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Showing: 361 - 390 of 1076 results

  1. Dos & Don'ts When Publishing a Scientific Manuscript

    Type
    Blog Post
    ...contributed by Maaike Pols, PhD, a Developmental Editor at F1000Research.  With many changes taking place...their funding should also be published. All these factors will influence your choice of journals to submit...communities. The ARRIVE guidelines for the reporting of laboratory animals during in vivo research and the CARE ... are two sets of guidelines frequently used by editors. Providing all this information makes your manuscript...who the reviewers are). If the reviewers and the editor decide that your manuscript needs to be revised...the conclusions of your paper. This will help the editor handling your manuscript decide on whether your... is appropriate for that journal. Argue with an editor or reviewer over their decision. If you do object...

  2. The Breast Cancer Microenvironment: A Tumor’s Backstage Team

    Type
    Blog Post
    ...proteins, such as human growth factor, vascular endothelial growth factor, and interleukin-6 (Witkiewicz... was contributed by Bárbara Pinho, a science communicator at the Portuguese science museum "Fábrica Centro...myofibroblasts, neuroendocrine, adipose, immune, inflammatory, angiogenic vascular, endothelial, and stromal... in increased expression of transforming growth factor-β signaling, possibly inducing the secretion of...seems to attack us by releasing mitogenic growth mediators and improving cancer cells proliferation.  How...enzymes and metabolism reprogramming aren’t the whole story. It’s essential for a tumor to spread and to resist... Pinho! Bárbara Pinho is currently a science communicator at the Portuguese science museum "Fábrica Centro...

  3. The Future of Research Symposium Boston 2015

    Type
    Blog Post
    ...is a STEM career counselor, Director of Education for the Jackson Laboratory for Genomic Medicine and a... successful and sustainable biomedical research sector at our first Future of Research symposium. The ...compulsory internship to be taken in an industry, regulatory, or clinical environment. It remains contested...the overall structure of the biomedical research sector, and what a tenable workforce structure may look...ideal and productive workforce look like for the sector – how many jobs are there for STEM graduates and...strong supporter of increasing the number of postdoctoral scientists at University of Maryland. Paula... at Scientific Meetings from Addgene Executive Director Joanne Kamens Learn how to be a successful manager...

  4. We’re Going Viral This Week!

    Type
    Blog Post
    ... be viral vector jokes and comics. Other new resources for researchers using viral vectors In addition...Addgene blog Download our Viral Vectors 101 eBook Find all of our viral vectors blog posts Learn more about...Starting today, our Twitter feed will be full of viral vector information. Each day, we’ll cover a different ...AddgeneGoesViral to find information on the basics of viral vectors, applications, and some new resources available...also investigates new strategies to improve viral vector production and data analysis. Our first paper came...

  5. Plasmids 101: Using Transposons in the Lab

    Type
    Blog Post
    ...in viral vectors, but easily fit in a TE. Transposons are also less likely than viral vectors to induce...DNA transposons are most commonly used in the laboratory for genome manipulation. When transposons are...transposon’s LTRs, similar to when packaging viral vectors.   Let’s take a closer look at three different ... in human cells at rates similar to retroviral vectors. The hyperactive version of the SB transposase,...efficiency in human cells similar to retroviral vectors. The hyperactive PB transposase (hyPB) is ~10-fold...transfer Transposons are an alternative to viral vector delivery of transgenes, like for iPSC reprogramming... piggyBac, which is a big advantage over viral vectors (~5 kB payload for AAV and ~8 kB payload for lentivirus...

  6. Sequencing Options for CRISPR Genotyping

    Type
    Blog Post
    ...Hendel et al. 2015). Low detection rates mean the investigator can be relatively certain that their samples...off-target mutations are essential data points for investigators looking to definitively link genotype and phenotype...Targeted amplicon sequencing doesn’t tell the whole story Figure 1: Schematic representations of the...viable options for multiplex sequencing in many laboratories. Nevertheless, unbiased detection isn’t as sensitive...genome-wide unbiased methods. However, most investigators use single cell clones for in vitro CRISPR experiments... Hough. We additionally thank Monica Sentmanat, Victor Dillard, and Ayokunmi Ajetunmobi for their contributions... Hough is a Biochemistry PhD candidate in the laboratory of Prof Steve Jackson at the Gurdon Institute...

