Tag Archives: Michigan State University

Agriculture and gene editing … shades of the AquAdvantage salmon

Salmon are not the only food animals being genetically altered (more about that later in this post) we can now add cows, pigs, and more.

This November 15, 2018 article by Candice Choi on the Huffington Post website illustrates some of the excitement and terror associated with gene editing farm animals,

A company wants to alter farm animals by adding and subtracting genetic traits in a lab. It sounds like science fiction, but Recombinetics sees opportunity for its technology in the livestock industry.

But first, it needs to convince regulators that gene-edited animals are no different than conventionally bred ones. To make the technology appealing and to ease any fears that it may be creating Franken-animals, [emphasis mine] Recombinetics isn’t starting with productivity. Instead, it’s introducing gene-edited traits as a way to ease animal suffering.

“It’s a better story to tell,” said Tammy Lee, CEO of the St. Paul, Minnesota-based company.

For instance, animal welfare advocates have long criticized the way farmers use caustic paste or hot irons to dehorn dairy cows so the animals don’t harm each other. Recombinetics snips out the gene for growing horns so the procedure is unnecessary. [emphases mine]

Last year, a bull gene-edited by Recombinetics to have the dominant hornless trait sired several offspring. All were born hornless as expected, and are being raised at the University of California, Davis. Once the female offspring starts lactating, its milk will be tested for any abnormalities.

Another Recombinetics project: castration-free pigs.

When male piglets go through puberty, their meat can take on an unpleasant odour, something known as “boar taint.” To combat it, farmers castrate pigs, a procedure animal welfare advocates say is commonly performed without painkillers. Editing genes so that pigs never go through puberty would make castration unnecessary.

Also in development are dairy cows that could withstand higher temperatures, so the animals don’t suffer in hotter climates. [emphasis mine]

..

Before food from gene-edited animals can land on dinner tables, however, Recombinetics has to overcome any public unease about the technology.

Beyond worries about “playing God,” it may be an uncomfortable reminder of how modern food production already treats animals, said Paul Thompson, a professor of agriculture at Michigan State University.

“There’s an ethical question that’s been debated for at least the last 20 years, of whether you need to change the animal or change the system,” Thompson said.

Support for gene editing will also likely depend on how the technology is used: whether it’s for animal welfare, productivity or disease resistance. In August, a Pew study found 43 per cent of Americans supported genetically engineered animals for more nutritious meat.

Choi has written an interesting article, which includes a picture of the hornless cows embedded in the piece. One note: Choi makes reference to a milk glut. As far as I’m aware that’s not the case in Canada (at this time) but it is a problem in the US where in 2015 (?) farmers dumped some 43  million gallons of milk (October 12, 2016 article by Martha C. White for Money magazine).

As for the salmon, I’ve covered that story a few times during its journey to being approved for human consumption i Canada (my May 20, 2016 posting) to the discovery in 2017 that the genetically modified product, AquAdvantage salmon, had been introduced into the market, (from my Sept. 13, 2017 posting; scroll down about 40R of the way),

“Since the 2016 approval, AquAdvantage salmon, 4.5M tonnes has been sold in Canada according to an Aug. 8, 2017 article by Sima Shakeri for Huffington Post …”

After decades of trying to get approval by in North America, genetically modified Atlantic salmon has been sold to consumers in Canada.

AquaBounty Technologies, an American company that produces the Atlantic salmon, confirmed it had sold 4.5 tonnes of the modified fish on August 4 [2017], the Scientific American reported.

The fish have been engineered with a growth hormone gene from Chinook salmon to grow faster than regular salmon and require less food. They take about 18 months to reach market size, which is much quicker than the 30 months or so for conventional salmon.

The Washington Post wrote AquaBounty’s salmon also contains a gene from the ocean pout that makes the salmon produce the growth hormone gene all-year-round.

The company produces the eggs in a facility in P.E.I. [Prince Edward Island; a province in Canada], which is currently being expanded, and then they’re shipped to Panama where the fish are raised.

….

There was a bit of a kerfuffle about the whole affair but it seems Canadians have gone on to embrace the genetically modified product. At least that’s Christine Blank’s perspective in her Sept. 13, 2018 article (Canada, US embrace AquAdvantage GMO salmon, Brazil and China may be next) for the Genetic Literacy Project website,

Genetically modified salmon firm AquaBounty has found “very enthusiastic” buyers in Canada, according to president and CEO Ronald Stotish.

The first sale of the Maynard, Massachusetts, U.S.A.-based firm’s AquAdvantage salmon was made last June [2017], when unnamed buyers in Canada bought five metric tons at the going rate of traditional farmed Atlantic salmon, according to the company. Since then, AquaBounty has sold 10 additional metric tons of its AquAdvantage salmon to buyers in Canada

Meanwhile, Stotish revealed that AquAdvantage will be sold in the U.S. through established distributors.

