...detection had over 1,000 authors. The chapter on deep learning addresses the dilemma of creating a technology... “The most obvious future consequence of the undermining of the scientific process and the marginalization... the summer of 2020 that the consequences of undermining science are even more immediate and dire than...himself has written entire books about optogenetics. Defining science and summarizing its past, present, and...task to set oneself. As a scientist who enjoys learning a little bit about many different things (part...

...plasmid cloning blog posts Resources on Addgene.org Find protocols for molecular biology and cloning Read... use a phenol chloroform extraction to remove remaining proteins and RNase. Finally, DNA is precipitated...into this mixture to absorb the nucleic acids. Containinants bind cellulose less tightly than nucleic acids..., as detected by qPCR, but this did not reduce cloning efficiencies.  When compared to fresh columns, ...

...standard in their bicinchoninic acid assay (BCA) to normalize samples before running a western blot. Standard...provide some general considerations for scientists planning to use them in their assays.  What is a standard... above 0.95.    Additional considerations When running assays that rely on a standard curve, it is critical...program. Summary Few things in the lab are more disheartening than seeing a potentially exciting result quashed...

... direct RNA-guided transposition. By natively combining the DNA integration capabilities of transposases...with Type I-F INTEGRATE using a single plasmid containing a multi-spacer CRISPR array. Workflow and...s41586-019-1323-z Peters JE, Makarova KS, Shmakov S, Koonin EV (2017) Recruitment of CRISPR-Cas systems by ...Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F (2019) RNA-guided DNA insertion with...science.aax9181 Strecker J, Ladha A, Makarova KS, Koonin EV, Zhang F (2020) Response to Comment on “RNA-...

... genome. These off-target sequences may be unintentionally mutated along with the desired target locus...sequences when used in place of wild-type SpCas9. The remaining variants (VQR, EQR, and VRER) recognize novel ...Staphylococcus aureus (Sa) NGRRT or NGRRN Neisseria meningitidis (Nm or Nme) NNNNGATT Campylobacter jejuni...Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F (2015) In vivo genome editing...Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (2015) Cpf1 Is a Single RNA-Guided ...

...HypaCas9, are great choices. Check out our SpCas9 containing plasmids, optimized for a variety of species....critical enzymatic residues has been converted to an alanine (D10A or H840A), changing its double-strand cut...available. This system utilizes an RNA template containing the desired edit adjoined to the sgRNA, a reverse....   Ok, I have a Cas9! What do i do next? Designing or selecting a sgRNA Addgene may carry a validated...expression systems Addgene carries a variety of Cas9 containing plasmids that have been optimized for expression...

...checkpoint.  The plasmid is self-transmissible, meaning that the plasmid is conjugative and carries the...inducibility (Toh et al. 2023), and additional cloning sites (Keen 1988).  Find broad host range recombinant... Origin of the Broad Host Range Plasmid RK2: Positioning of Various Motifs is Critical for Initiation ...1988). Improved broad-host-range plasmids for DNA cloning in Gram-negative bacteria. Gene, 70(1), 191–197...R. (1988). Chapter 15—Broad-Host-Range Plasmid Cloning Vectors for Gram-Negative Bacteria. In R. L. Rodriguez...

...identifies nine enemies that stand in the way of creative thinking. I won’t go through all nine here, but...found that many researchers feel they lack formal training in a variety of transferable skills. At Addgene...absolutely a transferable skill developed during PhD training. Creativity is required to develop new projects...’re stuck drawing stick figures, remember your training as a scientist has been building your creativity...

... shift to remote learning due to COVID-19. We had many protocols for plasmid cloning and working with ...details about personal protective equipment to learning about how to use a tissue culture hood and other...on our Protocols page and YouTube page.  Happy learning, and welcome to the lab bench, new scientists!...

...involves the introduction of a transgene construct containing fluorescent proteins (XFP) of different colors...not undergo recombination can be detected by immunostaining of the truncated YFP. In Thy1-Brainbow mice...are that it does not use ubiquitous promoters, meaning that not all cell types can be labeled, and that...labels Drosophila neurons at the neuroblast stage, meaning that neurons of the same lineage will express the... a plasmid construct called Zebrabow-GateDest containing an RFP, CFP, and YFP downstream of a ubiquitous...

