Tag Archives: University of Queensland

Desalination waste as a useful resource?

For anyone not familiar with the concept, it’s possible to remove salt from water to make it potable (i.e., drinkable). With growing concerns about water shortages worldwide, turning the ocean into something drinkable is seen as a reasonable solution. One of the problems associated with the solution is waste. As you can see in this post, it’s a big problem.

Illustration depicts the potential of the suggested process. Brine, which could be obtained from the waste stream of reverse osmosis (RO) desalination plants, or from industrial plants or salt mining operations, can be processed to yield useful chemicals such as sodium hydroxide (NaOH) or hydrochloric acid (HCl). Credit: Illustration courtesy of the researchers [downloaded from https://www.sciencedaily.com/releases/2019/02/190213124439.htm]

A February 13, 2019 news item on ScienceDaily announced research from MIT (Massachusetts Institute of Technology) into research on desalination and waste,

The rapidly growing desalination industry produces water for drinking and for agriculture in the world’s arid coastal regions. But it leaves behind as a waste product a lot of highly concentrated brine, which is usually disposed of by dumping it back into the sea, a process that requires costly pumping systems and that must be managed carefully to prevent damage to marine ecosystems. Now, engineers at MIT say they have found a better way.

In a new study, they show that through a fairly simple process the waste material can be converted into useful chemicals — including ones that can make the desalination process itself more efficient

A February 13, 2019 MIT news release (also on EurekAlert), which originated the news item, describes the work in detail,

The approach can be used to produce sodium hydroxide, among other products. Otherwise known as caustic soda, sodium hydroxide can be used to pretreat seawater going into the desalination plant. This changes the acidity of the water, which helps to prevent fouling of the membranes used to filter out the salty water — a major cause of interruptions and failures in typical reverse osmosis desalination plants.

The concept is described today in the journal Nature Catalysis and in two other papers by MIT research scientist Amit Kumar, professor of mechanical engineering John. [sic] H. Lienhard V, and several others. Lienhard is the Jameel Professor of Water and Food and the director of the Abdul Latif Jameel Water and Food Systems Lab.

“The desalination industry itself uses quite a lot of it,” Kumar says of sodium hydroxide. “They’re buying it, spending money on it. So if you can make it in situ at the plant, that could be a big advantage.” The amount needed in the plants themselves is far less than the total that could be produced from the brine, so there is also potential for it to be a saleable product.

Sodium hydroxide is not the only product that can be made from the waste brine: Another important chemical used by desalination plants and many other industrial processes is hydrochloric acid, which can also easily be made on site from the waste brine using established chemical processing methods. The chemical can be used for cleaning parts of the desalination plant, but is also widely used in chemical production and as a source of hydrogen.

Currently, the world produces more than 100 billion liters (about 27 billion gallons) a day of water from desalination, which leaves a similar volume of concentrated brine. [emphases mine] Much of that is pumped back out to sea, and current regulations require costly outfall systems to ensure adequate dilution of the salts. Converting the brine can thus be both economically and ecologically beneficial, especially as desalination continues to grow rapidly around the world. “Environmentally safe discharge of brine is manageable with current technology, but it’s much better to recover resources from the brine and reduce the amount of brine released,” Lienhard says.

The method of converting the brine into useful products uses well-known and standard chemical processes, including initial nanofiltration to remove undesirable compounds, followed by one or more electrodialysis stages to produce the desired end product. While the processes being suggested are not new, the researchers have analyzed the potential for production of useful chemicals from brine and proposed a specific combination of products and chemical processes that could be turned into commercial operations to enhance the economic viability of the desalination process, while diminishing its environmental impact.

“This very concentrated brine has to be handled carefully to protect life in the ocean, and it’s a resource waste, and it costs energy to pump it back out to sea,” so turning it into a useful commodity is a win-win, Kumar says. And sodium hydroxide is such a ubiquitous chemical that “every lab at MIT has some,” he says, so finding markets for it should not be difficult.

The researchers have discussed the concept with companies that may be interested in the next step of building a prototype plant to help work out the real-world economics of the process. “One big challenge is cost — both electricity cost and equipment cost,” at this stage, Kumar says.

