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We narrowed to 511 results for: ATO

Showing: 31 - 60 of 511 results

  1. Early Career Researcher Toolbox: Free Online Molecular Biology Tools

    Type
    Blog Post
    Published
    Sept. 12, 2023, 1:15 p.m.
    ...In-Fusion cloning molar ratio calculators Lab math calculators These calculators can help you with common...lab. Molarity calculator Promega's Biomath Calculators Primer resuspension calculator (sign-in required...Golden Gate Reactions Cloning ligation reaction calculators These links can help you calculate how much insert...assembly, or In-Fusion cloning.  NEB Ligation Calculator: This tool works for any cloning method. You ...required.)  DailyCalcs Science Calculator app for iPhone Reagent and Data Repositories These links can help...

  2. Rewiring Metabolic Circuitry with CRISPR RNA Scaffolds [Video]

    Type
    Blog Post
    Published
    April 7, 2015, 4:21 p.m.
    ...transcriptional regulator to modulate expression at that locus. The use of regulators allows a greater...shifted in recent years toward tinkering with regulatory networks and multiplex gene control. However,...approaches are often met with the challenges of regulatory bottlenecks and their scope is limited by the...scaffolds that can recruit various transcriptional regulators (Zalatan et al. 2015).  These scaffolds are stretches...levels dependent upon the type of transcriptional regulator or the number of designed scaffold binding sites...with distinct programs controlled by each dCas9 regulatory switch. By no means limited to the field of metabolic...scaffolds can recruit various transcriptional regulators to alter gene expression at the targeted site...

  3. Addgene's Cancer Collection Pages Connect the Research Community

    Type
    Blog Post
    Published
    Sept. 6, 2016, 2:30 p.m.
    ...to their laboratory. A single mouse click on a gene of interest will direct the investigator to a list... cancer are yielding promising results in the laboratory, and Addgene is accelerating this research by...proto-oncogenes and tumor suppressors to the accelerator and brake pedal of a vehicle, respectively. In... (now an oncogene), this is analogous to the accelerator of a vehicle being stuck down. Similarly, a mutation...cells still need to successfully infiltrate the circulatory or lymph systems to spread, or metastasize. Many...Many cancerous cells will die trying, as the circulatory and lymph systems are not ideal environments ...involved in the Ras pathway alone and thousands of investigators studying them, how do we ensure that the research...

  4. CRISPR 101: Which Cas9 Do I Choose for My CRISPR Experiment?

    Type
    Blog Post
    Published
    Oct. 13, 2022, 1:45 p.m.
    ...target genes using dCas9-based activators The simplest of the dCas9 activators consists of dCas9 fused to ... dCas9 and antibody-activator fusion proteins. The Synergistic Activation Mediator complex, generally ...exploited to localize factors such as transcriptional activators and repressors to target genes. Repressing target...activation domain - VP64.  Later generations of activators include the SunTag system which facilitates recruitment...generally the strongest activator, consists of a dCas9-VP64 fusion and a modified gRNA that is capable of interacting...with an additional RNA-binding transcriptional activator. Plasmids for activating target genes in a variety...fusion, both targeted to the promoter region. Cas9 activators include Cas9 fused to VP64, VP64 along with other...

  5. Hot Plasmids - October 2022

    Type
    Blog Post
    Published
    Oct. 6, 2022, 1:15 p.m.
    ... voltage indicator: JEDI-2P  by: Brian O'Neill  The François St-Pierre lab and collaborators have successfully...what you'll find in this post: Improved voltage indicator: JEDI-2P Novel class of light-gated potassium...successfully developed an improved voltage indicator (GEVI) called JEDI-2P. Using a custom, high-throughput...predecessor GEVIs (called ASAP 1 and 2), they found an indicator that is optimized for 2-photon imaging of voltages...screen for improved genetically-encoded voltage indicators (GEVIs) based on the ASAP sensors. The resultant...Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell, 18, 3408... cations. B) Cortical slice of HcKCR1-EYFP and tdTomato expressed layer 2/3 neurons in mouse. C) Action...

  6. Recombinase-based State Machines Enable Order-dependent Logic in vivo

    Type
    Blog Post
    Published
    July 28, 2016, 2:30 p.m.
    ...massive amount of information regarding which regulatory proteins, signaling molecules, mutations, and...paper (1). Lastly, it is possible to build gene regulatory RSMs (GRSMs, the subset of RSMs that regulate...also demonstrates that genetic parts (genes, terminators, and promoters) may be interweaved onto a GRSM...parts used in this paper (recognition sites, terminators, promoters, and genes) were built with flanking...them. We recommend using strong, directional terminators and promoters with buffer sequences on their ...ends (for insulation). A list of promoters and terminators used in our GRSM registers can be found in Table... parts (recognition sites, promoters, genes, terminators, etc) are composed. Fear not – the state machine...

