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  2. Networking Follow-up: I Met a Person. Now What?

    Type
    Blog Post
    ...defunct (but fun) plug-in called Maps.  Figure 1: See a starfish? This is actually a map of Joanne ...FiercePharma), or sign up to be alerted about their new publications via Pubmed, so you can congratulate them when...

  3. Improving Transduction Efficiency with Exosome AAVs

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    Blog Post
    ...vector-exosomes), exosome AAVs, or exo-AAVs (Figure 1). The researchers discovered that these particles ...the classical purification protocol involving iodixanol gradients. The current purification protocols for...particles accumulate inside the producer cells and purification protocols often describe a process that begins...lysis to release AAV particles with subsequent purification steps. It’s also possible for AAV vectors to... This is particularly useful for therapeutic applications in vivo where endogenous anti-AAV antibodies...Adrienn, et al. "Virus vector-mediated genetic modification of brain tumor stromal cells after intravenous...

  4. From Lab Bench to Leadership: Transitioning into Management as a PhD

    Type
    Blog Post
    ...pitfalls? Here's what you need to know.   Figure 1: Management can seem a mystery at first! Image used...cohesive team environment. Neglecting communication skillsClear communication is the backbone of effective management...management. Miscommunication often arises when managers fail to set expectations or provide timely feedback...firsthand when it took me some time to adapt to the communication style of a new, junior team member who had values...and leveraging tools like the Myers-Briggs Type Indicator or DISC assessments can help you navigate team...

  5. Visualizing Genomic Loci with CRISPR-Sirius

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    Blog Post
    ...the guides are relatively unstable.   Figure 1: CRISPRainbow labeling. Two MS2, PP7, or boxB sequences...The catalytically dead Cas9 protein (dCas9) is well known for its ability to bind DNA targets without...has been widely adapted for a wide variety of applications: base editing, CRISPR activation and inhibition... (B) CRISPR-Sirius used to visualize relative locations of the subtelomeric region of the pericentromeric...al. “CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging.” Nature Methods 15 (2018)...

  6. DAP arrays for multiplex gene editing

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    Blog Post
    ... genes with a single viral vector.   Fig. 1: Schematic of multiplex gene editing with DAP array...packaged into viral vectors for potential in vivo applications or multiplex CRISPR screening.   Using tRNAs...multiplex genome engineering of crops or allow for sophisticated CRISPR screenings that would perturb the unprecedented...and efficient in plasmid and viral vectors. In applications when repetitive tRNA sequences must be avoided...construct DAP array for multiplex gene editing applications, we provide detailed manual and online design...

  7. Hot Plasmids - January 2023

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    Blog Post
    ...as an endogenous RNA imaging tool.   Fig. 1: Csm, shRNA, and Cas13 were compared head-to-head ...antibodies may just not perform as well in one application as another, so it is always best to have options...for mEGFP-HRas (from Plasmid 18662). See the Applications section on the Anti-GFP [N86/8R] page for more...fluorescent proteins (FPs) necessary for many of these applications have lagged. Fixation, chemical staining, and...well-suited for the demands of advanced microscopy applications such as super resolution, electron, and expansion...

  8. The CRISPR Software Matchmaker: A New Tool for Choosing the Best CRISPR Software for Your Needs

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    Blog Post
    ...databases, EENdb (published 1 Jan 2013, no longer available), is a simple catalogue of reported sgRNA designs...follow him on Twitter @CMacPhD.          References  1. Ghorbal, Mehdi, et al. "Genome editing in the human...into this category describe how the user is expected to interact with the software. This category is important... CRISPR software submissions. With few prior publications to go on, a submitted manuscript could only ... solutions that facilitate most experimental applications in CRISPR engineering. When compared to that...easy to fault the lack of features in a single application. The question is then, should we use all tools...novo sgRNA design, I again separate it into two categories. On the one hand we have software tools that ...

  9. Antibodies 101: Flow Cytometry Controls

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    Blog Post
    ...settings with experimental samples. Figure 1: Example flow plots for a single color control. A)...ll need a few controls specific to flow as an application. These controls will allow you to distinguish...commercial antibody pages. Flow cytometry can be a complicated and daunting process. Controls like single color...