The team also continues to look at the possibility of extracting other, lower-concentration materials from the brine stream, he says, including various metals and other chemicals, which could make the brine processing an even more economically viable undertaking.

“One aspect that was mentioned … and strongly resonated with me was the proposal for such technologies to support more ‘localized’ or ‘decentralized’ production of these chemicals at the point-of-use,” says Jurg Keller, a professor of water management at the University of Queensland in Australia, who was not involved in this work. “This could have some major energy and cost benefits, since the up-concentration and transport of these chemicals often adds more cost and even higher energy demand than the actual production of these at the concentrations that are typically used.”

The research team also included MIT postdoc Katherine Phillips and undergraduate Janny Cai, and Uwe Schroder at the University of Braunschweig, in Germany. The work was supported by Cadagua, a subsidiary of Ferrovial, through the MIT Energy Initiative.

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

Direct electrosynthesis of sodium hydroxide and hydrochloric acid from brine streams by Amit Kumar, Katherine R. Phillips, Gregory P. Thiel, Uwe Schröder, & John H. Lienhard V. Nature Catalysis volume 2, pages106–113 (2019) DOI: https://doi.org/10.1038/s41929-018-0218-y Published 13 February 2019

This paper is behind a paywall.

Monitoring forest soundscapes for conservation and more about whale songs

I don’t understand why anyone would publicize science work featuring soundscapes without including an audio file. However, no one from Princeton University (US) phoned and asked for my advice :).

On the plus side, my whale story does have a sample audio file. However, I’m not sure if I can figure out how to embed it here.

Princeton and monitoring forests

In addition to a professor from Princeton University, there’s the founder of an environmental news organization and someone who’s both a professor at the University of Queensland (Australia) and affiliated with the Nature Conservancy making this of the more unusual collaborations I’ve seen.

Moving on to the news, a January 4, 2019 Princeton University news release (also on EurekAlert but published on Jan. 3, 2019) by B. Rose Kelly announces research into monitoring forests,

Recordings of the sounds in tropical forests could unlock secrets about biodiversity and aid conservation efforts around the world, according to a perspective paper published in Science.

Compared to on-the-ground fieldwork, bioacoustics –recording entire soundscapes, including animal and human activity — is relatively inexpensive and produces powerful conservation insights. The result is troves of ecological data in a short amount of time.

Because these enormous datasets require robust computational power, the researchers argue that a global organization should be created to host an acoustic platform that produces on-the-fly analysis. Not only could the data be used for academic research, but it could also monitor conservation policies and strategies employed by companies around the world.

“Nongovernmental organizations and the conservation community need to be able to truly evaluate the effectiveness of conservation interventions. It’s in the interest of certification bodies to harness the developments in bioacoustics for better enforcement and effective measurements,” said Zuzana Burivalova, a postdoctoral research fellow in Professor David Wilcove’s lab at Princeton University’s Woodrow Wilson School of Public and International Affairs.

“Beyond measuring the effectiveness of conservation projects and monitoring compliance with forest protection commitments, networked bioacoustic monitoring systems could also generate a wealth of data for the scientific community,” said co-author Rhett Butler of the environmental news outlet Mongabay.

Burivalova and Butler co-authored the paper with Edward Game, who is based at the Nature Conservancy and the University of Queensland.

The researchers explain that while satellite imagery can be used to measure deforestation, it often fails to detect other subtle ecological degradations like overhunting, fires, or invasion by exotic species. Another common measure of biodiversity is field surveys, but those are often expensive, time consuming and cover limited ground.

Depending on the vegetation of the area and the animals living there, bioacoustics can record animal sounds and songs from several hundred meters away. Devices can be programmed to record at specific times or continuously if there is solar polar or a cellular network signal. They can also record a range of taxonomic groups including birds, mammals, insects, and amphibians. To date, several multiyear recordings have already been completed.

Bioacoustics can help effectively enforce policy efforts as well. Many companies are engaged in zero-deforestation efforts, which means they are legally obligated to produce goods without clearing large forests. Bioacoustics can quickly and cheaply determine how much forest has been left standing.

