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We narrowed to 847 results for: CAL;

Showing: 281 - 300 of 847 results

  1. Chromoproteins: Colorful Proteins For Molecular Biology Experiments

    Type
    Blog Post
    Published
    Feb. 4, 2020, 2:15 p.m.
    ...What’s behind these sights are an abundance of biological molecules like chromoproteins, fluorescent proteins...proteins and luminescence have been widely used in biological research for a long time, chromoproteins are ...just now being developed for a broad range of biological inquiries.  What is a chromoprotein and how ...photosynthetic activity. This still allows photosynthetically active wavelengths to reach zooxanthellae...the Sea AnemoneCnidopus Japonicus. Journal of Biological Chemistry 281:37813–37819 . https://doi.org/10.1074...Pigments of Pocilloporid and Acroporid Corals. The Biological Bulletin 189:288–297 . https://doi.org/10.2307...chromoproteins for bacterial synthetic biology. Journal of Biological Engineering, 12(1). https://doi.org/10.1186/s13036...

  2. Selecting Your Plasmid Purification Kit

    Type
    Blog Post
    Published
    May 27, 2025, 1:15 p.m.
    ...such small amounts of DNA (often on the picogram scale) that most quality issues are negligible. That said...small amount of DNA (in the nanograms to micrograms scale depending on the experiment), but issues with DNA... large amounts of DNA (easily in the micrograms scale and up). But perhaps more importantly, the DNA needs...the clean-up stage, plasmid purification kits typically use one of two common approaches — columns or ... result in incomplete lysis. You may be able to scale the amount of buffers used to ensure proper lysis...appropriate amount of beads and a suitable magnet as you scale up. Table 1: Standard Prep Kit Capacities* Prep...and Milllipore Sigma’s GenElute™ kits were all specifically designed with environmental sustainability in...

  3. INTEGRATE: Bacterial Genome Engineering Using CRISPR-Transposons

    Type
    Blog Post
    Published
    Dec. 7, 2020, 2:53 p.m.
    ...candidate in the Sternberg Lab at Columbia University Medical Center. DNA transposons are ubiquitous genetic ...a multi-spacer CRISPR array. Workflow and technical considerations Making insertions in bacterial ...into cells and plate overnight Screen colonies phenotypically or by PCR/sequencing While CRISPR-transposons...few important details. For transposons to be specifically recognized during transposition, genetic cargos...Additionally, these transposon also exhibit something called target immunity, whereby multiple proximal insertions...Leveraging a unique marriage between distinct biological elements, CRISPR-transposons excel at programmable...candidate in the Sternberg Lab at Columbia University Medical Center. He currently studies CRISPR biology and...

  4. Uncovering Ancestral Bias in CRISPR Research

    Type
    Blog Post
    Published
    Nov. 29, 2022, 2:15 p.m.
    ...kind of biological framework, suggested to them that their findings may be the result of a technical artifact...Biomedical research has a long and well-documented history of racial bias, which still impacts and influences..., by extension, race. Many researchers do large-scale CRISPR screens in cancer cell lines, looking to ... Aaron knew that their study had significant statistical limitations, and expected to find only a few,...Seeking an explanation  First, they looked for a biological explanation, a relationship between the genetic...far larger and more complex problem endemic to biomedical research: pervasive bias that is easy for researchers...

  5. Viral Vectors 101: The Retroviral Lifecycle

    Type
    Blog Post
    Published
    July 27, 2023, 1:15 p.m.
    ...reverse-transcribed piece of DNA called a “provirus.” This DNA is synthesized inside of what is called the “target cell...The Retroviridae (commonly called retrovirus) family — of which HIV is a member — may seem like an unlikely...retroviral vectors and 2.) a subclass of retroviruses called the lentiviruses (like HIV-1) — that have been ...(Prussin et al., 2015), only a small fraction typically cause disease. The gamma-retroviruses have their...transduction by vectors (which we sometimes still call “infection” as a shorthand, although it is not quite... proteins encoded by complex retroviruses. Microbiological Reviews, 56(3), 375–394. https://doi.org/10.1128...

  6. Plasmids 101: Protein tags

    Type
    Blog Post
    Published
    Dec. 11, 2014, 4:26 p.m.
    ...purification (TAP) once referred specifically to a combo tag comprised of a calmodulin binding peptide (CBP), a...to) purification, detection, solubilization, localization, or protease protection. Thus far Plasmids 101...overexpress and purify proteins can face any number of technical challenges depending on their protein of interest...consider junk protein. Though there are a number of chemical and peptide-based proteosome inhibitors, glutathione... relatively small sequence of amino acids, is basically a molecular leash for your protein. If you’re ...want to combine a fluorophore with a tag that localizes your protein to the nucleus? Or you want multiple...

  7. Grad School Advice Part 1: Picking a Lab and a Project

    Type
    Blog Post
    Published
    Sept. 1, 2016, 2:30 p.m.
    ...Harvard Medical School, and is currently a fellow in clinical genetics at the University of California, Los...Vincent and Niroshi Senaratne, from the Biological and Biomedical Sciences program at Harvard University...the Program in Genetics and Genomics at Harvard Medical School. He studies developmental gene regulation...

