...photobiology: why use light? In synthetic biology and bioengineering, scientists seek to directly probe and build...problems; inexpensive tools such as LEDs can be engineered to deliver precise, consistent, and controllable.... Complicated patterns of light intensity and wavelength can be used to study dynamic processes. Conversely...Conversely, varied input patterns may also be used to engineer new pathways with sophisticated gene expression... of edge detection. Tabor et al. subsequently engineered a second photosensitive TCS activated by green...-friendly. They experimented with the promoter strength of various components, removing inducible promoters...could be made suitable for various scientific or engineering applications.   References Refactoring and optimization...

... in a variety of cells and organisms. However, lengthy genetic payloads and insufficient transcription...assembled tRNA-gRNAs is placed downstream of a lengthy promoter, which is used to drive the expression...efficient MBE with such a strategy, the need for lengthy promoters, such as U6 or EF1α promoters, has limited...derived from human or plant source), by tuning the length of 5’ leader sequences of a given tRNA to achieve...either from human or plant sources) in both the strength as a promoter and the activity to release gRNAs...results of their MBE efforts, the Gao Lab also engineered a DAP array for prime editing, achieving up to...also enable more convenient multiplex genome engineering of crops or allow for sophisticated CRISPR screenings...

...Cas9 and Cas12a, creates challenges for in vivo delivery and cell engineering applications. CasMINI, a...gene perturbation The Penn State Protein Ladder Engineered miniature CRISPR-Cas system for mammalian genome...flexible, modular tool for labeling. Here, Liu et al. engineer a chimeric single chain variable fragment (scFv...gels and can be detected on Western blots via engineered immunoglobulin binding domains.  Santilli, R.T.... https://doi.org/10.1038/s41598-021-96051-x Engineered miniature CRISPR-Cas system for mammalian genome... Figure 4: Overview of CasMINI for genome engineering applications. Image from Xiaoshu, et. al. 2021...system opens up new possibilities in both cell engineering and gene therapy.  Xiaoshu X, et al. Molecular...

...technology since its initial applications for genome engineering in 2012.  Many of these advances have stemmed... of dCas9; and 2) CRY2FL-VP64, a fusion of full-length CRY2 and the transcriptional activator domain VP64...PAM and had similar targeting specificity as full-length Cas9 (flCas9). When triggered by blue light (470nm...light-dependent (Yu et al., 2020). To express the N-Cas9, Haifeng Ye’s lab used the bacterial phytochrome BphS which...employed a photoactive strategy which had been engineered from naturally occurring photoactive proteins... specific site on the Cas9, the group used an engineered pyrrolysyl tRNA/tRNA synthetase pair which would... Grimm D, Correia BE, Eils R, Niopek D (2018) Engineered anti-CRISPR proteins for optogenetic control ...

...has developed a miniature Cas system (CasMINI) engineered from the uncultivated archaea Cas12f (Un1Cas12f1... system. The CasMINI system was developed by engineering the Cas12f scaffold gRNA and making strategic...CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs Yong-Sam Kim’s lab also created a ...the gRNA scaffold through five rounds of gRNA engineering.  They did not modify the Cas12f1 enzyme. The...facilitate its packaging into virus-like particles. Feng Zhang’s lab adapted the native PEG10 RNA sequences...plasmid tools to optimize prime editing systems. Engineered pegRNAs improve prime editing efficiency In the...the 3’ end with a structured RNA motif. These engineered pegRNAs (epegRNAs) protect the RNA from degradation...

...while writing each section. Research challenge The Research Challenge motivates the request for application...creates strong, well-directed meaning and delivers strength to the sentence. Below are the typical sections...how you, the expert, will address the research challenge. Now is the time to make bold statements. While...solution is the best approach to the research challenge. Demonstrating expertise in the field and past...how your innovation will address a variety of challenges and impact the field - its encouraged to dream...time budget writer, you may find this section challenging because it’s hard to determine the exact value... differs from publication writing and may be challenging to master at first. Additionally, reach out to...

