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  1. CRISPR Activation: A Practical Guide

    Type
    Blog Post
    Published
    Aug. 18, 2016, 2:30 p.m.
    ...experiments (Konermann et al., 2014, Chavez et al., 2014, Chavez et al., 2016) along with a belief that...doi.org/10.1038/nmeth.3312 Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque...contributed by guest bloggers Marcelle Tuttle and Alex Chavez, researchers at the Wyss Institute for Biologically...increase gene expression at certain loci to create changes in phenotypes. For example, CRISPR activation has...to differentiate induced pluripotent stem cells (Chavez et al., 2015) into neuronal cells by activating... constructs, however, Cas9 allows you to easily change the sequence targeted by the activator by simply...Tanenbaum et al., 2014, Gilber et al, 2014), and VPR (Chavez et al., 2015)) are good choices across multiple...
  2. 27 Hot Plasmids from 2016

    Type
    Blog Post
    Published
    Dec. 22, 2016, 3:03 p.m.
    ...quantification of enhancer activity have remained challenging due to the variable availability of enhancer ...this type. They were also able to functionally characterize positive hits. This work has been published ... the yeast vacuole, as well as to examine the mechanisms behind autophagic pathways. Rosado, et al. Autophagy...Takashi Yamamoto pcDNA-TAL-NC2, pCAGGS-TAL-NC2 Charles Gersbach pcDNA3.1-GoldenGate, pcDNA3.1-GoldenGate-VP64...pTALYM3, pTALYM4 Boris Greber pTAL7a, pTAL7b Michal Zurovec pBlue-TAL Nathan Lawson pJDS Series ...and provides a new method for generating protein chains or clusters. Veggiani, et al. Proc Natl Acad Sci...pharmaceutical industry, depend on the yeast, Saccharomyces cerevisiae, as a key host for the production...
  3. Stem Cell Models for Disease & Open Science: Interview with Darrell Kotton

    Type
    Blog Post
    Published
    July 7, 2017, 1:32 p.m.
    .... Listen to the interview with Darrell Kotton Chapter 1: Introduction to Darrell Kotton and the Boston...develop therapies to treat disease in the lung. Chapter 2: Balancing research with medical practice as ...becoming an MD but later got obsessed with research. Chapter 3: How all basic research ends up being translational...translational. Ex: the discovery of GFP. Chapter 4: Goals of the Center for Regenerative Meidince - Understanding...for Regenerative Medicine accelerates research. Chapter 5: Research currently under way in the Kotton Lab...understand the biology of certain lung diseases. Chapter 6: Near-term possibilities for using engineered...the retina have cell-based therapies underway. Chapter 7: Generating entire lungs using a decellurized...
  4. SciComm with the Experts at Science in the News Part 2

    Type
    Blog Post
    Published
    April 27, 2017, 2:30 p.m.
    ... the News Chapter 1: Introduction - Vini and Amy tell us a little about themselves. Chapter 2: What is...will the effects of climate change make put Cambridge underwater? Chapter 8: Work-Life Balance - Vini ...organize evens where scientists can grab a beer and chat about their work at a local bar. It doesn't have...great science communication tips or listen to the chapters we've broken down below for specific topics discussed...next generation of science communicators. In this chapter we learn about some of their events - science seminars...popular topics from the Science by the Pint series. Chapter 4: The SITN Podcast, Sit'N Listen - In their podcast...Episodes are driven by narrative and story telling. Chapter 5: The SITN Blog - Vini and Amy describe how the...
  5. Tips for Getting a Faculty Position

    Type
    Blog Post
    Published
    July 20, 2023, 1:15 p.m.
    ...Talk." 4. The chalk talk, simple in principle The first question I usually get about chalk talks is, what... whether there is chalk. Sometimes. It can also be a slide deck, markers, etc. Chalk or markers force ... Developing your Chalk Talk These items should be part of the beginning of your chalk talk. These should... This edition has substantial expansions on the chalk talks and Zoom interviews sections, along with new...what is a Chalk Talk? It is a 60-90 min session with department members to discuss your research plans...alternatives for an approach, if asked. The key to a chalk talk is to effectively convey your message. Key ...human disease" is vague. Instead, consider "A mechanistic understanding of this system will provide the...
  6. Savvy Advocates Needed to Navigate a Scientific Enterprise in Flux

