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Showing: 601 - 650 of 698 results
  1. Savvy Advocates Needed to Navigate a Scientific Enterprise in Flux

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    Blog Post
    .... Follow David on Twitter @driglar.   References: 1. Alberts, Bruce, et al. "Rescuing US biomedical research...for affecting change. On Friday, the symposium includes a panel discussion and keynote by former congressman...towards solutions. The 2015 Boston FoR meeting was designed to explore areas where further data is necessary...for students interested in leading the process despite the recent advance. Similarly, grad students throughout...development and implementation of new strategies designed to cope with current increases. These two rulings...
  2. 15 Hot Plasmids from 2017

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    Blog Post
    ...base editors with editing windows as small as 1-2 nucleotides! To reduce off-target effects associated with...Lower on-target activity than BE3; editing window ~1-2 nt  87438  pET42b-HF-BE3  HF-Cas9 (NGG)  Very ...cassette via Cre recombination. Each knockout includes unique barcodes and universal priming sites to ensure ... the Chi-Bin Chien lab (Kwan et al., 2007) and includes four promoters, six fluorophores with nonoverlapping...The set of CyRFP constructs available at Addgene includes bacterial and mammalian mCyRFP1 or CyRFP1 expression...codons) with kanamycin cassettes and were carefully designed to allow for easy removal of the resistance cassette...essential in B. subtilis 168. Each individual strain includes a xylose-inducible dCas9 paired with a single,...
  3. Tips for Using BLAST to Verify Plasmids

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    Blog Post
    ...most comprehensive for searching. Timesaving Tip #1: If you know the species that your sequencing result...terrific getting-started guide for BLAST, which includes a simple explanation of the different BLAST programs...matrix BLOSUM62, but you may want to check the description of the other matrices to see if another would...alternatives Depending on your sequencing result and desired analysis, BLAST may not always be your optimal ...
  4. RaPID Detection of RNA-protein Interactions

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    Blog Post
    ...for RaPID is an RNA motif of interest. See figure 1 below for details on the key components of RaPID. ...novel RNA-protein interactions, Ramanathan et al. designed an RNA bait containing three well conserved but...
  5. Antibodies 101: ELISA (Enzyme-linked Immunosorbent Assay)

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    Blog Post
    ... to the use of multiple antibodies. Figure 1: Overview of using Sandwich ELISA to quantitatively...ELISA is a modification of the sandwich ELISA as described here, the direct and indirect ELISA (more details...
  6. Uncovering Ancestral Bias in CRISPR Research

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    Blog Post
    ... digging deeply into their data.     Fig. 1: Genomic fraction for each of five major ancestry ... reference?  The CRISPR guides used in the screens they analyzed were designed to have a perfect match...African descent have approximately 20% more single nucleotide polymorphisms (SNPs) that map to guides in the...accounted for in the CRISPR guides they used, leading to mismatches between the guides and the lines’ genomes...modify the CRISpick algorithm to prevent guides from being designed that target regions with high genomic...coming through an unexpected source: the CRISPR guides, short pieces of RNA that bind to a cell’s DNA,...x-axis) which SNPs map to thetargeting sequences of guides across 8 CRISPR libraries. Samples are divided ...
  7. Science communication: 9 Strategies to Get Your Foot in the Door

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    Blog Post
    ...started:  Subscribe to Career Blog Posts from Addgene 1) Twitter – Get your voice out there Here’s one thing... Guardian, BBC Breakfast or the Londonist. BBC provides a peak into their day-to-day business with popular...Co-Ordinating Centre for Public Engagement (NCCPE) provides on-site courses in public engagement for institutions...
  8. Reaching out to China: Canton Nucleic Acids Forum (CNAF) 2015

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    Blog Post
    ...viruses - 2 cas systems regulate at the DNA level and 1 at the RNA level. Udi Qimron from Tel Aviv University...plasmids, especially those of the CRISPR variety (see slides from my talk below). Largely organized by Dmitry...CRISPR regions of the prokaryotic genome. Then he desribed how P. furiosus has systems to defend against ...
  9. Illuminating Epigenetics with A FRET Based Biosensor