  10. Plasmids 101: Blue-white Screening

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    Blog Post
    ...and also by a lactose analogue, IPTG (isopropyl β-D-1-thiogalactopyranoside). (To be completely accurate...insert. All colonies on this plate should be blue, indicating that your IPTG and x-gal are working as they ...of false positives: Blue-white screening only indicates the presence of AN insert, not necessarily YOUR...

  11. Will You Be My Mentor? Finding and Asking for Mentoring Support

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    Blog Post
    ...Networking 101-Building Relationships for Success”. Choose 1-2 tactics to try. One of my favorites is making the...great way to get started with mentoring. Read this Catalyst Report “Making Mentoring Work” to learn about ...tapping into it and helping make it work by being an educated mentee. Other opportunities: Try virtual mentoring...

  12. Summer SciComm: Preprints

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    Blog Post
    ...medRxiv.org) in the past few years.   Figure 1: Stand aside, CERN — it's a new age of accelerating...their CV or grant applications. A number of organizations (such as ASAPbio) advocate for preprints, and...the most important part of your research is communicating the results of the work. Yes, those control ...any impact! There are lots of ways scientists communicate with each other: from formal mechanisms like ...poster or talk, or submitting patent or grant applications; to informal settings like lab meetings, social...of the most significant shifts in scientific communication is the rising use of preprints, or scientific...publishing in a journal.  Accelerating scientific communication Preprints have been common in fields like math...

  13. Antibodies 101: Selecting the Right Antibody

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    Blog Post
    ...antibody that doesn't work for your application.      Fig. 1: Antibody Selection Flow Chart  ...your specific application. Consider also that there may be variations within an application. Take immunohistochemistry...website highlights a variation of your application, a publication successfully used it in a similar way...choosing an appropriate antibody first look at the application-specific data provided on the manufacturer’s ... a linear antigen tend to work very well for applications that denature a protein to its primary (linear...the most similar to yours. Take a look at the publications cited on the manufacturer’s website, which may...plan to. To secondary or not to secondary?  The application will also determine whether you should use an...

  14. Plasmids 101: Cre-lox

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    Blog Post
    ...techniques?  Let us know in the comments! References 1. Bacteriophage P1 site-specific recombination. I. ...recombinase catalyzes the site specific recombination event between two loxP sites, which can be located either...maintained).  Translocation: If the sites are on separate DNA molecules, a translocation event is generated...important plasmid elements – promoters, origins of replication, protein tags, and antibiotic resistance markers...creating (excuse the pun) specific, targeted DNA modifications in transgenic animals, embryonic stem cells,...proteins or co-factors, thus allowing for broad applications in a variety of experiments. LoxP (locus of ...and the canonical loxP sequence is ATAACTTCGTATA-GCATACAT-TATACGAAGTTAT. The loxP sequence does not occur...

  15. Visualizing Protein Turnover In Situ

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    Blog Post
    ... contact her at [email protected]. References 1. Dieterich, Daniela C., et al. "In situ visualization...This application of AHA labeling is known as fluorescence noncanonical amino acid tagging (FUNCAT, Dieterich...experiments. Visualizing newly synthesized proteins with FUNCAT Professor Schuman’s technique applies metabolic...the whole de novo synthesized proteome. However, FUNCAT alone cannot be used to determine the turnover ...specific protein. Professor Schuman’s lab showed that FUNCAT’s usefulness can be extended to determine the turnover...ligation assay (PLA). The clever combination of FUNCAT and PLA PLA was originally published by the Söderberg...DNA strands take part in rolling circle DNA amplification. The amplified DNA segment is labeled with fluorescent...

  16. Viral Vectors 101: Types of viruses

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    Blog Post
    ...efficiently with adenovirus and AAV.   Table 1: Types of viruses and their features Choosing ...injections, or the location of a specific cell type doesn’t always lend itself to direct application of virus. ...addition of a helper virus or plasmid allows it to replicate episomally, essentially remaining an extrachromosomal...extrachromosomal part of the host genome that can replicate and divide along with the endogenous DNA. AAV also...gamma-retro viruses. This is large enough for many applications, but in some cases multiple AAVs (co-infection...and AAV. If you’re wondering more about what applications these viruses are good for, we have plenty of...Adenovirus-Mediated Gene Delivery: Potential Applications for Gene and Cell-Based Therapies in the New...

