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We narrowed to 438 results for: ERG

Showing: 51 - 100 of 438 results

  1. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    ..., so it associates with random DNA sequences (Sternberg et al., 2014). The nuclease lobes are inactive...and active conformations (Bravo et al., 2022; Sternberg et al., 2015). The correct positioning of the ...before cleavage can occur (Jiang & Doudna, 2017; Sternberg et al., 2015).     Figure 8: Comparison...cellular recycling factors to release its handiwork (Sternberg et al., 2014). New discoveries on this topic are...and Computational Biology, National Institute of Allergy and Infectious Diseases. Resources and references...9), 839–843. https://doi.org/10.1038/nbt.2673 Sternberg, S. H., LaFrance, B., Kaplan, M., & Doudna, J.... 110–113. https://doi.org/10.1038/nature15544 Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C.,...

  2. Cloning Mammalian Cells with the Agarose Method

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    Blog Post
    ...blogger Iris Lindberg, Professor at the University of Maryland School of Medicine. In the Lindberg Lab we ...blogger Iris Lindberg, Professor at the University of Maryland School of Medicine. Iris Lindberg is a professor...PC12, Rin5F, Neuro2A and GH4C1, among others (see Lindberg papers in PubMed). While we found that nearly ...neural and endocrine cells. She can be emailed at ilindberg@som.umaryland.edu.   Additional Resources on the...

  3. Streaking for Single Colonies: The Streak Plate Challenge

    Type
    Blog Post
    ... any bacteriologist’s skill set. So when Dave Westenberg taught this concept in his microbiology lab course...wear a mask. (@GermJuggler) February 13, 2021 Westenberg, a Professor of Biological Sciences at Missouri...by using a thicker bacterial suspension,” says Westenberg. In addition to streaking for single colonies...them into different strains of E. coli,” says Westenberg. During the transformation experiment, he plans...efficiency.  Aside from the Streak Plate Challenge, Westenberg’s course includes Winogradsky columns and characterizing...

  4. Which Fluorescence Microscopy Technique is Best for Me?

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    Blog Post
    ...fluorescent microscopy. Collimated (non-converging or diverging) excitation light exits the microscope ...its unrivaled contrast, fluorescence imaging has emerged as the dominant light microscopy contrast technique...GFP. Because red light has approximately half the energy of blue light, two photons of red light are needed...Although the excitation light is completely reflected, energy is propagated into the sample via an evanescent...the fluorophore’s interaction with an evanescent energy field. Lightsheet microscopes that project ultra-thin...

  5. Meet an Addgenie: Insights into Grad School, Career Paths, and More

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    Blog Post
    ...after undergrad] was to learn and speak the language of science. I didn’t come out of [undergrad] feeling...solidified some concepts that are heard often during undergrad. Lauren Flynn is the Addgenie behind our...doctor. After taking a year break in between undergraduate school and studying for the MCAT, she decided...description.” Our resident bagel provider, source of energy, and conversation master knows that although her...

  6. CrispyCrunch: High-throughput Design and Analysis of CRISPR+HDR Experiments

    Type
    Blog Post
    ...science.   Acknowledgements Chan Zuckerberg Initiative Chan Zuckerberg Biohub Manuel Leonetti Ryan Leenay...Greg Dingle, a software engineer with the Chan Zuckerberg Initiative. We hereby announce the general availability... us your questions or comments to gdingle@chanzuckerberg.com. We're eager to hear your thoughts. Many...Greg Dingle is a software engineer with the Chan Zuckerberg Initiative, working on assignment at the Biohub...

  7. Minigenomes - a Safe Way to Study Dangerous Viruses Like the Ebola Virus

    Type
    Blog Post
    ...Cressey is a PhD Student in the labs of Dr. Elke Mühlberger and Dr. Rachel Fearns at Boston University School...Medicine, Department of Microbiology, National Emerging Infectious Disease Laboratories.  She is interested...The power of reverse genetics. Springer Berlin Heidelberg, 2004. 1-41. PubMed PMID:15298166. 3. Hoenen,...21699921. PubMed Central PMCID: PMC3586226. 4. Mühlberger, Elke, et al. "Comparison of the transcription... 9971816. PubMed Central PMCID: PMC104478. 5. Mühlberger, Elke. "Filovirus replication and transcription...

