...in comparison to protein-coding genes (Rinn and Chang 2012). Scientists have determined the function ...completely disrupt expression of the transcribed ncRNA (Jiang et al. 2014).  Simple knock-out experiments are .... doi:10.3390/ncrna7040079 Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS. Fitness effects of CRISPR...(5):573. doi:10.1038/s41587-020-0428-0 Rinn JL, Chang HY. Genome Regulation by Long Noncoding RNAs. Annual...10.1146/annurev-biochem-051410-092902 Liu Y, Cao Z, Wang Y, et al. Genome-wide screening for functional long...Nature. 2016;539(7629):452. doi:10.1038/nature20149 Jiang Q, Meng X, Meng L, et al. Small indels induced by...2015;6. doi:10.3389/fpls.2015.01001 Ho TT, Zhou N, Huang J, et al. Targeting non-coding RNAs with the CRISPR...

...Note: Cpf1 is also called Cas12a. In 2015, Feng Zhang’s lab characterized two Cpf1 nucleases, distant cousins... staggered fashion, creating a 5 nucleotide 5’ overhang 18-23 bases away from the PAM. Cpf1’s staggered...gene delivery due to their low immunogenicity and range of serotypes allowing preferential infection of ...regulatory elements. To solve this problem, the Zhang lab has previously used SaCas9 (1053 aa/3.2 kb) ...transgene insertion mediated by Cpf1-generated overhangs. Exploring the efficiency of these two processes...SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. Cpf1 Is a Single RNA-Guided Endonuclease of a...Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath ...

...specific tissues where they can scan for any signs of danger. In this post we’ll focus on how fluorescent proteins...GFP and its derivatives by the late Roger Tsien changed everything. For the first time, fluorescent proteins...Blue-green fluorescent proteins like EGFP Yellow-orange fluorescent proteins like TagRFP, tdTomato, DsRed...tdKatushka2 (Drobizhev et al. 2011) The commonly used orange and red fluorescent proteins are excited by 750...imaging studies with blue or cyan proteins without changing excitation wavelength (Salomonnson et al. 2012...it has been shown that even a small incremental change of the excitation wavelength can significantly ...Ubow mouse strain has been created to fate map Langerhans cells and follicular dendritic cells within the...

...a cell and understand how protein localization changes over time.Hallmarks of fluorescent protein timers...they predominantly fluoresce a second color. This change is usually hypothesized to be a result of chromophore...embryos. Of course, timers may be sensitive to changes in oxygen, temperature, and pH, but timer activity...and the formation of limbs are correlated with changes in gene expression. In a developing embryo, for...long-lived transcription factors control gross changes in gene expression as new body sections are formed...Alexey, et al. ""Fluorescent timer": protein that changes color with time." Science 290.5496 (2000): 1585...Fedor V., et al. "Monomeric fluorescent timers that change color from blue to red report on cellular trafficking...

...the human genome Wang, T., Antonacci-Fulton, L., Howe, K. et al. The Human Pangenome Project: a global...diligent scientist, they sought to understand these strange results by digging deeply into their data.   ...Samples are divided into those of African ancestry(orange) and those of other ancestry groups (grey). ...Cancer Data Science team at Broad, they were able to change their analysis to use a corrected genome map. Now...ignored. Working with Lia Petronio and Katherine Huang from Broad’s Pattern team, they designed a tool ...Boyle, Joshua Dempster, Lia Petronio, Katherine Huang, Alham Saadat, Thomas Green, Adam Brown, John G ...

...Did you notice the “Filter By…” options changed when we changed from searching for viral preps instead ...assembled a series of screenshots to highlight changes to both the design and functionality of searches...of plasmids? The available filtering options now change dynamically based on the type of material and specific...for details). The following screenshots show the range of different terms we can use to find materials ...exact plasmid you need. The ability to apply a wide range of filters isn’t new to Addgene’s plasmid search...you may find the available categories and filters change as we now only show options relevant to your current...