  8. Controlling for Off-target Effects with a New Genome-wide CRISPR Screen Design

    Type
    Blog Post
    Published
    Sept. 13, 2018, 1:55 p.m.
    ...results (i.e. mistakenly calling a gene a hit when really it’s not). In practical terms, this means that... approach for identifying genes involved in a biological process. These screens provide an alternative...cutting than full-length guides (19-20bp)?  Small-scale studies (Tsai et al., Fu et al.) suggest 17-19 bp...non-targeting guides on screen analysis and hit calling. 5,644 non-targeting guides and 6,750 safe-targeting...ricin screen. When safe-targeting guides are used to call hits from the growth screen, p-values were less ...References 1. Morgens, David W., et al. "Genome-scale measurement of off-target activity using Cas9 toxicity...

  9. Hot Plasmids Spring 2024

    Type
    Blog Post
    Published
    May 23, 2024, 1:15 p.m.
    ...Emily Bentley Building on their CROPseq method for optical pooled CRISPR screening, Paul Blainey’s lab has...multiplexing approach to Cas9-based pooled CRISPR screens called CROPseq-multi (Walton et al. 2024). This platform...compatible with enrichment, single-cell sequencing, and optical pooled screens in human cells. Addgene offers vectors...one of the virus’s most abundant proteins and a critical component for viral genome packaging. Addgene ...Genetic modification of microglial immune cells is critical for central nervous system research; however, ...cells.      Figure 5: A) Representative confocal images showing GFP expression from ssAAV5s with...gene of interest, reducing the immunogenicity typically associated with viral vector-based therapies. ...

  10. Grad School Advice Part 2: Building Community

    Type
    Blog Post
    Published
    Oct. 6, 2016, 2:30 p.m.
    ...Harvard Medical School, and is currently a fellow in clinical genetics at the University of California, Los...Niroshi Senaratne and Ben Vincent from the Biological and Biomedical Sciences program at Harvard University...the Program in Genetics and Genomics at Harvard Medical School. He studies developmental gene regulation...

  11. The Fluorescent Vegetables in Aptamer Soup

    Type
    Blog Post
    Published
    Jan. 29, 2019, 2:27 p.m.
    ...able to bind to a small molecule derivative of GFP called 3,5-difluoro-4-hydroxybenzylidene imidazolinone...intracellular locations using Cas9 and track the localization of the complex. Broccoli, the other green fluorescent...Broccoli, and useful for quantitative studies. Specifically, Corn was developed to quantify RNA transcription...high-affinity complex for RNA labeling and tracking." ACS chemical biology 9.10 (2014): 2412-2420. PubMed PMID: 25101481...and directed evolution." Journal of the American Chemical Society 136.46 (2014): 16299-16308. PubMed PMID...di-GMP and cyclic AMP-GMP." Journal of the American Chemical Society 135.13 (2013): 4906-4909. PubMed PMID:...a photostable RNA–fluorophore complex." Nature chemical biology 13.11 (2017): 1187. PubMed PMID: 28945233...

  12. Tips for Getting a Faculty Position

    Type
    Blog Post
    Published
    July 20, 2023, 1:15 p.m.
    ...colleges, private universities, and medical schools. I will emphatically deny that I have a magic formula..." manual on applying for faculty positions in biomedical science. My motivation was to share my experiences...told all of the nuances of the research in as technical of language as possible. Seriously. My suggested... trying to say X." She would then look at me quizzically and ask why I didn't just say that? Bottom line...especially helpful. I set out to make something practical and accessible. If there's something you come ...the Janelia Research Campus of the Howard Hughes Medical Institute. His interests include the quality control...

  13. Plasmids 101: Expressing shRNAs for RNA Interference

    Type
    Blog Post
    Published
    June 17, 2025, 1:15 p.m.
    ...structures that are processed by a ribonuclease called Dicer. In a great simplification of the process...pri-miRNA, which is then processed by a complex called Drosha to pre-miRNA. miRNA plasmids are engineered...backbone Choosing the promoter Mature siRNAs typically range from 19–22 nucleotides and are 100% complementary...’t just use the mature sequence in a plasmid and call it a day. You need to include both sides of the ...for quick in vitro experiments. shRNA plasmids typically use RNA polymerase III promoters, which transcribe... versatile gene-silencing machine. Journal of Biological Chemistry, 284(27), 17897–17901. https://doi.... DICER: structure, function, and regulation. Biophysical Reviews, 13(6), 1081–1090. https://doi.org/10.1007...

