...molecular language shared by every living thing fit onto a single lecture slide. That shared language is the...to our Viral Vectors 101 series. Are broad host range plasmids shuttle vectors? While it’s technically... to say that shuttle vectors have a “broad host range,” these terms are typically used in different (though...(though overlapping) ways. Broad host range plasmids are those that can replicate in multiple kinds of...incredible that my cells “speak” the same molecular language as the tree outside my window! Whatever you use...

...will always be that way. Things change and processes often have to change with them. If you can, set aside...concept and pare it down until you have something tangible and applicable to your situation.   Thinking Outside...creative when you don’t believe you have the power to change anything. You may not have the highest position...received, understand that people can be resistant to change. Ask your peers or your superiors to explain their...unworkable idea into a viable solution.  Anticipate Change Just because a process is working, doesn’t mean...

...critical regions of plasmids deposited with us via Sanger sequencing, while more recently we have moved to...design, we were free to use multiple programming languages (Python, Perl, Java, R, etc.) in our pipeline.... to translate or convert programs to a uniform language.  The modern architecture of Nextflow included...Python scripts, queried our database with SQL or Django, and executed code in Jupyter notebooks using familiar...Since a Nextflow process can utilize any scripting language that can be executed on Linux, we created our ...through much trial and error to learn the scripting language, but our path forward was clear: to build one ...

...increase gene expression at certain loci to create changes in phenotypes. For example, CRISPR activation has... constructs, however, Cas9 allows you to easily change the sequence targeted by the activator by simply...Voges M, Schäfer C, Spohn M, Stucka R, Hauber J, Lange UC (2016) Targeted HIV-1 Latency Reversal Using ... Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F (2014) Genome-scale transcriptional activation...doi.org/10.1016/j.cell.2014.09.039 Wong N, Liu W, Wang X (2015) WU-CRISPR: characteristics of functional...doi.org/10.1186/s13059-015-0784-0 Zetsche B, Volz SE, Zhang F (2015) A split-Cas9 architecture for inducible...

...This technique uses the trace file generated in Sanger sequencing and a simple algorithm to quantify editing... to amplify the target region of interest. Then Sanger sequence the PCR product of both an unedited population...enzyme screening is sensitive to single base pair changes, but the edit must occur at an existing restriction...simultaneously validate edits and look for off-target changes. This method requires a set of control cells to...option, you can still detect off-target effects with Sanger sequencing, provided you have some idea of where...where off target editing may occur, allowing you to Sanger sequence a manageable number of the higher probability...

...Brainbow-3.0, but with mOrange2, EGFP and mKate2 as the fluorophores; mOrange2 is the default state. In...first fluorescent protein in the construct, OFP (orange), is expressed when Cre is absent; stochastic Cre... both fluorescence and sequence overlap (coral mOrange2, jellyfish EGFP, and sea anemone mKate2.) They...proteins in the nervous system. Livet J, Weissman TA, Kang H, Draft RW, Bennis RA, Sanes JR, Lichtman JW. Nature.... Pan YA, Freundlich T, Weissman TA, Schoppik D, Wang XC, Zimmerman S, Ciruna B, Sanes JR, Luchtman JW...

... problem, how can one little change make a difference? Individual changes to our behavior can lead to ...By initiating little changes in ourselves, we can both influence others to change their behavior and we... Recycling and Innovations posts. Making small changes in your daily habits can feel ineffective or unimportant...

...Addgene saw big changes in 2022, from the launch of a new material to the redesign of a community resource...around the world, are learning to navigate the changes brought about by the pandemic. As we adjust, we...reflecting on how to help scientists in this rapidly changing environment. In particular, we are working to ...learn from, and a compelling future to plan in the changing landscape of science. We are therefore embarking...to serve the scientific community as we grow and change to meet its ever-evolving needs. For now, we have...

...doi.org/10.1074/jbc.M101559200 Wang, Z., Zhu, T., Rehman, K. K., Bertera, S., Zhang, J., Chen, C., Papworth,... material, and variations between serotypes can change how the viral particle sneaks its way into cells...pUCmini-iCAP-AAV9.452sub.LUNG1 Goertsen et al., 2022 Pancreas AAV6, AAV8 Wang et al., 2006 Retina 7M8 Dalkara et al., 2013 ...doi.org/10.1016/j.cell.2021.08.028 Tervo, D. G. R., Hwang, B.-Y., Viswanathan, S., Gaj, T., Lavzin, M., Ritola...Lindo, S., Michael, S., Kuleshova, E., Ojala, D., Huang, C.-C., Gerfen, C. R., Schiller, J., Dudman, J. ...