“Companies are adopting zero deforestation commitments, but these policies do not always translate to protecting biodiversity due to hunting, habitat degradation, and sub-canopy fires. Bioacoustic monitoring could be used to augment satellites and other systems to monitor compliance with these commitments, support real-time action against prohibited activities like illegal logging and poaching, and potentially document habitat and species recovery,” Butler said.

Further, these recordings can be used to measure climate change effects. While the sounds might not be able to assess slow, gradual changes, they could help determine the influence of abrupt, quick differences to land caused by manufacturing or hunting, for example.

Burivalova and Game have worked together previously as you can see in a July 24, 2017 article by Justine E. Hausheer for a nature.org blog ‘Cool Green Science’ (Note: Links have been removed),

Morning in Musiamunat village. Across the river and up a steep mountainside, birds-of-paradise call raucously through the rainforest canopy, adding their calls to the nearly deafening insect chorus. Less than a kilometer away, small birds flit through a grove of banana trees, taro and pumpkin vines winding across the rough clearing. Here too, the cicadas howl.

To the ear, both garden and forest are awash with noise. But hidden within this dawn chorus are clues to the forest’s health.

New acoustic research from Nature Conservancy scientists indicates that forest fragmentation drives distinct changes in the dawn and dusk choruses of forests in Papua New Guinea. And this innovative method can help evaluate the conservation benefits of land-use planning efforts with local communities, reducing the cost of biodiversity monitoring in the rugged tropics.

“It’s one thing for a community to say that they cut fewer trees, or restricted hunting, or set aside a protected area, but it’s very difficult for small groups to demonstrate the effectiveness of those efforts,” says Eddie Game, The Nature Conservancy’s lead scientist for the Asia-Pacific region.

Aside from the ever-present logging and oil palm, another threat to PNG’s forests is subsistence agriculture, which feeds a majority of the population. In the late 1990s, The Nature Conservancy worked with 11 communities in the Adelbert Mountains to create land-use plans, dividing each community’s lands into different zones for hunting, gardening, extracting forest products, village development, and conservation. The goal was to limit degradation to specific areas of the forest, while keeping the rest intact.

But both communities and conservationists needed a way to evaluate their efforts, before the national government considered expanding the program beyond Madang province. So in July 2015, Game and two other scientists, Zuzana Burivalova and Timothy Boucher, spent two weeks gathering data in the Adelbert Mountains, a rugged lowland mountain range in Papua New Guinea’s Madang province.

Working with conservation rangers from Musiamunat, Yavera, and Iwarame communities, the research team tested an innovative method — acoustic sampling — to measure biodiversity across the community forests. Game and his team used small acoustic recorders placed throughout the forest to record 24-hours of sound from locations in each of the different land zones.

Soundscapes from healthy, biodiverse forests are more complex, so the scientists hoped that these recordings would show if parts of the community forests, like the conservation zones, were more biodiverse than others. “Acoustic recordings won’t pick up every species, but we don’t need that level of detail to know if a forest is healthy,” explains Boucher, a conservation geographer with the Conservancy.

Here’s a link to and a citation for the latest work from Burivalova and Game,

The sound of a tropical forest by Zuzana Burivalova, Edward T. Game, Rhett A. Butler. Science 04 Jan 2019: Vol. 363, Issue 6422, pp. 28-29 DOI: 10.1126/science.aav1902

This paper is behind a paywall. You can find out more about Mongabay and Rhett Butler in its Wikipedia entry.

***ETA July 18, 2019: Cara Cannon Byington, Associate Director, Science Communications for the Nature Conservancy emailed to say that a January 3, 2019 posting on the conservancy’s Cool Green Science Blog features audio files from the research published in ‘The sound of a tropical forest. Scroll down about 75% of the way for the audio.***

Whale songs

Whales share songs when they meet and a January 8, 2019 Wildlife Conservation Society news release (also on EurekAlert) describes how that sharing takes place,

Singing humpback whales from different ocean basins seem to be picking up musical ideas from afar, and incorporating these new phrases and themes into the latest song, according to a newly published study in Royal Society Open Science that’s helping scientists better understand how whales learn and change their musical compositions.

The new research shows that two humpback whale populations in different ocean basins (the South Atlantic and Indian Oceans) in the Southern Hemisphere sing similar song types, but the amount of similarity differs across years. This suggests that males from these two populations come into contact at some point in the year to hear and learn songs from each other.