  8. Transferable Skills Guide: Time Management

    Type
    Blog Post
    ...skills, but I’ve learned a lot since my days as an undergrad working with cancer cell lines. As I started planning...useful tasks. The quick accomplishments will likely energize you. For example, let's say you’re doing a multi-day...that should help keep you content and give you the energy to finish any additional work you might need to... all if I’d planned appropriately. Back in my undergrad days, I had general goals for my experiments, ...to it each day. Once you get over the activation energy barrier that comes with making ANY progress, the...

  9. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    ...intracellular domain of an endogenous GPCR, such as adrenergic receptors. When exposed to light, there is a ...Figure 3: Chimeric OptoXR incorporating rhodopsin undergoes a conformational change when exposed to blue-light.../978-1-0716-0755-8_2 Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., & Deisseroth, K. (2005). Millisecond-timescale..., N., Berthold, P., Ollig, D., Hegemann, P., & Bamberg, E. (2003). Channelrhodopsin-2, a directly light-gated...Dieter, A., Pieper, F., Sims, R., Tenedini, F., Bergs, A. C. F., Bendifallah, I., Zhou, F., Zeitzschel...

  10. Hot Plasmids: Spring 2025

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    Blog Post
    ...proteins (GPC1, GPC3, and GPC4). All IPI antibodies undergo extensive characterization at IPI as well as community-led...CRISPR homing of retroelements." The Abudayyeh-Gootenberg Lab developed this tool based on several new ...Lim, J., Hiraizumi, M., … Abudayyeh, O. O., & Gootenberg, J. S. (2025). Reprogramming site-specific retrotransposon... The enhancers span all four major classes of GABAergic interneurons — those marked by parvalbumin (PV...lysosomal-associated membrane protein 5 (LAMP5) — as well as cholinergic (choline acetyltransferase, ChAT) neurons. The...

  11. Typing CRISPR Systems

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    Blog Post
    ...archaeal immune systems has led to extreme sequence divergence that requires a multi-pronged analysis to sort...References and Resources References Abudayyeh, O. O., Gootenberg, J. S., Essletzbichler, P., Han, S., Joung, J...doi.org/10.1126/science.1231143 Cox, D. B. T., Gootenberg, J. S., Abudayyeh, O. O., Franklin, B., Kellner...Makarova, K. S., Koonin, E. V., Abudayyeh, O. O., & Gootenberg, J. S. (2021). Programmable RNA targeting with...nar/gkz1197 Samai, P., Pyenson, N., Jiang, W., Goldberg, G. W., Hatoum-Aslan, A., & Marraffini, L. A. ...

  12. Understanding GPCR Signaling Using TRUPATH

    Type
    Blog Post
    ...Bioluminescence Resonance Energy Transfer (BRET). BRET is similar to Förster Resonance Energy Transfer (FRET), ...fluorophore. The difference for BRET is that the energy transfer is between a luminescent donor and a fluorescent...protein dissociation by bioluminescence resonance energy transfer 2, or BRET2. With binding of the drug,...

  13. Single-cell tracking of lineage and identity with CellTag

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    Blog Post
    ...CellTagD13), which is when the iEP phenotype typically emerges. Every three days, a sample of cells was collected...expression changes of more than 100,000 cells undergoing iEP conversion, the Morris Lab found that cells... to uncover two distinct trajectories of MEFs undergoing iEP conversion, but CellTag could be used to ...study other biological processes where cells are undergoing identity changes, such as the differentiation...

  14. CRISPR Methods for Bacteria: Genome Engineering, CRISPRa, CRISPRi, Base Editing, and More

    Type
    Blog Post
    ...transposons, the Sternberg and Zhang labs developed CRISPR-transposons. The Sternberg lab's system called...and Gram-positive bacteria Jason Peters, Oren Rosenberg, and Carol Gross used two different genetic systems...References Bikard D, Euler CW, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, Fischetti VA, Marraffini LA (2014..., Engel JN, Dutton RJ, Grossman AD, Gross CA, Rosenberg OS (2019) Enabling genetic analysis of diverse...

  15. Simple CRISPR-based Epigenetic Editing: dCas9-directed DNA Demethylation

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    Blog Post
    ...suddenly cool: DNA methylation. In 1983, Andrew Feinberg and Bert Vogelstein showed, for the first time...methylation detected in a human disease: cancer (Feinberg & Vogelstein 1983). The floodgates, as they say...methylated strand is diluted to undetectable amounts: ergo, DNA demethylation! With optimization, this method...827. https://doi.org/10.1038/s41588-020-0639-9.  Feinberg A, Vogelstein B (1983) Hypomethylation distinguishes...