...SpCas9 variants effectively double the targeting range of CRISPR/Cas9 within the human genome. Another ...guide or leave a comment below. Note: Jennifer Tsang and Mary Gearing contributed to the update of this...Kellner MJ, Regev A, Lander ES, Voytas DF, Ting AY, Zhang F (2017) RNA targeting with CRISPR–Cas13. Nature... Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F (2017) RNA editing with CRISPR-Cas13. Science ...publication at Addgene. Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, Zeina CM, Gao X, Rees HA, Lin ...Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F (2015) In vivo genome editing using Staphylococcus...SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (2015) Cpf1 Is a Single RNA-Guided Endonuclease...

...Transient reporter for editing enrichment (TREE) The Wang and Brafman lab developed a transient reporter for...’ after a C-to-T base editing event. This edit changes the histidine to a tyrosine generating a GFP variant...target specific loci of interest in the genome. The Wang and Brafman lab showed that GFP positive cells isolated...subsequent base editing efficiency. TLDR: TREE from the Wang and Brafman lab uses an engineered BFP variant that...https://doi.org/10.1093/nar/gkaa124 Martin AS, Salamango DJ, Serebrenik AA, Shaban NM, Brown WL, Harris....org/10.1038/s41598-018-36739-9 St. Martin A, Salamango D, Serebrenik A, Shaban N, Brown WL, Donati F,...K, Tekel SJ, Brookhouser N, Schwarz G, Nguyen T, Wang X, Brafman DA (2019) A transient reporter for editing...

...2.7 to Python 3.5. There are significant changes to the language and it took us a total of two years, from...of 40 minutes to 10 minutes. While users can’t tangibly see these improvements, you are benefited with...the flexibility to adapt and easily respond to changing needs of the teams at Addgene. Another advantage...only do the dishes once a month, resulting in a dangerous mountain of dirty dishes or you could choose to...updated in several years) or they make significant changes that make it incompatible with our software. When...you, which brings me to my next analogy. Human languages evolve over time, for example from Ancient Greek...

...-884. PubMed PMID: 12718874. Yang, Junjie, Weihong Jiang, and Sheng Yang. "mazF as a counter-selectable...systems have been used as biological tools for a wide range of applications in molecular biology or in vivo ...production of MazE, the toxin becomes active. Shen Yang’s lab made use of mazF as a counterselectable marker...100% stability after five days. Jeff Hasty and Sangeeta N. Bhatia also used the hok/sok toxin-antitoxin... Jennifer Tsang...

...light scattered by that cell at a low angle (FSC) or large angle (SSC) (Figure 1). FSC values depend on...is scattered forward at a low angle (FSC) or to the side at a large angle (SSC). FSC and SSC depend on ...software in order to generate signals in a reasonable range. If colleagues in your group already have experience...ll notice that while the height of your events changes, the separation pattern of positive vs. negative...live population from my live-dead staining. (B) Changing the y-axis from SSC to FSC can alter the positioning...

...sensor relies on a change in localization to the cell membrane and not a direct change in the fluorescent...biosensor that has a binding affinity close to the range of concentrations expected in your samples. Higher...operating at the outer edge of the sensor’s dynamic range. With this in mind, Ed Boyden and colleagues set...family of fluorescent potassium indicators with a range of binding affinities (Torres Cabán et al. 2022)...sensors with lower binding affinities to broaden the range of applications. Image reproduced from Torres Cabán... B) LiLac responses are highly resistant to pH changes. Image adapted from Koveal et al. 2022, under CC-BY...

...Cary Valley, Shreya Vedantam, Michelle Cronin, and Angela Abitua Thanks to a team effort from the Addgenies...Negative Selection for Plasmid Cloning by Jennifer Tsang There are many strategies for finding your clones...Proteins: mNeonGreen, mTFP1, and mWasabi by Jennifer Tsang Learn about mNeonGreen, mTFP1, and mWasabi and ...Precision and Flexibility to CRISPR Editing by Jennifer Tsang Prime editing is a new CRISPR technique from David...insertions, deletions, and all possible base-to-base changes.   1. Plasmids 101: Transformation, Transduction... Jennifer Tsang...