    Type
    Blog Post
    Published
    Sept. 13, 2016, 2:30 p.m.
    ...Symposium Boston 2016 Changes since the Future of Research Symposia Ongoing challenges facing the scientific... us to discuss advocacy efforts toward positive change in the scientific enterprise and the way it is ...to learn tangible skills necessary for affecting change. On Friday, the symposium includes a panel discussion...initiated. Recent developments promise to further change the landscape facing all scientists, both young...available avenue. Interestingly, both of these changes share a common thread that has the potential to...for the future No matter your opinion on these changes, it is likely that the shifts caused to the practical...landscape of the scientific enterprise will provide challenges and opportunities for us all.  For example, implementation...
  7. To Codon Optimize or Not: That is the Question

    Type
    Blog Post
    Published
    Nov. 12, 2020, 2:15 p.m.
    ...1793-7 Dresios J, Chappell SA, Zhou W, Mauro VP (2005) An mRNA-rRNA base-pairing mechanism for translation...they are incorporated into the growing polypeptide chain. One part of the tRNA contains the anticodon,  a...may be found at very different levels (Mauro and Chappell, 2014). Due to this variation in tRNA expression... synthesis. A ribosome interacts with mRNA and charged tRNAs to build a peptide. Image from Mariana Ruiz...gene engineering to improve gene expression by changing synonymous codons based on an organism's codon...Lester’s lab optimized the C. elegans GluCl ion channel genes for expression in mammalian cells. This was... in a 6-9 fold increase in expression of these channels providing scientists with the ability to selectively...
  8. Antibodies 101: Introduction to Antibodies

    Type
    Blog Post
    Published
    Jan. 19, 2021, 2:15 p.m.
    ...region. Two immunoglobulin (Ig) heavy chains and two Ig light chains make up each antibody molecule. The...the Ig heavy chains, and the rest of the Fab regions are completed with the Ig light chains. The variable...diagram of an antibody including Fc, Fab, heavy chain, light chain, constant region, variable region   The... Nanobodies are the variable heavy chain fragment of heavy chain camelid antibodies (Hcab) (Arbabi-Ghahroudi...variable region of the heavy and light chain determine what antigen the antibody recognizes and binds to. ...The constant region of the heavy chain determines the antibody’s isotype - that is, one of five broad ...for specificity and sensitivity, for example by changing certain amino acids to improve its stability. ...
  9. A Career in Grants: How To Become a Grant Professional

    Type
    Blog Post
    Published
    Aug. 20, 2015, 2:30 p.m.
    ...Follow Jo on Twitter @JM_Grants and follow Grantchat @Grant_Chat    Additional Resources Read other Career...seekers to use online applications with significant character limits for the written portion of the grant application...government grantmakers. We keep up-to-date on the changing guidelines and regulations impacting grant management...degrees, foundations, coaching and even Twitter Chats dedicated to the Grant Profession.  Demand for grant...government. Throughout these moves and program changes, I learned to write grants for health, housing,...within the city infrastructure. My career path changed when I was asked if I would consider consulting... started my own grant consulting firm, a Twitter Chat, and then our grant training and mentoring. How ...
  10. Antibodies 101: Epitope Availability

    Type
    Blog Post
    Published
    Jan. 11, 2022, 2 p.m.
    ...proteins change configurations or binding partners, the epitopes available for binding change as well....often change shapes and epitope accessibility naturally, by binding to other proteins, changing locations...well. If this change hides the epitope that the antibodies used to recognize the protein, your antibody will... you're working with antibodies.) Conformation changes usually fall into one of two categories: ones induced...  First, let’s think about induced conformation changes. Several types of assays, such as ELISAs and Westerns... some of the bonds keeping the protein folded, changing it from its native state to a less folded, or ...and a more accurate separation of proteins by mass:charge ratio in an SDS-page gel. As the protein unfolds...
  11. 22 Hot Plasmid Technologies from 2014