  16. Adapting Toehold Switches to Detect Zika Virus

    Type
    Blog Post
    ...Health Organization has declared a global health emergency and called for the fast-tracked development of... was underscored by the potential scale of the emerging outbreak, as many as 2.2 billion people globally...prototyping and sensor assembly pipeline for future emerging pathogens or health crises. Many thanks to our..., and self-assembly for applications in health, energy, and sustainability.   References 1. Pardee, Keith...

  17. Chromoproteins: Colorful Proteins For Molecular Biology Experiments

    Type
    Blog Post
    ... visible and infrared light to dissipate excess energy at wavelengths of low photosynthetic activity. ...lifetime imaging microscopy-based Förster resonance energy transfer (FLIM-FRET) in living cells (Figure 4)...10.1074/jbc.m606921200 Dove SG, Takabayashi M, Hoegh-Guldberg O (1995) Isolation and Partial Characterization...48604-4 Salih A, Larkum A, Cox G, Kühl M, Hoegh-Guldberg O (2000) Fluorescent pigments in corals are photoprotective...

  18. Getting to Know Expansion Microscopy

    Type
    Blog Post
    ...fluorescent proteins (Gambarotto, et al. 2019; Tillberg, et al. 2016). That being said, the anchoring,.../doi.org/10.1371/journal.pbio.3001020  Chen F, Tillberg PW, Boyden ES (2015) Expansion microscopy. Science...//doi.org/10.7554/elife.73775  Dani A, Huang B, Bergan J, et al (2010) Superresolution Imaging of Chemical...101796. https://doi.org/10.1016/j.mex.2022.101796  Tillberg PW, Chen F, Piatkevich KD, et al (2016) Protein-retention...

  19. Negotiating Work and Life: How to Find the Joy

    Type
    Blog Post
    ...real goal. We are all constantly negotiating our energy and attention. The goal is to maximise the time...Check out Joanne's Reddit AMA Managing time and energy between work and the rest of life is sometimes ...will worry less about how they will handle an emergency and this will make you much more confident about...daughter vehemently reminded her doctor that she was allergic to penicillin – I am much less worried knowing...

  20. 15 Hot Plasmids from 2017

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    Blog Post
    ...specific neuronal subtypes such as inhibitory GABA-ergic interneurons, Gordon Fishell’s lab has developed... you to target and functionally manipulate GABA-ergic interneurons across species and will undoubtedly...You can find the AAV vectors for infecting GABA-ergic interneurons here. Dimidschstein J, et al. Nature... use as a donor in FRET (fluorescence resonance energy transfer) and FLIM (Fluorescence Lifetime Imaging...Under the supervision of Dr. Tan, a team of undergraduates created DNA ladders (aka DNA molecular weight...

  21. The PAM Requirement and Expanding CRISPR Beyond SpCas9

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    Blog Post
    ...update of this post. References Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto...://doi.org/10.1186/s13059-018-1591-1 Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung...nature26155 Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova...://doi.org/10.1126/science.aba8853 Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, ...

  22. New CRISPR Tools: Cas7-11 and PASTE

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    Blog Post
    ...and expand our current knowledge. The Abudayyeh-Gootenberg lab (also called the AbuGoot lab), a joint lab...lab run by Omar Abudayyeh, PhD, and Jonathan Gootenberg, PhD, focuses exclusively on this space — developing...Gardner A, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS. Programmable RNA targeting with the single-protein...Adrianna E. Zepeda, Kevin Holden, Jonathan S. Gootenberg, Omar O. Abudayyeh. Drag-and-drop genome insertion...

  23. Technologies Enabled by NanoLuc® Luciferase

    Type
    Blog Post
    ...through a process known as bioluminescent resonance energy transfer (BRET). The fluor then emits light at ...release have been made using fluorescent resonance energy transfer (FRET) probes. These probes generally ...FRET signal. FRET is a non-radiative transfer of energy from one fluorescent protein to a compatible fluorescent...other fluorescent probes but can still transfer energy to the fluorescent protein acceptor. NLuc is an...