...10.1186/1471-2105-7-85Zhu G; Chang Y; Zuo J, Dong X, Zhang M, Hu G, Fang F. Fudenine, a C-terminal truncated...effects, cation concentrations and a temperature range) to predict PCR melting curves and dynamic melting... the board. If the samples or sample conditions change, the multiplexed protocol may have to be re-optimized..., which gives an RQ value representing the fold change of each sample compared to your control. But as...Wong, 2018.    🔥Hot Tip🔥 Negative fold changes in ΔΔCT are represented by RQs between 0 and 1.... during analysis can allow you to see this fold change as a positive difference (RQ>1), which may be easier...

...undergoes a conformational change in response to the molecule it detects. This change then generates a reporter...sensing domain induces changes in a fluorescent signal based on ligand presence or changing cellular conditions... calcium induces CaM/RS20 interaction, thereby changing the FP’s structural organization and activating... or transcriptional activation, conformational changes, translation, and protein translocation. Targeting...

...positive outcome if the employee sees that real change is possible in your eyes so their confidence is...feedback is a very effective way to bring about change in behaviors and habits in a nonthreatening way... would you do differently? Beware of indirect language You must be honest about performance problems.... I see is managers who hint at or use indirect language to talk about real performance issues. Watch this...this little video to learn more about indirect language from Steven Pinker. As a manager you must be able...There is place in human discourse for indirect language, but it is not the way to go when giving feedback...

..., Wu X, Jiang W, Marraffini LA, Zhang F. Science. 2013 Jan; 339 (6121): 819–23. Mali P, Yang L, Esvelt...other CRISPR subtypes. Still, the large and dynamic range of CRISPR systems between and within prokaryotic...http://en.wikipedia.org/wiki/File:Crispr.png Barrangou R, Horvath P. Science. 315, 2007 Jan; 1709–1712...CRISPRdb. Date: 2013-09-18. Makarova K, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, Moineu...

...resolution. In this setup, gels have an increasing range of acrylamide content from top to bottom allowing...allowing a mix of proteins with a broad size range to be separated on a single gel.  Immobilizing proteins ...process is very effective in transferring a broad range of protein sizes but takes hours to overnight.  ...available dry blotting systems efficiently transfer a range of protein sizes in minutes without any transfer...being used and may require some trial and error (Yang et al., 2012).  Choosing your primary antibody Once...addition to protein abundance, westerns detect changes to a protein’s post-translational modifications...4350–4354 . https://doi.org/10.1073/pnas.76.9.4350 Yang P-C, Mahmood T (2012) Western blot: Technique, theory...

... The authors share a wealth of data on ... The language is ... The general representation of data is.....couple of sentences - even if written in a clumsy language make it much easier for me to go back and finish...about the paper after my initial read, adjust my language in the first (and clunky) version of my general...general comments and adjust them if my opinion changed after this more detailed look.        Encourage...try to stay away from the loaded and judgemental language. In each peer-review, I try to mention what I ... Tester, where she focuses on (1) salt-induced changes in root-to-shoot ratio in Arabidopsis, (2) expression...

...awarded to study 31 rare diseases,” said Claudia OuYang, BeHEARD Co-Director in a release. The research...developing metastatic melanomas and other cancers. Joshua Wang (bottom right), also of the Wistar Institute, says... broadly. “This [award] is pretty great for us,” Wang said. “We were planning on and looking at a bunch...number of stressors, including emotional stress or changes in temperature.  “The disease was first described...a rare disease that can cause hearing loss and changes in coloring of the hair, skin, and eyes. The researchers...of Waardenburg syndrome (WS4) by Pediatrician Duangrurdee Wattanasirichaigoon carried different mutations...