“Once [AquaBounty salmon] is established in the market, the option for branding as a ‘sustainably produced’ food item can be considered,” he told investors.

Alex Gillis’ June 5, 2018 article for Macleans magazine suggests that Canadians may be a bit more doubtful about GM (genetically modified) salmon than Stotish seems to be believe,

An Ipsos Reid poll conducted for the Canadian Biotechnology Action Network in 2015 suggested that Canadians are concerned about GM foods, in spite of government assurances that they’re safe. About 60 per cent of respondents opposed genetically modifying crops and animals for food; nearly half supported a ban on all GM food. More than 20 years of surveys indicate that the vast majority of Canadians want to know when they’re eating GMOs. Fully 88 per cent of those polled in the 2015 survey said they want mandatory labelling.

Their concern hasn’t escaped the notice of those who raise and sell much of the salmon consumed in this country. Five years ago, Marine Harvest, one of the world’s largest producers of farmed salmon, called for labelling of GMOs. Today, it says that it doesn’t grow, sell or research GM salmon, a policy it shares with major salmon producers in Canada. And most big grocery retailers have stated they don’t want GM salmon. When contacted by Maclean’s for this story, Metro, Sobeys, Wal-Mart and Loblaws—four of Canada’s five largest food retailers—declared that none of AquaBounty’s GM salmon from 2017 was sold in their stores, saying neither Sea Delight Canada nor Montreal Fish Co. supplied them with Atlantic salmon at the time.

“I’m happy to report that we don’t source salmon from these two companies,” says Geneviève Grégoire, communications adviser with Metro Richelieu Inc., which operates or supplies 948 food stores in Quebec and Ontario, including Metro, Super C, Food Basics, Adonis and Première Moisson. “As we said before, we didn’t and will not sell GM Atlantic salmon.”

If you’re looking for a more comprehensive and critical examination of the issue, read Lucy Sharratt’s Sept. 1, 2018 article for the Canadian Centre for Policy Alternatives (CCPA).

Artificial intelligence used for wildlife protection

PAWS (Protection Assistant for Wildlife Security), an artificial intelligence (AI) program, has been tested in Uganda and Malaysia. according to an April 22, 2016 US National Science Foundation (NSF) news release (also on EurekAlert but dated April 21, 2016), Note: Links have been removed,

A century ago, more than 60,000 tigers roamed the wild. Today, the worldwide estimate has dwindled to around 3,200. Poaching is one of the main drivers of this precipitous drop. Whether killed for skins, medicine or trophy hunting, humans have pushed tigers to near-extinction. The same applies to other large animal species like elephants and rhinoceros that play unique and crucial roles in the ecosystems where they live.

Human patrols serve as the most direct form of protection of endangered animals, especially in large national parks. However, protection agencies have limited resources for patrols.

With support from the National Science Foundation (NSF) and the Army Research Office, researchers are using artificial intelligence (AI) and game theory to solve poaching, illegal logging and other problems worldwide, in collaboration with researchers and conservationists in the U.S., Singapore, Netherlands and Malaysia.

“In most parks, ranger patrols are poorly planned, reactive rather than pro-active, and habitual,” according to Fei Fang, a Ph.D. candidate in the computer science department at the University of Southern California (USC).

Fang is part of an NSF-funded team at USC led by Milind Tambe, professor of computer science and industrial and systems engineering and director of the Teamcore Research Group on Agents and Multiagent Systems.

Their research builds on the idea of “green security games” — the application of game theory to wildlife protection. Game theory uses mathematical and computer models of conflict and cooperation between rational decision-makers to predict the behavior of adversaries and plan optimal approaches for containment. The Coast Guard and Transportation Security Administration have used similar methods developed by Tambe and others to protect airports and waterways.

“This research is a step in demonstrating that AI can have a really significant positive impact on society and allow us to assist humanity in solving some of the major challenges we face,” Tambe said.

PAWS puts the claws in anti-poaching

The team presented papers describing how they use their methods to improve the success of human patrols around the world at the AAAI Conference on Artificial Intelligence in February [2016].

The researchers first created an AI-driven application called PAWS (Protection Assistant for Wildlife Security) in 2013 and tested the application in Uganda and Malaysia in 2014. Pilot implementations of PAWS revealed some limitations, but also led to significant improvements.

Here’s a video describing the issues and PAWS,

For those who prefer to read about details rather listen, there’s more from the news release,

PAWS uses data on past patrols and evidence of poaching. As it receives more data, the system “learns” and improves its patrol planning. Already, the system has led to more observations of poacher activities per kilometer.

