Host-released microRNA taken up by gut bacteria for bacterial gene regulation

Cell Host & Microbe | The Host Shapes the Gut Microbiota via Fecal MicroRNA

The host gut microbiota varies across species and individuals but is relatively stable over time within an individual. How the host selectively shapes the microbiota is largely unclear. Here, we show that fecal microRNA (miRNA)-mediated inter-species gene regulation facilitates host control of the gut microbiota. miRNAs are abundant in mouse and human fecal samples and present within extracellular vesicles. Cell-specific loss of the miRNA-processing enzyme, Dicer, identified intestinal epithelial cells (IEC) and Hopx-positive cells as predominant fecal miRNA sources. These miRNAs can enter bacteria, such as F. nucleatum and E. coli, specifically regulate bacterial gene transcripts, and affect bacterial growth. IEC-miRNA-deficient (Dicer1ΔIEC) mice exhibit uncontrolled gut microbiota and exacerbated colitis, and WT fecal miRNA transplantation restores fecal microbes and ameliorates colitis. These findings identify both a physiologic role by which fecal miRNA shapes the gut microbiota and a potential strategy for manipulating the microbiome.

Civilization OS 2.0: super-efficient robots

Phys Org | Team reprograms social behavior in carpenter ants using epigenetic drugs

In Florida carpenter ant colonies, distinct worker castes called minors and majors exhibit pronounced differences in social behavior throughout their lives. In a new study published today in Science, a multi-institution team anchored at University of Pennsylvania found that these caste-specific behaviors are not set in stone. Rather, this pioneering study shows that social behavior can be reprogrammed, indicating that an individual's epigenetic, not genetic, makeup determines behavior in ant colonies.

Civilization OS 2.0: patching tools

Science | Biogenic tools for singlecell surgery

Miniaturization has created a world of new medical tools, from pill-cams that can be swallowed and used to photograph the digestive tract, to tiny robots used for minimally invasive surgery. Srivastava et al. pursued this to the level of operating on single cells through the creation of microdaggers. They started with microneedles extracted from plants that are composed of porous calcium oxalate and calcium carbonate. Coating the microneedles with a layer of iron and titanium allowed their manipulation by means of a magnetic field. The tip of the microdagger could drill into a cell, and the porous nature of the needles should make it possible to preload them to deliver drugs to individual cells.

Civilization OS 2.0: making useful things

Science | Printing ceramics into complex shapes

Some materials, such as thermoplastics and metals, are naturally suited to being 3D printed because the individual particles can be fused together by applying heat. In contrast, ceramics do not fuse together the same way. Eckel et al. developed a way to pattern specific preceramic monomers using either 3D printing or stereolithography into complex, curved, and porous shapes. Upon heating, they observed almost no shrinkage, and the formed parts showed exceptional thermal stability.

Civilization OS 2.0: CRISPR getting crisper

Science | Making the correct cut

The CRISPR/Cas system is a prokaryotic immune system that targets and cuts out foreign DNA in bacteria. It has been adopted for gene editing because it can be designed to recognize and cut specific locations in the genome. A challenge in developing clinical applications is the potential for off-target effects that could result in DNA cleavage at the wrong locations. Slaymaker et al. used structure-guided engineering to improve the specificity ofStreptococcus pyogenes Cas9 (SpCas9). They identified enhanced-specificity variants (eSpCas9) that display reduced off-target cleavage while maintaining robust on-target activity

Civilization OS 2.0: hydrogen nano-reactor

Indiana University | IU scientists create 'nano-reactor' for the production of hydrogen biofuel

BLOOMINGTON, Ind. -- Scientists at Indiana University have created a highly efficient biomaterial that catalyzes the formation of hydrogen -- one half of the "holy grail" of splitting H2O to make hydrogen and oxygen for fueling cheap and efficient cars that run on water.

A modified enzyme that gains strength from being protected within the protein shell -- or "capsid" -- of a bacterial virus, this new material is 150 times more efficient than the unaltered form of the enzyme.

The process of creating the material was recently reported in "Self-assembling biomolecular catalysts for hydrogen production" in the journal Nature Chemistry.

"Essentially, we've taken a virus's ability to self-assemble myriad genetic building blocks and incorporated a very fragile and sensitive enzyme with the remarkable property of taking in protons and spitting out hydrogen gas," said Trevor Douglas, the Earl Blough Professor of Chemistry in the IU Bloomington College of Arts and Sciences' Department of Chemistry, who led the study. "The end result is a virus-like particle that behaves the same as a highly sophisticated material that catalyzes the production of hydrogen."

Other IU scientists who contributed to the research were Megan C. Thielges, an assistant professor of chemistry; Ethan J. Edwards, a Ph.D. student; and Paul C. Jordan, a postdoctoral researcher at Alios BioPharma, who was an IU Ph.D. student at the time of the study.