  7. Design Tips for Prime Editing

    Type
    Blog Post
    ...nick, and monitor indel frequencies (Anzalone et al., 2019). Figure 6: Prime editors bound to ... Figure 4: Editing the PAM prevents the prime editor from re-engaging with DNA it has already edited...to pegRNAs drive editing (left), while prime editors bound to sgRNAs only drive nicking (right). Start ...opposite strand. Created with BioRender.com. MMR inhibitors PE4 and PE5: These approaches inhibit MMR to...inhibited. Created with BioRender.com. RNA protectors epegRNAs: epegRNAs include structured motifs...primer binding site (Nelson et al., 2022). PE7: This editor includes the fused RNA-binding protein La to protect...software, however. You may find it useful to ask a mentor what software tools they recommend — feel free ...

  8. Plasmids 101: The Wide World of Natural Plasmids

    Type
    Blog Post
    ...cells survive their own secretions. Pro tip! Historically, colicin-producing plasmids have been referred...referred to as “Col plasmids” or “Col factors.” Virulence plasmids: microbial infection Virulence plasmids...other molecules to host organisms. For instance, vectors derived from the Agrobacterium Ti virulence plasmid... through direct contact. That’s conjugation! F factors can also be integrated into the bacterial chromosome...developing new cloning techniques based on these vectors (Shareck et al., 2004). Plasmid categorization...the many plasmid tools available in the Addgene repository. To learn more about some other common plasmid...Auriol, P., Vogel, T. M., & Simonet, P. (2001). Laboratory-scale evidence for lightning-mediated gene transfer...

  9. Savvy Advocates Needed to Navigate a Scientific Enterprise in Flux

    Type
    Blog Post
    ...Washington Office Ben Corb - Director of Public Affairs at ASBMB Adam Fagen, PhD - Director, Early Career Scientist..., these issues which will continue to shape the sector throughout their careers (McDowell et al, F1000Research...working group (National Academy of Sciences. “The Postdoctoral Experience Revisited” 2014 Appendix B p93-95...funding and funding mechanisms require an engaged sector with effective advocacy skills. Advocating for ...Scientist Segment at AAAS Marnie Gelbart, PhD - Director of Programs at Personal Genetics Education Project...their respective fields: David Cameron, PhD - Director of Media Communications, Harvard University Ray...Advocate with the Perfect Science Talk Find a Good Mentor ...

  10. Adapting Toehold Switches to Detect Zika Virus

    Type
    Blog Post
    ...Diagnostics will play an important role in helping to monitor and slow this spread until vaccine programs can... switches for pathogen detection In 2014, as postdoctoral fellows with Jim Collins and Peng Yin at the.... The first was a new class of programmable riboregulators, called toehold switches, which allow for the...allowed gene circuits to be deployed out of the laboratory in a cell-free and biosafe format that was stable...circuit-based sensors to be used outside of the laboratory. The detection threshold for these RNA sequences...the technology through product development, the regulatory process, and manufacturing so that we can get...Leslie Dan Faculty of Pharmacy at the University of Toronto. His research is focused on developing cell-free...

  11. Cpf1 Update: Comparison to Cas9 and NgAgo

    Type
    Blog Post
    ...deliver in low-capacity vectors like AAV. AAV (adeno-associated viral vectors) are commonly used for in...Background Read About CRISPR Competitor NgAgo Learn How You Can Use piggyBac Vectors in Genome Editing Resources...preferential infection of certain tissues. However, these vectors have a low genetic capacity of ~4.5 kb. At 4.1 ...barely fits into AAV when you add in a gRNA and regulatory elements. To solve this problem, the Zhang lab...previously used SaCas9 (1053 aa/3.2 kb) with AAV vectors for efficient postnatal editing. LbCpf1 and AsCpf1...SpCas9. These nucleases should fit well into AAV vectors, especially given that Cpf1 gRNAs are also shorter...