  24. Plasmids 101: Dimers and Multimers

    Type
    Blog Post
    ...: 797459. Berg CM, Liu L, Coon M, Strausbaugh LD, Gray P, Vartak NB, Brown M, Talbot D, Berg DE. pBR322...frequently in plasmids with large inserts (>7 kb)(Berg et al., 1989), direct repeats (Ribeiro et al., 2009...and define recA-independent mechanisms. Avoid overgrowing the bacterial culture Another way to prevent ...

  25. FLEx Technology and Optogenetics: Flipping the switch on gene expression with high spatial and temporal resolution

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    Blog Post
    ...light-sensitive proteins that absorb photons for energy conversion or the induction of intra- or intercellular...shorter than 5 kb (Hirsch et al., 2016; Hudry and Vandenberghe, 2019). How to achieve strong opsin expression...PubMed PMID: 26135556. Hudry, Eloise, and Luk H. Vandenberghe. "Therapeutic AAV gene transfer to the nervous...Juarez, Barbara, and Ming-Hu Han. "Diversity of dopaminergic neural circuits in response to drug exposure...

  26. Illuminating Choices: A Guide to Selecting Fluorescent Dyes and Ligands

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    Blog Post
    ...emitting a photon with slightly less energy due to non-radiative energy losses. This difference in emission...ensure accurate tagging. In Fluorescence Resonance Energy Transfer (FRET) applications, the dyes need to ...excitation and emission profiles to enable effective energy transfer, which is key to observing interactions...

  28. Embracing Serendipity: A Crucial Element in the PhD Journey

    Type
    Blog Post
    ... its confines. The beauty of serendipity often emerges at the intersections of disciplines. Cast your ... capture fleeting thoughts and connections that emerge during moments of inspiration. Additionally, journaling...serendipity. However, the best discoveries often emerge when we allow ourselves the freedom to explore ...

  30. Three Tips for Preventing Viral Plasmid Recombination in Your Samples

    Type
    Blog Post
    ...sequences. Repeating sequences within a plasmid can undergo intramolecular DNA recombination. This naturally...two repeating elements love each other very much undergo recombination, two smaller plasmids are formed....To reduce recombination, it is important to not overgrow the plasmid at 37°C. Some researchers find that...

  31. Mentoring for Scientists: I Have a Mentor, What Now?

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    Blog Post
    ... An undergraduate can mentor a high school student, a graduate student can mentor an undergraduate, a ... up on plans. Make a commitment to put time and energy into your mentoring relationships. You will only...

  32. The Crispr Babies Saga Shows the Need for Action, Not More Delays

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    Blog Post
    ...non-governmental groups with seeking “public views on emerging IVF techniques designed to prevent the transmission... a controversial and ethically fraught rapidly emerging technology. We could do this for CRISPR/Cas9 –...in the software industry to inform her work on emerging issues in novel technologies, including self-driving...

  33. R Bodies: Membrane-Rupturing Microscopic Tools

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    Blog Post
    ...Instead, R body monomers respond to pH changes by undergoing local conformational changes. These tiny movements...decades, and they were known to be resistant to detergents and degradation under a variety of conditions...conditions. More speculatively, R bodies might endow divergent organisms with new functions. For inspiration,...

  34. Viral Vectors 101: Systemic Capsids

    Type
    Blog Post
    ...ll provide information about commonly used and emerging capsids to help you decide which ones may be suitable... of published descriptions of commonly used or emerging capsids. Selected capsids are further highlighted... regional bias towards the cortex and thalamus emerges. AAV-PHP.eC effectively transduces neurons and ... Moncada-Reid, C., Eid, F.-E., Walkey, C. J., Ljungberg, M. C., Lagor, W. R., Heaney, J. D., Chan, Y. ... Sakopoulos, S., Schneider, G., Stevenson, O., Vergara, J., Sharma, J., Zhang, Q., Franken, T. P., Smith...

  35. Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens

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    ...just such a system, which they call CRISPR/Cas9 Synergistic Activation Mediator or SAM. SAM is an engineered...distinct effector domains that work together synergistically, modeled after natural transcription activation... J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F. Nature. 2015...

  36. Rabies and Neuronal Tracing

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    ...cargoes, genetically engineered neurotropic viruses emerged as powerful tools for visualizing neural connectivity...monosynaptic tracing to identify inputs to two major dopaminergic cell populations in two specific brain regions...617–623. Pubmed PMID 19349161.  2. Deshpande A, Bergami M, Ghanem A, Conzelmann KK, Lepier A, Götz M, Berninger...

