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Check in w. Reversing the Biosphere

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Veronique Greenwood, 19 Apr 2018, Quanta, How many genes do cells need? Maybe almost all of them, here.

By knocking out genes three at a time, scientists have painstakingly deduced the web of genetic interactions that keeps a cell alive. Researchers long ago identified essential genes that yeast cells can’t live without, but new work, which appears today in Science, shows that looking only at those gives a skewed picture of what makes cells tick: Many genes that are inessential on their own become crucial as others disappear. The result implies that the true minimum number of genes that yeast — and perhaps, by extension, other complex organisms — need to survive and thrive may be surprisingly large.

About 20 years ago, Charles Boone and Brenda Andrews decided to do something slightly nuts. The yeast biologists, both professors at the University of Toronto, set out to systematically destroy or impair the genes in yeast, two by two, to get a sense of how the genes functionally connected to one another. Only about 1,000 of the 6,000 genes in the yeast genome, or roughly 17 percent, are considered essential for life: If a single one of them is missing, the organism dies. But it seemed that many other genes whose individual absence was not enough to spell the end might, if destroyed in tandem, sicken or kill the yeast. Those genes were likely to do the same kind of job in the cell, the biologists reasoned, or to be involved in the same process; losing both meant the yeast could no longer compensate.

Queensland University of Technology, 2 May 2018, Phys.org, Math sheds light on how living cells ‘think’, here.

Queensland University of Technology (QUT) researcher Dr. Robyn Araujo has developed new mathematics to solve a of how the incredibly complex biological networks within cells can adapt and reset themselves after exposure to a new stimulus.

Her findings, published in Nature Communications, provide a new level of understanding of cellular communication and cellular ‘cognition’, and have potential application in a variety of areas, including new targeted cancer therapies and drug resistance.

 

Carrie Arnold, 2 May 2018, Quanta, Cells talk in a language that looks like viruses, here.

For cells, communication is a matter of life and death. The ability to tell other members of your species — or other parts of the body — that food supplies are running low or that an invading pathogen is near can be the difference between survival and extinction. Scientists have known for decades that cells can secrete chemicals into their surroundings, releasing a free-floating message for all to read. More recently, however, scientists discovered that cells could package their molecular information in what are known as extracellular vesicles. Like notes passed by children in class, the information packaged in an extracellular vesicle is folded and delivered to the recipient.

The past five years have seen an explosion of research into extracellular vesicles. As scientists uncovered the secrets about how the vesicles are made, how they package their information and how they’re released, it became clear that there are powerful similarities between vesicles and viruses.

A small group of researchers, led by Leonid Margolis, a Russian-born virologist at the National Institute of Child Health and Human Development (NICHD), and Robert Gallo, the HIV pioneer at the University of Maryland School of Medicine, has proposed that this similarity is more than mere coincidence. It’s not just that viruses appear to hijack the cellular pathways used to make extracellular vesicles for their own production — or that cells have also taken on some viral components to use in their vesicles. Extracellular vesicles and viruses, Margolis argues, are part of a continuum of membranous particles produced by cells. Between these two extremes are lipid-lined sacs filled with a variety of genetic material and proteins — some from hosts, some from viruses — that cells can use to send messages to one another.

Megan Molteni, 3 May 2018, Wired, Biology will be the next great computing platform, here.

In some ways, Synthego looks like any other Silicon Valleystartup. Inside its beige business park facilities, a five-minute drive from Facebook HQ, rows of nondescript black server racks whir and blink and vent. But inside the metal shelving, the company isn’t pushing around ones and zeros to keep the internet running. It’s making molecules to rewrite the code of life.

Crispr, the powerful gene-editing tool, is revolutionizing the speed and scope with which scientists can modify the DNA of organisms, including human cells. So many people want to use it—from academic researchers to agtech companies to biopharma firms—that new companies are popping up to staunch the demand. Companies like Synthego, which is using a combination of software engineering and hardware automation to become the Amazon of genome engineering. And Inscripta, which wants to be the Apple. And Twist Bioscience, which could be the Intel.

 Carol Lynn Curchoe, 20 May 2018, Medium, Top 10 Crispiest CRISPR Applications, here.

Watch my full CRISPR address at The Oxford Union here.https://youtu.be/QW2TU3p7uyA

There is a heady and hysterical goldrush to CRISPR ALL THE THINGS. And with good reason. These are not your grandpa’s GMOs.

“Second-generation” genome-editing tools can now precisely convert a single base into another without the need for double strand break or incorporating a gene from another organism. At the drop of a “nickase,” C can be converted to T, and A to G, generating a STOP codon and abolishing the need for complex knockout — strategies. (Review CRISPR fundamentals here.)

Like the immeasurable heaven of the Laniakea supercluster, the applications of CRISPR seem to know no bounds. But, the most exciting applications for CRISPR have little to do with gene editing. At the rate of CRISPR publications (1000s per year), you may forgive yourself for not being able to stay up on the literature.

I have compiled some of my favorite (for about a minute) CRISPR applications. The breathless future of CRISPR means these will likely be overturned faster than an ubiquitinated protein.

 

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