  12. The Materials Science of Optogenetics Experiments

    Type
    Blog Post
    ..., 50ms “off”.  A pulse generator such as the A.M.P.I Master-9 Pulse Stimulator, which can control output...cable is threaded through—and fixed to—an optical insulator called a ferrule (below). The fiber optic cable...Channelrhodopsin 2 (Chr2) has been expressed in the motor cortex of a mouse. Upon connection of the ferrule...to give the animal the full range of motion, a commutator allows the patch cable to connect to the laser...University of Michigan and he is currently a Postdoctoral Fellow in the lab of Mary Jeanne Kreek at the... 1. Gutierrez DV, et al. Optogenetic control of motor coordination by Gi/o protein-coupled vertebrate ... neurons. Current protocols in neuroscience / editorial board, Jacqueline N Crawley  [et al]. 2012;Chapter...

  13. 10 Basic tips for mammalian cell culture

    Type
    Blog Post
    ...Keep the hood clean Hoods should not be used as storage cabinets. Clutter not only makes it difficult to...air conditioning on) so leave them in a sterile incubator. This also means that any medium or washing buffer...entering the hood and when putting them into the incubator). It also helps to get familiar with the morphology...results. Most cell culture media contain the pH indicator phenol red (pH range 6.0 (yellow) - 8.0 (red))...aliquot them into a number of vials, freeze them, and store all but one in liquid nitrogen. The frozen vials...master stock. This ensures that you have many cells stored in their original condition and can replace your...with the Agarose Method Plasmids 101: Mammalian Vectors Resources on Addgene.org Find mammalian plasmids...

  14. 3D Printing Meets CRISPR Cas9

    Type
    Blog Post
    ...development programs for bioscience educators. Using these hands-on tools, educators introduce their students to...This post was contributed by Tim Herman, director of the MSOE center for BioMolecular Modeling and the...dangerous. Subscribe to CRISPR Blog Posts How do educators and students use molecular models?   We created...something tangible. Under the guidance of a trained educator, these instances of focused attention become magical... their labs. Soon after we began working with educators in our Center for BioMolecular Modeling, we spun...our guest blogger Tim Herman! TIm Herman is the director of the MSOE center for BioMolecular Modeling and...Addgene.org Visit Our CRISPR Guide Page CRISPR/Cas9 History Browse All CRISPR Plasmids and Resources ...

  15. Starter guide to induced pluripotent stem cells (iPSCs) part 1:  A renaissance in regenerative medicine

    Type
    Blog Post
    ... was contributed by Kusumika (Kushi) Mukherjee, editor of Trends in Pharmacological Sciences, a Cell Press...Shinya Yamanaka’s lab, where the reprogramming factors were delivered via retroviral infection [8]. The...Kushi) Mukherjee. Kusumika (Kushi) Mukherjee is the Editor of Trends in Pharmacological Sciences, a Cell Press...communication and publishing after completing her postdoctoral training from Massachusetts General Hospital...PMCID: PMC2752493. 4. Bongso, A. and M. Richards, History and perspective of stem cell research. Best Pract...embryonic and adult fibroblast cultures by defined factors. Cell, 2006. 126(4): p. 663-76. PubMed PMID: 16904174... cells from adult human fibroblasts by defined factors. Cell, 2007. 131(5): p. 861-72. PubMed PMID: 18035408...

  16. Experimenting with New Careers while in Grad School

    Type
    Blog Post
    ...guest blogger Melanie Fox, founder and executive director of Central Indiana Science Outreach and a Postdoc...professional development I had a wonderfully supportive mentor and graduate office. I cannot stress how important...my blog helped immensely when CINSO started brainstorming the resources we wanted to provide online. ...in real time! I follow great online science communicators like Phil Plait @BadAstronomer, Emily Graslie...when I was trying to find local informal science educators, and ever since, the State Museum has been the...week. I gained experience explaining science to visitors of all ages, learned a lot about the dinosaurs...Melanie Fox is currently the founder and executive director of Central Indiana Science Outreach and a Postdoc...

  17. PITChing MMEJ as an Alternative Route for Gene Editing

    Type
    Blog Post
    ...making it easier to construct targeting vectors. Addgene depositor Takashi Yamamoto’s lab has harnessed ...cloned into a vector containing Cas9 and the PITCh-gRNA. Step 3: Contransfect the PITCh vector with the vector...just upstream of a stop codon. Briefly, the PITCh vector should be constructed with 5’ and 3’ microhomology...PITCh Step 1: Generate microhomologies in the PITCh vector ~20 bp 5’ and 3’ microhomologies are added to ..., and this construct is inserted into the PITCh vector via In-Fusion or SLIC cloning. Step 2: Design an... vector carrying Cas9 and the PITCh- and locus-specific gRNAs Step 4: Select for puromycin resistant cells...

