...self-assembling protein (SAP) such as a bacteriophage shell protein or a bacterial microcompartment protein. The ...fluorescent proteins into one particle within the cell, the lab fused the red fluorescent protein (RFP) to... (DCDC), relies on the assembly of fluorescent proteins into one bright particle that segregates into ...PubMed Central PMCID: PMC6467691. Takahashi, Melissa K., et al. "A low-cost paper-based synthetic biology...systems in bee gut microbiome species such as Snodgrassella alvi and Gilliamella apicoli. The plasmids could...

...necessary to visualize expression of fluorescent proteins, for example, as many viral particles must infect...infect a cell to achieve visible expression of the protein. However, expression of receptors may not need ...In the case of channelrhodopsins, fewer channel proteins are required for the transduced cell to become...become light responsive than fluorescent proteins required to get a good fluorescent signal. It may not be...to improve AAV production.     References 1.Clark, K. Reed. "Recent advances in recombinant adeno-associated... by an anterograde AAV was shown to drop off drastically with lower titers. As you can see in figure 2...

...the viral protein reverse transcriptase (RT). In the case of a natural virus, both the protein and the ...while missing the polymerase gene may seem like a mystery. But it’s simple. The RT protein is made by a separate... there is a turn of phrase — “pseudotransduction” — to describe the direct protein transfer of RT, which...two strands of viral RNA and of the viral RT protein (Faras et al., 1973). Interestingly, retroviruses ...from step 2 will be integrated by the viral integrase protein (IN) during step 3 (King et al., 2008) (Hu...the fact that the virus must have its structural proteins expressed from a reverse-transcribed piece of ...gene therapy vector! For viral vectors, only the protein for reverse transcriptase (RT) is present in the...

...small (12-15 kDa) single-domain proteins that can bind effectively to protein targets, similar to how antibodies... sybodies against membrane proteins Developing antibodies against proteins embedded in membranes is tricky...candidate sybodies in their coat protein to screen for binding to the target protein. The protocol describes going...identified nanobodies that bind to coronavirus spike proteins (Wrapp et al., 2020), which sit on the surface...host cells. To do this, they injected the spike protein from two different coronaviruses into a llama over...special camelid antibodies that bind to the spike proteins in cell culture, and inhibit these viruses.  ...antibodies against unstable targets like membrane proteins that may unfold due to camelid high body temperature...

.... Spike protein, variants, and pseudotyping The SARS-CoV-2 virus depends on its spike protein to bind ...spike protein was developed based on 100 structure-guided spike designs and has improved protein yields...and identified interactions of these proteins with human proteins. Their deposited plasmids expressed ... more about mapping the SARS-CoV-2 - human protein-protein interaction Find tips for remote collaborations...over 75 countries. Figure 1: SARS-CoV-2 proteins and other components. Image from Maya Kostman ...scientists have developed ways to pseudotype the spike protein onto another virus. With the pseudovirus, scientists...pseudotyping lentivirus with the SARS-CoV-2 spike protein. They deposited the plasmids used for this study...

...processes: cell wall synthesis, DNA replication, or protein synthesis. Because they target such generic processes...References 1. Citorik, Robert J., Mimee, Mark, and Timothy K. Lu. “Sequence-specific antimicrobials using efficiently-delivered...Hiroki, Sebastien Lemire, Diana P. Pires, and Timothy K. Lu. “Engineering Modular Viral Scaffolds for Targeted...resistance, mediated by a single base pair change in DNA gyrase, CRISPR phagemids were cytotoxic only for resistant...

...GO works by affecting protein translation of different reporter proteins. Protein translation requires ...the translation of any detectable protein, not just fluorescent proteins. Figure 4: Reporters in Gene...codon to initiate protein expression, it can be used for an array of detectable proteins including fluorescent...fluorescent proteins, antibiotic resistance, and luciferase. References Gaudelli NM, Komor AC, Rees HA,...monitors APOBEC (a family of cytidine deaminase proteins) and Cas9-mediated editing in real time (St. Martin... editing capability of the seven human APOBEC3 proteins, finding that APOBEC3A and APOBEC3bctd are the...reporter that is converted into BFP (blue fluorescent protein) upon CRISPR/Cas9 homology directed repair (HDR...