    Type
    Blog Post
    Published
    Jan. 6, 2015, 5:21 p.m.
    ...family of plasmids by offering a lentivirus-based mechanism for sgRNA delivery and providing a means for large...mutant S65T-GFP, and the subsequent biochemical characterization, has enabled scientists to engineer a wide...Branchiostoma floridae, named bfloGFPs. They went on to characterize the structural and spectral properties of two...a mutant of the fluorescent protein dsRed that changes irreversibly its color from green to red when it... show its usefulness in cell culture to report changes in mitochondrial turnover and transport. pMitoTimer...degradation in vitro and in vivo. Merged green and red channel fluorescence images of C2C12 cells stably expressing...alternative pathway or induce other compensatory mechanisms. How can protein function be dissected while ...
  12. Fluorescent Proteins 101: Photoactivatable Fluorescent Proteins

    Type
    Blog Post
    Published
    April 25, 2017, 2:30 p.m.
    ...) are fluorescent proteins that display unique changes in their spectral properties upon exposure to a...fluorescent states to high fluorescence states, they can change from one fluorescent color to another, or their...Activating Light Pre/ Post Color Contrast (Fold Change in Fluorescence) Brightness Excitation/ Emission...usually preferred for studying single protein characteristics, as the monomeric state is less likely to interfere.... By generating monomeric PA-FPs, there is less chance that the chimeric protein will oligomerize, disrupting...super-resolution imaging usually have the following characteristics-high contrast ratios, bright fluorescence, ...
  13. Typing CRISPR Systems

    Type
    Blog Post
    Published
    March 18, 2025, 1:15 p.m.
    ...a decade of frenzied interest in bacterial and archaeal immune systems. During this time, scientists discovered... discovered many related immune mechanisms that could target foreign DNA with unique properties. This ...fast evolution of these adaptive bacterial and archaeal immune systems has led to extreme sequence divergence...share sequence similarity but are grouped due to mechanisms of action and other analyses. This also means...identified CRISPR-Cas in bacteria and nearly 100% in archaea, though Class 1 remains largely underutilized compared... These subtypes have similar compositions and mechanisms, with the biggest differences being the components... contain a distinct Cas7-type gene. The exact mechanism of type IV systems is not known, but it’s suspected...
  14. Story of a SynBio Startup: RevBio's Epiphany (or Lack Thereof)

    Type
    Blog Post
    Published
    June 5, 2014, 3:32 p.m.
    ... that changes color, but the experience is invaluable. This opportunity has given us the chance to develop... careers in order to head to Ireland and take a chance as entrepreneurs. To make things more interesting...product no one has ever seen before (flowers that change color throughout the day) and doing this with very...our lives and took this daring risk? What moment changed our whole outlook on the possibilities in life ...published a paper a year (or less) and limited the exchange of information to the public and to other academic... publish or attend conferences makes it very challenging to compete in today’s tough academic or industry...team. We have confidence that we can take on any challenge and quickly become experts in something, even ...
  15. Future of Research Conference - Remarkable Opening Session

    Type
    Blog Post
    Published
    Oct. 7, 2014, 3 p.m.
    ...science publishing system needs to be changed.  Dr. Bourne charged the audience to use their useful energy...things off, “We are all capable of contributing to change.”  Check out Joanne's Reddit AMA The keynote speaker...spoke eloquently and vehemently about the need for change.  Dr. Bourne strongly believes this is an amazing...PI driven basic research, there is resistance to change, public support is weak, government support is ...is “feckless”.  So what can be done?  He charged the postdocs to “Grab ahold of your destinies” and also...engaged in training excellence to begin effecting change.  Panelists call for action Each of the speakers...graduate students and postdocs in their labs. Dr. Richard Roberts, CSO of New England Biolabs, gave examples...
  16. AAVs CREATed for Gene Delivery to the CNS and PNS