...structure-guided engineering of the PAM-interacting domain of Cas9. After multiple rounds of engineering, they developed...the "perfect" guide sequence for your genome engineering experiment. With CRISPR entering the clinic for... Nureki lab generated SpCas9-NG, a rationally engineered Cas9 with NG PAM compatibility, as the name implies...R.A. et al. PAM-flexible genome editing with an engineered chimeric Cas9. Nat Commun 14, 6175 (2023). DOI...Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 368,290-296(2020...Plasmids available here)   Nishimasu, H., et al.,Engineered CRISPR-Cas9 nuclease with expanded targeting ...Requirement and Expanding Beyond Cas9 xCas9: Engineering a CRISPR Variant with PAM Flexibility History...

...proteins or TALE proteins, proteins had to be re-engineered for each gene, making wide-scale gene activation...gene activation: rather than requiring protein engineering for each loci, CRISPR/Cas systems only require...methods rely on fusion proteins while others re-engineer components of Cas systems themselves. SunTag, ...Mediator (SAM) Description SAM uses specially engineered sgRNAs to increase transcription. This is done... through creating a dCas9/VP64 fusion protein engineered with aptamers that bind to MS2 proteins. These...activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Research 41:...Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517:583–588 . https...

... Kucera, M.Sc. and Eric Cantor, Ph.D. from New England Biolabs. Golden gate assembly limitations Embraced... assemblies that enable biosynthetic pathway engineering and optimization. However, current best practices... reduced these limitations through the use of engineered Type IIS restriction enzymes and careful choice...redesign was guided by both advances in the re-engineering of the original BsaI-HF® Type IIS restriction...In conjunction with BsaI-HFv2 (NEB #R3733), re-engineered to provide improved Golden Gate performance, ... Kucera, M.Sc. and Eric Cantor, Ph.D. from New England Biolabs. Becky Kucera is a Principal Development...Development focusing on DNA cloning and assembly, New England Biolabs, Inc.         Eric Cantor is a molecular...

...recombinant protein purification and metabolic engineering. If instead you want to build genetic circuits...biology MoClo applications, but there are more! Engineering disease resistance through gene stacking, increasing...localization signals, plant markers, and reporters (Engler et al., 2014). This kit is a great starter for ...vectors, several delivery systems which can be engineered into the TUs, and even viral gene silencing vectors...kit has a focus on transformation and genome engineering. This is a specialized system with parts including...confined to that arena! The Mammalian Toolkit was engineered specifically for the types of expression and ...Multiplex MoClo Toolkit for Extensive and Flexible Engineering of Saccharomyces Cerevisiae.” ACS Synthetic Biology...

...excitation wavelength (Salomonnson et al. 2012). They can also be excited efficiently at wavelengths between...development of cell sorters together with the engineering of fluorescently labelled antibodies made it ... lymph nodes at different times after antigen challenge, scientists were able to track where GFP labelled...et al. 2016, Cavanagh et al. 2008)? Technical challenges of two photon microscopy Intravital imaging is... at steady state or under physio-pathological challenge. However technical specificities have to be taken... also important to finely tune the excitation wavelength as it has been shown that even a small incremental...incremental change of the excitation wavelength can significantly affect emission intensities from fluorescent...

...Ellis does research in synthetic biology and bioengineering including a recent effort to construct a synthetic... SynBio. Chapter 3: Synthetic biology as the engineering of biology at the level of DNA using modular,...in the Ellis lab including yeast and E. coli engineering, microbial cooperation, and antibiotic production...lectures synthetic biology for the Department of Bioengineering. He graduated from Oxford University and then...supervision of Prof Jim Collins and specialising in engineering gene regulation in yeast. Dr. Ellis is now one...undergraduate projects. Special thanks to our sound engineer/producer, Eddy Page! Edward B. Page is a Digital...Production Specialist at Addgene. He is the audio engineer and producer for the Addgene Podcast.      Additional...

...University, Jieze Zhang, an intern in the Yang Lab, and Sheng Yang, a professor in synthetic biology from the ...pEcCas/pEcgRNA system. This system works well for engineering single genome edits but the double strand breaks...interrupt genes (or gene clusters) in metabolic engineering. So far, we’ve used the MUCICAT system in two...compared to the industrial strain. In our metabolic engineering case study of N-acetylglucosamine biosynthesis... systems to choose from. Ready for metabolic engineering with improved cargo dedicated to gene (cluster... optimizing strains with low efficiency.       Sheng Yang obtained his Ph.D. from Shanghai Institute ... phenotypes and to design a new generation of engineered cells for green chemistry and biomedical applications...