  17. A Quick Guide to a Career in Software Product Management

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    Blog Post
    ...PM--Catch up. Finish any communications with my UK team members before they log off for the day. 1:45 ...getting to talk to so many different people! I communicate with customers, software developers, as well ...from interacting with others, and have strong communication skills to tailor your message to any type of... to solve is clear, but the solution is more complicated. You’ll need to be creative to be able to work...team in the UK is five hours ahead, so I’m always catching up in the morning! 9:00 AM--Technical implementation...out. 4:00 PM--Respond to customer help tickets. Catch up on customer help tickets, and respond when I ...technology, software, and science. She loves to advocate for the customer and help build software and technology...

  18. Viral Vectors 101: Viral Vector Elements

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    Blog Post
    ...guide outlines these components.     Fig. 1 - Viral vector components of retrovirus  Adeno-associated...ITRs serve as a type of origin of replication to initiate replication of the dsDNA virus. Viral packaging...plasmid while the other plasmids with packaging or replication components are called helper plasmids. Below,... production, they can be helpful for certain applications and aid in ease of use. Our lentiviral guide...AAV are rep and cap. Rep is required for viral replication and also aids in infrequent genome integration...a helper plasmid and mediate efficient viral replication. More information on these viral genes is available...particles. E2A/E2B are responsible for viral replication, with E2B being the primary viral polymerase....

  19. GCE4All: Making Genetic Code Expansion Accessible

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    Blog Post
    ...non-canonical amino acid at the site of interest (figure 1). While the codon used is often one of the three stop... its function, mimic a biologically relevant modification, or add in fluorescent or chemically reactive...function relationships or, in more practical applications, allow a protein to be more effectively used... you do to any number of experiments with. The catch The rapid expansion of GCE led to the creation of... of many new tools and potential applications. But this focus on development, along with the inherent ...’t give it a try. Optimization Why is GCE so complicated? Well, while the techniques are straightforward...ligation through introducing ncAAs with protein modifications of interest or any of a huge variety of ncAAs...

  20. 7 Tips to Secure a STEAM Internship This Summer

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    Blog Post
    ...advice below:  1. Eligibility check Scrutinize every opportunity prior to starting an application to assess...your application a whole week before the deadline. The day of submission, review your application with... their dream.  To help students focus on the application process, and simplify access to academic resources... detailed. Beyond the resume, a cover letter communicates your interest in a specific program, and institution...February represent peak season for internship applications. Thus these noble individuals are inundated ... with a stellar letter of support.        5. Application submission  Set a calendar reminder for every...about outreach among low-income communities to educate parents about resources that can help their children...

  21. Antibodies 101: Secondary Antibodies

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    Blog Post
    ...with each protein of interest.    Figure 1: The direct approach (left) versus the indirect approach... antibodies may be indicated on occasion, usually after other signal amplification techniques have been...IgG2 or IgG4. This can be important for some applications. Assay use While secondary antibodies are useful..., the flexibility of their use varies across applications. Western blots, for instance, almost always ...For the latter three, secondary antibodies are indicated when the protein of interest is found in low amounts...been ruled out.  Ease of access Signal amplification isn’t the only benefit of secondary antibodies. Finding...quantitative analysis of a sample. Instead, relative quantification can be done using either the direct or the ...

  22. Advice for Starting a Biotech Company from a Grad Student turned Entrepreneur

    Type
    Blog Post
    ...prove the technology. This transition takes around 1 – 2 years. The product is the measure of success...competitions. After much learning, the focus of the application was changed, but Sample6 still leverages the ...fit for this set of technologies, effectively communicating the advantages embodied, and driving the enterprise...He explained that entrepreneurs must clearly communicate their idea at various levels of complexity and...backgrounds how amazing their idea is. While communication styles in academia and industry vary drastically...biggest challenge during this time was learning to communicate effectively to non-scientific audiences. "There...for the company; this will help avoid future complications and potential conflicts that waste money and...