The genetic material used to create the enzyme, hydrogenase, is produced by two genes from the common bacteria Escherichia coli, inserted inside the protective capsid using methods previously developed by these IU scientists. The genes, hyaA and hyaB, are two genes in E. coli that encode key subunits of the hydrogenase enzyme. The capsid comes from the bacterial virus known as bacteriophage P22.

The resulting biomaterial, called "P22-Hyd," is not only more efficient than the unaltered enzyme but also is produced through a simple fermentation process at room temperature.

Civilization OS 2.0: DNA - the most relevant build tool

Science Direct | DNA nanotechnology: new adventures for an old warhorse

As the blueprint of life, the natural exploits of DNA are admirable. However, DNA should not only be viewed within a biological context. It is an elegantly simple yet functionally complex chemical polymer with properties that make it an ideal platform for engineering new nanotechnologies. Rapidly advancing synthesis and sequencing technologies are enabling novel unnatural applications for DNA beyond the realm of genetics. Here we explore the chemical biology of DNA nanotechnology for emerging applications in communication and digital data storage. Early studies of DNA as an alternative to magnetic and optical storage mediums have not only been promising, but have demonstrated the potential of DNA to revolutionize the way we interact with digital data in the future.

for those that have been watching, the newest component to Civilization OS 2.0

Berkeley Lab | How to Train Your Bacterium

Trainers of dogs, horses, and other animal performers take note: a bacterium namedMoorella thermoacetica has been induced to perform only a single trick, but it’s a doozy. Berkeley Lab researchers are using M. thermoacetica to perform photosynthesis – despite being non-photosynthetic – and also to synthesize semiconductor nanoparticles in a hybrid artificial photosynthesis system for converting sunlight into valuable chemical products.

“We’ve demonstrated the first self-photosensitization of a non-photosynthetic bacterium, M. thermoacetica, with cadmium sulfide nanoparticles to produce acetic acid from carbon dioxide at efficiencies and yield that are comparable to or may even exceed the capabilities of natural photosynthesis,” says Peidong Yang, a chemist with Berkeley Lab’s Materials Sciences Division, who led this work.

“The bacteria/inorganic-semiconductor hybrid artificial photosynthesis system we’ve created is self-replicating through the bio-precipitation of cadmium sulfide nanoparticles, which serve as the light harvester to sustain cellular metabolism,” Yang says. “Demonstrating this cyborgian ability to self-augment the functionality of biological systems through inorganic chemistry opens up the integration of biotic and abiotic components for the next generation of advanced solar-to-chemical conversion technologies.”

a soft, juicy target

Dark Reading (Information Week) | Project 'Gridstrike' Finds Substations To Hit For A US Power Grid Blackout

Turns out free and publicly available information can be used to determine the most critical electric substations in the US, which if attacked, could result in a nationwide blackout.

Remember that million-dollar Federal Energy Regulatory Commission (FERC) study in 2013 that found that attacks on just nine electric substations in the US could cause a blackout across the entire grid? Well, a group of researchers decided to see just what it would take for a small group of domestic terrorists to identify the US's most critical substations -- using only free and public sources of information.

While FERC relied on confidential and private information in its shocking report and spent a whopping $1 million in research, researchers at iSIGHT Partners used only so-called open-source intelligence, at a cost of just $15,000 total for 250 man-hours by their estimates. The Wall Street Journal, which obtained and first reported on the confidential FERC report, never publicly revealed the crucial substations ID'ed by FERC for obvious reasons, nor does iSIGHT plan to disclose publicly the ones it found.

Sean McBride, lead analyst for critical infrastructure at iSIGHT, says the goal of his team's so-called "Gridstrike" project was to determine how a small local-grown terror group could sniff out the key substations to target if it were looking to cause a power blackout -- either via physical means, a cyberattack, or a combination of the two. "How would an adversary go about striking at the grid?" McBride said in an interview with Dark Reading. He will speak publicly for the first time about the Gridstrike research next week at the S4x2016 ICS/SCADA conference in Miami.

The iSIGHT researchers drew from a combination of publicly available transmission substation information, maps, Google Earth, and grid congestion documentation, and drew correlations among the substations that serve the top ten cities in the US. They then were able to come up with 15 substations that serve as the backbone for much of the electric grid: knocking out those substations would result in a nationwide blackout, they say.

FERC's report had concluded that the US could suffer a nationwide blackout if nine of the nation's 55,000 electric transmission substations were shut down by attackers.

"We looked at maps and tried to … identify [power] generation facilities, and looked up both centers and what substations are in the middle that would make high-value targets," for example, McBride says. "We tried to identify which substations have the highest number of transmission lines coming in and out," as well, and weighed their significance.