Its key technical advance lies in its ability to incorporate complex terrain information, including the topography of protected areas. That results in practical patrol routes that minimize elevation changes, saving time and energy. Moreover, the system can also take into account the natural transit paths that have the most animal traffic – and thus the most poaching – creating a “street map” for patrols.

“We need to provide actual patrol routes that can be practically followed,” Fang said. “These routes need to go back to a base camp and the patrols can’t be too long. We list all possible patrol routes and then determine which is most effective.”

The application also randomizes patrols to avoid falling into predictable patterns.

“If the poachers observe that patrols go to some areas more often than others, then the poachers place their snares elsewhere,” Fang said.

Since 2015, two non-governmental organizations, Panthera and Rimbat, have used PAWS to protect forests in Malaysia. The research won the Innovative Applications of Artificial Intelligence award for deployed application, as one of the best AI applications with measurable benefits.

The team recently combined PAWS with a new tool called CAPTURE (Comprehensive Anti-Poaching Tool with Temporal and Observation Uncertainty Reasoning) that predicts attacking probability even more accurately.

In addition to helping patrols find poachers, the tools may assist them with intercepting trafficked wildlife products and other high-risk cargo, adding another layer to wildlife protection. The researchers are in conversations with wildlife authorities in Uganda to deploy the system later this year. They will present their findings at the 15th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2016) in May.

“There is an urgent need to protect the natural resources and wildlife on our beautiful planet, and we computer scientists can help in various ways,” Fang said. “Our work on PAWS addresses one facet of the problem, improving the efficiency of patrols to combat poaching.”

There is yet another potential use for PAWS, the prevention of illegal logging,

While Fang and her colleagues work to develop effective anti-poaching patrol planning systems, other members of the USC team are developing complementary methods to prevent illegal logging, a major economic and environmental problem for many developing countries.

The World Wildlife Fund estimates trade in illegally harvested timber to be worth between $30 billion and $100 billion annually. The practice also threatens ancient forests and critical habitats for wildlife.

Researchers at USC, the University of Texas at El Paso and Michigan State University recently partnered with the non-profit organization Alliance Vohoary Gasy to limit the illegal logging of rosewood and ebony trees in Madagascar, which has caused a loss of forest cover on the island nation.

Forest protection agencies also face limited budgets and must cover large areas, making sound investments in security resources critical.

The research team worked to determine the balance of security resources in which Madagascar should invest to maximize protection, and to figure out how to best deploy those resources.

Past work in game theory-based security typically involved specified teams — the security workers assigned to airport checkpoints, for example, or the air marshals deployed on flight tours. Finding optimal security solutions for those scenarios is difficult; a solution involving an open-ended team had not previously been feasible.

To solve this problem, the researchers developed a new method called SORT (Simultaneous Optimization of Resource Teams) that they have been experimentally validating using real data from Madagascar.

The research team created maps of the national parks, modeled the costs of all possible security resources using local salaries and budgets, and computed the best combination of resources given these conditions.

“We compared the value of using an optimal team determined by our algorithm versus a randomly chosen team and the algorithm did significantly better,” said Sara Mc Carthy, a Ph.D. student in computer science at USC.

The algorithm is simple and fast, and can be generalized to other national parks with different characteristics. The team is working to deploy it in Madagascar in association with the Alliance Vohoary Gasy.

“I am very proud of what my PhD students Fei Fang and Sara Mc Carthy have accomplished in this research on AI for wildlife security and forest protection,” said Tambe, the team lead. “Interdisciplinary collaboration with practitioners in the field was key in this research and allowed us to improve our research in artificial intelligence.”

Moreover, the project shows other computer science researchers the potential impact of applying their research to the world’s problems.

“This work is not only important because of the direct beneficial impact that it has on the environment, protecting wildlife and forests, but on the way that it can inspire other to dedicate their efforts into making the world a better place,” Mc Carthy said.

The curious can find out more about Panthera here and about Alliance Vohoary Gasy here (be prepared to use your French language skills). Unfortunately, I could not find more information about Rimbat.

Listening to bacteria for superior organic nanowires

Researchers at Michigan State University (MSU; US) claim to have  discovered organic nanowires that are superior to the engineered kind according to a March 24, 2016 news item on ScienceDaily,

A microbial protein fiber discovered by a Michigan State University scientist transports charges at rates high enough to be applied in humanmade nanotechnologies.

The discovery, featured in the current issue of Scientific Reports, describes the high-speed protein fiber produced by uranium-reducing Geobacter bacteria. The fibers are hair-like protein filaments called “pili” that have the unique property of transporting charges at speeds of 1 billion electrons per second.

