Researchers in the lab of Rice’s Jeffrey Hartgerink have figured out how to 3D-print the well-defined structures using a self-assembling peptide ink. “Eventually, the goal is to print structures with cells and grow mature tissue in a petri dish. These tissues can then be transplanted to treat injuries, or used to learn about how an illness works and to test drug candidates,” said Adam Farsheed, a Rice bioengineering graduate student and lead author of the study, which appeared in Advanced Materials.

“There are 20 naturally occurring amino acids that make up proteins in the human body,” Farsheed said. “Amino acids can be linked together into larger chains, like Lego blocks. When amino acid chains are longer than 50 amino acids, they are called proteins, but when these chains are shorter than 50 amino acids they are called peptides. In this work, we used peptides as our base material in our 3D-printing inks.”

Developed by Hartgerink and collaborators, these “multidomain peptides” are designed to be hydrophobic on one side and hydrophilic on the other. When placed in water, “one of the molecules will flip itself on top of another, creating what we call a hydrophobic sandwich,” Farsheed said.

These sandwiches stack onto one another and form long fibers, which then form a hydrogel, a water-based material with a gelatinous texture that can be useful for a wide range of applications such as tissue engineering, soft robotics and wastewater treatment.

Multidomain peptides have been used for nerve regeneration, cancer treatment and wound healing, and have been shown to promote high levels of cell infiltration and tissue development when implanted in living organisms.

“We know that the multidomain peptides can safely be implanted in the body,” Farsheed said. “But what I was looking to do in this project was to go in a different direction and show that these peptides are a great 3D-printing ink.

“It might be counterintuitive since our material is so soft, but I recognized that our multidomain peptides are an ideal ink candidate because of the way they self-assemble,” he continued. “Our material can reassemble after being deformed, similar to how toothpaste forms a nice fiber when pushed out of a tube.”

Farsheed’s mechanical engineering background allowed him to take an unconventional approach when testing his hypothesis.

“I had more of a brute-force engineering approach where instead of chemically modifying the material to make it more amenable to 3D printing, I tested to see what would happen if I simply added more material,” he said. “I increased the concentration about fourfold, and it worked extremely well.

“There have been only a handful of attempts to 3D-print using other self-assembling peptides, and that work is all great, but this is the first time that any self-assembling peptide system has been used to successfully 3D-print such complex structures,” Farsheed continued.

The structures were printed with either positively charged or negatively charged multidomain peptides, and immature muscle cells placed on the structures behaved differently depending on the charge. Cells remained balled up on the substrate with a negative charge, while on the positively charged material the cells spread out and began to mature.

“It shows that we can control cell behavior using both structural and chemical complexity,” Farsheed said.

Hartgerink is a professor of chemistry and bioengineering and associate chair for undergraduate studies. Farsheed is a bioengineering graduate student and lead author on the study. Additional study co-authors are undergraduate student Adam Thomas and graduate student Brett Pogostin.

The National Institutes of Health (R01 DE021798) and the National Science Foundation Graduate Research Fellowships Program supported the research.

In a new study Professor Nick Wilson, from the University of Otago and independent researcher Dr Matt Boyd, from Adapt Research in New Zealand, say five island nations, including New Zealand, could be well placed to continue to produce food despite the reduced sunlight and cooler temperatures caused by soot in the atmosphere following a nuclear war in the Northern Hemisphere. Australia (an island continent), Iceland, Vanuatu and the Solomon Islands were also likely to have robust food self-sufficiency, even in an extreme nuclear winter.

Their research is published in the international journal Risk Analysis.

Professor Wilson says while New Zealand was likely to continue to be able to produce enough food, its production and distribution was still threatened by the country’s extreme dependence on imported commodities, such as refined fuel.

The researchers investigated the impact of abrupt sunlight reducing scenarios caused by nuclear war, super volcano eruptions or asteroid impacts on agricultural production globally. They applied published crop models under ‘nuclear winter’ conditions to 38 island nations, combining this with other methods to estimate the food calorie supply. They also assessed a range of resilience factors that might protect countries from the impacts of a nuclear winter.

Dr Boyd says although some other nations would likely be able to produce enough food, other factors, such as the collapse of industry and social functioning placed their resilience in doubt.

Professor Wilson says the findings are consistent with a 1980s study on the impact of nuclear war on New Zealand, although the country’s resilience has declined since then as its dependence on imported diesel and digital infrastructure has grown.