  23. Hot Plasmids - March 2020 - base editors, GEVI, MoClo, and optogenetics

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    Blog Post
    ...native peptide bond at the split site. Figure 1: The base editor is split into two plasmids and co-transfected...voltage indicator Article contributed by Shreya Vedantam Genetically encoded voltage indicators (GEVIs)...fluorescent optics. Existing red fluorescent voltage indicators, however, fall short compared to GFP-based sensors...linker between them. The Ace-mScarlet voltage indicator works like many FRET-opsin GEVIs. With an increase...channelrhodopsins. Find the Ace-mScarlet voltage indicator plasmids at Addgene! Beck et al., Sci Report 2019...increasingly been recognized for its biotechnological applications including conversion of CO2 into water and electrical...the N-terminus of Cre (CreN) are fused to the truncated Phytochrome B (PhyBΔ) and the active protein binding...

  24. Stabilized Bacterial Promoters: Constant Gene Expression at any Copy Number

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    Blog Post
    ...give these stabilized promoters a try. References 1. Segall-Shapiro, Thomas H., Eduardo D. Sontag, and...rounds of replication are initiated before the cell has divided. This means that genes located near the...problems. Rapidly dividing cells initiate genome replication more than once per cell division and thus, genes...genes closer to the origin of replication will be overrepresented compared to those further away. As a...maximal gene expression near genomic origins of replication, the stabilized promoters created by Segall-Shapiro...the control of IPTG. Because RepA is a plasmid replication initiator protein, they could alter copy number...

  25. The Importance of High Titer for AAV Transductions

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    Blog Post
    ...methods to improve AAV production.     References 1.Clark, K. Reed. "Recent advances in recombinant adeno-associated... Protocols for Work with Virus Watch Our AAV Purification Video ...

  26. Four Factors that Differentiate the Stem Cell Field

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    Blog Post
    ...regarding what makes this group of researchers special: 1. Stem cell scientists care deeply about ethics Ethics... have profound impacts on the development of applications with the potential to save lives. While most...

  28. Cas13d: Small RNA-targeting CRISPR enzymes for transcriptome engineering

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    Blog Post
    ... Effectors.” Cell (2018) pii: S0092-8674(18)30207-1. PubMed PMID: 29551272 Plasmids from this paper ...for pre-clinical and clinical applications of dCasRx. The identification of Type VI Cas13d enzymes is ...RspCas13d. RspWYL1 also increased EsCas13d activity, indicating that WYL domain-containing proteins may be broader...even when guides were tiled across a target RNA, indicating that this enzyme does not cleave at a predictable...target essentially any RNA in a cell. Since catalytically dead dCasRx maintains its RNA-binding properties...

  29. Choosing a CRISPR Nuclease: Site Accessibility, Specificity, and Sensitivity

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    Blog Post
    ...sites that were previously unavailable. Figure 1: The PAM sequence that the Cas nuclease recognizes...to generate a genomic alteration at a specific location, it must be accessible by Cas9. Our previous blog...off-target activity, which may be undesirable in many applications. At the time of our first blog post on choosing...CRISPR-Cas9 to increase its specificity." Nature communications 9.1 (2018): 3048. PubMed PMID: 30082838. PubMed...CRISPR-Cas12b for human genome editing." Nature communications 10.1 (2019): 212. PubMed PMID: 30670702. PubMed...

  30. How to Keep a Lab Notebook for Bioinformatic Analyses

    Type
    Blog Post
    ...the output of the analysis performed in experiment 1. Use camelCase: In camelCase, each subsequent word..., specific goal for each analysis will help you locate relevant information in the future. Approach:...folders and files that you see on your desktop. The location of your master directory or folder for all of ...simple .txt document. Record the name, date, and location of all analyses (see above). Give every experiment.... She is particularly interested in science communication and epigenetics. Follow her on twitter @kc_palozola...
Showing: 571 - 600 of 727 results