  7. Plasmids 101: Inducible Promoters

    Type
    Blog Post
    Published
    Jan. 18, 2018, 2:34 p.m.
    ...the activator protein cannot bind. After an inducer binds to the activator protein, the activator protein...In this system, the activator rtTA (reverse tetracycline-controlled transactivator) is normally inactive...protein purification. When arabinose is absent, regulatory protein AraC binds O and I1 sites upstream of...addition to arabinose, cAMP complexed with cAMP activator protein (CAP) can also stimulate AraC binding ...research. Promoter Subtype Promoter Example Activator Addgene Plasmid/Kit Alcohol-regulated AlcA...

  8. Truncated gRNAs for Regulating Gene Expression

    Type
    Blog Post
    Published
    Jan. 10, 2017, 3:37 p.m.
    ...cut either strand of DNA. Traditional Cas9 regulators In addition to its utility in making targeted...to DNA, Cas9 can be reprogrammed to serve as a regulator of gene expression. Its catalytic domains can ...fused to effector domains such as transcriptional activators or repressors. These fusion proteins retain the... generate a potent Cas9-based transcriptional regulator without making any functional changes to Cas9....adapter capable of recruiting a transcriptional activator, robust regulation of gene expression is observed...the truncated gRNA recruits a transcriptional activator to the Cas9-gRNA complex. When this complex is...of the Addgene Scientific Advisory Board. His laboratory at Columbia University is focused advancing scientific...

  9. Transgenic Organisms, Cas9 Gene Drives, and Appropriate Safeguards

    Type
    Blog Post
    Published
    May 22, 2015, 4:58 p.m.
    ...carrying a synthetic gene drive were to escape the laboratory, the drive could eventually spread through the...mistake would necessarily extend far beyond the laboratory and seriously damage public trust in scientists... can spread through populations of transgenic laboratory organisms but not wild organisms. For example...synthetic sequence will only spread in transgenic laboratory populations with that sequence2. Both methods...Reproductive confinement involves working with laboratory organisms that can't reproduce with wild ones...confinement seeks to keep the organisms in the laboratory. It varies by organism, but your local biosafety...population and immunizes it against the first drive. Laboratories interested in building candidate gene drives...

  10. Isolating Genomic Regions of Interest with the CRISPR System

    Type
    Blog Post
    Published
    May 30, 2019, 12:44 p.m.
    ...the Tapscott Lab identified regulators of DUX4, a transcriptional regulator that when inappropriately expressed...activation using a fusion to a transcriptional activator such as VP64 (Gilbert et al., 2013), or repression...region to inhibit association of transcriptional activators (Qi et al., 2013). However, the fusion of dCas9...specific genomic region In 2013, the Hodaka Fujii Laboratory first described a method to purify a specific...lab is CRISPR affinity purification in situ of regulatory elements (CAPTURE) (Liu et al., 2017). This system...additional research conducted in the Hodaka Fujii Laboratory, please also see our interview with Dr. Fujii...immunoprecipitation identifies miR483 as an epigenetic modulator of IGF2 imprinting in tumors." Oncotarget 8.21...

  11. Simplify Cloning with in vivo Assembly

    Type
    Blog Post
    Published
    Oct. 18, 2018, 12:37 p.m.
    ...  Javier García-Nafría is an investigator scientist at the MRC Laboratory of Molecular Biology. He is ... Watson and Javier García-Nafría from the MRC Laboratory of Molecular Biology. Plasmid cloning is an essential...with successful recombination reported in all laboratory E. coli strains tested so far. The use of this...low cost and can be immediately adopted by any laboratory. All procedures are performed using the same...the homologous region (calculated using Oligo Calculator). Insertions - To insert short sequences of ... Watson and Javier García-Nafría from the MRC Laboratory of Molecular Biology. Jake Watson is a postdoctoral...postdoctoral researcher in neurophysiology at the MRC Laboratory of Molecular Biology. He is currently investigating...

