...Continued development of new allelic exchange vectors Allelic exchange is a great technique for the scarless...scarless mutations, both in stand-alone systems (Jiang et al., 2013), and those which increase the efficiency...modification. This technique is frequently called allelic exchange. Here, a mutated allele introduced from a conjugative...off-target mutations. Ultimately, successful allelic exchange requires two sequential homologous recombination...counterselection vector is the pDS132 sacB-based allelic exchange vector. This vector contains sacB, an chloramphenicol... colonies isolated are those where the allelic exchange vector has undergone single crossover and integrated...develop these negative selection markers for allelic exchange. To do this, we performed the following modifications...

...define plasmid host range, identify a few of the features that confer broad host range in plasmids in nature...features to create broad host range recombinant vectors.  A plasmid’s host range is determined by the different... plasmids have a narrow host range, while others have a broad host range and can replicate and stably ...identified as broad host range plasmids. The properties that influence host range are not fully understood...examples of a narrow host range plasmid with only one ori and a broad host range plasmid with multiple oris...broad host range replicons, recombinant vectors can be modified further to increase the range of hosts ...Recombinant vectors that are made from broad host range plasmids are more stable, can be easily cloned in...

...different points on this salary range. We have been able to gather data on changes to salary for some of the...Additional Career Posts on the Addgene Blog How did this change in labor laws come about? In March 2014, the White...Institutions are now preparing to comply with the changes to the law on Dec 1st, according to guidance issued...stipend levels. In theory, therefore, the salary changes expected for postdocs in many cases should be as...to gauge exactly how postdoctoral salaries are changing. Transparent salary information for postdoctoral...policies are one indicatator of how salaries may changes due to the FLSA. In 2014, 89% of institutions had...actions for junior scientists and for academia Changes are afoot for the postdoc population, and it is...

...viral sequences (e.g. promoters) can be studied by changing the minigenome cis-acting sequences and monitoring...

.../gmab036 Zhang Y, Sun X, Wang Q, Xu J, Dong F, Yang S, Yang J, Zhang Z, Qian Y, Chen J, Zhang J, Liu Y...Sichuan Normal University, Jieze Zhang, an intern in the Yang Lab, and Sheng Yang, a professor in synthetic ...References and Resources References: Jiang Y, Chen B, Duan C, Sun B, Yang J, Yang S (2015) Multigene Editing in....1128/aem.04023-14 Li Q, Sun B, Chen J, Zhang Y, Jiang Y, Yang S (2021) A modified pCas/pTargetF system... Y, Tao R, Jiang Y, Yang J, Yang S (2020) Multicopy Chromosomal Integration Using CRISPR-Associated Transposases...contributed by guest bloggers, Yiwen Zhang, a Ph.D. candidate in the Yang Lab, Qi Li, a lecturer at Sichuan...following changes. In pCas9, we 1) replaced the promoter of gRNA-pMB1 with PrhaB, 2) changed the replicon...

...broad): somatic and visceral sensory ganglia, type II spiral ganglion neurons Mice, rats No (mechanism... 4d, Jang et al., 2023). When combined with a specific promoter, AAV-PHP.AX shows greater changes in specificity...Chen, X., Ravindra Kumar, S., Adams, C. D., Yang, D., Wang, T., Wolfe, D. A., Arokiaraj, C. M., Ngo, V... Bindu, D. S., Zhang, M., Taskin, N., Goertsen, D., Shay, T. F., Sullivan, E. E., Huang, S.-F., Ravindra...Cummins, A., Chen, Y., Fan, Y., Zhang, Q., Sharma, J., Duan, Y., Wang, L., Feng, G., Chen, Y., Ip, N. ...D., Dobreva, T., Huang, Q., Ding, X., Luo, Y., Einarsson, P. H., Greenbaum, A., Jang, M. J., Deverman,...

....2013.04.025 Zhang X, Liang P, Ding C, Zhang Z, Zhou J, Xie X, Huang R, Sun Y, Sun H, Zhang J, Xu Y, Songyang...10.1038/s41467-017-02706-7 Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-Step...new technology to engineer mouse models (Wang et al., 2013, Yang et al., 2013). Like everyone else in the... Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex Genome Engineering...Kutny PM, Maser RS, Dion SL, Lamont JD, Zhang Y, Perry GA, Wang H (2016) Generating Mouse Models Using ...Dion SL, Kutny PM, Zhang Y, Cheng AW, Jillette NL, Malhotra A, Geurts AM, Chen Y-G, Wang H (2015) Efficient... https://doi.org/10.1534/genetics.115.176594 Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R...

