...chromosomes. These long range DNA interactions are often detected with chromosome conformation capture (3C) based... of the drawbacks of 3C methods, but could only detect chromatin interactions at one location in the genome...CAPTURE 2.0, an updated version of CAPTURE that detects chromatin interactions at hundreds of loci at once... The chromatin “picture” is then developed by detecting these chimeric DNA fragments by PCR or next-generation...Cross-links are reversed so that DNA fragments can be detected by PCR or deep sequencing. A drawback of the...of CAPTURE 2.0 CAPTURE 2.0’s increased rate of detecting chromatin interactions opens the door for answering...proof-of-concept experiment to show that CAPTURE 2.0 could detect multiple chromatin interactions at once. Chromatin...

...the detection of RNA, dsDNA, and now ssDNA. By comparing the ability of Cas12 and Cas14 to detect SNPs...adaptive immune systems that provide bacteria protection against infectious agents. Several enzymes behind...fantastic add-on to a diagnostic toolkit, called DETECTR, which has been created by the authors. This kit...kit uses Cas12 and Cas13 to quickly detect the presence of infectious organisms (ex: SARS-CoV-2) and genetic...SNPs using the DETECTR kit, the authors showed that improved specificity of Cas14 enables high-fidelity ...high-fidelity SNP genotyping. The development of  Cas14-DETECTR will soon enable the quick and efficient diagnoses...resources on the Addgene Blog Learn more about DETECTR Browse all of the CRISPR blog posts Download our...

...implications of using these technologies, but also the rapidity of the technologies’ adoption by the scientific...amongst the Nobel prize winners for developing the technology. Though these case studies are “old,” they lead...significantly over the last decade. He describes the detection of gravitational waves--a story I was much less...around the world. The paper describing the waves’ detection had over 1,000 authors. The chapter on deep learning...learning addresses the dilemma of creating a technology that could eventually replace scientists themselves...Addgene’s role in the rapid dissemination of these technologies, proposing that “Addgene, with its easy, fast...CRISPR-Cas plasmids, has been a key driver of the technology.” As an Addgene vet of 12 years, I’m very familiar...

... into plasmid DNA. In high throughput cloning techniques, although the specific sequences of the genetic...proteins and the availability of powerful imaging technologies, the combination of multiple fluorescent protein...-throughput cloning. MXS Chaining is one such technique and has been used to produce complex fluorescent...constructs. These fluorescent reporters can be used to detect structure and protein localization, as well as ...show robust labeling, with strong expression and detection of each fluorophore at the respective subcellular...that the separate modules combined using these techniques are free of specific restriction enzyme recognition...High Throughput Cloning Strategies Method Technology Pros Cons References Golden Gate Type II restriction...

... to) purification, detection, solubilization, localization, or protease protection. Thus far Plasmids ...proteins, which are sometimes used as tags for detection; however, those are just one (admittedly large...overexpress and purify proteins can face any number of technical challenges depending on their protein of interest...one-step purification with glutathione, can also protect against proteolysis. That’s one form of instability...it’s a good one), then your first step towards detecting, immunoprecipitating, or purifying that protein...Stability Good for purification with glutathione; protects against proteolysis, but may reduce solubililty... improves solubility; good for antibody-based detection SUMO ~100 amino acid protein  12 Stability At...

...thanks to these technologies but many questions remain. The use of other technologies such as optogenetics... cellular movements in the immune system. The techniques used here could be adapted to studying other ...labeled cells? 1. Epifluorescence microscopy This technique uses a fluorescence microscope where the light...excitation microscopy is a fluorescence imaging technique that allows imaging of living tissue up to about...from this volume. The consequence is that you can detect signal in thick specimens. See the video below ...monitor cellular movements in real time. This technique was first Introduced to immunology by three papers...papers in the journal Science in 2002. Now, this technique and the in vivo live-cell imaging (intravital ...

...not to say that the technique doesn’t have its limitations or that other technologies need to be discarded...relatively cheap (compared to many other technologies and techniques in the sciences). But how exactly does...the history of neuroscience research we have a technology that allows us to show causality in neural circuits...interest. Despite its power and versatility, the technique is remarkably straightforward to learn and relatively...behavioral optogenetics in order to implement the technique in my lab at The Rockefeller University. In this...exactly do you want to use optogenetics for? The technique is non-trivial; you don’t want to spend months...stereotaxic surgery is a neuroscience research technique often used beyond just optogenetics. Successful...

...University of Science and Technology in Shijiazhuang, defended the technology in a news article in Nature..., NgAgo. As you might expect with any nascent technology, researchers are having trouble getting NgAgo...early successes, and to find out what delivery techniques researchers are using. The detailed results of...Mary Gearing and discusses a newer, CRISPR-based technique to generate C->T or G->A transitions in a target...target sequence in live cells. This technique uses catalytically inactive CRISPR endonuclease (dCas9) fused...in this informative post. Interestingly, this technology may make some uses of Site Directed Mutagenesis...Software for Biology Adapting Toehold Switches to Detect Zika Virus As always, if you have any questions...