A March 24, 2016 MSU news release, which originated the news item, provides more information,

“This microbial nanowire is made of but a single peptide subunit,” said Gemma Reguera, lead author and MSU microbiologist. “Being made of protein, these organic nanowires are biodegradable and biocompatible. This discovery thus opens many applications in nanoelectronics such as the development of medical sensors and electronic devices that can be interfaced with human tissues.”

Since existing nanotechnologies incorporate exotic metals into their designs, the cost of organic nanowires is much more cost effective as well, she added.

How the nanowires function in nature is comparable to breathing. Bacterial cells, like humans, have to breathe. The process of respiration involves moving electrons out of an organism. Geobacter bacteria use the protein nanowires to bind and breathe metal-containing minerals such as iron oxides and soluble toxic metals such as uranium. The toxins are mineralized on the nanowires’ surface, preventing the metals from permeating the cell.

Reguera’s team purified their protein fibers, which are about 2 nanometers in diameter. Using the same toolset of nanotechnologists, the scientists were able to measure the high velocities at which the proteins were passing electrons.

“They are like power lines at the nanoscale,” Reguera said. “This also is the first study to show the ability of electrons to travel such long distances — more than a 1,000 times what’s been previously proven — along proteins.”

The researchers also identified metal traps on the surface of the protein nanowires that bind uranium with great affinity and could potentially trap other metals. These findings could provide the basis for systems that integrate protein nanowires to mine gold and other precious metals, scrubbers that can be deployed to immobilize uranium at remediation sites and more.

Reguera’s nanowires also can be modified to seek out other materials in which to help them breathe.

“The Geobacter cells are making these protein fibers naturally to breathe certain metals. We can use genetic engineering to tune the electronic and biochemical properties of the nanowires and enable new functionalities. We also can mimic the natural manufacturing process in the lab to mass-produce them in inexpensive and environmentally friendly processes,” Reguera said. “This contrasts dramatically with the manufacturing of humanmade inorganic nanowires, which involve high temperatures, toxic solvents, vacuums and specialized equipment.”

This discovery came from truly listening to bacteria, Reguera said.

“The protein is getting the credit, but we can’t forget to thank the bacteria that invented this,” she said. “It’s always wise to go back and ask bacteria what else they can teach us. In a way, we are eavesdropping on microbial conversations. It’s like listening to our elders, learning from their wisdom and taking it further.”

Asking what else bacteria can teach us? That’s a lovely thought and  different from the still common ‘let’s wipe them all out’ approach to bacteria. It suggests scientific research that is more amenable to sharing the planet with all forms of life.

Here’s a link to and a citation for the paper,

Thermally activated charge transport in microbial protein nanowires by Sanela Lampa-Pastirk, Joshua P. Veazey, Kathleen A. Walsh, Gustavo T. Feliciano, Rebecca J. Steidl, Stuart H. Tessmer, & Gemma Reguera. Scientific Reports 6, Article number: 23517 (2016) doi:10.1038/srep23517 Published online: 24 March 2016

This paper is open access.

Nanorobotic approach to studying how skin falls apart

Scientists have combined robotic techniques with atomic force microscopy to achieve understanding of how skin falls apart at the nanoscale. From a Sept. 11, 2014 news item on Azonano,

University at Buffalo researchers and colleagues studying a rare, blistering disease have discovered new details of how autoantibodies destroy healthy cells in skin. This information provides new insights into autoimmune mechanisms in general and could help develop and screen treatments for patients suffering from all autoimmune diseases, estimated to affect 5-10 percent of the U.S. population.

“Our work represents a unique intersection between the fields of biology and engineering that allowed for entirely new investigational strategies applied to the study of clinical disease,” says Animesh A. Sinha, MD, PhD, Rita M. and Ralph T. Behling Professor and chair of the Department of Dermatology in the UB School of Medicine and Biomedical Sciences and senior author on the study.

A Sept. 9, 2014 University of Buffalo news release by Ellen Goldbaum (also on EurekAlert dated Sept. 10, 2014), which originated the news item, describes the condition and the research in more detail,

PV [Pemphigus Vulgaris] results in the often painful blistering of the skin and mucous membranes. Generally treated with corticosteroids and other immunosuppressive agents, the condition is life-threatening if untreated.

Sinha’s research team, in collaboration with scientists at Michigan State University, describe the use of atomic force microscopy (AFM), a technique originally developed to study nonbiological materials, to look at cell junctions and how they rupture, a process called acantholysis.

“It has been very difficult to study cell junctions, which maintain the skin’s barrier function by keeping cells attached to each other,” says Sinha. “These junctions, micron-sized spots on cell membranes, are very complex molecular structures. Their small size has made them resistant to detailed investigation.”

Sinha’s interest lies in determining what destroys those junctions in Pemphigus Vulgaris.