... problem when the excitation wavelength is shifted to longer wavelengths. Therefore, the use of bright...binds a synthetic, fluorescent analogue have been engineered (Thorn, 2017). These fluorescent analogues are...28 kDa protein that resembles a cylinder with a length of 4.2 nm and a diameter of about 2.4 nm (Hink ...above. The smallest tags are peptides that are engineered to bind specifically and with high affinity to...., 2017) may improve detection. Since longer wavelengths have better tissue penetration, (infra)red fluorescent...usually dim relative to fluorescent probes, recent engineering efforts have increased the brightness of these...fluorescent proteins, biosensors, and optogenetic tools engineered from phytochromes." Chemical reviews 117.9 (2017...

...repair and genome engineering CRISPR-Cas9 has revolutionized the genome engineering world and made targeted...immediately applicable in DSB-induced genome engineering, it has biological importance for the repair ...CRISPR forum moderated by the Zhang lab CRISPR Challenges: Standardization and HDR CrispyCrunch Optimizing... (2018). Pubmed. CRISPR References: Genome engineering using the CRISPR-Cas9 system. Ran FA, et al. ...546; (2015). PubMed. Optimization of Genome Engineering Approaches with the CRISPR/Cas9 System. Li, K...PubMed. Making designer mutants in model organisms. Peng, Y. et al. Development 141; (2014). PubMed. Enhancing..., et al. Poster at Keystone Precision Genome Engineering. 2017.  Easi-CRISPR: a robust method for one-...

...summarizes Zalatan JG, et al.'s recent paper, "Engineering Complex Synthetic Transcriptional Programs with...However, these approaches are often met with the challenges of regulatory bottlenecks and their scope is ... ‘biofactories’, most successes in metabolic engineering have been limited to the overexpression of various...host-independent, beyond the oft published metabolic engineering realm of S. cerevisiae and E. coli. The utility...scRNA design is readily apparent in metabolic engineering. The authors elegantly demonstrated the potential...By no means limited to the field of metabolic engineering, this is such a powerful and flexible technique... 1173-1183. (2013). PubMed. Zalatan, J. G. Engineering Complex Synthetic Transcriptional Programs with...

...or intentional release of engineered organisms. “Is [the organism] engineered? Where did it come from? ...reached out to MIT labs in the Synthetic Biology Engineering Research Consortium. That is how Aditya Kunjapur...organism in the lab. Predicting lab-of-origin of engineered DNA This isn’t the only time researchers have...plasmid datasets) to predict the lab-of-origin of engineered DNA. Both of these groups have generated robust...complementary tools in a time where biological engineering and synthetic biology is expanding rapidly.  ...Deep learning to predict the lab-of-origin of engineered DNA." Nature communications 9.1 (2018): 3135....

...theoretically, at least) fully and freely engage or disengage at will.  Informal education is education...typically ad hoc, for learners who can choose to engage or disengage with a very high level of independence, such...than average and are more likely to spend time engaging with science communication efforts.  Scientific...however, many others partner with formal learning to engage students at all levels.      Jargon is field-specific...space for people outside of the primary audience to engage if they so wish. (And let’s be honest: are you ...

... versatility of the engineered SpCas9-NG and its variants can be used to engineer specific sites that ...Expanding the targeting range of CRISPRCas9 by engineering SpCas9 Article contributed by Shreya Vedantam...editing. PAM sequences can be from 2-6 base pairs in length and follow the DNA sequence targeted by the Cas9...PAM to recognize the target. Osamu Nureki’s lab engineered SpCas9 (SpCas9-NG) with relaxed preferences for...recognizes NG rather than NGG. In addition to the engineered SpCas9, they also fused the SpCas9-NG with the... promoters and enhancers, or have attempted to engineer loops to create genomic interactions that wouldn...

... genetic engineering, with the ultimate objective of genome design.” It’s genetic engineering on a genomic...needed for anyone to begin considering genetic engineering projects in a very big way. In one of his latest... with Cas9 guided by different promoters. The challenge in building genetic circuits is getting enough...scale could be created. Someone could take on an engineering project including hundreds of genes and regulation...complete toolbox for taking on very large genetic engineering projects. Addgene: How easy is it to do this ...animals make. That will be an outcome of genetic engineering.   Thank you to Chris Voigt for speaking with...