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Thursday, April 20, 2017

SHERLOCK to detect early circulating tumor DNA

Early detection of circulating tumor DNA is quite challenging. Read this comment in Cell:

And here comes SHERLOCK(Specific High Sensitivity Enzymatic Reporter UnLOCKing)!
from Nucleic acid detection with CRISPR-Cas13a/C2c2,  a study leaded by Feng Zhang in MIT.

Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting CRISPR effector Cas13a (previously known as C2c2) exhibits a “collateral effect” of promiscuous RNAse activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity. We use this Cas13a-based molecular detection platform, termed SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing), to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify cell-free tumor DNA mutations. Furthermore, SHERLOCK reaction reagents can be lyophilized for cold-chain independence and long-term storage, and readily reconstituted on paper for field applications.

This may be a game-changer in the field.

several very interesting histone modification (epigenetics) papers

If you have read my previous post Misconcept of epigenetics , you will know that: histone modification is not epigenetics!

However, recently, four papers in Science actually showed that histone modifications actually have a component of inheritance:

Causal role for inheritance of H3K27me3 in maintaining the OFF state of a Drosophila HOX gene

DNA sequence-dependent epigenetic inheritance of gene silencing and histone H3K9 methylation

Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA

Transgenerational transmission of environmental information in C. elegans

and one paper in Molecular Cell:

SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication

one more on Nature Genetics:

Interestingly, all the studies were carried out on model organisms: Drosophila and C.elegans!

Read this blog post if you are into this question: what is epigenetics ?

Wednesday, April 19, 2017

sshfs on ubuntu and ssh key

Two things I want to keep a note here:

First, if you ever have set up a shh key for connecting to remote server, you need to be aware that password-less shh key only works when your home directory on the server is not 777 (writable by others).

see this stackexchange post .

Second, I was following to set up sshfs on my ubuntu machine. I put down a gist below.