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    Blog Post
    ...treatment and improving patients lives. References 1. Ong-Abdullah, Meilina, et al. "Loss of Karma transposon... of the DNA with a high frequency of C and G nucleotides). The conversion of cytosine to 5-methylcytosine..., which binds selectively to lysine-methylated peptides. This construct is in the middle of a FRET pair...
  10. Capturing a Moment with Marc Zimmer’s “The State of Science”

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    Blog Post
    ...in restraint. The very first subheading in Chapter 1 asks “What is science?” That’s a very big question... Zimmer provides several. In Part Three of the book, called simply “Old Science,” he describes the now...teaching and communicating science for over two decades, attempts to answer it in five paragraphs, with...recent resurgence of “Do-It-Yourself Science” described in Chapter 3, and of course the rapidly changing... science.”  The three chapters in this section describe the challenges of trusting science in a “fake ...changed significantly over the last decade. He describes the detection of gravitational waves--a story ...collaboration from scientists around the world. The paper describing the waves’ detection had over 1,000 authors. ...
  11. Viral Vectors 101: Chemogenetics

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    Blog Post
    ...impacts of neural circuits on behavior. Figure 1: An overview of the chemogenetics system. Why use...DREADDs DREADDs DREADDS, or designer receptors exclusively activated by designer drugs, are G protein-coupled...Relationship Studies for Designer Receptors Exclusively Activated by Designer Drugs. ACS Chemical Neuroscience...Chemogenetics has become a popular tool in the field as it provides a noninvasive method for manipulating cell activity...Roth's and Takafumi Minamimoto's lab called deschloroclozapine (DCZ) shows promise as a CNO alternative ... Gomez J, Ramirez M, Hu X, Galvan A, Basu J, Michaelides M, Sternson S (2019) Ultrapotent chemogenetics...Conditional expression and signaling of a specifically designed Gi-coupled receptor in transgenic mice. Nature...
  12. xCas9: Engineering a CRISPR Variant with PAM Flexibility

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    Blog Post
    ... NGT PAM GAA PAM GAT PAM xCas9 3.7 41 (1) 32 (1.6) 13 (2.1) 38 (4.5) 7.2 (5.2) ...insertion site, the corresponding gRNA might be undesirable due to potential off-target sites or low predicted..., resulting in lower overall genome frequency. Despite the progress we’ve made, there is still a need ...bacterial polymerase subunit ω. This construct is designed to activate transcription from the accessory plasmid... stringency and promoting survival of only the broadest-targeting variants. For the final round of evolution...spectinomycin resistance. xCas9 3.7 showed the broadest PAM range, recognizing NG, NNG, GAT, and CAA PAMs...scaffold. With an NGG PAM, xCas9 3.7-VPR constructs modestly outperformed SpCas9-VPR in activating transcription...
  13. Rabies and Neuronal Tracing

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    Blog Post
    ... questions of how the brain operates. References 1. Callaway EM. Transneuronal Circuit Tracing with Neurotropic...widely used in neuroscience. In this post, I’ll describe how rabies virus (RABV) can be used in the brain... by modifying the wild-type RABV genome, which encodes a single envelope protein called rabies glycoprotein... neurons integrated into the brain over time (Deshpande et al., 2013). The study found that at early time...Dec; 18(6): 617–623. Pubmed PMID 19349161.  2. Deshpande A, Bergami M, Ghanem A, Conzelmann KK, Lepier ...Pubmed PMID 26190977. 6. Osakada F, Callaway EM. Design and generation of recombinant rabies virus vectors...
  14. Polymerase Chain Reaction Overview and Applications

    Type
    Blog Post
    ...target DNA quickly and accurately.  Figure 1: Steps in PCR reaction   This process of denaturation...addition to Taq DNA polymerase, PCR requires free nucleotides (dNTPs), template DNA to amplify from and unique...polymerases require an existing strand of DNA to add nucleotides to.  Using these reagents and a series of heating...protocol page, protocol video and reference on how to design PCR primers.  Types of PCR Since the invention ...  Digital droplet PCR or ddPCR is a method that provides ultrasensitive and absolute nucleotide concentration...Polymerase Chain Reaction (PCR) Protocol: How to Design a primer  Molecular Biology Reference Molecular...
  15. Hot Plasmids and Viral Preps - May 2021