...avidin-biotin technology to improve cell adhesion on nanofibrous matrices.” Journal of Nanobiotechnology 13.1 ...in molecular biology for an array of different techniques and protocols. In this post we will discuss the...interaction with avidin for molecular biology and biotechnology purposes.  Once a polypeptide is biotinylated...reporter is then added to the reaction for easy detection. The multiple biotin binding sites found on avidin...amplification during these experiments. During detection, a biotinylated reporter enzyme that is pre-incubated...amplification of the reporter signal and easier detection. This strategy is referred to as the Avidin-Biotin...Zhu, Y. “A non-radioactive method for small RNA detection by northern blotting.” Rice 7.1 (2014): 1–7. PubMed...

...in the malaria community for the better (Nat. Biotechnol., 2014). Given the timing, it shouldn’t be a ...causes malaria). I attribute their success to technical expertise, thoughtful single guide RNA (sgRNA)...yet. As a genome editing tool, the CRISPR/Cas9 technology has been surrounded by a whirlwind of research...but generally rely on less powerful algorithms to detect off-targets. The few offline tools available mostly... sgRNAcas9. Top tools for transferring CRISPR technology to a new organism: For obvious reasons you can...developed with the purpose of applying CRISPR technologies to new organisms and will help you whether you...Report your findings to help everyone else. CRISPR technology has reached into so many different communities...

...schedule times to write.  Pomodoro technique timer  One time management technique that you can use as part of...of your writing schedule is the Pomodoro technique, which is when you spend 25 minutes focusing on a task... tomato or “Pomodoro” kitchen timer that the technique’s developer used as a university student.   ...Hemingway Editor  This is a free web-based tool for detecting the readability of your writing. It makes suggestions...suggestions Hemmngway makes (it wasn’t designed for technical writing), it’s great at flagging passive voice...jargon, this tool can help you avoid overusing technical terms when writing for a general audience. The...Simple tricks for time management: the pomodoro technique": This podcast talks more about using the Pomodoro...

...science and biotech due to its fermentation abilities and other useful traits. The “biotech yeast” You...You’re probably wondering if the “biotech yeast” is S. pombe or S. cerevisiae. Actually, it’s neither. .... The most commonly used yeast by biotech and pharmaceutical companies is K. phaffii (formerly known as... and advancements in other biomass production techniques in the following decades, Phillips made the decision...they abandoned the system. Since then, multiple biotech and pharmaceutical companies (along with some research...recombinant proteins by the pharmaceutical and biotech industries as a protein expression workhorse. This...Riley, R., et al., Comparative genomics of biotechnologically important yeasts. Proc. Natl. Acad. Sci.,...

...translation, but a visual technique to study translation remained elusive. Two techniques developed by Addgene...mRNAs are digested with ribonucleases, ribosomes protect the segments of mRNA to which they are bound. These...translational frequency. Although highly useful, this technique requires extensive sample processing to avoid ...-mRNA complexes. Recent work has adapted this technique to monitor local translation and determine if ... single RFP-labeled osk and Oskar protein were detected at the posterior pole. Oskar protein levels were...compartment. Despite these limitations, these techniques represent powerful tools for studying translation...Protein Plasmids Check Out Other Hot Plasmid Technologies ...

...particularly interested in DNA sequencing tech, and the intersection of technology, software, and science. She loves... software product manager at Oxford Nanopore Technologies. If the first thing you hear when someone says...undergraduate research straight to a lab career at a biotech company, I always assumed I’d work one or two years.... Now, in my current role at Oxford Nanopore Technologies, I work with our customers in the US to learn...m always catching up in the morning! 9:00 AM--Technical implementation review. The developers discuss ...Field-based Product Manager at Oxford Nanopore Technologies for the North America region. She is particularly... for the customer and help build software and technology tools with the customer in mind. You can follow...

...to look towards genetic code expansion (GCE): techniques in which non-canonical amino acids (ncAAs, also...allow a protein to be more effectively used in a technology or as a therapeutic.  A (very) brief history ...seminal paper from Peter Schultz’s lab describing a technique that allowed for intentional incorporation of ...expansion occurred, with hundreds of new ncAAs and techniques being developed. In the mid-aughts, the first... mostly accessible to experts. That many GCE technologies have idiosyncrasies presents a significant barrier...wishing to use it as a tool. In short, while the technical skills needed to perform GCE are essentially those...Optimization Why is GCE so complicated? Well, while the techniques are straightforward, the systems – the cells ...