... and a protein standard. The density of the antibody bands can be measured against the protein standard...predict the molar absorption coefficient of a protein. Protein Sci. 1995 Nov;4(11):2411-23. doi: 10.1002/... A. Pathak, Christopher J. Roberts, Prasad S. Sarangapani, Protein aggregation, particle formation, characterization...applications you are planning, cost, and the amount of protein you need to produce.  The most common yeast strain...pastoris) because it secretes fewer of its own proteins, making the purification process simpler. Due ...incubation time to maintain cell viability and increase protein production (Schwarz et. al., 2020). Harvest and...quantification. Many spectrophotometers have an IgG protein setting. If yours does not, be sure to set the ...

...tetR with the C-terminal domain of VP16 (virion protein 16), an essential transcriptional activation domain...effectors for Tet transregulators. Krueger C, Pfleiderer K, Hillen W, Berens C. Biotechniques . 2004 Oct;37(4...additional selection options third-generation rtTA On Fraser 44012 pInducer20 Lentiviral vector for shRNA expression...single copy in mammalian cells; Expresses firefly luciferase hairpin and GFP under pTREtight promoter None...pSBtet-GP Sleeping Beauty transposon system; has luciferase in cloning site; see article for additional selection.... Bockamp E, Maringer M, Spangenberg C, Fees S, Fraser S, Eshkind L, Oesch F, Zabel B. Physiol Genomics...

...detect, purify, quantify, deplete, and visualize proteins of interest (Greenfield, 2014). Traditionally,...chain for the antibody and when translated into protein will assemble into a fully functional antibody....encoded in a plasmid. (Right) An assembled antibody protein binds an antigen. Image from Fvasconcellos. ...genes for antibody expression. If starting from a protein sample (for instance, affinity purified antibodies...well in animals because of similarities to host proteins. After the antibody of interest has been cloned..., Manning CF, Nguyen JT, Bechtold H, Dumitras C, Gong B, Nguyen K, van der List D, Murray KD, Engebrecht...

...there are many protein-based toxin-antitoxin systems. One of the most well known protein-based toxin-antitoxin...specific sequences in RNA resulting in a blockage of protein synthesis. The antitoxin MazE, which binds and ...Toxin-antitoxin systems are not just restricted to the protein realm. Let’s take a look at a toxin-antitoxin system...additions to constructs that are used to drive high protein expression in vivo. Expression plasmids are often...PMC39188. Kamada, Katsuhiko, Fumio Hanaoka, and Stephen K. Burley. "Crystal structure of the MazE/MazF complex...more stable than the methyltransferase. When a plasmid is lost, the methyltransferase is degraded and/or... replication by binding the GyrA subunit of DNA gyrase and trapping it in the cleaved complex. This results...

...cells in a population. It can be used to measure protein expression, identify rare cells, or even sort out...Alyamani, A., Kalamegam, G., Ahmed, F., Abbas, M., Sait, K., Anfinan, N., Al-Wasiyah,  mohammad khalid, Huwait...i1.23 Jhunjhunwala, S., Aresta-Dasilva, S., Tang, K., Alvarez, D., Webber, M., Tang, B., Lavin, D., Veiseh... J. A., Campillo, J., Moya-Quiles, M., Minguela Puras, A., Pons, J. A., & Muro, M. (2018). In vitro intracellular...

...Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm...below affect continuous cellular processes (e.g., protein synthesis), while amp only affects the cell wall...Kanamycin, or kan, is an aminoglycoside which inhibits protein synthesis. The kan resistance gene, NPTII, facilitates...streptomycin Spectinomycin and streptomycin both inhibit protein synthesis as their mode of action and have a very...gene provides zeocin resistance by expressing a protein that directly binds to zeocin, preventing it from.... M., Piccinini, T. E., Lammel, C. J., Hadley, W. K., & Brooks, G. F. (1986). Effect of storage temperature...entirely detoxified, even when Sh ble is expressed (Trastoy et al). Thus, it may not be a good choice for experiments...

...to modified proteins called histones. We can detect modified histones with “GPS for proteins,” ChIP-seq... compute coordinates for genetic elements like protein, RNA, and DNA (Table 1). As with GPS in the real...techniques Technique What It Locates ChIP-seq Proteins (for our example later, histones) ChiRP-seq ...For details on DNA compaction and the structural proteins that make it possible, see the appendix DNA is... you run a ChIP-seq experiment (think “GPS for proteins”) for NANOG, an essential transcription factor...epigenomics: H3 – one of NANOG’s associated histone proteins K4 and K27 – locations of the amino acid lysine... is a combination of coiled DNA and structural proteins called histones. Chromatin folds into secondary...