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    Blog Post
    ...(RBD) of the viral spike protein.   Figure 1. (A) SARS-CoV-2 RBD DMS Library generation and sequencing...library, each plasmid encodes the mutated spike protein and a barcode, and is designed so that the SARS-CoV....1074/jbc.RA120.01289     Novel protein cage provides simple enzyme protection in yeast bioproduction...enzymes in a reaction pathway, the MPyV system provides a simple, efficient method for protecting a single...- Ampl133 targets S. cerevisiae genes with 6-12 guides per gene where gRNA expression is induced by anhydrous...
  16. Addgene's Cancer Collection Pages Connect the Research Community

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    Blog Post
    ... education and scientific writing.     References 1. Martz, Colin A., et al. "Systematic identification...die from cancer-related complications each year. Despite these grim statistics, new strategies for attacking...cancers, especially those of the pancreas and colon. Despite the prevalence of Ras mutations in a variety of... enabled researchers to begin discovering and designing molecules that are showing some promise in their...in the screenshot below). Currently, the page includes interactive maps for the Ras, mTor, and p53 pathways...
  17. A Guide to Starting Your Own Journal Club

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    Blog Post
    ...for your first journal club to begin! Figure 1: Discussing next-generation sequencing at the Addgene... on single papers could be more important.  Any slides, presentations, recordings, and other materials...those who were unable to attend. We capture the desktop and audio recordings of the meeting using teleconferencing... ensure that the journal club is useful for the widest audience, you should get feedback from those who...served. I hope that with some of the information described above you feel empowered to start your own journal...
  18. CRISPR 101: Ribonucleoprotein (RNP) Delivery

    Type
    Blog Post
    ...genome engineering and microbiology.     References 1. Chen, Sean, et al. "Highly efficient mouse genome...transfecting cells with a plasmid, such as PX459, which encodes Cas9 and contains a site for inserting a custom...targeted approach using RNPs has recently been described in vitro, with the hope of eventually using this...expertise. Final thoughts The Cas9-gRNA RNP method provides scientists with an additional means to deliver...other CRISPR delivery techniques Find tips on gRNA design Resources on Addgene.org Browse all CRISPR plasmids...
  19. CRISPR 101: Targeting Non-Coding RNAs with CRISPR/Cas9

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    Blog Post
    ...off-target effects (Zibitt et al. 2021).    Figure 1: A schematic illustration of CRISPR/Cas9-based approaches...non-coding RNAs (lncRNA). lncRNAs are over 200 nucleotides in length and lack an open reading frame, so ...transcription machinery of a target gene or DNA that codes for ncRNA. CRISPRa, on the other hand, recruits ...which targets RNA instead of DNA and selectively degrades RNA molecules. This system is often used to knock...
  20. Hot Plasmids and Viral Preps - January 2021

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    Blog Post
    ...article, they investigated three Casɸ orthologs, Casɸ-1, Casɸ-2, and Casɸ-3. This system is notable for several... Parts. This library delivers 2 randomly paired guides per construct and allows a reduced scale in screens...
  21. Plasmids 101: Shuttle Vectors

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    Blog Post
    ...many mammalian vectors are designed to shuttle between species. Figure 1: Shuttle vectors are vectors...affects all kingdoms of life. Of course, that includes you. Besides the risk to the researcher, Zeocin has been...host’s replication machinery. A shuttle vector designed for unrelated bacteria should include oris for...target species. Fun fact! Plant vectors are usually designed to shuttle between E. coli and Agrobacterium tumefaciens...protects against any of them. But different aminoglycosides work on different host species: kanamycin targets...media that supplies the key nutrient. The vector provides the missing synthesis machinery, and the cells...image for individual analysis. A shuttle vector designed for this approach in a mammalian cell experiment...
  22. New Optimized Genome-wide CRISPRko, CRISPRi, and CRISPRa Libraries

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    Blog Post
    ...and primary cells. References 1. Doench, John G., et al. "Rational design of highly active sgRNAs for CRISPR-Cas9...These libraries utilize optimized sgRNAs that were designed based on the rules identified in Doench et al....1,000 non-coding control sgRNAs. This library was designed to improve on-target activity while reducing off-target...with 6 sgRNAS, highlighting the benefit of sgRNA design in CRISPR libraries. Thus, the Brunello library... that if an essential gene plays a role in the desired screening phenotype, it may be missed because it's... the sgRNA metrics, confirming again that sgRNA design plays a significant role in library efficiency....CRISPRa, sgRNAs were targeted between 150-75 nucleotides upstream of the TSS. Similar to the Brunello ...
  23. The Challenges of Cell Culture