“We haven’t understood why some antibodies generated by the condition cause blisters and why other antibodies it generates do not,” says Sinha.

By studying the connections between skin cells using AFM and other techniques that probe cells at the nanoscale, Sinha and his colleagues report that pathogenic antibodies change structural and functional properties of skin cells in distinct ways.

“Our data suggest a new model for the action of autoantibodies in which there are two steps or ‘hits’ in the development of lesions,” says Sinha. “The first hit results in the initial separation of cells but only the pathogenic antibodies drive further intracellular changes that lead to the breaking of the cell junction and blistering.”

The researchers examined the cells using AFM, which requires minimal sample preparation and provides three-dimensional images of cell surfaces.

The AFM tip acts like a little probe, explains Sinha. When tapped against a cell, it sends back information regarding the cell’s mechanical properties, such as thickness, elasticity, viscosity and electrical potential.

“We combined existing and novel nanorobotic techniques with AFM, including a kind of nanodissection, where we physically detached cells from each other at certain points so that we could test what that did to their mechanical and biological functions,” Sinha adds.

Those data were then combined with information about functional changes in cell behavior to develop a nanomechanical profile, or phenotype, for specific cellular states.

He also envisions that this kind of nanomechanical phenotyping should allow for the development of predictive models for cellular behavior for any kind of cell.

“Ultimately, in the case of autoimmunity, we should be able to use these techniques as a high-throughput assay to screen hundreds or thousands of compounds that might block the effects of autoantibodies and identify novel agents with therapeutic potential in given individuals,” says Sinha.  “Such strategies aim to advance us toward a new era of personalized medicine”.

I found some more information about the nanorobotics technique, mentioned in the news release, in the researchers’ paper (Note: A link has been removed),

Nanorobotic surgery

AFM-based nanorobotics enables accurate and convenient sample manipulation and drug delivery. This capability was used in the current study to control the AFM tip position over the intercellular junction area, and apply vertical indentation forces, so that bundles of intercellular adhesion structures can be dissected precisely with an accuracy of less than 100 nm in height. We used a tip sharp enough (2 nm in tip apex diameter) to penetrate the cell membrane and the intermediate filaments. It has been shown that intermediate filaments have extremely high tensile strength by in vitro AFM stretching [19]. Thus, the vertical force and moving speed of the AFM cantilever (0.06 N/m in vertical spring constant) was controlled at a vertical force of 5 nN at an indentation speed of 0.1 µm/s to guarantee the rupture of the filament and to partially dissect cell adhesion structures between two neighboring cells.

For those who want to know more, here’s a link to and a citation for the paper,

Nanorobotic Investigation Identifies Novel Visual, Structural and Functional Correlates of Autoimmune Pathology in a Blistering Skin Disease Model by Kristina Seiffert-Sinha, Ruiguo Yang, Carmen K. Fung, King W. Lai, Kevin C. Patterson, Aimee S. Payne, Ning Xi, Animesh A. Sinha. PLOSONE Published: September 08, 2014 DOI: 10.1371/journal.pone.0106895

This is an open access paper.

Call for papers (IEEE [Institute for Electrical and Electronics Engineers] 10th annual NEMS conference in 2015

The deadline for submissions is Nov. 15, 2014 and here’s more from the notice on the IEEE [Institute for Electrical and Electronics Engineers] website for the IEEE-NEMS [nano/micro engineered and moecular systems] 2015,

The 10th Annual IEEE International Conference on Nano/ Micro Engineered and Molecular Systems (IEEE-NEMS 2015)
Xi’an, China
April 7-11, 2015
http://www.ieee-nems.org/2015/

The IEEE International Conference on Nano/Micro Engineered and Molecular Systems (IEEE-NEMS) is a series of successful conferences that began in Zhuhai, China in 2006, and has been a premier IEEE annual conference series held mostly in Asia which focuses on MEMS, nanotechnology, and molecular technology. Prior conferences were held in Waikiki Beach (USA, 2014), Suzhou (China, 2013), Kyoto (Japan, 2012), Kaohsiung (Taiwan, 2011), Xiamen (China, 2010), Shenzhen (China, 2009), Hainan Island (China, 2008), Bangkok (Thailand, 2007), and Zhuhai (China, 2006). The conference typically has ~350 attendees with participants from more than 20 countries and regions world-wide.

In 2015, the conference will be held in Xi’an, one of the great ancient capitals of China. Xi’an has more than 3,100 years of history, and was known as Chang’an before the Ming dynasty. Xi’an is the starting point of the Silk Road and home to the Terracotta Army of Emperor Qin Shi Huang.

