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TypeBlog PostPublishedFeb. 9, 2021, 2:15 p.m....at odd times, new strategies can make socially distanced work more creative. An example could be making...signal the approach of a brain break, where everyone stands up, disappears from the video, and prepares a coffee...brainstorm on data in smaller groups, where for instance the presence of the PI in the main room inhibits...these weird times of shift working and social distancing. The take home message is the approaches/tools...
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Networking Follow-up: I Met a Person. Now What?
TypeBlog PostPublishedJan. 12, 2021, 2:15 p.m....give rise to a starfish shape. You can ask me about the different arms of this starfish sometime, but... plug-in called Maps. Figure 1: See a starfish? This is actually a map of Joanne Kamen's LinkedIn... it is completely impossible for me or anyone to stay in touch with all of their connections on a regular... -
Optimizing Donor DNA for Enhanced CRISPR Genome Editing
TypeBlog PostPublishedMarch 24, 2016, 2:30 p.m....efficiency of these editing reactions is low. Understanding the biological cause of this repair bias is ... reinforce a key scientific principle: that understanding a biological process in detail often suggests... efficiency of sequence replacement by HDR. Understanding Cas9 biophysics enhances HDR We first measured...released strand, 127bp in length, With 36bp on the PAM-distal side of the break and 91bp on the PAM-proximal ... -
How to Lead a Great Meeting
TypeBlog PostPublishedFeb. 9, 2016, 3:30 p.m.... the purpose of the meeting: Begin meetings by stating “The purpose of this meeting is to _________." ... what you need to accomplish to get to the next stage, and then adjourn. Define the tone of the meeting...template for project meetings. Team Meetings: For standing team meetings, provide agenda sections for each...meeting. Accountability: At your next meeting, start by checking in on the action items from last meeting... -
A Practical Approach to Choosing the B(right)est Fluorescent Protein
TypeBlog PostPublishedJune 1, 2017, 2:30 p.m....at (and through) a couple of models. Before you start a new project with fluorescent proteins, the best...this series of posts are (i) brightness, (ii) photostability and (iii) aggregation tendency. Brightness...Without further information about properties like photostability or aggregation tendency, our choice would be...Goedhard and Marieke Mastop! Joachim Goedhart is an assistant professor at the Section of Molecular Cytology... -
Plasmids 101: Inducible Promoters
TypeBlog PostPublishedJan. 18, 2018, 2:34 p.m....promoters. Others are only active under specific circumstances. In this post, we’ll discuss inducible promoters...promoters, which can be switched from an OFF to an ON state, and how you might use these in your research. When...negative control. Positive inducible In the OFF state, the promoter is inactive because the activator ...transcription. Negative inducible In the OFF state, the promoter is inactive because a bound repressor... -
Viral Vectors 101: Gamma-Retroviral Packaging Systems
TypeBlog PostPublishedAug. 6, 2024, 1:15 p.m....This method utilizes a packaging cell line that stably expresses Gag-Pol and/or Env, eliminating the need...packaging cell line developed by Garry Nolan at Stanford (Swift, 2001) contains Gag-Pol and either an ecotropic...differentiated (non-dividing) cells. Both lentiviruses and standard γ-retroviruses use the Gag, Pol, and Env genes...provirus. 3’ LTR Terminates transcription started by 5' LTR by the addition of a poly A tract just... -
Viral Vectors 101: Inverted Terminal Repeats
TypeBlog PostPublishedOct. 19, 2023, 1:15 p.m....virus. Since the WT sequence is relatively unstable, a more stable 130 bp version is used in most plasmids...recombinant-deficient bacterial strains such as NEB Stable, Stbl3, JC8111, SURE2, or XL10-Gold will help to...sequences can sometimes be removed to improve vector stability and sequencing results. Next-generation sequencing... -
Viral Vectors 101: Viruses as Biological Tools
TypeBlog PostPublishedMarch 21, 2023, 1:15 p.m....infect cells and deliver cargo, it’s important to understand their differences to choose the best one for ...viruses Retroviruses are a family of viruses that stably integrate their genome into the host genome, setting... Type of Virus Pros Cons Retrovirus Stable Gene Expression Broad Tropism Only Infects ...virus safety and viral applications to help you start (safely!) thinking about the possibilities. Ready... -
Antibodies 101: Buffers, Storage, and Conjugates
TypeBlog PostPublishedFeb. 1, 2022, 2:15 p.m....reaction to understand if any of your buffer components could affect the reaction. For instance, sodium azide...either testing the antibody efficacy through a standard curve, another quick experiment, or using a different... to use, not sensitive to light in its inactive state, and cheap. Unless there’s a specific reason you... -
Hot Plasmids December 2018 - C. elegans RNAi, TurboID, Detecting Viral Outbreaks, and Protein Binding Specificity Tools