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    Blog Post
    ...testing. You can find Nick on LinkedIn. References 1. Skloot, Rebecca, and Bahni Turpin. The immortal life...contamination and match their original description. The oldest, largest, and most diverse of these repositories...culture in the present day Cell culture is a widespread tool used in the fields of oncology, virology...problems surrounding cell culture over the last few decades some pharmacologists have tended to avoid cell ...International Cell Line Authentication Committee includes a database listing all cross contaminated or misidentified...comparable studies to be performed on a cell line even decades after it is initially isolated. Regrettably this...Master and Working stocks to work from. The future Attitudes are changing but yet more is needed to convince...
  24. Bacterial Toxin-antitoxin Systems as Molecular Biology Tools

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    Blog Post
    ...plasmids are passed down through generations (Figure 1). These so called “plasmid addiction systems” require...than plasmids without this DNA. They eventually designated this fragment as the ccdB region (for “coupled... serves as a counterselectable marker in the destination vector. Successful cloning occurs when the ccdB...restriction endonucleases in plasmid addition was first described by studies of EcoRI and Bsp6I in Escherichia coli...systems. As with the other toxin-antitoxin systems described above, one part of the pair is more stable than...toxin-antitoxin system discovered. Unlike the systems just described, the hok/sok systems consist of three components...long-term experiments. They’ve also helped researchers design and optimize cloning methodologies using counterselection...
  25. An Inside Look into Addgene's Dev Team

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    Blog Post
    ... done and we’re onto the next story. Figure 1: Addgene’s Agile Approach Sharing is caring There...released a major redesign of how search works on our site. For Addgenies, development includes everything from...experience and the overall soundness of the software design. Each of us brings slightly different cognitive...Addgene. Another advantage of Scrum is that it provides transparency to everyone involved about the status... on a new feature. We start with a story that describes the feature and what the criteria is for accepting...our users, we are able to make informed software design choices, resulting in software that helps our users...
  26. Bioinformatics at Addgene

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    Blog Post
    ...drives our bioinformatics needs       Fig. 1: QC'ing data at Addgene is like standing under a Niagara...of data. In this two-part blog series, we will describe the importance of bioinformatics at Addgene and...each week. Our internal software was originally designed to help us work in large formats, such as 96-well...Thanks to the flexibility inherent in Nextflow’s design, we were free to use multiple programming languages...alone! The benefits of containers are they are designed to ‘contain,’ in a complete package, all of the... who or which computer ran the process. Another design choice we appreciated about Nextflow was how effortless...small with a print statement and tested that the desired data was available so we felt confident we were...
  27. Plasmids 101: Codon usage bias

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    Blog Post
    ...inclusion bodies and is folding properly. References 1. Angov, Evelina, et al. "Heterologous protein expression...features to consider when designing a full gene. A non-exhaustive list includes: Codon abundance relative...that their codons are more appropriate for the desired expression host. This is known as “codon optimization...as easy as it sounds. Even for relatively short peptides, there can be many possible ways to encode them...every amino acid I’d like to encode,” but, as described above, not every region of a protein should necessarily...PubMed Central PMCID: PMC4794256. This review provides a great overview of codon usage bias 8. Tuller...
  28. INTEGRATE: Bacterial Genome Engineering Using CRISPR-Transposons

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    Blog Post
    ... end sequences (R and L ends).  Figure 1: (A) Components involved in each type of CRISPR-Transposon...human therapeutics (e.g. using Sleeping Beauty). Despite their diverse utility, DNA transposons have been...(V. cholerae INTEGRATE - hereafter VchINT) and encodes a Type I-F CRISPR-Cas system. The four major components...the same promoter, and a donor plasmid (pDonor) encodes the mini-transposon. pEffector and pDonor can also...: Clone spacer(s) into the CRISPR array Clone desired DNA cargo into the mini-transposon Transform plasmid...even very large genetic cargo, at one or multiple desired genomic loci. Many applications of these systems...
  29. Plasmids 101: The Promoter Region – Let's Go!