We now invite contributions describing the latest scientific and technological research results in subjects including, but are not limited to:

  • Nanophotonics
  • Nanomaterials
  • Nanobiology, Nanomedicine, Nano-bio-informatics
  • Micro/Nano Fluidics, BioMEMS, and Lab-on-Chips
  • Molecular Sensors, Actuators, and Systems
  • Micro/Nano Sensors, Actuators, and Systems
  • Carbon Nanotube/Graphene/Diamond based Devices
  • Micro/Nano/Molecular Heat Transfer & Energy Conversion
  • Micro/Nano/Molecular Fabrication
  • Nanoscale Metrology
  • Micro/Nano Robotics, Assembly & Automation
  • Integration & Application of MEMS/NEMS
  • Flexible MEMS, Sensors and Printed Electronics
  • Commercialization of MEMS/NEMS/Nanotechnology
  • Nanotechnology Safety and Education

Important Dates:

Nov. 15, 2014 – Abstract/Full Paper Submission
Dec. 31, 2014 – Notification of Acceptance
Jan. 31, 2015 – Final Full Paper Submission

We hope to see you at Xi’an, China, in April 2015!

General Chair: Ning Xi, Michigan State University, USA
Program Chair: Guangyong Li, University of Pittsburgh, USA
Organizing Chair: Wen J. Li, City University of Hong Kong, Hong Kong
Local Arrangement Chair: Xiaodong Zhang, Xi’an Jiaotong University, China

The 2015 IEEE-NEMS webpage offers more general information about the conference,

The IEEE-NEMS is a key conference series sponsored by the IEEE Nanotechnology Council focusing on advanced research areas related to MEMS, nanotechnology, and molecular technology. … The conference typically has ~350 attendees with participants from more than 20 countries and regions world-wide.

Good luck!

Good lignin, bad lignin: Florida researchers use plant waste to create lignin nanotubes while researchers in British Columbia develop trees with less lignin

An April 4, 2014 news item on Azonano describes some nanotube research at the University of Florida that reaches past carbon to a new kind of nanotube,

Researchers with the University of Florida’s [UF] Institute of Food and Agricultural Sciences took what some would consider garbage and made a remarkable scientific tool, one that could someday help to correct genetic disorders or treat cancer without chemotherapy’s nasty side effects.

Wilfred Vermerris, an associate professor in UF’s department of microbiology and cell science, and Elena Ten, a postdoctoral research associate, created from plant waste a novel nanotube, one that is much more flexible than rigid carbon nanotubes currently used. The researchers say the lignin nanotubes – about 500 times smaller than a human eyelash – can deliver DNA directly into the nucleus of human cells in tissue culture, where this DNA could then correct genetic conditions. Experiments with DNA injection are currently being done with carbon nanotubes, as well.

“That was a surprising result,” Vermerris said. “If you can do this in actual human beings you could fix defective genes that cause disease symptoms and replace them with functional DNA delivered with these nanotubes.”

An April 3, 2014 University of Florida’s Institute of Food and Agricultural Sciences news release, which originated the news item, describes the lignin nanotubes (LNTs) and future applications in more detail,

The nanotube is made up of lignin from plant material obtained from a UF biofuel pilot facility in Perry, Fla. Lignin is an integral part of the secondary cell walls of plants and enables water movement from the roots to the leaves, but it is not used to make biofuels and would otherwise be burned to generate heat or electricity at the biofuel plant. The lignin nanotubes can be made from a variety of plant residues, including sorghum, poplar, loblolly pine and sugar cane. [emphasis mine]

The researchers first tested to see if the nanotubes were toxic to human cells and were surprised to find that they were less so than carbon nanotubes. Thus, they could deliver a higher dose of medicine to the human cell tissue.  Then they researched if the nanotubes could deliver plasmid DNA to the same cells and that was successful, too. A plasmid is a small DNA molecule that is physically separate from, and can replicate independently of, chromosomal DNA within a cell.

“It’s not a very smooth road because we had to try different experiments to confirm the results,” Ten said. “But it was very fruitful.”

In cases of genetic disorders, the nanotube would be loaded with a functioning copy of a gene, and injected into the body, where it would target the affected tissue, which then makes the missing protein and corrects the genetic disorder.

Although Vermerris cautioned that treatment in humans is many years away, among the conditions that these gene-carrying nanotubes could correct include cystic fibrosis and muscular dystrophy. But, he added, that patients would have to take the corrective DNA via nanotubes on a continuing basis.

Another application under consideration is to use the lignin nanotubes for the delivery of chemotherapy drugs in cancer patients. The nanotubes would ensure the drugs only get to the tumor without affecting healthy tissues.

Vermerris said they created different types of nanotubes, depending on the experiment. They could also adapt nanotubes to a patient’s specific needs, a process called customization.

“You can think about it as a chest of drawers and, depending on the application, you open one drawer or use materials from a different drawer to get things just right for your specific application,” he said.  “It’s not very difficult to do the customization.”