The study titled “Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins” appears in the latest edition of the Royal Society Open Science journal. The authors are: Melinda L. Rekdahl, Carissa D. King, Tim Collins, and Howard Rosenbaum of WCS (Wildlife Conservation Society); Ellen C. Garland of the University of St. Andrews; Gabriella A. Carvajal of WCS and Stony Brook University; and Yvette Razafindrakoto of COSAP [ (Committee for the Management of the Protected Area of Bezà Mahafaly ] and Madagascar National Parks.

“Song sharing between populations tends to happen more in the Northern Hemisphere where there are fewer physical barriers to movement of individuals between populations on the breeding grounds, where they do the majority of their singing. In some populations in the Southern Hemisphere song sharing appears to be more complex, with little song similarity within years but entire songs can spread to neighboring populations leading to song similarity across years,” said Dr. Melinda Rekdahl, marine conservation scientist for WCS’s Ocean Giants Program and lead author of the study. “Our study shows that this is not always the case in Southern Hemisphere populations, with similarities between both ocean basin songs occurring within years to different degrees over a 5-year period.”

The study authors examined humpback whale song recordings from both sides of the African continent–from animals off the coasts of Gabon and Madagascar respectively–and transcribed more than 1,500 individual sounds that were recorded between 2001-2005. Song similarity was quantified using statistical methods.

Male humpback whales are one of the animal kingdom’s most noteworthy singers, and individual animals sing complex compositions consisting of moans, cries, and other vocalizations called “song units.” Song units are composed into larger phrases, which are repeated to form “themes.” Different themes are produced in a sequence to form a song cycle that are then repeated for hours, or even days. For the most part, all males within the same population sing the same song type, and this population-wide song similarity is maintained despite continual evolution or change to the song leading to seasonal “hit songs.” Some song learning can occur between populations that are in close proximity and may be able to hear the other population’s song.

Over time, the researchers detected shared phrases and themes in both populations, with some years exhibiting more similarities than others. In the beginning of the study, whale populations in both locations shared five “themes.” One of the shared themes, however, had differences. Gabon’s version of Theme 1, the researchers found, consisted of a descending “cry-woop”, whereas the Madagascar singers split Theme 1 into two parts: a descending cry followed by a separate woop or “trumpet.”

Other differences soon emerged over time. By 2003, the song sung by whales in Gabon became more elaborate than their counterparts in Madagascar. In 2004, both population song types shared the same themes, with the whales in Gabon’s waters singing three additional themes. Interestingly, both whale groups had dropped the same two themes from the previous year’s song types. By 2005, songs being sung on both sides of Africa were largely similar, with individuals in both locations singing songs with the same themes and order. However, there were exceptions, including one whale that revived two discontinued themes from the previous year.

The study’s results stands in contrast to other research in which a song in one part of an ocean basin replaces or “revolutionizes” another population’s song preference. In this instance, the gradual changes and degrees of similarity shared by humpbacks on both sides of Africa was more gradual and subtle.

“Studies such as this one are an important means of understanding connectivity between different whale populations and how they move between different seascapes,” said Dr. Howard Rosenbaum, Director of WCS’s Ocean Giants Program and one of the co-authors of the new paper. “Insights on how different populations interact with one another and the factors that drive the movements of these animals can lead to more effective plans for conservation.”

The humpback whale is one of the world’s best-studied marine mammal species, well known for its boisterous surface behavior and migrations stretching thousands of miles. The animal grows up to 50 feet in length and has been globally protected from commercial whaling since the 1960s. WCS has studied humpback whales since that time and–as the New York Zoological Society–played a key role in the discovery that humpback whales sing songs. The organization continues to study humpback whale populations around the world and right here in the waters of New York; research efforts on humpback and other whales in New York Bight are currently coordinated through the New York Aquarium’s New York Seascape program.

I’m not able to embed the audio file here but, for the curious, there is a portion of a humpback whale song from Gabon here at EurekAlert.