...10.1016/j.stem.2014.04.020 Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak...30nt from the proximal ends of the repair template (Yang et al., 2013). This means that, for gene editing...the so-called base editor Cas9, which makes DNA changes in the absence of dsDNA breaks (Rees et al., 2018...Kim-Kiselak C, Briggs AW, Rios X, Huang P-Y, Daley G, Church G (2013) Optimization of scarless human stem cell...

...Proteins For Molecular Biology Experiments by Jennifer Tsang Chromoproteins are a subset of the fluorescent ...many molecular biology methods such as allelic exchange, FRET, and synthetic biology. 7. 25 Work From...From Home Tips for Scientists by Jennifer Tsang These tips were written early on in the pandemic. Later...Quantification Methods to Consider by Jennifer Tsang The nanodrop vs. spec debate dominates DNA quantification... Jennifer Tsang...

...expression vector for CRISPR nuclease, SpCas9 from the Zhang Lab. It's name, though a little confusing to the... is a modified version of CAG promoter that the Zhang lab has tested in a variety of mammalian cell lines...component of most CRISPR systems and generates double strange breaks at target sites 5' of the 5'NGG3' PAM sequence... can be modified for viral trasduction (see the Zhang Lab's Nature Protocols Paper for more information... all of these variants, as well as links to the Zhang Lab's Nature Protocols Publication describing them...

...domain is interesting because by changing certain amino acids you can change the specificity,” explained Zhanar...she hopes will change the intracellular localization of RNA. “You can think of changing bases to other...binds a consecutive base in its RNA target. By changing amino acids, it’s possible to produce a protein...

...graduate student Silvana Konermann first entered Feng Zhang’s lab at MIT, the use of customizable DNA-binding...new. Now, Konermann and her colleagues including Zhang and Mark Brigham have taken the technology to another...literally at the flip of a (blue) light switch. Zhang’s team devised the plasmids now available in Addgene...introducing the optogenetic tool, Konermann and Zhang showed they could package LITEs in viral vectors...specific epigenetic modifications in the genome,” Zhang said in MIT’s press release. In an accompanying ...

...fluorescent tags in neurons. Their toolkit named ORANGE (Open Resource for the Application of Neuronal ...in neurons.  Read the paper in bioRxiv Find the ORANGE toolkit   Cas9/gRNA ribonucleoprotein delivery...plasmids   Cytosine deaminase for RNA editing Feng Zhang’s lab previously developed a programmable adenosine-to-inosine...system is called RNA Editing for Specific C-to-U Exchange, or RESCUE. Read the paper in Science Find RESCUE... Jennifer Tsang...

...References Feng, J., Zhang, C., Lischinsky, J. E., Jing, M., Zhou, J., Wang, H., Zhang, Y., Dong, A., Wu,...generating variants with improved affinity and dynamic range of both nLightG and nLightR, and may soon have a...Wu, Z., Wu, H., Chen, W., Zhang, P., Zou, J., Hires, S. A., Zhu, J. J., Cui, G., Lin, D., Du, J., & Li,...

...stars Tom Hanks as the protagonist (Langdon). The plot involves Langdon chasing an anti-villain geneticist...CBE) use a cytidine deaminase to introduce a C→T change at precise locations in the genome. This was soon...Hugo De Vries: from the theory of intracellular pangenesis to the rediscovery of Mendel. Comptes Rendus ...Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (2013) Genome engineering using the CRISPR-Cas9...EJ, Lee AH, Amora R, Miller JC, Leung E, Meng X, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Meyer BJ (2011...

...chemistry. The society currently has 352 members, ranging from undergrad all the way up to professors. Oxford...Oxford currently has around 700 members and hosts a range of scientific meetings for students to attend. It...society provides talks and career support for a range of different scientific disciplines, as well as ... opportunities for society members as well as arranging collaborations and conferences for their students...Synthetic Biology Society also aims to develop a range of talks for both students and the general public...

...the success of the change in expression of GFP, for the stop codon should have changed from “TGA” to “TGG...without requiring a double-stranded break. The Xiao Wang Lab has recently deposited a set of plasmids that...-020-00929-7    The CRISPR corner By Jennifer Tsang New CRISPR plasmids are always being added to the...identification of essential MYC binding sites in a wide range of human cells.  A new pooled library from Junjie...

... Research is Advocating for Change Within the Sciences Learn How Changing Labor Laws Can Effect Postdoc...editors) can move slowly, news about possible broad changes to policies seems to break everyday. Many researchers...active and involved if we wish to make positive change. Below I present perspectives on the March for ...cause autism to politicians saying that climate change is a hoax. This has culminated in the current President...before the House Science Committee about climate change. All the scientists – including global warming ...