Ancient Firefly Genes Resurrected & Protein Folding Problem Solved?
By: Niko Mccarty
Tags: Research, News, Biotechnology, Newsletter, Science

🧫 Rapid-Fire Highlights

More research & reviews worth your time

A brief letter to the editor, at Nature Biotechnology, argues that, as DNA synthesis becomes more common, it could be exploited to create pathogenic organisms. The authors argue that such biothreats are possible because “there are no comprehensive databases of pathogenic sequences, and the guidelines — unenforced outside of US National Institutes of Health (NIH) grantees — are outdated.” Nature Biotechnology (Open Access). Link

CRISPR-Cas9 often basks in the limelight, and for good reason. But have you considered the historical events that propelled the discovery of guide RNAs? An intriguing article, by André Schneider, takes a closer look at these crucial CRISPR components. EMBO Reports. Link

An opinion piece argues that the scientific quest to build synthetic life — that is, a replicating cell, built from chemical components — should be carefully considered and regulated. By creating life in the lab, the authors say that: “This blurring of boundaries may in turn change our views and values towards life.” That statement, at least, is not a new opinion. Trends in Biotechnology (Open Access). Link

Baker’s yeast (S. cerevisiae) were engineered to manufacture “bikaverin, a tetracyclic polyketide with antibiotic, antifungal and anticancer properties” at a titer of 202.75 mg/L using glucose or galactose as the carbon source. Nature Communications (Open Access). Link

Engineers have created a genetic circuit, in photosynthetic cyanobacteria, that can oscillate a gene’s expression with the cell’s circadian rhythm. That is, a gene was turned on and off with the rising and setting of the sun. To build it, the researchers used dCas9 and a guide RNA to construct a NAND genetic logic gate that was hooked up to a circadian promoter (“the purF gene; peak expression at dawn”). ACS Synthetic Biology. Link

George Church’s group has unveiled the ‘Human TFome’, which is a collection of 1,564 transcription factor genes found in human cells. They tested the library of transcription factors in three different types of human pluripotent stem cells, discovering that “290 TFs, including 241 that were previously unreported” were able to induce the cells to differentiate in 4 days. They also used some of the transcription factor genes to program the stem cells to differentiate into neurons, fibroblasts, and other types of cells. Nature Biotechnology. Link

The liver is built from two types of cells: hepatocytes and ductal cells. A new paper explains how to turn human hepatocyte cells into organoids, and also includes instructions for knocking out or modifying multiple genes at once, with CRISPR, in these organoids. Be warned: “The protocols to genome engineer human liver ductal organoids and human fetal hepatocyte organoids take 2–3 months.” Nature Protocols. Link

In a brilliant new study, researchers used a modified version of the FISH method (which stands for fluorescence in situ hybridization) to study the spatial networks of microbes in mouse guts. They found that, when a mouse is treated with antibiotics, the spatial networks of bacteria in the gut are profoundly disrupted. The researchers also used the method to study the microbiome living on human teeth. Nature. Link

Synthetic silks could, one day, be turned into printable ink and loaded into 3D printers at home. Imagine creating an ultra-sturdy, but lightweight, shirt in your living room. That’s (kind of) the topic of this compelling review. Trends in Biotechnology. Link

A huge CRISPR activation screen experiment, using deactivated Cas9, was performed to study which transcription factors — proteins that control a gene’s expression — are involved in determining how a stem cell changes into a neuron. Duke University also published a press release on this study. Cell Reports (Open Access). Link

Researchers have engineered E. coli bacteria to produce dihydroquercetin — a flavonoid found in onions, milk thistle and tamarind seeds — in a one-step enzymatic reaction from glycerol. To do that, they took a gene from Arabidopsis thaliana, a type of weed, and expressed it in the bacterial cells. bioRxiv (Open Access). Link

Cytokines are itty-bitty proteins that act as signaling, or ‘immunomodulation’, compounds. That is, they play a role in the immune system, and tweak how it responds to foreign bacterial or viral invaders, among other things. A new Perspective article takes a look at how synthetic biology can be used to tune and tweak cytokine signaling and, thus, control an immune response. Science (Open Access). Link

Peroxisomes are organelles that float in the cytoplasm of eukaryotic cells. For a new study, researchers engineered peroxisomes, in yeast, to produce geranyl diphosphate — a critical starting point for manufacturing loads of different chemicals, like cannabinoids, camphor, and menthol. PNAS. Link

Take a dozen yeast cells, and let them divide. If you watch very carefully (with a microscope), you will notice that each cell in the population divides at a different time; their division is asynchronous. For a new study, researchers placed genetically-engineered yeast cells into a microfluidic device, attached the device to a microscope, and carefully controlled their growth medium to determine when each cell divides. In other words, they built an automated, robotic system to synchronize yeast cell divisions. Cyber-Yeast! bioRxiv (Open Access). Link

A new Perspective article discusses the myriad biological problems that can be solved, or studied, by constructing genomes from scratch. This piece comes at an intriguing time, especially as researchers wait to hear about final results from the Synthetic Yeast 2.0 project, which aims to build a modified version of the Baker’s yeast genome from scratch. Nature Communications (Open Access). Link

For a new study, researchers used a deep learning model — trained on 20,000 mRNA datasets, taken from seven organisms, including bacteria and humans — to predict the number of mRNA transcripts from a DNA sequence alone. That is, given only a DNA sequence, the researchers can predict how many mRNA copies it will produce. Nature Communications (Open Access). Link

When engineering a cell, researchers often want to pack proteins together, really closely, to speed up a chemical reaction. For a new preprint, researchers created light-inducible cellular compartments. When they shine light on E. coli cells, a desired protein can very quickly form a compartment in the cytosol, enhancing the reaction efficiency. When they stop shining the light, the proteins disperse back into the cytosol after about 15 minutes. bioRxiv (Open Access). Link