...3’ flaps containing the edited sequence anneal with each other, while the 5’ flaps containing the original...First, twin prime editing installs two sequences containing attB/P recombinase landing sites on opposite ...recombinase integrates a sequence from a donor plasmid containing a complementary site into the genome at this ...rat brain sections stained with Anti-GFAP. The staining patterns from recombinant antibodies produced ...

...been around since 1975 thanks to the Nobel prize winning work of Milstein and Köhler who developed hybridoma...by infecting bacteria for additional rounds of panning and scFv characterization.    Figure 2: ...by infecting bacteria for additional rounds of screening. Created with Biorender.com.   Some phage ...and VH sequences. Phage display also allows for screening scFv generated from the B cell antibody genes ...Gąciarz A, Ruddock LW (2017) Complementarity determining regions and frameworks contribute to the disulfide...

...months. Jennifer and I spent about an hour that morning scrambling. Everything we had set up involved multiple...adapted for video making.   Cycle One: The Ironing Board Control Center With the pandemic in full ...that included iPad and her laptop raised on an ironing board, giving it the perfect height (Fig. 2). We...to think of something else.   Figure 2: Ironing boards. Good as a WFH desk, and as a video control...smooth filming in the future, but we were finally refining the process down to a place I could be happy with...

...around 20 minutes, they are perfect for molecular cloning and metabolic engineering.  The E. coli genome ....  Check out Addgene’s collection of plasmids containing Rattus norvegicus genes! Mexican axolotl (Ambystoma...community.  The Arabidopsis genome project marked the beginning of widespread Arabidopsis genetics research development...out the GreenGate Toolkit which allows for easy cloning of constructs specifically designed for use in ...Xing, X.-H. (2018). Pooled CRISPR interference screening enables genome-scale functional genomics study...

...iBiology which hosts an amazing amount of useful, entertaining science lab, career, and policy content. Watch...presentation appropriately.  Find out who will be listening.  Are they early, mid, or late career?  Will many...force it. You can always relate to scientists by explaining how your work fits in the bigger science picture...that this might sound condescending, consider explaining the term on a slide but not reading the explanation...practice. I always take a poll of scientists in training to see how many in my audiences have given a 50...

...pSer-incorporated proteins requires a molecular toolkit containing the OTS, an appropriate bacterial host strain...The pCRT7 NT TOPO vector contains a mutant pSer-containing GFP that can be used as a positive control during... researchers can run samples on SDS-PAGE gels containing Phos-Tag, a small molecule that binds specifically...that wasn’t originally a serine (e.g. mutating a threonine residue to a phosphoserine) to control for effects...large proteins by Western blotting using Phos-tag containing gel." Nat. Protoc. doi 10 (2008). Journal. Resources...

...knockout mouse in about 3 months. Image courtesy of Wenning Qin. Single-stranded DNA repair templates Short...electroporation methods using in mouse transgenics. Designing an Easi-CRISPR knock-in allele To design a knock-in...make the first two bases of the left homology arm guanine (i.e. GG); this design has been shown to increase..., you can add a silent PAM or guide mutation. Designing an Easi-CRISPR conditional allele The design for... can amplify the desired region using primers containing the homology arms on both sides and the T7 promoter...

...Off-target effects” a vague catch-all term for unintended consequences in an experiment. For CRISPR work...In other words, they can sometimes localize to unintended sites with sequence similarity to the on-target...on-target site. When a CRISPR-Cas system localizes to unintended sites and performs its programmed function there...not Homologous Recombination or Alternative End Joining, two alternative pathways. See (Guo et al, 2023...factor, etc.) this control is usually not very meaningful. Unfortunately, there really aren’t any effective...

... aim of improving professional development and training in a globalized world where individuals can exchange...IMP 2014-15, University of Valencia): “At the beginning, I registered at IMP to have an opportunity to...throughout the entire year. In addition to their direct training role as mentors to Spanish mentees, mentors also...addition to a pre-program self-assessment survey defining expectations of the program and their baseline...resources, and entrepreneurial visions thereby opening new frontiers for young talent around the world...

...Crystal developed her management skills - training, learning from peers, and being receptive to those ...experiment. Chapter 6: Advice to scientists who are planning on working in industry. The importance of recognizing...our Mentoring for Scientists Series Learn about Turning Your PhD into a Career with Joanne Kamens' AMA ...