...transition While a PhD equips you with exceptional technical skills, transitioning into management often means...stepping into unfamiliar territory. Unlike solving technical problems in the lab, management involves a different...time, I discovered that I not only enjoyed the technical aspects of my work but also found fulfilment in...believe management is the next logical step after technical mastery. However, being a great scientist doesn...your team's—can lead to frustration. Clinging to technical tasksDelegation can feel unnatural for those accustomed...careers evolve, many professionals move between technical and managerial roles, and I've witnessed several...management and choose to focus on it, moving away from technical work. On the other hand, it’s perfectly valid ...

...you want to read more content related to CRISPR technology, subscribe to our CRISPR blog content.   In this... dCas12f to VP64. Read the paper in Nature Biotechnology Find the Cas12f-GE plasmids Programmed genome...of target genes and cell types. Their Nature Biotechnology paper showcases an improved design of the guide...RNA motif. These engineered pegRNAs (epegRNAs) protect the RNA from degradation by cellular exonucleases...editing efficiency. Read the paper in Nature Biotechnology Find the epegRNA plasmids Enhanced prime editing...editing efficiency. The lab also optimized the architecture and amino acid sequence of the prime editor,... paired pegRNAs.  Read the paper in Nature Biotechnology Find the PRIME-del plasmids  Deletion and replacement...

...Gibson Assembly Cloning and Gateway® cloning technologies, as well as several others. Each method is unique...biologists have harnessed it to evolve cloning technology. CcdB: A potent toxin... The ccdB gene, located...operon, codes for the antitoxin protein (CcdA) that protects the cell against the toxic CcdB. Cells that lose...thoroughly screen colonies for the insert. Gateway® technology (developed by InvitrogenTM) is essentially a ...check out Addgene’s Choosing a Molecular Cloning Technique page and the Addgene Blog for a variety of useful...Positive Selection of Recombinant DNA by CcdB.” Biotechniques. 1996 Aug;21(2):320-3. PubMed PMID: 8862819....Resources on Addgene.org Choose a Molecular Cloning Technique Find Plasmid Cloning Protocols Check Out All of...

... CRISPR-based cytosine base editing. Nature Biotechnology, 41(5), 663–672. https://doi.org/10.1038/s41587...activity and therapeutic application. Nature Biotechnology, 38(7), 892–900. https://doi.org/10.1038/s41587...concurrent adenine and cytosine editing. Nature Biotechnology, 38(7), 861–864. https://doi.org/10.1038/s41587...engineered Cas9-cytidine deaminase fusions. Nature Biotechnology, 35(4), 371–376. https://doi.org/10.1038/nbt...optimization and ancestral reconstruction. Nature Biotechnology, 36(9), 843–846. https://doi.org/10.1038/nbt...editors generated from TadA variants. Nature Biotechnology, 41(5), 686–697. https://doi.org/10.1038/s41587...editor with low off-target activity. Nature Biotechnology, 41(5), 673–685. https://doi.org/10.1038/s41587...

...Harshana S De Silva Feelixge. Gene therapy technologies hold great promise for improving or potentially...Rapid advances in next generation sequencing technologies have allowed scientists to quickly identify ...retroviral vectors. However, many diseases require techniques that can deliver gene therapies directly to the...Adeno-associated virus (AAV) – based delivery techniques may hold the key. In the simplest form, translating...been challenging. A variety of vector delivery technologies have been investigated including lentiviruses... delivery tools such as nanoparticles. These technologies can have serious adverse effects, and their ...discovered frequently and recent advances in AAV technology have enabled us to generate new and refined forms...

...develop this idea, Drs. Koeris and Lu founded the biotech startup company, Novophage. As you'll hear Dr. ...therapeutics to developing phage-based tools for detecting pathogens in food products. Along the way, the... Koeris' decided to develop phage for use in a biotech startup 12:16 - 15:15 : Why Sample 6 began to develop...Sample 6 16:27 - 18:02 : Benefits of the Sample 6 technology and how It works 18:02 - 19:56 : Why Sample 6... could succeed in the market or to focus on a technology that one is passionate about developing? 38:00... Advisory Board and how he hopes to help young biotech entrepreneurs.   We'd like to thank Dr. Koeris...Sample 6 website Check out Dr. Koeris' Website, biotechstart.org Read Sample 6's Paper on Bacteriophage-based...

... covers a brief review of different basic BE technologies and their adaptation for plant genome editing...presence of nucleosome or other proteins. You can detect base editing as early as 48-72 hours post-transformation...site, RE analysis of PCR product could be used to detect success. Although there is a slim chance of generating...State University Kutubuddin Molla is an Ag-biotechnologist in the National Rice Research Institute, Cuttack...CRISPR-Cas9 cytidine deaminase fusion." Nature biotechnology 35.5 (2017): 441. PubMed PMID: 28346401. 6. ...with a Cas9-cytidine deaminase fusion." Nature biotechnology 35.5 (2017): 438. PubMed PMID: 28244994. 7. ...fusion of nCas9 and human APOBEC3A." Nature biotechnology (2018). PubMed PMID: 30272679. 8. Hua, Kai, ...