    Type
    Blog Post
    Published
    Sept. 28, 2017, 2:01 p.m.
    ...3b in Chan et al.   To achieve the full diversity of colors AND sparse labeling of neurons , Chan et al...both the CNS (figure 5 in Chan et al) and the PNS (supplemental figure 8 of Chan et al). These new AAVs ...figure 5 and supplemental figure 8 in Chan et al).  References 1. Chan, KY, Jang MJ, Yoo BB, et al. Engineered...3) they have limited toxicity. However, a key challenge of using AAVs for neuroscience research is the...the Gradinaru Lab at Caltech stepped up to the challenge. Find the PHP Plasmids Here! Their Solution: ...the cell type of interest, which, in the case of Chan et al, was neurons and astrocytes. Why screen for...high doses of this viral cocktail are injected, by chance lots of individual cells will be transduced with...
  17. Using AAV for Neuronal Tracing

    Type
    Blog Post
    Published
    Aug. 9, 2018, 1:04 p.m.
    ...transport suggest that there are several parallel mechanisms in place (for review see Maday et al., 2014)....neuroscientists for some time due to their advantageous characteristics for brain research and their ability to introduce...2010), AAV8, -9 (Masamizu et al., 2011); AAV5 (Aschauer et al., 2013). Anterograde transport has been ...California Institute of Technology generated novel AAVs (Chan et al., 2017) that express one of a few different...are capable of synaptic spread. The underlying mechanisms of trans-synaptic trafficking are not fully understood...these two modes of transport may share common mechanisms. Rare observations like these may be a starting...brain. A better understanding of the routes and mechanisms of intracellular transport of AAV could facilitate...
  18. Optogenetics + CRISPR, Using Light to Control Genome Editing

    Type
    Blog Post
    Published
    Sept. 3, 2020, 12:15 p.m.
    ...Single-chain Cas9 photoswitches Photoactivation of Cas9 can also be achieved using single-chain fusion...Can be used for in vivo models Single-chain Photoswitchable Cas9 Richter et al., 2016 tsRC9 RsLOV ...Bratovič M, Charpentier E, Möglich A (2013) Engineering of temperature- and light-switchable Cas9 variants...Y, Liu Y, Qi LS, Lin MZ (2017) A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible...Moritoshi Sato’s lab at the University of Tokyo and Charles Gersbach’s lab at Duke University developed similar...Their most successful design utilized Magnet photoswitchable proteins derived from the fungal photoreceptor...instead of nMagHigh1-C714, generating paCas9-2. This change did not significantly alter the system’s efficiency...
  19. Fluorescent Protein Travel Awards - FLiPs and Fluorescent Protein Biosensors

    Type
    Blog Post
    Published
    July 27, 2017, 1:11 p.m.
    ...work in Michael Lin’s lab at Stanford, Xin Zhou greatly expanded that list by using photoswitchable fluorescent...apply fluorescent proteins everyday.  The late Michael Davidson and Roger Tsien played enormous roles ...To honor their legacy, we recently launched the Michael Davidson and Roger Tsien Commemorative Travel Awards...this post, we’re proud to announce our first two Michael Davidson and Roger Tsien Commemorative Travel Awardees...turned the enzymes back on. Xin termed these photoswitchable enzymes Fluorescent Light-inducible Proteins...various designs, Xin has been able to develop photoswitchable Intersectin, Cdc42, Raf1, Mek1, Mek2, Cdk5,... You can learn more about Xin’s work with photoswitchable components of the ERK signaling pathway in ...
  20. CRISPR 101: Homology Directed Repair

    Type
    Blog Post
    Published
    Jan. 26, 2023, 2:15 p.m.
    ...ultraviolet light. In this post, we will describe the mechanism of homology directed repair, one of the repair...template for repair and is thus the more accurate mechanism for DSB repair. The process is generally error-free...the template DNA. There are several unique HDR mechanisms, but all templated-repair pathways have these...process Homology directed repair pathways HDR mechanisms can be divided into two main camps: non-conservative... conservative. The conservative methods are characterized by use of a homologous donor (e.g., sister chromatid...single strand annealing (SSA), an error prone mechanism that notably does not require a donor template... (SDSA) pathway SDSA is a conservative repair mechanism which exclusively yields non-crossover events....
  21. Podcast: Interview with Addgene's Founders