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

    Type
    Blog Post
    Published
    April 8, 2025, 1:15 p.m.
    ... why you might want to be careful relying on so called “housekeeping proteins.” Fully quantifying a western... later steps in this chain (blue) to infer or calculate things about earlier ones. In practice, multiple...popular choices for loading controls. These are often called “housekeeping proteins” and are detected with an... will almost certainly be overloaded. One paper called this problem “the most common error associated ...Data is presented as mean ± SEM. Adapted from Analytical Biochemistry, vol 440, Gilda, J. E., & Gomes,...loading control to β-actin for Western blots. Analytical Biochemistry, 440(2), 186–188. https://doi.org...Antibodies 101: The Basics of Western Blotting Technical Design of a Western Blot Troubleshooting and Optimizing...

  15. Antibodies 101: Beyond Surface Labeling

    Type
    Blog Post
    Published
    June 27, 2024, 1:15 p.m.
    ...populations; for example, CD8+ T (“T killer”) cells. Typically, you would label the CD8 co-receptor protein on...of interest via FACS using negative selection is called dump gating. Let’s say we want to sort out all ...cell membrane but inside the cell. Due to their chemical nature, antibodies cannot penetrate the cell membrane...intracellular labeling with antibodies requires chemically pre-treating the cells to allow for entry of ...esterified dyes that can enter cells freely are typically used. Inside the cell, the ester group is cleaved...intracellular labeling protocol is necessary, requiring chemical treatment of the cells after surface labeling....Associate in the lab of Arlene Sharpe at Harvard Medical School. His projects include investigating negative...

  16. How to Negotiate a Successful Lab Start Up Budget

    Type
    Blog Post
    Published
    Sept. 1, 2015, 2:30 p.m.
    ...where you can start to identify which items aren’t critical to your research success. If you can get away ...resources to keep, and which ones to abandon. It’s critical to make these decisions in the following order... budget can help you compare the monetary and empirical value that helps you determine whether or not ...know how to decide which components are the most critical to your research, negotiations can be much easier...negotiating finances, instead of solely discussing numerical values, try to keep conversations focused on research...saving the institute time and energy that would typically be wasted going through some of the questions ...is your goal, then understanding your needs is critical to a successful negotiation and collaboration....

  17. Optogenetics + CRISPR, Using Light to Control Genome Editing

    Type
    Blog Post
    Published
    Sept. 3, 2020, 12:15 p.m.
    ...temporal and spatial control. Optogenetics uses genetically encoded tools, such as microbial opsins, to control...light-inducible heterodimerizing cryptochrome 2 (CRY2) and calcium and integrin-binding protein 1 (CIB1) proteins....this approach. This study generated the first optically active saCas9 protein. Stop light! Photoactive...different approach. These researchers used a genetically encoded photocaging technique to insert a light-removable...light-removable protecting group, specifically a nitrobenzyl photocaged lysine (PCK), on the Cas9 protein...Hemphill et al. presented data showing that this genetically encoded, photocaged Cas9 system could silence...editing and transcription. Label genomic loci Photochemical Control Hemphill et al., 2015   Nitrobenzyl-caged...

  18. CRISPR/Cas9 FAQs Answered!

    Type
    Blog Post
    Published
    March 13, 2014, 4:08 p.m.
    ...it's usually more efficient than plasmid donor. Typical design is to have 50–80 bp of homology arms on ...changes (>100 bp insertions or deletions), we typically use plasmid donor, with two homology arms on each...transfection in cells like HEK, we use around 400 ng of a typical size (~5 kb) donor plasmid with Cas9/sgRNAs vector...plasmids. For ssDNA oligo design, the Zhang lab typically uses around 100–150 bp total homology. The mutation... giving 50–75 bp homology arms. The Zhang lab typically use PAGE purified long oligos. For large changes...100 bp insertions or deletions), the Zhang lab typically uses a plasmid donor, with two homology arms on...like HEK, the Zhang lab uses around 400 ng of a typical size (~5 kb) donor plasmid with Cas9/sgRNAs vector...

  19. Bringing Sustainable Practices to the Lab: Innovations

    Type
    Blog Post
    Published
    March 7, 2019, 2:39 p.m.
    ...you’ve saved. Repurposing regulated medical waste Regulated medical waste (RMV), which we collect in those...scores products by their environmental impact on a scale of 1-10: the lower the score, the lower the environmental...companies to obtain these labels! Reusing plastic Historically, scientists washed and reused materials such...flow cytometers. These fluidic machines handle biological samples and are cleaned between each use. You...those red biohazard bags, typically is destined for a landfill. However, Triumvirate Environmental developed...

  20. What's New in CRISPR - December 2019

    Type
    Blog Post
    Published
    Dec. 17, 2019, 2:37 p.m.
    ...deaminase (TadA) to a catalytically impaired Streptococcus pyogenes Cas9. They called this editor Target-...-to-inosine (A-to-I) RNA editor called REPAIR by fusing catalytically inactivated RNA-targeting Cas13 ...plasmids available at Addgene. We will still periodically focus on specific CRISPR plasmid tools more ...editor still retains A-to-I editing. This system is called RNA Editing for Specific C-to-U Exchange, or RESCUE...
Showing: 281 - 300 of 847 results