody, ** = recombinant antibody. Figure adapted from Biddle et al., 2024.   Once an...separation between the wild-type and the KO population (Figure 1), further optimization can be performed to both...it can be a real challenge to troubleshoot RNAi failures. Potential explanations for RNAi not reducing ...

...that overcomes many of those limitations (Figure 1). Figure 1: Opto-katanin induces fast, localized microtubule...specific place and time. Future studies with these CIB1-Rabs in other contexts are sure to reveal even more...cytoskeleton. They provide cells with physical structure, separate chromosomes during mitosis, support ...regions, laser ablation can damage other cellular structures, and genetic mutations are not easily reversible...roles played by microtubules, Opto-katanin will surely be useful for a wide variety of experiments. Opto-RhoGEFs... GEF to a specific area at the plasma membrane (Figure 2). Just express the plasma membrane-localized ...your cells will be ready for the spotlight.    Figure 2: Opto-RhoGEFs to control Rho GTPase activity....

...kDa. GFP and its homologues have a beta-barrel structure. Although the beta barrel has no strong affinity...binding sites per unit.  There are several ways to measure stickiness. In vitro, ultracentrifugation or gel...dimerization (Shaner et al., 2008 - supplementary figure C). However, these assays are qualitative. The ...Reticulum (OSER) assay (Costantini et al., 2012) measures homodimerization of FPs targeted to the endoplasmid...sequences or (ii) designed to form an inert, unstructured peptide and therefore consisted of glycines,... GFP sticks out and can be considered a linker (figure 1). In fact, for several FRET biosensors (yellow...Golgi, whereas the mVenus-APT1 fusion does not (figure 2). In the mVenus-APT1, a lipidation motif, which...

...gleaned from the literature and engagement with researchers who study the protein or structure of interest....alleninstitute.org. A classic challenge in cell biology is making sure that what we observe through the microscope represents...case of protein tagging to elucidate cellular structures. Overexpression methods flood the cell with protein...visualize the precise location of the protein or structure of interest. Endogenous gene tagging is an ideal.... Furthermore, the quality control necessary to ensure the edited cells are behaving normally can be prohibitively...tagged are widely recognized markers of cellular structures, we provide guidance on how to make your own ... Collection Fluorescent tagging strategy Figure 1: Gene editing is the addition of a useful coding...

...variants:   Figure 2: Inner mitochondrial membranes imaged with structured illumination microscopy...incubation, even with multiplexed guides. Figure 1: A) Cell-penetrating Cas9, fused to HIV TAT, ...primary cells using peptide-assisted genome editing. Nature Biotechnology, 10.1038/s41587-023-01756-1. https...Although it quickly saw wide interest, its dimeric nature can interfere with some applications. Several labs...molecular fusion and membrane-targeting applications. Nature Methods, 1–9. https://doi.org/10.1038/s41592-023...2023). A monomeric StayGold fluorescent protein. Nature Biotechnology, 1–4. https://doi.org/10.1038/s41587...observed in young macaques and vascular bias in mature marmosets. CAP-Mac also robustly expressed fluorescent...

...the proper controls needed to pressure-test your FRET assay to make sure it is working? This article addresses...resonance energy transfer measurements of ryanodine receptor type 1 structure using a novel site-specific...donor/acceptor fluorophores (Stryer, 1978), a measurement that is unaffected by intervening proteins, lipid...blog has an excellent primer on FRET and how to measure it). Molecular mailbox: How to get your fluorophore... on the same street as the donor), then FRET measurements are possible. In fact, even if the majority ...properly targeted donor/acceptor pairs, then any measureable FRET will be swamped out by a sea of uncoupled..., but even these modifications can affect the structure or function of certain proteins. Rather than shove...

...commonly called “triple plasmid transfection” (Figure 1).    Figure 1: Overview of key steps of AAV production...understand how different titers are measured. A TCID50 measurement reports an infectious titer, meaning...Whitney, O., Walther, N., & Maurer, A. C. (2023). Transgene Expression in Cultured Cells Using Unpurified ...with standard molecular biology tools and tissue culture experience. Here, we’ll go over the basics of rAAV...rAAV production.  Of course, you will want to make sure that your final stocks only contain rAAV. To minimize...contamination, use appropriate decontamination procedures (Korte et al., 2021) for all disposable items...into contact with the rAAV and apply common cell culture practices diligently throughout the production ...

... efficiencies using sequence features and DNA repair determinants. Nature Biotechnology 2023, 1–11. https... evaluate all of the pegRNAs in one experiment (Figure 1). Through this method, we found key determinants...Once we had our datasets with all the different features and editing efficiencies, we could train our prediction...very diverse edit types and cell contexts. Figure 1: High-throughput screening of pegRNA efficiency...downstream flanking sequences to their input string (Figure 2). This string can then be used as input for the...e.g., top 5) and test them in their labs. Figure 2: Guidelines to predict pegRNA efficiencies with...Mathis et al., 2024) and concurrent research by the Shendure lab (Li et al., 2024) have highlighted how chromatin...

...introduced mutations that drive leukemia (Figure 3). Figure 3: Using LARRYv2 libraries for state-...expansion cultures. A) Experimental design. B) UMAP of cell states in ex vivo expansion cultures from days...maintaining high brightness and fast maturation time (Figure 1). See the paper for more details on small differences...mGold2t depending on the application. Figure 1: Super-resolution imaging of actin filaments ...yellow fluorescent proteins for extended imaging. Nature Communications, 16(1), 3241. https://doi.org/10.1038... an RNA guide (known as an omega RNA, or ωRNA) (Figure 2), but TnpB is small enough to be carried by viral...less than a third of the size of Cas9). Figure 2: Comparison of TnpB (A) and Cas9 (B) genome editors...