  12. 6 Tips for Analyzing and Troubleshooting Sanger Sequencing Results

    Type
    Blog Post
    Published
    June 26, 2014, 2:23 p.m.
    ...to always look closely at the trace file (or chromatogram) of the sequencing results you get back from...facility. When it comes to DNA sequencing the chromatogram is your visual control. And, like all controls...controls, missing out is a big mistake. Chromatograms come to the rescue for analyzing and troubleshooting...But look closer, the overlapping peaks in the chromatogram suggest the results are not as certain as the... of the following programs to view your .ab1 chromatogram file 4Peaks (Mac) SnapGene Viewer (Mac/PC) ...peak, don’t be shy. Feel free to edit it. Most chromatogram viewing programs (even the free ones) allow ...allowing us to share it with our readers! The chromatograms in this article were created with SnapGene. ...

  13. Hot Plasmids - August 2020

    Type
    Blog Post
    Published
    Aug. 18, 2020, 1:15 p.m.
    ...mDlx-GFP, hDlx-FLEX-GFP, hDlx-Flex-dTomato, mDlx-GCaMP6f, hDlx-GiDREADD-dTomato and mDlx-ChR2-mCherry. Find... a cell. The Goedhart lab, Gadella lab, and collaborators have an ongoing effort to improve genetically...by one-step immobilized metal ion adsorption chromatography (IMAC) using Ni-NTA magnetic beads. Workflow...multiplexed gRNAs and of dCas9 fusions. The dCas-KRAB activator and the dCas-VPR repressor are introduced into...an EGFP reporter. Expression of the dCas9-KRAB activator or dCas9-VPR repressor in hPSCs is also driven...expression. This includes a CRISPRi-based synthetic oscillator, bistable network, stripe pattern-forming incoherent...calcium sensors (jYCaMP1), variants of the calcium indicator jGCaMP7, that are optimized for excitation wavelengths...

  14. Plasmids 101: The Promoter Region – Let's Go!

    Type
    Blog Post
    Published
    April 3, 2014, 8:05 p.m.
    ...controlled by still other regulatory factors: enhancers, boundary elements, insulators, and silencers; however...tetracycline operators. Transcription can be turned on or off depending on what tet transactivator is used....the promoter (RNA polymerase binding site) and operators (response elements). Promoters are about 100 to...expression Promoter from T7 bacteriophage plus lac operators Negligible basal expression when not induced. ...RNA polymerase, which is also controlled by lac operator. Can be induced by IPTG. Commonly found in pET...pET vectors. Very tightly regulated by the lac operators. Good for modulating gene expression through varied...

  15. Tetbow: Bright Multicolor Labeling for Neuronal Tracing

    Type
    Blog Post
    Published
    Jan. 24, 2019, 2:24 p.m.
    ... introduced, stochasticity will result in a combinatorial expression of these three genes with different...inherently low. This is because the stochastic and combinatorial expression of fluorescent proteins is only possible...original method, we used the Tetracycline trans-activator system to boost the expression levels, and we ...we named the system Tetbow (Tetracycline trans-activator Brainbow) (Sakaguchi et al., 2018) (Figure 1)....sensory systems focusing on the functional and anatomical maturation of the olfactory system.      Takeshi...University. His lab has been studying functional and anatomical aspects of sensory circuit development using ...Livet, Jean, et al. "Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous...

  16. Cultivating Community Science at BosLab

    Type
    Blog Post
    Published
    Nov. 2, 2017, 1:35 p.m.
    ...fully-equipped laboratory for citizen scientists. In addition to maintaining a laboratory to support both... of independent Do-it-Yourself (DIY) biology laboratories working towards enabling everyone to participate... set on top of filing cabinets, a rickety old incubator, a few pipettes, and some home-made equipment....Anyone can become a member of BosLab and previous laboratory experience is not required. Our members are skilled...have non-traditional scientists working in our laboratory! Don’t worry though, we make sure that everyone...a co-organizer at BosLab, a community biotech laboratory in Somerville MA. Follow her on twitter at @ZebraElement...

  17. Mycoplasma Contamination: Where Does It Come From and How to Prevent It

    Type
    Blog Post
    Published
    Oct. 8, 2020, 1:15 p.m.
    ...include the laboratory personnel, the serum, the cell culture media, water baths, incubators, etc. Contamination... in a single incubator since it increases the risk of cross-contamination. CO2 incubators should be cleaned...Contamination! Tissue culture media often have indicators included in the media that turns yellow from ...proliferating shortly. Once they are present in the laboratory environment, they are difficult to eradicate....tighten the flask cap before placing them in the incubators. This will also solve the problem of contamination...airflow and the lab facility periodically. The CO2 incubators, used for maintaining cell lines, must not be...