  38. 5 Tips for Troubleshooting Viral Transductions

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    Blog Post
    ...obstacles when working with virus: 1. Viral vectors undergo DNA rearrangements. Depending on the composition...repeat sequences present in the LTR, the vector may undergo genomic rearrangements during replication. To avoid...immunotherapy." Acute Leukemias VIII. Springer Berlin Heidelberg, 2001. 291-306. PubMed PMID: 10634178. 8. Murnane...

  39. 3D Printing Meets CRISPR Cas9

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    Blog Post
    ...surface of the protein where the nascent polypeptide emerges from the exit channel.   He then said “I hadn’t...accurately suggests the potential of this protein to undergo conformational shifts. This backbone model of Cas9...conformational gymnastics that this protein must undergo as it interrogates your genome. If you are interested...

  40. Quick Guide to Working with Drosophila Part 1: Getting Started with Flies

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    Blog Post
    ...takes roughly 10 days for an egg to develop and emerge as an adult fly at 25°C. At low temperatures like...the day and throughout daytime. They mostly stop emerging at night. An incubator with a light cycle makes...makes for very predictable work! When flies first emerge, their bodies will be very light in coloration ...

  41. Viral Vectors 101: Producing Your rAAV

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    ... media, while others remain cell-associated (Vandenberghe et al., 2010). For certain in vitro and in vivo...rAAV sample has to be digested with DNase before undergoing titering, to remove residual plasmid DNA carried...Article 10. https://doi.org/10.1089/hum.2009.223 Vandenberghe, L. H., Xiao, R., Lock, M., Lin, J., Korn, M...

  43. Transferable Skills Guide: Managing a Team

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    Blog Post
    ...I knew that when I was “managing” a couple of undergrads back in grad school. Both were hard-working scientists-in-training...reviewing the results of my Myers-Briggs test:  my undergrads were different people! More specifically, they...time I could likely have retained this talented undergrad. The point here is managing is not “one size ...

  44. AAVs in Retinal Gene Therapy

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    ...Pigmentosa. I quickly became fascinated by this emerging technology and its potential for the treatment...cost of clinical development. As a result, Luk Vandenberghe and colleagues at MEEI co-founded a non-profit...approves gene therapy for blindness 2. Gene Therapy emerges from disgrace to be the next big thing, again 3...

  45. An Introduction to Adenovirus

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    ... zoonotic? A systematic review of the evidence. Emerg Microbes Infect, 8(1), 1679–1687. https://doi.org...of a Cytopathogenic Agent from Human Adenoids Undergoing Spontaneous Degeneration in Tissue Culture. Proc...M., Foresythe, A., Huh, H. J., Bazinet, A. L., Bergman, N. H., Bull, R. L., Garcia, K. Y., Goodrich, J...

  47. Great Results Start with Great Standard Curves

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    Blog Post
    ...their viruses; food allergy labs use standard curves with ELISAs to measure allergen concentrations in ...What do a viral vector production facility, food allergy testing lab, and the grad student down the hall...

  48. CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics

    Type
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    ...third chromosome, ten base pairs in length. An emerging family of sequencing techniques function as a ...coordinates into meaningful experiments. Table 1: An emerging family of "GPS for the genome" techniques Technique...going. Appendix DNAse Hypersensitive Sites and Intergenic CRISPRs Yours truly generated the DHS data set...

  49. Fluorescent Proteins 101: Green Fluorescent Protein (GFP)

    Type
    Blog Post
    ...the earliest uses of GFP. Fluorescence resonance energy transfer (FRET): This is used to study the interactions...proteins or between two domains of a protein that undergoes conformational change. Typically, two fluorescent...come into close proximity, the two halves of EGFP undergo folding, maturation, and fluorescence. Biosensors...

  50. CRISPR 101: Targeting RNA with Cas13a (C2c2)

    Type
    Blog Post
    ...molecules of an RNA species with high specificity (Gootenberg et al., 2017). This system, dubbed SHERLOCK (...Find plasmids from this paper at Addgene.  3. Gootenberg, Jonathan S., et al. "Nucleic acid detection ...plasmids from this paper at Addgene. 6. Shmakov, Sergey, et al. "Discovery and functional characterization...
Showing: 51 - 100 of 438 results