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

Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins by Melinda L. Rekdahl, Ellen C. Garland, Gabriella A. Carvajal, Carissa D. King, Tim Collins, Yvette Razafindrakoto and Howard Rosenbaum. Royal Society Open Science 21 November 2018 Volume 5 Issue 11 https://doi.org/10.1098/rsos.172305 Published:28 November 2018

This is an open access paper.

Clay nanosheets and world food security

This is some interesting agricultural research from Australia. From a Jan. 11, 2017 news item on phys.org,

A University of Queensland team has made a discovery that could help conquer the greatest threat to global food security – pests and diseases in plants.

Research leader Professor Neena Mitter said BioClay – an environmentally sustainable alternative to chemicals and pesticides – could be a game-changer for crop protection.

“In agriculture, the need for new control agents grows each year, driven by demand for greater production, the effects of climate change, community and regulatory demands, and toxicity and pesticide resistance,” she said.

“Our disruptive research involves a spray of nano-sized degradable clay used to release double-stranded RNA, that protects plants from specific disease-causing pathogens.”

The research, by scientists from the Queensland Alliance for Agriculture and Food Innovation (QAAFI) and UQ’s Australian Institute for Bioengineering and Nanotechnology (AIBN) is published in Nature Plants.

A Jan. 11, 2017 University of Queensland press release, which originated the news item, provides a bit more detail,

Professor Mitter said the technology reduced the use of pesticides without altering the genome of the plants.

“Once BioClay is applied, the plant ‘thinks’ it is being attacked by a disease or pest insect and responds by protecting itself from the targeted pest or disease.

“A single spray of BioClay protects the plant and then degrades, reducing the risk to the environment or human health.”

She said BioClay met consumer demands for sustainable crop protection and residue-free produce.

“The cleaner approach will value-add to the food and agri-business industry, contributing to global food security and to a cleaner, greener image of Queensland.”

AIBN’s Professor Zhiping Xu said BioClay combined nanotechnology and biotechnology.

“It will produce huge benefits for agriculture in the next several decades, and the applications will expand into a much wider field of primary agricultural production,” Professor Xu said.

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

Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses by Neena Mitter, Elizabeth A. Worrall, Karl E. Robinson, Peng Li, Ritesh G. Jain, Christelle Taochy, Stephen J. Fletcher, Bernard J. Carroll, G. Q. (Max) Lu & Zhi Ping Xu. Nature Plants 3, Article number: 16207 (2017) doi:10.1038/nplants.2016.207 Published online: 09 January 2017

This paper is behind a paywall.

I don’t usually do this but here’s the abstract for the paper,

Topical application of pathogen-specific double-stranded RNA (dsRNA) for virus resistance in plants represents an attractive alternative to transgenic RNA interference (RNAi). However, the instability of naked dsRNA sprayed on plants has been a major challenge towards its practical application. We demonstrate that dsRNA can be loaded on designer, non-toxic, degradable, layered double hydroxide (LDH) clay nanosheets. Once loaded on LDH, the dsRNA does not wash off, shows sustained release and can be detected on sprayed leaves even 30 days after application. We provide evidence for the degradation of LDH, dsRNA uptake in plant cells and silencing of homologous RNA on topical application. Significantly, a single spray of dsRNA loaded on LDH (BioClay) afforded virus protection for at least 20 days when challenged on sprayed and newly emerged unsprayed leaves. This innovation translates nanotechnology developed for delivery of RNAi for human therapeutics to use in crop protection as an environmentally sustainable and easy to adopt topical spray.

It helps a bit but I’m puzzled by the description of BioClay as an alternative to RNAi in the first sentence because the last sentence has: “This innovation translates nanotechnology developed for delivery of RNAi … .” I believe what they’re saying is that LDH clay nanosheets were developed for delivery of RNAi but have now been adapted for delivery of dsRNA. Maybe?

At any rate this paper is behind a paywall.

Australia’s nanopatch: a way to eliminate needle vaccinations

Tristan Clemons has written a Nov. 9, 2016 essay for The Conversation on one of my favourite stories, the nanopatch,

Who likes getting a needle? I know I definitely don’t.

Someone else who doesn’t is Mark Kendall from the University of Queensland, winner of the Young Florey Medal 2016.

Mark’s work in developing the nanopatch has provided a clear pathway for vaccine delivery science to move beyond 160 year-old needle and syringe technology.