    Type
    Blog Post
    Published
    April 13, 2018, 12:51 p.m.
    ...founders Podcast breakdown Intro Chapter 1 - Who are Addgene's Founders? Chapter 2 - The process of founding...ensuring that success Chapter 6 - Developing Addgene’s Brand and culture Chapter 7 - Building Addgene ...distribution!) Chapter 8 - Opportunities to create repositories with other materials Chapter 9 - The Founders... came from and how the idea got off the ground Chapter 3 - Addgene as a leader in standardized tech transfer...transfer and the adoption of the UBMTA Chapter 4 - Developing Addgene as a modern e-commerce company and... and establishing credibility Chapter 5 - Realizing that Addgene would be successful and the importance...and beyond - Ginkgo, Tufts Launchpad, and more Chapter 10 - Addgene's Future, the research team, and the...
  22. Chromoproteins: Colorful Proteins For Molecular Biology Experiments

    Type
    Blog Post
    Published
    Feb. 4, 2020, 2:15 p.m.
    ...jellyfish Cassiopea xamachana. Marine Biology 94:423–430 . https://doi.org/10.1007/bf00428249 Chan MCY, Karasawa...-colored protein from the jellyfish Cassiopea xamachana (Blanquet and Phelan, 1987). Eight years later...of chromoproteins were identified in sea anemone (Chan et al., 2006). Why do these organisms have chromoproteins...specific purposes.     Chromoproteins for allelic exchange Figure 3: pTOX plasmids expressing amilCP... create negative selection markers for allelic exchange. These vectors contain a toxin gene (regulated...rhamnose-inducible promoter) and a chromoprotein gene. Allelic exchange occurs through two sequential homologous recombination... the tsPurple chromoprotein.  Find the allelic exchange vectors here! ShadowR, a novel FLIM-FRET acceptor...
  23. Magnetic Control of Proteins: More than a Dream

    Type
    Blog Post
    Published
    Sept. 24, 2024, 1:15 p.m.
    ...identify how MagLOV’s structure changes under magnetic field. Such changes could be harnessed or enhanced... Entropy as a Proposed Gating Mechanism for Magnetogenetic Ion Channels. Biophysical Journal, 116(3), ... good ol’ EGFP — showed a slight but detectable change in fluorescence when a small magnet was passed ...Fluorescence intensity of EGFP-FlavinTag in E. coli changes in response to a ~25 mT magnet. Gray regions indicate...could be expressed and purified. Although a ~1% change in signal might not make a very powerful tool, ... Q513K, G528K, D540M) that shows a fluorescence change of ~75% in response to the magnetic field (Figure...MagLOV-based tools, just as light-induced conformational changes are the basis of many optogenetic tools. And, since...
  24. Lambda Red: A Homologous Recombination-based Technique for Genetic Engineering

    Type
    Blog Post
    Published
    Dec. 15, 2016, 3:57 p.m.
    ...flank the desired change with 4-5 silent changes in the wobble codons, i.e. make changes to the third base... translated protein.  These changes can be 5’ or 3’ of the desired change.   Table 1: Overview of ds- ...sequences, point mutations or other small base pair changes, and the addition of protein tags. It also has ...to restriction enzyme cloning where the genetic changes occur in a test tube. The donor DNA substrate only...ssDNA substrate is best for point mutations or changes of only a few base pairs.  dsDNA Substrate dsDNA...prone to mutations and will have more unintended changes to their genomes. 2) Designing ssDNA oligos that... to generate insert ssDNA Point mutations or changing a few nucleotides 0.1-1% or 25-50% when activation...
  25. FLEx Technology and Optogenetics: Flipping the switch on gene expression with high spatial and temporal resolution

    Type
    Blog Post
    Published
    Oct. 17, 2019, 12:28 p.m.
    ...bacteriorhodopsins, halorhodopsins, and channelrhodopsins, the first two found in the Archaea, the third in green algae...). These proteins control the flow of electric charges across cell membranes and maintain membrane potential... 2012). For example, blue light activates channelrhodopsins that, in turn, trigger neural excitation, ... promoter upstream of an opsin gene (e.g., channelrhodopsin-2, ChR2) fused to a reporter gene (e.g., mCherry...vectors to study the neural circuitry behind the mechanisms of sleep and anesthesia. In Cre transgenic mice...vectors to answer this question, mapping and characterizing the activity of the DA neurons of the VTA. ...optogenetics to understand the cellular and molecular mechanisms of the brain in vivo. Many thanks to our guest...
  26. Sonic Hedgehog? Sleeping Beauty? Learn About the Genes Behind Addgene’s Conference Room Names