...the steps and technical considerations are directly applicable to the rat [6]. Technical differences include..., regardless of the type of behavior, certain technical considerations still apply. Testing stimulation...is wrong or 2) there is some problem with the technical implementation of your optogenetics setup (viral...difficult as it seems. Like every other advanced technique in neuroscience it has a bit of a steep learning...neuroscience sub-discipline that has published using the technique and ask if they would be willing to teach you....performed in this species. However, transgenic rat technology is improving and may one day reach the sophistication... et al. "Recombinase-driver rat lines: tools, techniques, and optogenetic application to dopamine-mediated...

... that brings to light the cellular world. The technique allows you to ask questions like: “Where does ...within a cell,” “Does this disease change the architecture of my cells,” or “How does this mutation impact...whole organism. But, as with any antibody-based technique, validation and proper experimental design are... a future blog post to learn more about these techniques!  Direct vs. indirect immunofluorescence There...approach than direct IF, so we will focus on this technique here. One of the reasons that indirect IF is more...Figure 2. For a deeper dive into the steps and techniques, see Im, et al. 2019.  Fixation Good fixation...has shed some light on immunofluorescence. The technique can provide you not only answers to your most ...

... system will you use to detect your fluorescent protein? The type of detection method depends on what ...Experiment  Detection Method Notes Quantification of a process Plate-based assays (plate reader) Detect the... are biological tools that monitor a process or detect a given molecule. The sensor component is usually...conformational change in response to the molecule it detects. This change then generates a reporter signal. ...have summarized some of the common fluorescent detection methods and the types of experiments they are ...

... of this approach is SnapGene’s algorithm for detecting common features. This algorithm enables one of...identified common variants, and then crafted a detection algorithm that tolerates occasional mismatches...to require at least 96% sequence identity when detecting a reference feature. For a coding sequence feature...feature that may be used to make fusion genes, detection needs to occur even if one or two codons are missing...versions of common coding sequence features, so our detection system was enhanced to allow searches for a perfect...sequenced strains through our mismatch tolerant detection algorithm and thereby speed up the annotation ... see an opportunity to harness common feature detection in a new way, please contact us at snapgene.com...

... that works for your application, specifically detects your protein, is species compatible, and doesn’...review the most common tags, the antibodies used to detect them, and how they can fix your antibody woes.   ...antibodies for the purpose of purification or detection of the tagged protein. These peptides consist ...an antibody. Tags can enable the separation of detection of a mutant protein vs. endogenous WT levels of... blog, though, we are focusing on tagging for detection purposes (stay tuned for our affinity purification... be more!) to a protein’s termini to increase detection. The tag can also be removed by treating the protein...fundamentals to commercial systems. Appl Microbiol Biotechnol. (2003) 60:523-533 DOI: 10.1007/s00253-002-1158...

...replicates such as multiple mice in each group and C, technical replicates or repeated measurements will increase... in biological experiments. Replicates can be technical or biological and are included to improve the ...therefore the statistical power of an experiment. Technical replicates are repeated measurements of the same...nonspecifically through the Fc, allowing you to detect this undesirable interaction. When non-specific...with the preadsorbed antibody. If a signal is detectable, it is likely due to binding interactions outside...the signal measured. If a nonspecific signal is detected, the level of noise will determine whether it ...flow cytometry. A viability control allows you to detect dead or dying cells so that you can base your analysis...

...wasn’t that easy. In the 1980s, gene targeting technology was invented to introduce specific changes into...into the mouse genome. With these early technologies, a researcher would first introduce a mutation into...transgenic offspring. Although powerful, this technology is cumbersome to use, not that efficient, often...first exposure to CRISPR when he used this new technology to engineer mouse models (Wang et al., 2013, ...others around the world. Yes, finally, we have a technology, CRISPR, that is simple in concept, straightforward...electroporated into the oviduct of pregnant females, a technique called Genome editing via Oviductal Nucleic Acids... germline transmission of the transgene, this technique is still in need of improvement. Also when working...

...molecular biology labs. Recent and rapid advances in technologies that permit large-scale creation and synthesis...overcome crucial challenges in NGS by developing technologies that can help unlock the potential of modern...develop and apply our plexWell™ Library Preparation Technology for NGS-based sequencing and confirmation of ...plexWell™ in more detail, and how we are using this technique in our partnership with Addgene to sequence large...large numbers of plasmids. plexWell™ technology overview For any NGS experiment, the DNA sample being...samples. As mentioned above, one of the primary technical benefits of plexWell™ is that normalized libraries... and CEO of seqWell, Inc. He is a sequencing technologist and computational biologist with a passion for...