… There are approximately 20,000 projections per square centimeter on each patch, each around 60 to 100 micrometres in length. One micrometre is one million times smaller than a metre, so the height of these tiny spikes is approximately the width of a human hair.

The nanopatch is produced using a technique known as “deep reactive ion etching”, which essentially makes use of ions (charged atoms) in an electric field to selectively etch the surface of a material away. Controlling the electric field and the ions allows a high degree of control, so the microprojections are regularly spaced and of similar dimensions.

An added advantage of this approach is it has been used in the electronic circuit and solar energy industries for many years, and has the potential for increasing the scale of production.

The tiny projections on each nanopatch are invisible to the naked eye, but are long enough to breach the outermost skin layer, the stratum corneum. The stratum corneum is a layer of dead skin cells which acts as the first barrier in protecting us from infection and skin water loss.

The nanopatch projections penetrate through the stratum corneum to reach the living skin layers directly below, the epidermis and the dermis. In the epidermis are several types of immune cells that are vital for the vaccine to work.

Hence the nanopatch is well suited to the delivery of vaccines where targeting immune cells is vital for vaccination success. Examples include influenza, polio and cholera.

Mark Kendall and his colleagues have shown they are able to coat nanopatch microprojections with a vaccine, apply the nanopatch to the skin and achieve vaccination with one tenth to one thirtieth of the dose required using traditional needle and syringe approaches.

… it’s more than just a good idea. Mark Kendall and his colleagues are now running human clinical trials of nanopatches in Brisbane, and the WHO is planning a polio vaccine trial in Cuba in 2017.

The latest information I have about this research is from a Feb. 26, 2016 University of Queensland press release,

Needle-free Nanopatch technology developed at The University of Queensland has been used to successfully deliver an inactivated poliovirus vaccine.

Delivery of a polio vaccine with the Nanopatch was demonstrated by UQ’s Professor Mark Kendall and his research team at UQ’s Australian Institute for Bioengineering and Nanotechnology, in collaboration with the World Health Organisation, the US Centres for Disease Control and Prevention, and vaccine technology company Vaxxas.

Professor Kendall said the Nanopatch had been used to administer an inactivated Type 2 poliovirus vaccine in a rat model.

“We compared the Nanopatch to the traditional needle and syringe, and found that there is about a 40-fold improvement in delivered dose-sparing,” Professor Kendall said.

“This means about 40 times less polio vaccine was needed in Nanopatch delivery to generate a functional immune response as the needle and syringe.

“To our knowledge, this is the highest level of dose-sparing observed for an inactivated polio vaccine in rats achieved by any type of delivery technology, so this is a key breakthrough.”

The next step will be clinical testing.

Dr David Muller, first author of the research published in Scientific Reports, said the work demonstrated a key advantage of the Nanopatch.

“The Nanopatch targets the abundant immune cell populations in the skin’s outer layers; rather than muscle, resulting in a more efficient vaccine delivery system,” he said.

Clinical success and widespread use of the Nanopatch against polio could help in the current campaign to eradicate polio. It could be produced and distributed at a cheaper cost, and its ease of use would make it suitable for house-to-house vaccination efforts in endemic areas with only minimal training required.

World Health Organisation Global Polio Eradication Initiative Director Mr Michel Zaffran said only Afghanistan and Pakistan remained polio-endemic, but all countries were at risk until the disease was eradicated everywhere.

“Needle-free microneedle patches such as the Nanopatch offer great promise for reaching more children with polio vaccine as well as other antigens such as measles vaccine, particularly in hard-to-reach areas or areas with inadequate healthcare infrastructure,” Mr Zaffran said.

Nanopatch technology is being commercialised by Vaxxas Pty Ltd, which has scaled the Nanopatch from use in small models to prototypes for human use.

Vaxxas CEO Mr David Hoey said the first human vaccination studies are scheduled for this year [2016].

“Key attributes of the Nanopatch, including its ease of use and potential to not require refrigeration, could improve the reach and efficiency of vaccination campaigns in difficult-to-reach locations, including those where polio remains endemic,” Mr Hoey said.