...02050-w Yi, Z., Zhang, X., Wei, X., Li, J., Ren, J., Zhang, X., Zhang, Y., Tang, H., Chang, X., Yu, Y., ...01595-6 Ye, L., Zhao, D., Li, J., Wang, Y., Li, B., Yang, Y., Hou, X., Wang, H., Wei, Z., Liu, X., Li, Y.,...Hong, M., Luan, C., Gao, H., Ru, G., Guo, X., Zhang, D., Zhang, S., Li, C., Wu, J., Randolph, P. B., Sousa... Y., Zhou, X., Chang, C., Chen, G., Liu, W., Li, G., Fan, X., Sun, M., Miao, C., Huang, Q., Ma, Y., Yuan...Yuan, F., & Chang, X. (2024). Protein language models-assisted optimization of a uracil-N-glycosylase ... H., Li, G., Zhou, J., Yuan, Y., Zhang, H., Shi, L., Yao, X., & Yang, H. (2023). Programmable deaminase-free...https://doi.org/10.1093/nsr/nwad143 Tong, H., Wang, H., Wang, X., Liu, N., Li, G., Wu, D., Li, Y., Jin, ...

...the study of heritable changes in gene expression that do not involve any changes to DNA sequence (Epigenetics...modifications can result in phenotypic changes without any change in genotype. Epigenetic modifications...reduces the risk of dangerous DNA damage. If the way DNA is wrapped around histones changes, then gene expression...Epigenetic changes have been discovered to play a large role in a variety of diseases, ranging from cancer...epigenetic changes were statistically significantly associated with reduced life-span, but no changes in the... visualize changes in gene expression and may lead to the development of a whole new range of methods ...expression can change as well. The more frequently and tightly bound DNA is to histones, the more compacted...

... designing your overhang sets. But are those rules the best way to design GGA overhang sets, particularly...(1) don’t use the same overhang twice; (2) avoid palindromes; (3) no overhangs with the same three nucleotides...number of overhangs, three or four base-pair sequences, and exclude or include specific overhang sequences...2018, they published a paper profiling four base overhang ligation (Potapov et al., 2018), which showed ...two nucleotides in the same position; (5) avoid overhangs with either 0% or 100% GC.) In fact, the NEB® ...that high-fidelity reactions could be done using overhang sets that broke rules 3—5. Fidelity, it turns ...design high-fidelity Golden Gate Assemblies and overhang sets: NEBridge Ligase Fidelity Viewer™; NEBridge...

..., Han, H., Li, Y., Wang, L., Chen, G., Ma, X., Geng, H., Huang, W., Pang, X., Yang, Z., … Li, D. (2020...mediate a C to T change (or a G to A change on the opposite strand). ABEs make an A to G change (or a T to ...science.aba8853 Zhang, X., Zhu, B., Chen, L., Xie, L., Yu, W., Wang, Y., Li, L., Yin, S., Yang, L., Hu, H....out of 12 possible base-to-base changes. The other 8 base-to-base changes require Base Transition Editors... Ru, G., Meng, H., Yan, Y., Hong, M., Zhang, D., Luan, C., Zhang, S., Wu, H., Gao, H., Bai, S., Li, C....to C change on the opposite strand). Both are base transition editors: converting one purine base to the...purine-to-purine or pyrimidine-to-pyrimidine base changes. Solid red arrows indicate a conversion directly...

...aptamer, Mango, binds to multiple derivatives of thiazole orange (TO) and fluoresces in the orange or red... and orange fluorescent aptamers Corn was described in the same study as Red Broccoli and Orange Broccoli...fluoresce in the red and orange channels, respectively. Both Red Broccoli and Orange Broccoli are derived ...(Autour et al., 2018). Three variants of Mango, coined Mango II, III, and IV, were then identified through...that bind metabolites, leading to conformational changes that control the expression of coding RNA. Spinach-based...molecule. Notably, like Broccoli, Red Broccoli and Orange Broccoli are not photostable, and were presented...et al., 2014). While 10 derivatives of TO exist, Mango is most frequently used with TO1-biotin or TO3-biotin...

...4811-9-39 Gao Q, Xu W, Yan T, Fang X, Cao Q, Zhang Z, Ding Z, Wang Y, Wang X (2019) Rescue of a plant cytorhabdovirus... Lowder LG, Zhang D, Baltes NJ, Paul JW III, Tang X, Zheng X, Voytas DF, Hsieh T-F, Zhang Y, Qi Y (2015... crops to increase agricultural yield (Wang et al., 2016; Wang et al., 2014). While it is certainly possible.... https://doi.org/10.1038/s41467-020-15731-w Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Liu Y-G, Zhao...doi.org/10.1371/journal.pone.0154027 Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu J-L (2014) Simultaneous...https://doi.org/10.1038/nature.2016.19754 Zhang H, Demirer GS, Zhang H, Ye T, Goh NS, Aditham AJ, Cunningham... of reasons to consider using genome editing to change the genetic code of plants, including the development...