  18. CRISPR 101: Mammalian Expression Systems and Delivery Methods

    Type
    Blog Post
    ...conjunction with activator or repressor domains to control gene expression. Base editors can help you make... in a single lentiviral transfer vector or separate transfer vectors. May contain reporter gene (e.g. ...experiment As with any experiment, there are many factors that need to be considered during the planning ... that would work for your system. Addgene has depositor submitted protocols and links to a CRISPR forum...Components of System Application Mammalian expression vector Promoter driving Cas9 expression can be constitutive...CRISPR elements are inserted into an AAV transfer vector and used to generate AAV particles. Transient or...

  19. Drew Endy Introduces the Biobrick Public Agreement Plasmid Collection

    Type
    Blog Post
    ...Science describing the development of “transcriptors,” transistor-like digital genetic switches that enable...Stanford develops engineered DNA systems capable of storing data and computing inside living cells. He's also...cellular computing. These logic gates built from transcriptors are now available at Addgene through the Biobrick...world using words like OR and AND. These logical operators are so useful they are implemented in most materials...the beginnings of computational logic and data storage. What we don't have are the keyboards and displays...mining. There is an absolutely incredible hidden story here. The parts we are releasing simply plug into... plants. We are really plugging into the "stuff sector" if you will, making chemicals and materials, and...

  20. Custom CRISPR Screens & the Green Listed Software

    Type
    Blog Post
    ...signaling pathway with many receptors, signaling molecules, transcription factors, and ligands. The presenter... unbiased discovery. With these screens, the investigator generates a cell population where all genes ...contexts. Most of the immune cells we study are migratory, and their exact localization is important for...types of interactions to a large extent involve receptors expressed on the cell surface. Thus, a screen ...targets, preferentially those for which validated inhibitors or even approved drugs already exist. If you ...The gRNA oligos are subsequently cloned into your vector of choice using the adapter sequences that you ...strategies related to other nucleases as well as inhibitory and activating approaches.  Many thanks to our...

  21. Visualizing Your Plasmid Request Data

    Type
    Blog Post
    ... for depositing labs to its website, allowing depositors to download their plasmid request data, as a ...information can be of personal interest to the depositor, but it can also be valuable data to share in ...total requests, total countries represented by requestors, year of first reagent sent, year with most reagents...is launched, it will show my data by default. Depositors can download their CSV file from Addgene by following...Dashboard After the upload, the name of the depositor and the date of downloading the CSV is shown (...and the source code is available in the Github repository (you can find the link in the upper right hand...dashboard useful when analyzing and sharing your own depositor metrics!  About the Author Joachim Goedhart is...

  22. Summer SciComm Series: Modes of Communication

    Type
    Blog Post
    ...including the internet!) can vary depending on factors like socioeconomic status and geographic location...communication should be fun and engaging for the communicator as well as the audience, so pick a mode of communication...restrictions (or both!) will be a major limiting factor at multiple points. Before you embark on a project... convey enough information to tell a compelling story in an image or do you need a full exhibit? In a ....  Static. Can be difficult to convey an entire story or context via still images. Some things cannot ...information. Primarily useful for data-focused stories. In-person lectures, presentations, etc… Low... Low barrier to entry for both audience and communicators. Well-developed content creation platforms.  ...

  23. Great Results Start with Great Standard Curves

    Type
    Blog Post
    ...What do a viral vector production facility, food allergy testing lab, and the grad student down the hall... curves in their day-to-day work. Indeed, viral vector production facilities frequently use qPCR with ...with each step of the series diluted by the same factor. For example, Figure 1 depicts a 2-fold dilution... standard curves vary depending on a number of factors, including the user, equipment, assay incubation...measure.  Dynamic range depends on a number of factors, including the dilution series of the standard ...standard curve dilution series with lower dilution factors. If the unknown sample’s measurement is too high...assays you will be using ahead of time to see what factors may impact the dynamic range of the assay. Try ...