The work was funded by the World Health Organisation, Vaxxas, Rotary District 9630 and the Rotary Foundation.

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

Inactivated poliovirus type 2 vaccine delivered to rat skin via high density microprojection array elicits potent neutralising antibody responses by David A. Muller, Frances E. Pearson, Germain J.P. Fernando, Christiana Agyei-Yeboah, Nick S. Owens, Simon R. Corrie, Michael L. Crichton, Jonathan C.J. Wei, William C. Weldon, M. Steven Oberste, Paul R. Young, & Mark A. F. Kendall. Scientific Reports 6, Article number: 22094 (2016) doi:10.1038/srep22094 Published online: 25 February 2016

This paper is open access.

As befitting a ‘favourite story’, I’ve been following it for a number of years starting with this April 23, 2009 posting (scroll down about 25% of the way) although you might prefer to read this more substantive July 26, 2010 posting. The last time (Aug. 3, 2011 posting) I featured the story, it was to announce an investment of AUD $15M in Vaxxas (Kendall is not listed as member of the company) in order to bring the nanopatch to market.

The nanostructure of cellulose at the University of Melbourne (Australia)

This is not the usual kind of nanocellulose story featured here as it doesn’t concern a nanocellulose material. Instead, this research focuses on the structure of cellulose at the nanoscale. From a May 21, 2015 news item on Nanotechnology Now,

Scientists from IBM Research and the Universities of Melbourne and Queensland have moved a step closer to identifying the nanostructure of cellulose — the basic structural component of plant cell walls.

The insights could pave the way for more disease resistant varieties of crops and increase the sustainability of the pulp, paper and fibre industry — one of the main uses of cellulose.

A May 21, 2015 University of Melbourne press release, which originated the news item, describes some of the difficulties of analyzing cellulose at the nanoscale and the role that IBM computer played in overcoming them,

Tapping into IBM’s supercomputing power, researchers have been able to model the structure and dynamics of cellulose at the molecular level.

Dr Monika Doblin, Research Fellow and Deputy Node Leader at the School of BioSciences at the University of Melbourne said cellulose is a vital part of the plant’s structure, but its synthesis is yet to be fully understood.

“It’s difficult to work on cellulose synthesis in vitro because once plant cells are broken open, most of the enzyme activity is lost, so we needed to find other approaches to study how it is made,” Dr Doblin said.

“Thanks to IBM’s expertise in molecular modelling and VLSCI’s computational power, we have been able to create models of the plant wall at the molecular level which will lead to new levels of understanding about the formation of cellulose.”

The work, which was described in a recent scientific paper published in Plant Physiology, represents a significant step towards our understanding of cellulose biosynthesis and how plant cell walls assemble and function.

The research is part of a longer-term program at the Victorian Life Sciences Computation Initiative (VLSCI) to develop a 3D computer-simulated model of the entire plant wall.

Cellulose represents one of the most abundant organic compounds on earth with an estimated 180 billion tonnes produced by plants each year.

A plant makes cellulose by linking simple units of glucose together to form chains, which are then bundled together to form fibres. These fibres then wrap around the cell as the major component of the plant cell wall, providing rigidity, flexibility and defence against internal and external stresses.

Until now, scientists have been challenged with detailing the structure of plant cell walls due to the complexity of the work and the invasive nature of traditional physical methods which often cause damage to the plant cells.

Dr John Wagner, Manager of Computational Sciences, IBM Research – Australia, called it a ‘pioneering project’.

“We are bringing IBM Research’s expertise in computational biology, big data and smarter agriculture to bear in a large-scale, collaborative Australian science project with some of the brightest minds in the field. We are a keen supporter of the Victorian Life Sciences Computation Initiative and we’re very excited to see the scientific impact this work is now having.”

Using the IBM Blue Gene/Q supercomputer at VLSCI, known as Avoca, scientists were able to perform the quadrillions of calculations required to model the motions of cellulose atoms.

The research shows that within the cellulose structure, there are between 18 and 24 chains present within an elementary microfibril, much less than the 36 chains that had previously been assumed.

IBM Researcher, Dr. Daniel Oehme, said plant walls are the first barrier to disease pathogens.