The next step in the research process is for Vermerris and Ten to begin experiments on mice. They are in the application process for those experiments, which would take several years to complete.  If those are successful, permits would need to be obtained for their medical school colleagues to conduct research on human patients, with Vermerris and Ten providing the nanotubes for that research.

“We are a long way from that point,” Vermerris said. “That’s the optimistic long-term trajectory.”

I hope they have good luck with this work. I have emphasized the plant waste the University of Florida scientists studied due to the inclusion of poplar, which is featured in the University of British Columbia research work also being mentioned in this post.

Getting back to Florida for a moment, here’s a link to and a citation for the paper,

Lignin Nanotubes As Vehicles for Gene Delivery into Human Cells by Elena Ten, Chen Ling, Yuan Wang, Arun Srivastava, Luisa Amelia Dempere, and Wilfred Vermerris. Biomacromolecules, 2014, 15 (1), pp 327–338 DOI: 10.1021/bm401555p Publication Date (Web): December 5, 2013
Copyright © 2013 American Chemical Society

This is an open access paper.

Meanwhile, researchers at the University of British Columbia (UBC) are trying to limit the amount of lignin in trees (specifically poplars, which are not mentioned in this excerpt but in the next). From an April 3, 2014 UBC news release,

Researchers have genetically engineered trees that will be easier to break down to produce paper and biofuel, a breakthrough that will mean using fewer chemicals, less energy and creating fewer environmental pollutants.

“One of the largest impediments for the pulp and paper industry as well as the emerging biofuel industry is a polymer found in wood known as lignin,” says Shawn Mansfield, a professor of Wood Science at the University of British Columbia.

Lignin makes up a substantial portion of the cell wall of most plants and is a processing impediment for pulp, paper and biofuel. Currently the lignin must be removed, a process that requires significant chemicals and energy and causes undesirable waste.

Researchers used genetic engineering to modify the lignin to make it easier to break down without adversely affecting the tree’s strength.

“We’re designing trees to be processed with less energy and fewer chemicals, and ultimately recovering more wood carbohydrate than is currently possible,” says Mansfield.

Researchers had previously tried to tackle this problem by reducing the quantity of lignin in trees by suppressing genes, which often resulted in trees that are stunted in growth or were susceptible to wind, snow, pests and pathogens.

“It is truly a unique achievement to design trees for deconstruction while maintaining their growth potential and strength.”

The study, a collaboration between researchers at the University of British Columbia, the University of Wisconsin-Madison, Michigan State University, is a collaboration funded by Great Lakes Bioenergy Research Center, was published today in Science.

Here’s more about lignin and how a decrease would free up more material for biofuels in a more environmentally sustainable fashion, from the news release,

The structure of lignin naturally contains ether bonds that are difficult to degrade. Researchers used genetic engineering to introduce ester bonds into the lignin backbone that are easier to break down chemically.

The new technique means that the lignin may be recovered more effectively and used in other applications, such as adhesives, insolation, carbon fibres and paint additives.

Genetic modification

The genetic modification strategy employed in this study could also be used on other plants like grasses to be used as a new kind of fuel to replace petroleum.

Genetic modification can be a contentious issue, but there are ways to ensure that the genes do not spread to the forest. These techniques include growing crops away from native stands so cross-pollination isn’t possible; introducing genes to make both the male and female trees or plants sterile; and harvesting trees before they reach reproductive maturity.

In the future, genetically modified trees could be planted like an agricultural crop, not in our native forests. Poplar is a potential energy crop for the biofuel industry because the tree grows quickly and on marginal farmland. [emphasis mine] Lignin makes up 20 to 25 per cent of the tree.

“We’re a petroleum reliant society,” says Mansfield. “We rely on the same resource for everything from smartphones to gasoline. We need to diversify and take the pressure off of fossil fuels. Trees and plants have enormous potential to contribute carbon to our society.”

As noted earlier, the researchers in Florida mention poplars in their paper (Note: Links have been removed),

Gymnosperms such as loblolly pine (Pinus taeda L.) contain lignin that is composed almost exclusively of G-residues, whereas lignin from angiosperm dicots, including poplar (Populus spp.) contains a mixture of G- and S-residues. [emphasis mine] Due to the radical-mediated addition of monolignols to the growing lignin polymer, lignin contains a variety of interunit bonds, including aryl–aryl, aryl–alkyl, and alkyl–alkyl bonds.(3) This feature, combined with the association between lignin and cell-wall polysaccharides, which involves both physical and chemical interactions, make the isolation of lignin from plant cell walls challenging. Various isolation methods exist, each relying on breaking certain types of chemical bonds within the lignin, and derivatizations to solubilize the resulting fragments.(5) Several of these methods are used on a large scale in pulp and paper mills and biorefineries, where lignin needs to be removed from woody biomass and crop residues(6) in order to use the cellulose for the production of paper, biofuels, and biobased polymers. The lignin is present in the waste stream and has limited intrinsic economic value.(7)