TypeBlog PostPublishedDec. 6, 2018, 1:34 p.m....phenotypes than standard RNAi protocols without the need for mutant genetic backgrounds. The standard RNAi vector...biochemical and biophysical study involving protein stability or binding experiments. Potential experiments ...perform using the purified domains include protein stability, small molecule binding screens, peptide arrays... -
Plasmids 101: Blue-white Screening
TypeBlog PostPublishedJune 4, 2015, 1:03 p.m....for colonies that contain your plasmid is a great start when cloning, but how about being able to choose..., and remain the lovely whitish-cream color of standard E. coli. On the other hand, intact β-galactosidase...colonies that not only have your plasmid (antibiotic resistance), but also confirm those plasmids have your insert...plasmid-containing cells without using antibiotic resistance. These rely on cell lines susceptible to or dependent... -
Rosella: A Fluorescent pH-Biosensor for Studying Autophagy
TypeBlog PostPublishedApril 13, 2017, 2:30 p.m....protein degradation due to other pathways, it is standard practice to compare degradation rates between ...identify because their contents can be at various stages of degradation. Additionally, electron microscopy...that affect autophagy (ATG) in yeast. Atg8p (“p” stands for protein) associates with autophagosomal membranes...green fluorescence. After 4 hours of nitrogen starvation to induce autophagy, red but not green fluorescence... -
Viral Vectors 101: An Introduction to AAV
TypeBlog PostPublishedMay 30, 2023, 1:15 p.m....weeks is the standard ballpark estimation. Once expressed, viral cargo is usually quite stable and in some...and promoter) for use in your experiment! As a starting point, we recommend checking the literature and...272. PubMed PMID: 12349826. Xiong, Wenjun, and Constance Cepko. "Distinct expression patterns of AAV8 vectors... -
Transferable Skills Guide: Problem Solving
TypeBlog PostPublishedNov. 30, 2021, 2:15 p.m....the problem and gather information to help you understand it. Step Two: Come up with and evaluate potential...You might do some background research to better understand it and come up with several hypotheses on the...problem solving process on your own, but you can start by paying attention to how your mentors reach solutions...to remember that you have these skills when you start applying and interviewing for new positions. Highlighting... -
Announcing the Winners of the 2021 Michael Davidson and Roger Tsien Commemorative Conference Awards
TypeBlog PostPublishedAug. 5, 2021, 12:15 p.m....will enable significant steps forward in our understanding of synaptic and circuit functions in health ...metabolites are vital for researchers to better understand the processes that happen inside the cell,” says...Together, this project will allow us to better understand how neuron activity changes following opioid ...improved voltage indicator coming from the screen to understand mouse cortical and hippocampal neural microcircuits... -
Tagging Optogenetics and Chemogenetics Receptors: Fluorescent Proteins and Other Options
TypeBlog PostPublishedMay 11, 2021, 1:15 p.m....interfere with fused protein function Under some circumstances, the fused fluorescent proteins can be a roadblock...that some fluorescent proteins can be, in some circumstances, detrimental to the expression of the protein...be beneficial in some types of experiments (for instance, when the fluorescence expressed in the neuropil...techniques, her research aims to gain a deeper understanding of the physiology and pathology of the basal... -
Hot Plasmids - March 2019 - Anti-CRISPR, 2in1 Cloning, Fluorescent Voltage Indicators, and Photoswitchable Proteins
TypeBlog PostPublishedMarch 19, 2019, 1:31 p.m....ratio, high sensitivity, responds quickly, is photostable, and is compatible with optogenetic control. ...proteins that bind to either the light- and dark- states of the photoswitchable cPYP, which changes in conformation... partners that bind to only the light- or dark- state of the photoswitchable proteins offers a powerful...binders (which bind to either the light- or dark- state of the photoswitchable proteins) fused to mVenus... -
Click Biology: How to Click and Play to Explore Biology
TypeBlog PostPublishedOct. 21, 2025, 1:15 p.m....product without a lot of left-over starting components. High rate constant— time is money and things move...Addgene can help with this!). Besides requiring stable covalent reactions, other required parameters of...Click Biology reactions. For basic research, the stable and selective reactions of these tags can help ... -
Plasmids 101: Cre-lox
TypeBlog PostPublishedJan. 13, 2015, 3:47 p.m.... of replication, protein tags, and antibiotic resistance markers (just to name a few). In this edition... I use Cre-lox? The Cre/lox system is a well-established research tool, especially in the field of mouse...targeting, targeted clones are selected for using a resistance marker; however, it is often desirable to remove...in certain cell or tissue types, during certain stages of development, or by making the Cre inducible ...