... SDS-PAGE, measure the protein content and normalize to ensure equivalent loading. Denature the samples...antibodies.   Figure 1: Overview of the Western blot process. The sample, a mixture of protein is separated...denaturing western, the protein is denatured to its primary structure and separated by size with smaller...western, the protein’s secondary and tertiary structures remain intact and the protein is separated through... expensive system-specific sandwiches.   Figure 2: The western blot dry apparatus includes a stack...its native state while a western blot detects denatured polypeptide chains. The protein regions available... antibody validation. This level of validation ensures that the antibody is staining the intended target...

...of Addgene’s work culture. Our developers are a diverse group of ethnicities, cultures, genders, educational... for working on a new feature. We start with a story that describes the feature and what the criteria ...stakeholder accepts the new feature as done and we’re onto the next story. Figure 1: Addgene’s Agile Approach...working on a feature, sometimes we have to take short cuts or add a band-aid to get a feature to work. We...number of stories we commit to for each sprint, to ensure we will have the capacity to finish all of the ...criteria is for accepting the feature as done correctly. These initial stories are usually a result of collaborations...step-by-step instructions on how to demonstrate the feature. For example, we recently reduced the number of...

...sequence (Zong et al., 2018) (see CBE-3 in Figure 3). Figure 3: Activity windows of plant base editors...excision repair mediated by uracil glycosylase (Figure 1). The presence of a uracil glycosylase inhibitor...generation of the desired T-A base pair. Figure 1: Transition mutation (C>T, G>A, A>G, and T>C)... that compete with the desired outcome are not pictured. Adenine base editors (ABE) What if you have...satisfactorily accepts DNA as its substrate (see figure 2).          The artificially evolved adenosine...genomic A-T base pair is converted to a G-C pair (Figure 1). As the cellular inosine excision repair is ...base editing platforms for plant systems.  Figure 2: Plant base editor platforms and their molecular...

...better at 30°C or room-temperature, which is accomplished by growing your culture to the desired density...previous Plasmids 101 blog, we reviewed the salient features of several popular strains of E. coli for DNA ...except ** which are K12 Strain Resistance Key Features Genotype Use BL21 (DE3)   Basic IPTG-inducible...Denotes the presence of an additional plasmid-- make sure to maintain this by growing on appropriate media...timing is important, as you typically want to make sure your cells have first reached an appropriate density...expression. If you wait too long to induce, your culture will start collecting dead cells, and, conversely...too early as there are not enough cells in the culture to make protein.  The DE3 lysogen/T7 promoter combination...

...acceptor fluorophore can be measured using microscopy techniques. FRET measurement sensitivity makes it suitable...one of the first techniques which enabled the measurement of single molecule interactions in living cells...living cells. Since then FRET has also been used to measure conformational changes, cleavage activity using...is still one of the best and most used pairs to measure FRET. The table below lists plasmids that can be...and Venus Other issues that can affect FRET measurements include: the brightness of a fluorophore pair...between FRET efficiency and cross-talk. Methods to Measure FRET for Cell Biology Studies Several methods have... have been used over the past 20 years to measure FRET and there is not one that is better than another...

...environments: corrosive pH ranges, crushing pressures, near-melting temperatures, tons of radiation, or freezing ...Sreepadmanabh M from IISER Bhopal. All illustrations / figures featured were designed by our team member Kallol Mozumdar... take bacteria out of their optimally suited temperature ranges and make them grow better at suboptimal...cold-loving) bacteria. These bacteria inhabit cold temperature locales and psychrophilic enzymes help them survive...next-door microbes which grow optimally in moderate temperatures (usually defined between a fairly nippy 20°C...materials degrade at a much slower rate under cold temperatures, and frigid conditions decrease the potential...mesophilic host systems. The so-called “regular” temperatures of growth, say around 37°C, is a far cry from...

...method does provide a quantitative measure of autophagy, it only measures bulk autophagy (as opposed to giving... Long-lived protein degradation: This approach measures the degradation rate of radio-labeled long-lived...long-lived proteins as a proxy for autophagy. Cells are cultured with isotope-labeled amino acids for several hours...by measuring the amount of radioactivity in the culture supernatant (this is indicative of protein degradation...out of this assay. This is also a quantitative measure of autophagy, but, like the protein degradation...degradation assay above, it’s slow and only measures bulk autophagy. Morphological assays Electron microscopy...method relies on the identification of autophagic structures based on morphology. Autophagosomes are relatively...

...articles, only 46% could be reproduced. In a recent Nature report from researchers at Amgen, it was stated...that only 11% of the academic research in the literature was reproducible by their groups. Finally results..., it will always be a part of everyday work to capture ideas, write down certain notes or brainstorm, ...functionalities i.e. main priorities of different ELN features, ranging from whether respondents saw them as ...term, so they need a solution for which they are sure that there will be no sharp changes in costs once...researchers to store everything in one place. From pictures to excel sheets, researchers today generate vast...Following these findings, we defined the priorities for future ELN development and developed the SciNote Electronic...

...with CRISPR–Cas13. Nature, 550(7675), 280–284. https://doi.org/10.1038/nature24049 Altae-Tran, H., Kannan... ideas for your own research! Classification Structure Principles of CRISPR classification While CRISPR...six types, 33 subtypes, and 17 variants. Figure 1: Overview of the CRISPR classification hierarchy...using a Cascade complex is tricky, as you need to ensure every unit of the complex expresses at similar ...components present in the Cascade complex. Figure 2: Schematic of a Cascade complex (blue subunits...CRISPR types do, due to a lack of canonical CRISPR features (Pinilla-Redondo et al., 2019; Moya-Beltrán et... most often found on plasmids. The many unique features of IV-A and IV-B have led to the hypotheses that...