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

    Type
    Blog Post
    Published
    March 3, 2020, 2:15 p.m.
    ...voltage indicator Article contributed by Shreya Vedantam Genetically encoded voltage indicators (GEVIs)...fluorescent optics. Existing red fluorescent voltage indicators, however, fall short compared to GFP-based sensors... sensors and blue-light-activated optogenetic actuators.  To overcome this overlap, Yiyang Gong’s lab ...linker between them. The Ace-mScarlet voltage indicator works like many FRET-opsin GEVIs. With an increase...channelrhodopsins. Find the Ace-mScarlet voltage indicator plasmids at Addgene! Beck et al., Sci Report 2019...cyanobacteria. This kit contains 96 parts including terminators and promoters, CRISPRi parts, selectable markers...

  19. Announcing the Winners of the 2021 Michael Davidson and Roger Tsien Commemorative Conference Awards

    Type
    Blog Post
    Published
    Aug. 5, 2021, 12:15 p.m.
    ...tag neurons activated by opioid withdrawal with tdTomato and assessed cFos expression. She will explore...periaqueductal gray (PAG), with red neurons expressing tdTomato and green neurons expressing cFos. Image from ...painful stimuli are processed by a network of excitatory and inhibitory neurons whose function and connectivity...where she engineers genetically encoded voltage indicators. Tian developed a video-based high-throughput...archaerhodopsin‑derived genetically encoded voltage indicator which had improved performance in live mouse brains... Currently, she is using the improved voltage indicator coming from the screen to understand mouse cortical...Tian. Figure 5: Citrine-tagged voltage indicator expressed in mouse cortex. Image from He Tian....

  20. Cancer and the Immune System: Deciphering the Relationship

    Type
    Blog Post
    Published
    March 14, 2017, 2:30 p.m.
    ...and helper T (Th) cells. These cells produce inflammatory cytokines - interleukin (IL)-12 and interferon... eliminate early stage cancer cells, chronic inflammatory responses can augment tumor growth. Indeed, ... to precede cancer development, for example, inflammatory bowel disease is associated with the onset of... 1 (CSF-1). Additionally, tumor cells recruit regulatory T cells (T-regs) into their microenvironment ...TGFβ is also known to change CD4+ Th cells into regulatory cells to suppress function. Creating Tolerance...cell-surface proteome to inhibit expression of co-stimulatory molecules needed for T cell effector function...identities based on their level of progression, anatomical location, characteristic (solid localized tumors...

  21. Viral Vectors 101: Calcium Sensors

    Type
    Blog Post
    Published
    Aug. 10, 2023, 1 p.m.
    ...crosslinking agent, a signaling ion, and an allosteric modulator. Because of its importance, scientists have developed... a calcium sensor Genetically encoded calcium indicators (GECIs) are fluorescent proteins linked to calcium...in living cells and organisms. Unlike chemical indicators, these DNA constructs can be delivered to intact...:509-18. Inoue M. Genetically encoded calcium indicators to probe complex brain circuit dynamics in vivo...Kanemaru K, Iino M. Genetically encoded fluorescent indicators for organellar calcium imaging. Biophysical journal...neuronal activity with genetically encoded calcium indicators. Cold Spring Harbor Protocols. 2012 Jun 1;2012...signaling using genetically targetable fluorescent indicators. Nature protocols. 2006 Aug;1(3):1057-65. Resources...

  22. 3D Printing Meets CRISPR Cas9

    Type
    Blog Post
    Published
    Oct. 17, 2017, 12:55 p.m.
    ...development programs for bioscience educators. Using these hands-on tools, educators introduce their students to...a backbone structure of a protein, based on its atomic coordinates. These wire models were useful in that...necessary to download a pdb file of the structure’s atomic coordinates, and “open” these structures with molecular...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...

  23. Tips to Make the Most of a Scientific Conference

    Type
    Blog Post
    Published
    May 23, 2019, 12:26 p.m.
    ...following: the elevator pitch, talks, the poster session, networking, and social media. The elevator pitch Before... Before the conference Practice your “elevator pitch,” the 30 - 60 second blurb you will use to introduce...work you are familiar with. You can tweak your elevator pitch slightly if you know a bit more about the...or talk. After the conference After using your elevator pitch several times at the conference, you might...might notice some trends. Were there parts of your elevator pitch where the other person seemed confused, ...questions. If you or your lab identifies a potential collaborator from the meeting, reach out to them, pointing...