...elegans. Other groups have used Mango to study RNA-protein complexes (Panchapakesan et al., 2017) and short...selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution...highly efficient RNA mimics of green fluorescent protein." Nature structural & molecular biology 21.8 (2014... Resources at Addgene.org Browse fluorescent protein plasmids and resources See all Jaffrey lab plasmids...additions to aptamer soup! References Alam, Khalid K., et al. "A fluorescent split aptamer for visualizing...developed to quantify RNA transcription by RNA Polymerase III. By expressing Corn under promoters for transcripts... transcripts uniquely transcribed by RNA Polymerase III (5S, tRNA and U6) and measuring Corn fluorescence...

...models for immunogenicity prediction of therapeutic proteins. European journal of pharmaceutics and biopharmaceutics...https://doi.org/10.3389/fddsv.2022.952326Joubert, M. K., Deshpande, M., Yang, J., Reynolds, H., Bryson, C...This allows scientists to get a more definitive grasp on the immunogenicity of the drug product while ...A Method Using Existing in silico Algorithm Infrastructure and a Vision for Future Enhancements. Frontiers...

...harmful weeds. The parasitic fusion is such that the two plants share RNA, proteins, and DNA. Euprymna...manipulated by injected RNA and can express fluorescent proteins. This lab has created an automated tank for feeding...the brain allows the squid to create a different protein. Did you know that most cephalopods die after they...systems for scientists and educational programs for K-12 students. You can see why I was excited to be invited... "for development of tools, approaches, and infrastructure necessary for direct tests of cause and effect...) -  perhaps you’ll choose to study Crepidula atrasolea or Prochlorococcus with your next project. Gymnotiformes...protocol community! Asclepias syriaca and Asclepias curassavica (Gerog Jander) Milkweed plants are known to many...

...Anti-Kv1.1 K+ channel [K20/78R] KCNA1 CMV Episodic ataxia James Trimmer 128627 Anti-Kv4.3 K+ channel [...Anti-Kv1.1 K+ channel [K20/78R-2b] KCNA1 CMV Episodic ataxia James Trimmer 206631 Anti-Kv4.3 K+ channel ...Anti-Kv1.1 K+ channel [K20/78R-1] KCNA1 CMV Episodic ataxia James Trimmer 206684 Anti-Kv4.3 K+ channel ...type, mutations, and/or tags such as fluorescent protein (FP) tags. Information on genes and associated ...ALS Rajat Rohatgi 107856 pHBS1052 TDP43 RRM-GFP R-K TARDBP CMV ALS Rajat Rohatgi 107857 pHBS952 TARDBP-Exon1...CMV ALS Rajat Rohatgi 118796 pHBS1388 TDP43 RRM-GFP K-R TARDBP CMV ALS Rajat Rohatgi 118797 pHBS1147 GFP-TDP43...LRRK2 CMV Parkinson's James Trimmer 177537 Anti-Kv3.3 K+ channel [N375/67R] KCNC3 CMV Spinocerebellar ataxia...

.... Once a co-repressor protein binds the repressor protein, the repressor protein can bind to the operator...activator protein is bound, turning transcription ON. When a repressor binds the activator protein, the activator... and largely defines the amount of recombinant protein that will be produced. Many commonly-used promoters... activator protein cannot bind the promoter sequence anymore and transcription is turned OFF. Negative...Negative Repressible: A repressor protein is present, but cannot bind the promoter sequence and transcription....1038/s41598-022-07852-7 De Boer, Herman A., Lisa K. Comstock & Mark Vasser. “The tac promoter: a functional...Promoters control the binding of RNA polymerase and transcription factors. Since the promoter region ...

...at the Institute for Protein Innovation (IPI), a Boston-based, nonprofit protein research institute, partnered...Table 1: IPI antibodies  Antibody Target Proteins Reactivity Isotype Source Species Anti-Integrin...plasmids. To encourage collaboration and education in protein science, IPI hosts events and training courses ...Faulds is a science writer at the Institute for Protein Innovation. She writes about all things IPI, from...References Hao, Y., Yan, J., Fraser, C., Jiang, A., Anuganti, M., Zhang, R., Lloyd, K., Jardine, J., Coppola...and morphed asymmetrically (Jo et al., 2022). By contrast, LVDP-binding integrin α4β1 required and conferred...