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    Blog Post
    ...mammalian expression from human elongation factor 1 alpha Constitutive  Tends to give consistent expression...insert into RNA. In practice, the term "promoter" describes the combination of the promoter (RNA polymerase...   Primarily used for RNA     transcript     Description Expression Additional considerations CMV General... phosphoglycerate kinase gene.  Constitutive  Widespread expression, but may vary by cell type. Tends ...promoters     Promoter     Primarily used for Description Expression Additional considerations T7 in ...identify the right tissue-specific promoters as described by researchers at the NIH here.  Note: A. Max...
  30. A Look Back at One Year of Plasmid Sharing for COVID-19 Research

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    Blog Post
    ... reached labs in over 75 countries. Figure 1: SARS-CoV-2 proteins and other components. Image from... developed based on 100 structure-guided spike designs and has improved protein yields and stability. ...Plasmids deposited from Alejandro Balazs’s lab includes those for generating pseudovirus and those encoding...Liu Y, Chou C-W, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, ...Finkelstein IJ, McLellan JS (2020) Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science...
  31. New CRISPR Tools: Cas7-11 and PASTE

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    Blog Post
    ... of low-toxicity RNA editing tools.   Fig. 1 Schematic of luciferase RNA knockdown assays using...The hardest part of any revolutionary discovery, including CRISPR, is turning potential into impact. ...two pieces: a single protein, computationally described as a fusion of four Cas7 proteins and a putative...RNA editing methods — streamlining experimental design and its potential for clinical applications. Specifically...high-fidelity rate. Both Cas7-11 and PASTE open up multitudes of possibilities at the bench and potentially...
  32. Data Freedom: The Expansion of Data Sharing in Research Publications

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    Blog Post
    ...processed since the declaration, only a small fraction (<1%) of authors have asked for advice about the scope...the time of manuscript submission. The rationale includes increasing the ability of reviewers (and, once...issue by requiring ever more condensed methods descriptions, legends and limiting numbers of figures such...could be mitigated by on-line services such as SlideShare, Figshare and Dataverse. Just as Addgene helps... raise the alpha isoform of GSK-3 to the same (deserved) stature as the beta isoform. Follow him on Twitter...
  33. SciComm: Taking Science to Elementary and Middle Schools

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    Blog Post
    ...can make this fun activity relate to STEM.” Figure 1 shows the activities we had for my school’s Math &... can teach  5-10 year olds in a single evening. Grades K-5 cover a broad range of attention spans, skill...CRISPR work? This section was essentially background slides getting everyone on the same page in terms of the... by running it by the teachers and sharing some slides on Twitter, where I was able to get some great ...
  34. Plasmids 101: Choosing an Antibiotic Resistance Gene

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    Blog Post
    ...antibiotic selection. Essentially, this gene is a 2-in-1 providing both bacterial and eukaryotic selection,...The NPTII gene confers resistance to several aminoglycosides, including G418 which is commonly used for ...DNA and generating DNA breaks. The Sh ble gene provides zeocin resistance by expressing a protein that...experiments in which off-target mutations are undesirable. Pros: Works across many species/systems. Cons...
  35. Course-Based Undergraduate Research Experiences (CUREs)

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    Blog Post
    ...two (Knutson et al., 2010a,b).      Fig. 1: Undergraduates in Provost’s CURE prepare to analyze...semester one and then proceed to use those skills to design and carry out their own novel experiments in semester...resources, offers mentoring for instructors, and provides opportunities for students to exchange ideas and...results in student learning gains and positive STEM attitudes in CUREs. CBE Life Sciences Education. 21(4):ar74...
  36. Antibodies 101: Immunoprecipitation

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    Blog Post
    ...antibody bonding strengths.    . Steps of an IP: 1) Protein extracts from cells or tissues contain a ...most situations.  A slightly different method is desirable if the antibody is expected to bind weakly to ...vary in shape and structure. Their porous surface provides a large area for binding, but antibodies conjugated... slightly higher, than those of agarose beads, despite the size difference. Magnetic beads are particularly...
  37. Viral Vectors 101: Preparing Pooled Libraries