    Type
    Blog Post
    Published
    April 2, 2019, 1:44 p.m.
    ...this is not a direct reference to the video game character but rather to an extremely important gene in animal...1980, when Christine Nusslein-Volhard and Eric Wiechaus first identified the hedgehog gene in Drosophila...that resembled a hedgehog (Nusslein-Volhard and Wiechaus, 1980). The mammalian hedgehog protein, sonic ...into vertebrate chromosomes via a cut and paste mechanism. Scientists reconstructed a transposase system...squash (Sqh) is the Drosophila Regulatory Light Chain (RMLC) of nonmuscle myosin II (Karess et al., 1991...plasmids in our inventory from the lab of Eric Wieschaus that express sqh.   cookie monster, a meiotic...required for spermatogenesis after a Sesame Street character? The scientists who discovered comr thought the...
  27. Hot Plasmids: Fall 2024

    Type
    Blog Post
    Published
    Nov. 21, 2024, 1:30 p.m.
    ...constant domains, the plasmids for the heavy chain and light chain are also available from Addgene!   ...disruption in M. abscessus  Bioluminescent reporter of mechanical forces   Epitope tag antibody collection grows...K., & Russell, W. C. (1987). Isolation and characterization of monoclonal antibodies to simian virus 5...of its biology, pathogenicity, and resistance mechanisms.     Figure 4. Overview of the dual-plasmid...10.1128/jb.00335-23.  Bioluminescent reporting of mechanical forces with PILATeS By Emily P. Bentley Time ... lab and collaborators have deposited a new mechanosensor called PILATeS, Pulling-Induced Luciferase Association...different contexts.   Figure 5: Left: Mechanism of the PILATeS tension sensor. The LgBiT (cyan...
  28. R Bodies: Membrane-Rupturing Microscopic Tools

    Type
    Blog Post
    Published
    April 14, 2016, 2:30 p.m.
    ...body monomers respond to pH changes by undergoing local conformational changes. These tiny movements are... much force can be generated by conformational changes in proteins? How can information propagate through... repeatedly extend and contract in response to changing pH, and they can rupture E. coli spheroplasts ...and retract over many microns in response to pH changes without the need for ATP or other chemical fuel...vasculature or extracellular matrices) in response to pH changes. Beyond these applications, purified R bodies ...bodies could also perform as actuators in microelectromechanical systems (MEMS) devices. They could be functionalized...
  29. 3 Tips to Improve HDR Efficiency for CRISPR Editing in Human Cells

    Type
    Blog Post
    Published
    Sept. 5, 2017, 1:58 p.m.
    ...introduction of specific sequence changes. To generate a specific sequence change the cell must undergo homology-directed...extensively for the purpose of making sequence-specific changes in human induced pluripotent stem cells (iPSCs)... (ssODN), which contains the intended sequence changes to be incorporated into the edited genome. In mammalian...CRISPR/Cas9 blocking mutations in either the PAM (changing one of the G’s to an A,T or C – but avoid NAG)... to be silent. In our view, it’s always best to change the PAM site, however we have also demonstrated...mismatch in the binding sequence, we recommend changing several bases as close to the PAM as possible ...blocking mutation together with the intended sequence change and screen a few hundred clones to find the right...
  30. March for Science

    Type
    Blog Post
    Published
    April 21, 2017, 2:30 p.m.
    ...warming The New York Times: With Trump in Charge, Climate Change References Purged from Website The Washington...reality – a government cannot declare that gravity change direction and make things fly up when we drop them...outcomes are actually possible for a given policy. In exchange, the government protects (and often funds [3])...scientists has been rising as evidence of climate change, the safety of genetically modified organisms (...90% of active research scientists believe climate change is mostly due to human activity while much less...administration’s actions, including taking down the climate change page on whitehouse.gov, freezing grants, and proposing...advocating for science education and literacy that this changes.  2) Lumping all scientists (and consequently their...
  31. Hot Plasmids: Summer 2024