Since hydroxyl and carboxyl groups in lignin facilitate functionalization, its compatibility with natural and synthetic polymers for different commercial applications have been extensively studied.(8-12) One of the promising directions toward the cost reduction associated with biofuel production is the use of lignin for low-cost carbon fibers.(13) Other recent studies reported development and characterization of lignin nanocomposites for multiple value-added applications. For example, cellulose nanocrystals/lignin nanocomposites were developed for improved optical, antireflective properties(14, 15) and thermal stability of the nanocomposites.(16) [emphasis mine] Model ultrathin bicomponent films prepared from cellulose and lignin derivatives were used to monitor enzyme binding and cellulolytic reactions for sensing platform applications.(17) Enzymes/“synthetic lignin” (dehydrogenation polymer (DHP)) interactions were also investigated to understand how lignin impairs enzymatic hydrolysis during the biomass conversion processes.(18)

The synthesis of lignin nanotubes and nanowires was based on cross-linking a lignin base layer to an alumina membrane, followed by peroxidase-mediated addition of DHP and subsequent dissolution of the membrane in phosphoric acid.(1) Depending upon monomers used for the deposition of DHP, solid nanowires, or hollow nanotubes could be manufactured and easily functionalized due to the presence of many reactive groups. Due to their autofluorescence, lignin nanotubes permit label-free detection under UV radiation.(1) These features make lignin nanotubes suitable candidates for numerous biomedical applications, such as the delivery of therapeutic agents and DNA to specific cells.

The synthesis of LNTs in a sacrificial template membrane is not limited to a single source of lignin or a single lignin isolation procedure. Dimensions of the LNTs and their cytotoxicity to HeLa cells appear to be determined primarily by the lignin isolation procedure, whereas the transfection efficiency is also influenced by the source of the lignin (plant species and genotype). This means that LNTs can be tailored to the application for which they are intended. [emphasis mine] The ability to design LNTs for specific purposes will benefit from a more thorough understanding of the relationship between the structure and the MW of the lignin used to prepare the LNTs, the nanomechanical properties, and the surface characteristics.

We have shown that DNA is physically associated with the LNTs and that the LNTs enter the cytosol, and in some case the nucleus. The LNTs made from NaOH-extracted lignin are of special interest, as they were the shortest in length, substantially reduced HeLa cell viability at levels above approximately 50 mg/mL, and, in the case of pine and poplar, were the most effective in the transfection [penetrating the cell with a bacterial plasmid to leave genetic material in this case] experiments. [emphasis mine]

As I see the issues presented with these two research efforts, there are environmental and energy issues with extracting the lignin while there seem to be some very promising medical applications possible with lignin ‘waste’. These two research efforts aren’t necessarily antithetical but they do raise some very interesting issues as to how we approach our use of resources and future policies.

ETA May 16, 2014: The beat goes on with the Georgia (US) Institute of Technology issues a roadmap for making money from lignin. From a Georgia Tech May 15, 2014 news release on EurekAlert,

When making cellulosic ethanol from plants, one problem is what to do with a woody agricultural waste product called lignin. The old adage in the pulp industry has been that one can make anything from lignin except money.

A new review article in the journal Science points the way toward a future where lignin is transformed from a waste product into valuable materials such as low-cost carbon fiber for cars or bio-based plastics. Using lignin in this way would create new markets for the forest products industry and make ethanol-to-fuel conversion more cost-effective.

“We’ve developed a roadmap for integrating genetic engineering with analytical chemistry tools to tailor the structure of lignin and its isolation so it can be used for materials, chemicals and fuels,” said Arthur Ragauskas, a professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology. Ragauskas is also part of the Institute for Paper Science and Technology at Georgia Tech.

The roadmap was published May 15 [2014] in the journal Science. …

Here’s a link to and citation for the ‘roadmap’,

Lignin Valorization: Improving Lignin Processing in the Biorefinery by  Arthur J. Ragauskas, Gregg T. Beckham, Mary J. Biddy, Richard Chandra, Fang Chen, Mark F. Davis, Brian H. Davison, Richard A. Dixon, Paul Gilna, Martin Keller, Paul Langan, Amit K. Naskar, Jack N. Saddler, Timothy J. Tschaplinski, Gerald A. Tuskan, and Charles E. Wyman. Science 16 May 2014: Vol. 344 no. 6185 DOI: 10.1126/science.1246843

This paper is behind a paywall.