“Islands such as New Zealand are often very dependent on imports of refined liquid fuel, may lack energy self-sufficiency and are susceptible to breakdowns and shortages of critical commodities. While New Zealand could divert a high proportion of its dairy exports to supply the local market, it lacks the ability to manufacture many replacement parts for farm and food processing machinery.”

Dr Boyd says the findings of the study reinforce the precarious position many countries would find themselves in during a global catastrophe.

“New Zealand has the potential to preserve an industrial society through this kind of catastrophe, but it is not ‘plug-and-play’. A decent amount of strategic planning needs to happen and across a long period of time, but this planning would have benefits in dealing with a wide range of extreme risks.”

Dr Boyd says the findings show there is a need to analyse nuclear winter and other abrupt sunlight reducing scenarios as part of a comprehensive national risk assessment.

“We are not aware of any plan for this kind of global catastrophe, including whether priorities for rationing have been considered.

“With the Government expected to release New Zealand’s first National Security Strategy this year it is important that the catastrophic risks associated with abrupt sunlight reducing scenarios do not slip through the cracks.”

A study, “Cell-Free Synthesis Goes Electric: Dual Optical and Electronic Biosensor vie Direct Channel Integration into a Supported Membrane Electrode,” was published Jan. 18 in the Synthetic Biology journal of the American Chemical Society.

The bioengineering feat described in the paper uses synthetic biology to re-create a cell membrane and its embedded proteins, which are gatekeepers of cellular functions. A conducting sensing platform allows for an electronic readout when a protein is activated. Being able to test if and how a molecule reacts with proteins in a cell membrane could generate a great many applications.

But embedding membrane proteins into sensors had been notoriously difficult until the study’s authors combined bioelectronic sensors with a new approach to synthesize proteins.

“This technology really allows us to study these proteins in ways that would be incredibly challenging, if not impossible, with current technology,” said first author Zachary Manzer, a doctoral student in the lab of senior author Susan Daniel, the Fred H. Rhodes Professor and director of the Robert Frederick Smith School of Chemical and Biomolecular Engineering at Cornell Engineering.

Proteins within cell membranes serve many important functions, including communicating with the environment, catalyzing chemical reactions, and moving compounds and ions across the membranes. When a membrane protein receptor is activated, charged ions move across a membrane channel, triggering a function in the cell. For example, brain neurons or muscle cells fire when cues from nerves signal charged calcium-ion channels to open.

The researchers have created a biosensor that starts with a conducting polymer, which is soft and easy to work with, on top of a support that together act as an electric circuit that is monitored by a computer. A layer of lipid (fat) molecules, which forms the membrane, lies on top of the polymer, and the proteins of interest are placed within the lipids.

In this proof of concept, the researchers have created a cell-free platform that allowed them to synthesize a model protein directly into this artificial membrane. The system has a dual readout technology built in. Since the components of the sensor are transparent, researchers can use optical techniques, such as engineering proteins that fluoresce when activated, which allows scientists to study the fundamentals via microscope, and observe what happens to the protein itself during a cellular process. They can also record electronic activity to see how the protein is functioning through clever circuit design.

“This really is the first demonstration of leveraging cell-free synthesis of transmembrane proteins into biosensors,” Daniel said. “There’s no reason why we wouldn’t be able to express many different kinds of proteins into this general platform.”

Currently, researchers have used proteins grown and extracted from living cells for similar applications, but given this advance, users won’t have to grow proteins in cells and then harvest and embed them in the membrane platform. Instead, they can synthesize them directly from DNA, the basic template for proteins.

“We can bypass the whole process of the cell as the factory that produces the protein,” Daniel said, “and biomanufacture the proteins ourselves.”

With such a system, a drug chemist interested in a particular protein implicated in a disease might flow potentially therapeutic molecules across that protein to see how it responds. Or a scientist looking to create an environmental sensor could place on the platform a particular protein that is sensitive to a chemical or pollutant, such as those found in lake water.

“If you think of your nose, or your tongue, every time you smell or taste something, ion channels are firing,” Manzer said. Scientists may now take the proteins being activated when we smell something and translate the results into this electronic system to sense things that might be undetectable with a chemical sensor.”

The new sensor opens the door for pharmacologists to research how to create non-opioid pain medicines, or drugs to treat Alzheimer’s or Parkinson’s disease, which interact with cell membrane proteins.

Surajit Ghosh, a postdoctoral researcher in Daniel’s lab, is a co-first author. Neha Kamat, assistant professor of biomedical engineering at Northwestern University, is a senior co-author of the paper.

