CRISPR-directed mitotic recombination enables genetic mapping without crosses

Linkage and association studies have mapped thousands of genomic regions that contribute to phenotypic variation, but narrowing these regions to the underlying causal genes and variants has proven much more challenging. Resolution of genetic mapping is limited by the recombination rate. We developed a method that uses CRISPR to build mapping panels with targeted recombination events. We tested the method by generating a panel with recombination events spaced along a yeast chromosome arm, mapping trait variation, and then targeting a high density of recombination events to the region of interest. Using this approach, we fine-mapped manganese sensitivity to a single polymorphism in the transporter Pmr1. Targeting recombination events to regions of interest allows us to rapidly and systematically identify causal variants underlying trait differences.

Practical Olefin Hydroamination with Nitroarenes

The synthesis and functionalization of amines are fundamentally important in a vast range of chemical contexts. We present an amine synthesis that repurposes two simple feedstock building blocks: olefins and nitro(hetero)arenes. Using readily available reactants in an operationally simple procedure, the protocol smoothly yields secondary amines in a formal olefin hydroamination. Because of the presumed radical nature of the process, hindered amines can easily be accessed in a highly chemoselective transformation. A screen of more than 100 substrate combinations showcases tolerance of numerous unprotected functional groups such as alcohols, amines, and even boronic acids. This process is orthogonal to other aryl amine syntheses, such as the Buchwald-Hartwig, Ullmann, and classical amine-carbonyl reductive aminations, as it tolerates aryl halides and carbonyl compounds.

Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference

The discovery that the machinery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 bacterial immune system can be re- purposed to easily create deletions, insertions and replacements in the mammalian genome has revolutionized the field of genome engineering and re- invigorated the field of gene therapy. Many parallels have been drawn between the newly discovered CRISPR-Cas9 system and the RNA interference (RNAi) pathway in terms of their utility for understanding and interrogating gene function in mammalian cells. Given this similarity, the CRISPR-Cas9 field stands to benefit immensely from lessons learned during the development of RNAi technology. We examine how the history of RNAi can inform today’s challenges in CRISPR-Cas9 genome engineering such as efficiency, specificity, high-throughput screening and delivery for in vivo and therapeutic applications.

A Mouse Geneticist’s Practical Guide to CRISPR Applications

RNA-guided gene drives can efficiently and reversibly bias inheritance in wild yeast

T4 phages against Escherichia coli diarrhea: Potential and problems

Quality-Controlled Small-Scale Production of a Well- Defined Bacteriophage Cocktail for Use in Human Clinical Trials

Phage Therapy - Reviews

1.

Experimental Phage Therapy on Multiple Drug Resistant Pseudomonas aeruginosa Infection in Mice

2013 paper -

Experimental phage therapy of burn wound infection: difficult first steps

Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing

Link (h/t: weigel Lab)

Highly-efficient Cas9-mediated transcriptional programming

Generating genetically modified mice using CRISPR/Cas-mediated genome engineering

Very good paper with detailed protocols -

CRISPR/cas9 Success Stories in Plasmodium

Lane-by-lane Sequencing Using Illumina's Genome Analyzer II

Non-random DNA fragmentation in next-generation sequencing

PacBio P4-C2, P5-C3, etc. - What Do They Mean?

We had been pondering about those cryptic terms and found by asking some people around that the P stands for polymerase and C stands for chemistry. Therefore, P4-C2 means polymerase of fourth generation and chemistry of second generation.

Three Amazing Applications of CRISPR/cas9

Changing genome in plants used to be incredibly difficult, but not any more. Here is an excellent review -

Highly Efficient Transformation of Diatom

Diatoms have very strong silicon cell walls. Transformation is not easy.

Type I, II and III CRISPR/cas Systems

In a 2011 paper, Makarova KS1, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV proposed a new system for classifying various CRISPR/cas systems in bacteria and archaea. The genetically engineered CRISPR/cas9 is from Type II.

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