  24. CRISPR Protocol for Genomic Deletions in Mammalian Cell Lines [Video]

    Type
    Blog Post
    Published
    Feb. 18, 2015, 3:09 p.m.
    ...The first is the study of non-coding regulatory elements. Regulatory DNA function is typically inferred ...bloggers! Daniel Bauer is a pediatric hematologist and principal investigator at Boston Children’s Hospital and...interested in exploring the function of non-coding regulatory elements in their native chromatin context. An...PhD student at Harvard Medical School in the laboratories of Stuart Orkin and Daniel Bauer. He received...

  25. Technologies Enabled by NanoLuc® Luciferase

    Type
    Blog Post
    Published
    Feb. 8, 2018, 12:17 p.m.
    ...employing optogenetic regulators to initiate the event being monitored. Optogenetic regulators respond to specific...initiation wavelengths, excitation of the optogenetic regulator leads to spurious activation of the FRET sensor...interested in using photoactivatable, optogenetic accuators to depolarize or hyperpolarize membranes. Traditional...wavelengths needed would also activate the optogenetic accuators. The researchers took a FRET reporter and adapted...biosensors that can even be paired with optogenetic regulators. Many of these tools are available from Addgene...2017) Genetically encoded bioluminescent voltage indicator for multi-purpose use in wide range of bioimaging...

  26. The Crispr Babies Saga Shows the Need for Action, Not More Delays

    Type
    Blog Post
    Published
    Dec. 20, 2018, 1:15 p.m.
    ...upon a moratorium until another meeting, three branches – a private funder, government regulators, and ...there was a generally agreed-upon international moratorium on utilizing CRISPR/Cas9 in humans. This topic...mtDNA transfer options being investigated; A UK regulatory body tasked two separate non-governmental groups...technology to research centers engaged in long-term, mandatory follow-ups and observational studies of the technique...stop punting decisions on scientific, ethical, regulatory, and general public consensus to the next meeting...

  27. Hot Plasmids - December 2019 - CRISPR pooled library, LipoGlo, CRISPRa, and Voltage Imaging Tools

    Type
    Blog Post
    Published
    Dec. 10, 2019, 1:58 p.m.
    ...lipoproteins, shuttles lipoproteins through the circulatory systems, but can also lead to the formation of...as both a powerful tool for generating complex regulatory systems and further the study of natural σ54-... PMID: 31451697. Genetically encoded voltage indicators for use in worms Article contributed by Brook...Brook Pyhtila Genetically encoded voltage indicators (GEVIs) change fluorescence in real time when neurons... excitation light intensities have made these indicators difficult to work with.  The Gottschalk lab has...microbial rhodopsin GEVIs in excitable cells of the nematode Caenorhabditis elegans. They have found several...

  28. Plasmids 101: Modular Cloning Applications and Kits

    Type
    Blog Post
    Published
    May 14, 2024, 1:15 p.m.
    ...site-specific recombinases, regulatory elements, developmental regulators, and lots of viral components...test many different combinations of promoters, terminators, solubility and purification tags, connectors... examine the effects of different promoters, terminators, enhancers, and cross-cassette interactions in...Standard and New E. Coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology... Signaling in CAR T Cells. Cold Spring Harbor Laboratory, 17 Feb. 2024. Crossref, https://doi.org/10.1101...Emerging CRISPR Technologies. Cold Spring Harbor Laboratory, 27 Oct. 2023. Crossref, https://doi.org/10.1016...

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

    Type
    Blog Post
    Published
    Jan. 31, 2019, 1:32 p.m.
    ...environmental modulation of hepatocellular cancer cell growth." Hepatology 54.4 (2011): 1237-1248. PubMed... 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...seems to attack us by releasing mitogenic growth mediators and improving cancer cells proliferation.  How... Pinho! Bárbara Pinho is currently a science communicator at the Portuguese science museum "Fábrica Centro...

  30. Hot Plasmids - October 2020

    Type
    Blog Post
    Published
    Oct. 13, 2020, 1:15 p.m.
    ...you'll find in this post: Tools for labeling excitatory inhibitory synaptic proteins Fluorescent protein...corner New from the viral service Labeling excitatory and inhibitory synaptic proteins with FingRs ...developed AAV vectors to selectively visualize excitatory and inhibitory synapses in the brain.  ...scaffolding proteins PSD95 and gephyrin to label excitatory and inhibitory synapses, respectively. Once expressed... fluorescent proteins targeting inhibitory or excitatory synapses or that are Cre-inducible, researchers... cycle in vivo, particularly if the cells are migratory or in deep tissues. To resolve this issue, Shangqin...
Showing: 31 - 60 of 511 results