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

    Type
    Blog Post
    ... the notation works? The + operator denotes intersection and the – operator denotes set difference. That...inclusive markers of regulatory regions in the genome, including enhancers, promoters, insulators, and more. I...proteins”) for NANOG, an essential transcription factor in embryonic stem cells (ESCs). Your ChIP-seq finds...of embryonic stem cells (ESCs) with a lentiviral vector, an attenuated retrovirus in the same family as...enhancers, lncRNAs, repetitive elements, repressors, insulators, and more. We know that this matter exists, but...criteria: no TTTTT allowed (this is a polymerase terminator), and no off-target effects for the identified...

  25. Save Time with Transient Plant Leaf Transformations

    Type
    Blog Post
    ...us. Use a well working vector system This allows you to quickly assemble vectors and test different ideas...MoClo system. The vectors mentioned in this blog post above are ready to use vectors, but with the MoClo...to quickly screen and investigate transcription factor candidates and the regulation of genes in the biosynthetic... region is transferred into the plant. In the laboratory we can utilize this natural process by replacing...and a vacuum is applied with a vacuum bell or desiccator. Successful infiltration can often be seen by...system you can easily and quickly create customized vectors. For more information on MoClo for plants, check...

  26. Transferable Skills Guide: External Collaborations

    Type
    Blog Post
    ...keeping track of speakers. During your graduate or postdoctoral work there are loads of opportunities to create... concrete happen. You may have more willing collaborators than you realize. Being at a university provides...meetings and take minutes. Get to know your collaborators from other institutions personally on conference...relationship with the perspective of my potential collaborators in mind. Being at a university allows you to...with people at your organization. You can meet collaborators  for lunch, make a point of talking to them ... different countries). Here social media is a connector and virtual meeting place: You can follow interesting...as messages and keep you up-to-date on your collaborators’ professional developments without directly ...

  27. Stem Cell Models for Disease & Open Science: Interview with Darrell Kotton

    Type
    Blog Post
    ...-funded Principle Investigator in the Kotton Laboratory and is the founding Director of the Center for...Darrell Kotton is the director of the Center for Regenerative Medicine at Boston University Medical School... Darrell recently joined the Addgene Board of Directors where he hopes to help keep us focused on our ...Darrell's goals as a member of the Addgene board of directors - increasing open source sharing and helping us...Medicine and in the Department of Pathology and Laboratory Medicine. He attends in the Medical Intensive...

  28. Plasmids 101: What is a plasmid?

    Type
    Blog Post
    ... referred to as “vectors” or “constructs.” To insert a gene of interest into a vector, scientists may ...plasmid with its elements described below.   Vector Element Description Origin of Replication (ORI...the target gene. Vital component for expression vectors: determines which cell types the gene is expressed...Regardless, once the cloning steps are complete, the vector containing the newly inserted gene is transformed...Fluorescent Protein (GFP) Plasmids 101: Luciferase Monitor the level of a chemical in a particular environment...about molecular cloning, how to choose a plasmid vector, molecular biology tools and references, and how...

  29. Understanding GPCR Signaling Using TRUPATH

    Type
    Blog Post
    ...they do so is through G protein-coupled receptors (GPCRs), receptors that play many roles in signaling processes...which a donor fluorophore is used to excite an acceptor fluorophore. The difference for BRET is that the... between a luminescent donor and a fluorescent acceptor. TRUPATH uses an updated version of BRET called...constructing 14 luciferase donor Rluc8-Gα chimeras, four acceptor GFP2-Gγ chimeras, and two untagged Gβ constructs...non-uniform across the transducerome for a specific receptor-ligand pair. They further used TRUPATH to analyze...Mitaku S (2002) Identification of G protein-coupled receptor genes from the human genome sequence. FEBS Letters...

  30. Hot Plasmids: FRET-Based Biosensors

    Type
    Blog Post
    ...upon an indicator they developed and published in 2010 for visualizing the transcription factor cAMP-responsive...Neurobiology has been working on genetically encoded indicators of calcium and other small molecules since the...Griesbeck is motivated by a particular interest in monitoring the activity and biochemistry of living neurons...imaging for beginners Griesbeck says his calcium indicators can be used in mouse, Drosophila, C. elegans,...while in principle adapting a FRET sensor for monitoring calcium versus zinc should require the simple... variants of mOrange2 and mCherry as donor and acceptor domains. He says, these new colors might now enable...
Showing: 361 - 390 of 1076 results