The study was funded by the National Science Foundation, the Air Force Office of Scientific Research, the American Heart Association, the National Institute of General Medical Sciences and the Defense Advanced Research Projects Agency.

In a new Northwestern University-led study, researchers have, for the first time, deciphered the metabolic mechanisms that enable C. testosteroni to digest the seemingly undigestible. This new information could potentially lead to novel biotechnology platforms that harness the bacteria to help recycle plastic waste.

The research will be published on Feb. 6 in the journal Nature Chemical Biology.

Comamonas species are found nearly everywhere — including in soils and sewage sludge. C. testosteroni first caught researchers’ attention with its natural ability to digest synthetic laundry detergents. After further analysis, scientists discovered that this natural bacterium also breaks down compounds from plastic and lignin (fibrous, woody waste from plants).

Although other researchers have worked to engineer bacteria that can breakdown plastic waste, Aristilde believes bacteria with natural abilities to digest plastics hold more promise for large-scale recycling applications.

“Soil bacteria provide an untapped, underexplored, naturally occurring resource of biochemical reactions that could be exploited to help us deal with the accumulating waste on our planet,” said Northwestern’s Ludmilla Aristilde. “We found that the metabolism of C. testosteroni is regulated on different levels, and those levels are integrated. The power of microbiology is amazing and could play an important role in establishing a circular economy.”

The study was led by Aristilde, an associate professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering, and Ph.D. student Rebecca Wilkes, who is the paper’s first author. The study included collaborators from University of Chicago, Oak Ridge National Laboratory and Technical University of Denmark.

Kicking sugar

Most projects to engineer bacteria involve Escherichia Coli because it is the most well-studied bacterial model organism. But E. Coli, in its natural state, readily consumes various forms of sugar. As long as sugar is available, E. Coli will consume that — and leave the plastic chemicals behind.

“Engineering bacteria for different purposes is a laborious process,” Aristilde said. “It is important to note that C. testosteroni cannot use sugars, period. It has natural genetic limitations that prevent competition with sugars, making this bacterium an attractive platform.”

What C. testosteroni really wants, though, is a different source of carbon. And materials such as plastic and lignin contain compounds with a ring of tasty carbon atoms. While researchers have known that C. testosteroni can digest these compounds, Aristilde and her team wanted to know how.

“These are carbon compounds with complex bond chemistry,” Aristilde said. “Many bacteria have great difficulty breaking them apart.”

Combining different ‘omics’

To study how C. testosteroni degrades these complex forms of carbon, Aristilde and her team combined multiple forms of “omics”-based analyses: transcriptomics (study of RNA molecules); proteomics (study of proteins); metabolomics (study of metabolites); and fluxomics (study of metabolic reactions). Comprehensive “multi-omics” studies are massive undertakings that require a variety of different techniques. Aristilde leads one of few labs that carries out such comprehensive studies.

By examining the relationship among transcriptomics, proteomics, metabolomics and fluxomics, Aristilde and her team mapped the metabolic pathways that bacteria use to degrade plastic and lignin compounds into carbons for food. Ultimately, the team discovered that the bacteria first break down the ring of carbons in each compound. After breaking open the ring into a linear structure, the bacteria continue to degrade it into shorter fragments.

“We started with a plastic or lignin compound that has seven or eight carbons linked together through a core six-carbon circular shape forming the so-called benzene ring,” Aristilde explained. “Then, they break that apart into shorter chains that have three or four carbons. In the process, the bacteria feed those broken-down products into their natural metabolism, so they can make amino acids or DNA to help them grow.”

Upcycling plastic waste

Aristilde also discovered that C. testosteroni can direct carbon through different metabolic routes. These routes can lead to useful by-products that can be used for industrially relevant polymers such as plastics. Aristilde and her team are currently working on a project investigating the metabolism that triggers this polymer biosynthesis.

“These Comamonas species have the potential to make several polymers relevant to biotechnology,” Aristilde said. “This could lead to new platforms that generate plastic, decreasing our dependence on petroleum chemicals. One of my lab’s major goals is to use renewable resources, such as converting waste into plastic and recycling nutrients from wastes. Then, we won’t have to keep extracting petroleum chemicals to make plastics, for instance.”

Aristilde is a member of the Institute for Sustainability and Energy at Northwestern’s Program on Plastics, Ecosystems and Public Health.