    Type
    Blog Post
    Published
    Aug. 27, 2024, 1:15 p.m.
    ...Engineered and evolved optimizations for prime editing CHARM: A compact epigenetic silencer Recombinant antibodies...in Xenopus nucleosomes and in complex with its chaperone NPM2, but the technique should be widely applicable...more complex protective methods or detergents like CHAPSO, while requiring a lower concentration of sample...  https://doi.org/10.1038/s41551-024-01227-1   CHARM: A compact epigenetic silencer By Emily P. Bentley...for Autoinhibition Release of Methyltransferase (CHARM), with several advantages over the earlier system...methyltransferase for epigenetic silencing, which can be toxic, CHARM uses a cofactor fused to a histone tail to recruit...potentially with multiplexed targets.   Figure 4: CHARM uses a fusion of the DNMT3L cofactor (D3L) with ...
  32. Enabling Precision Functional Genomics with the Target Accelerator Plasmid Collection

    Type
    Blog Post
    Published
    May 11, 2017, 2:30 p.m.
    ...precision medicine a reality. Challenges for cancer variant characterization For many years, we’ve hoped...report includes rare variants that haven’t been characterized? Some have developed exciting computational...algorithms, such as SIFT or PolyPhen to approach this challenge, using attributes of cancer variants such as evolutionary... or predicted deleteriousness of the amino acid change based on maps of protein structure. Sometimes this...Collection, that we hope researchers can use to characterize these variants in a high-throughput manner and...validation experiments. But, there have been two huge challenges preventing us from testing this hypothesis: ...Accelerator Plasmid Collections To overcome this first challenge, we’ve developed the Broad Institute Target Accelerator...
  33. Antibodies 101: Monoclonal Antibodies

    Type
    Blog Post
    Published
    June 29, 2021, 1:15 p.m.
    ...antibody.     Figure 2: Changes to the heavy chain or light chain genes within a hybridoma impacts...off-target effects. This is because there are more chances for these antibodies to recognize epitopes that...monoclonal antibodies. Genetic drift refers to changes in the nucleic acid sequence of the antibody-encoding...over time as the hybridoma cells divide. These changes can alter the antibody that is actually produced...produced by the hybridoma, meaning that there will be changes between lots over time. Specifically, the antigen-binding...antigen-binding sites of the antibody - the paratopes - may change and impact the specificity and avidity of the antibodies...be identified by sequencing the heavy and light chains. To circumvent any possible genetic drift, scientists...
  34. Fluorescent Proteins 101: Introduction to FRET

    Type
    Blog Post
    Published
    June 27, 2017, 1:03 p.m.
    ...donor-acceptor pair and a change in FRET efficiency correlates with a change in the distance and/or orientation...to a change in the environment which alters the FRET efficiency. Detecting certain cellular changes with...studying protein-protein interactions by measuring the change in FRET efficiency, from which conclusions regarding...error in suboptimal or undetectable FRET, well-characterized FRET reference standards can be used to validate...rearranging the start and end positions without changing the order of the amino acids in the protein) may...cellular processes and signaling cascades, quantify mechanical tension (a molecular “spring”) (Meng et al., ... et al. "A fluorescence energy transfer‐based mechanical stress sensor for specific proteins in situ."...
  35. Pathways Over Time Plasmids Engage Students in Functional Genomics Research

    Type
    Blog Post
    Published
    May 22, 2018, 1:38 p.m.
    ...., Bussey, H. et al. Functional characterization of the Saccharomyces cerevisiae genome by gene deletion...students (1, 2), but educators face significant challenges in designing suitable projects. In the O'Connor...methionine synthesis (5). The budding yeast, Saccharomyces. cerevisiae, makes a great reference organism...cerevisiae (Figure 1) occurs through a well-characterized pathway with multiple enzymatic steps (5). In... or not proteins from the fission yeast, Schizosaccharomyces pombe, have the same function as their counterparts... the Advancement of Science. (2011). Vision and Change in Undergraduate Biology Education: A Call to Action...yeast for budding geneticists: A primer on the Saccharomyces cerevisiae model system. Genetics 197, 33-48...
  36. Viral Vectors 101: Chemogenetics