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    Blog Post
    ...your virus. Let’s start there!     Figure 1: Flowchart showing the process for using pooled lentiviral... If not, our protocol on Lentivirus Production provides a general approach for producing lentivirus in...excellent protocol paper by the Feng Zhang lab describing construction, lentiviral production, transduction...the Broad Institute- A variety of protocols and guides regarding pooled libraries, from cloning a pooled...
  38. Protocol - How to Design Primers

    Type
    Protocol
    ...fragment that needs to be amplified should be within 1-10 kB in size. The structure of the primer should ...18-24 bases 40-60% G/C content Start and end with 1-2 G/C pairs Melting temperature (Tm) of 50-60°C Primer... Protocols Designing Primers How to Design a Primer You may also like...Tips on designing primers for PCR Protocols...Cloning by PCR Agarose Gel Electrophoresis Primer Design for PCR Oligonucleotide primers are necessary when... when running a PCR reaction. One needs to design primers that are complementary to the template region.... They are synthesized chemically by joining nucleotides together. One must selectively block and unblock...
  39. Transferable Skills: Negotiation

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    Blog Post
    ...dollar contracts behind closed doors. Fig. 1: The mythical land of negotiations.    You negotiate...specific details about the individuals, each example provides a scenario where both people get something valuable...
  40. A Career in Grants: How To Become a Grant Professional

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    Blog Post
    ...successful and meaningful career in the grants profession: 1. Build on your existing skills & passion  Skills such...LLC, a grant professional development firm that includes the social media community GrantChat. She has ... from administration and fundraising to program design and evaluation. She and her team at J. Miller &...
  41. Advancing Biology with Zebrafish: Genetic Tools for Developmental Studies and More

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    Blog Post
    ... such a popular model organism? Zebrafish (Figure 1) were initially recognized as a useful vertebrate ...deactivation method in zebrafish are short, modified oligonucleotides called morpholinos. When injected into zygotes...CRISPR/Cas9-mediated insertion of foreign DNA. Despite these caveats, several features of zebrafish—including...
  42. Viral Production at Addgene

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    Blog Post
    ...determine purity of the AAV preparation. Figure 1: Silver staining of purified and non-purified AAV ...protocols, titering methods, and quality control are described below. AAV Production AAV distributed by Addgene...) are generated from lentiviral preparations (described above) that are subject to a concentration step...
  43. Mesothelioma - Causes, Symptoms, and Treatment

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    Blog Post
    ...blood test for HMGB1, the high mobility group box 1 protein. Normally localized to the nucleus, if the...tumors.  This process is not quick. It can take decades from the first exposure to asbestos to the time...T-cells to more easily recognize and cause the destruction of cancer cells. Pembrolizumab has shown some...
  44. Filming Science Videos in the Age of Social Distancing

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    Blog Post
    ...again. Here’s that process!   Figure 1: The Design-Build-Test-Learn cycle adapted for video making...Good as a WFH desk, and as a video control center.   Cycle 2: Zooming Forward Design: We produced ... So, much like SynBio, it was time to start our Design-Build-Test-Learn cycles. If you’re not familiar...through. I know cameras, but we needed someone else. Design: Jennifer thankfully volunteered, and we decided...here, the operator is in a different room.   Design: The previous cycle made me realize we needed to...restrictions in place, most importantly, masks.  Besides the muffled voices beneath masks, humans rely on...reach for Addgene.  So, onto research! I needed to design a system that would allow me to set up a camera...
  45. Negotiating Work and Life: How to Find the Joy

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    Blog Post
    ...commandments for making it all work – most of the time. #1 Thou shalt find enjoyment in your work If you are ...that extra two miles which is way more fun. And despite those who may wish to tell you so – towel corners...
  46. 5 Reasons to Use Reddit for Science Communication

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    Blog Post
    ...first foray into Reddit. Here are some reasons why: 1. Reddit has a large and active community of people...They also host AMA forums where users can ask designated scientists anything about a particular topic....calendar invite over to the r/Science team with a description of our AMA and Joanne’s preferred time to start...was writing all day and straight on through her designated two hours for answering questions. She was able...toxic advisors, fruitless job searches, and even despair at having chosen an academic past. I hope I was...receive via email. The cool features are too many to describe here, but I have over 2,000 notes which Evernote...
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