.../acssynbio.7b00399 Li Q, Sun B, Chen J, Zhang Y, Jiang Y, Yang S (2021) A modified pCas/pTargetF system....org/10.1038/nbt.3043 Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA (2013) Programmable...doi.org/10.1038/s41467-018-04901-6 Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided ...homologous recombination in bacteria. These quirks change the way CRISPR-mediated genome engineering functions... to generate multiple mutations simultaneously (Jiang et al. 2013). Genome editing tools for bacteria ...coli and T. citrea scarless editing plasmids Sheng Yang’s lab describes a two-plasmid system that combines...system for scarless, iterative genome engineering (Jiang et al., 2015). pCas contains Cas9 and the phage ...

...-00745-y Zhang Y, Sun X, Wang Q, Xu J, Dong F, Yang S, Yang J, Zhang Z, Qian Y, Chen J, Zhang J, Liu Y... Y, Tao R, Jiang Y, Yang J, Yang S (2020) Multicopy Chromosomal Integration Using CRISPR-Associated Transposases...discovery of CRISPR-transposons by the Sternberg and Zhang labs (Peters et al., 2017; Klompe et al., 2019; ...and CAST (CRISPR-associated Transposase) by the Zhang group. Mechanism of CRISPR-transposons One of the... these systems have already been demonstrated, ranging from large genomic insertions and/or deletions,...multi-copy genomic integration of metabolic cassettes (Zhang et al. 2020); however, the technology potential ...Crits-Christoph A,  He C , Xu M, Zhou Z, Smock DC, Tang K, Owens TK, Krishnappa N, Sachdeva R, Deutschbauer...

...and single-stranded 5′ overhangs… but it doesn’t really matter if those overhangs perfectly match up. They...from its dependence on single-stranded overhangs. These overhangs must be accessible to allow for complementary...backbones, base pairing between these ~4 base overhangs isn’t strong enough to hold a plasmid together...be ligated. But in LIC, longer single-stranded overhangs can hold a nicked plasmid together long enough...) digested to create 10–12 base “chewed back” overhangs, they can be annealed, forming a circular product...limited by its sequence constraints. The long overhangs must not contain the dNTP present in the exonuclease...protocol itself is flexible. For one thing, those 5′ overhangs can be generated in several ways. One option, ...

...When we start thinking about languages, humans have two types of languages: one to communicate amongst ...then there are languages to communicate with other things. These are programming languages like Java or ...successful human-to-human languages. Who owns computer-programming languages? That's trickier. Sometimes...successful computer languages are free to use. Of the 15 most popular computer programming languages, 12 out of...earlier this year by the White House as a Champion of Change, a program created as part of President Barack ...genetically encoded functions - the words in our language for programming life - and they should be free...1854 was thinking about logic and analyzing human language and observed that we humans find it useful to ...

... Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex Genome Engineering...102–106 . https://doi.org/10.1038/nbt.3055  Wang D, Zhang F, Gao G (2020) CRISPR-Based Therapeutic Genome...gene delivery due to their low immunogenicity and range of serotypes allowing preferential infection of ... room for additional regulatory elements. Feng Zhang's group previously packaged Cas9 and multiple gRNAs...a smaller, but equally potent Cas9 protein, the Zhang lab took a different approach. They analyzed over...compare the off-target effects of SpCas9 and SaCas9, Zhang’s group used an approach called BLESS (direct in ... test the efficiency of AAV-SaCas9 in vivo, the Zhang lab created an all-in-one SaCas9 and sgRNA construct...

...21559-9 Huang, M. E., Qin, Y., Shang, Y., Hao, Q., Zhan, C., Lian, C., Luo, S., Liu, L. D., Zhang, S., Zhang... Zhang, Y., Wo, Y., Li, N., Wu, S., Gui, T., Wang, B., Luo, Y., Cai, Y., Liu, X., Xu, Z., … Meng, F.-L...10.1038/s41587-020-0609-x Yang, C., Dong, X., Ma, Z., Li, B., Bi, C., & Zhang, X. (2022). Pioneer Factor... Bi, C., & Zhang, X. (2021). Glycosylase base editors enable C-to-A and C-to-G base changes. Nature Biotechnology...bacteria and mammalian cells Researchers in the Xueli Zhang lab were making similar observations around the ...pioneered these editors (calling them GBEs), Xueli Zhang’s lab, returned with a unique approach to improving...binding to and remodeling inaccessible chromatin (Yang et al., 2022). Specifically, they found that the...