    Type
    Blog Post
    Published
    July 11, 2023, 1:15 p.m.
    ...the ion pore domain (IPD) of a channel, the PSAM acts as a gating mechanism to control ion flux. The system... endogenous gene expression, which can lead to changes in normal cell physiology and function (Saloman...to one receptor, so it is important to fully characterize the compound, or compounds, you choose to ensure...system allows you to directly manipulate ion channels. When working with PSAM receptors, your impact on...with. Combining a PSAM with the IPD of a cation channel, such as the serotonin 3 receptor, will promote...Alternatively, combining with the IPD of an anion channel, such as the glycine receptor, will promote hyperpolarization...doi.org/10.1523/ENEURO.0171-19.2019Jendryka M, Palchaudhuri M, Ursu D, van der Veen B, Liss B, Kätzel D,...
  37. Truncated gRNAs for Regulating Gene Expression

    Type
    Blog Post
    Published
    Jan. 10, 2017, 3:37 p.m.
    ...contributed by guest bloggers Alissa Lance-Byrne and Alex Chavez, researchers at the Wyss Institute for Biologically...double strand break (DSB) stimulates DNA repair mechanisms that can be exploited to either inactivate a ...alteration. Listen to Our Podcast Interview with Alex Chavez Figure 1: Schematic of native (nuclease-...different perturbations. Consider, for instance, the challenge of attempting to simultaneously and selectively...importantly, most Cas9 orthologs are less well characterized than the conventionally used SpCas9 (derived...transcriptional regulator without making any functional changes to Cas9. For instance, when native (nuclease-competent... our guest bloggers Alissa Lance-Byrne and Alex Chavez! Alissa Lance-Byrne is a graduate student at the...
  38. Antibodies 101: Producing Recombinant Antibodies

    Type
    Blog Post
    Published
    Aug. 13, 2024, 1:15 p.m.
    ... the production of Fab fragments where variable chains are secreted into the periplasmic space to be oxidized...transfection, depending on whether the heavy and light chain genes are contained to one plasmid or if they’ve...preferred buffer. If that’s the case, a buffer exchange can be performed using a desalting column or an...concentration to give your downstream applications the best chance at being successful.  Using a spectrophotometer...SDS-PAGE gel. Once stained, the heavy and light chains become visible alongside your ladder and a protein...Any bands on the gel beside the heavy and light chains can also be measured. Contaminating bands lower...western blot. This can be due to conformational changes in the antigen or lower detection sensitivity of...
  39. Using Video to Share Your Science: We Share Science

    Type
    Blog Post
    Published
    Nov. 3, 2016, 2:30 p.m.
    ...solutions to complex challenges. As a cross-disciplinary researcher, the challenge of keeping up on studies... Sharing your research with the world can be challenging. After months, or years, of grueling effort to... personnel, and sociology journals when I get a chance, but I know that there is much more research that...biology or international relations.  Many of the challenges in science today are too complex for any single...disciplines. Included in the article is an interactive chart where you can see the yearly interdisciplinarity...Out Addgene Videos Over at the Addgene Youtube Channel   After watching these trends for a few years, ...making publishing their research all the more challenging even when it is of quality). On the site you ...
  40. Transferable Skills Guide: Creativity

    Type
    Blog Post
    Published
    Jan. 18, 2022, 2:15 p.m.
    ...will always be that way. Things change and processes often have to change with them. If you can, set aside... needing to brainstorm with a team. One major challenge with these brainstorming sessions is avoiding ...person who submitted the idea did not have to be in charge of implementing it. The purpose of this form was...creative when you don’t believe you have the power to change anything. You may not have the highest position...received, understand that people can be resistant to change. Ask your peers or your superiors to explain their...unworkable idea into a viable solution.  Anticipate Change Just because a process is working, doesn’t mean...aside time to prepare for future challenges. This doesn’t have to be time-consuming or even very frequent...
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