“While we don’t fully understand the molecular pathway of pathogen infection and plant r

You can find out more about this work and affiliated projects at the Australian Research Centre (ARC) of Excellence in Plant Cell Walls.

Biofuels could be competitive with fossil fuels according to Australians

The University of Queensland’s Australian Institute for Bioengineering & Nanotechnology released a three-year study on biofuels and aviation fuel at a Weds., May 22, 2013 aviation environmental summit hosted by Boeing, according to a May 24, 2013 article by Steve Creedy for The Australian.com.au,

AVIATION biofuels produced in Australia using widely touted feedstocks and existing technology would be competitive only if crude oil was almost three times its present price, a three-year study by universities and industry has found.

The cheapest of three feedstocks studied, sugar cane, would be competitive if crude oil was at $US301 a barrel.

This increased to $US374 for oil-producing seeds from the pongamia tree and a huge $US1343 with microalgae. Brent crude is trading at about $US105 a barrel.

But technological improvements in key areas could significantly lower the price to $US168 for sugarcane, $US255 for pongamia seeds and $US385 for algae.

Peter Hannam’s May 22, 2013 article about the presentation for the Newcastle Herald provides some context for the airlines’ interest in biofuels,

… Nations and carriers continue to wrangle over rules to curb emissions. The European Union earlier this year suspended plans to impose emission permits for any flight arriving or leaving European airspace. The EU backed down after threats of non-compliance or retaliation from China, India and the US, although discussions continue for global restrictions to come into force from 2020.

As Creedy notes in his article, ” … technological improvements in key areas could significantly lower the cost …” and this would require funds. There isn’t any mention in either Creedy’s or Hannam’s article about increased funding.

You can find out more about the Queensland Sustainable Aviation Fuel Initiative here and this is where the group’s latest research study can be found,

Technoeconomic analysis of renewable aviation fuel from microalgae, Pongamia pinnata, and sugarcane by Daniel Klein-Marcuschamer, Christopher Turner, Mark Allen, Peter Gray, Ralf G Dietzgen, Peter M Gresshoff, Ben Hankamer, Kirsten Heimann, Paul T Scott, Evan Stephens, Robert Speight, and Lars K Nielsen.  Biofuels, Bioprod. Bioref.. doi: 10.1002/bbb.1404 Article First published online: 25 APR 2013

This study is behind a paywall.

Legend of the giant squid, a lesson for environmentalists on how to tell a science story

Mark Schrope has written a wonderful piece on the search for the giant squid in his Jan. 25, 2013 posting on Slate.com. It’s a story about adventure, myth, scientific pursuits, and, very cunningly, environmental issues.

I will excerpt a few bits from the piece but I encourage you to read it in its entirety,

Deep-sea biologist Edith Widder was working on a ship positioned off Japan’s Ogasawara Islands when Wen-Sung Chung asked her to step into the lab to see something. Cameras followed her as she got up. This was not unusual, since the Japan Broadcasting Commission (NHK) and the Discovery Channel were funding the expedition, which was being conducted from a research yacht named Alucia leased from a billionaire hedge fund owner. Chung was nonchalant, so it didn’t occur to Widder that she was about to see the culmination of a quest that has driven ocean explorers for more than a century. She thought maybe it was going to be video of a cool shark.

The purpose of the expedition was to capture footage of the enigmatic giant squid in its natural habitat. The animal can grow to 35 feet or longer, and its eye is as big as your head. But it lives about 1,000 feet below the surface and deeper, and it had only been glimpsed a few times at the surface and photographed alive once.

Widder is a world expert on bioluminescence, the light that countless marine animals use to communicate, especially in the dark world of the deep sea.

Schopes introduces a mystery, ‘What is Widder about to see?’, and then doesn’t answer it for several paragraphs while he explains who she is, her area of research, and the legend of the giant squid. Note: A link has been removed.

The giant squid has been the stuff of legend for about as long as people have sailed across oceans. Aristotle and Pliny the Elder described what may have been giant squid, which occasionally wash ashore or end up in fishermen’s nets, and the species is thought to be the origin of the Norwegian kraken myth.

Countless groups in past decades have tried to manufacture giant squid encounters, investing millions, getting all the best advice from the experts, only to come back as failed crusaders. One of the other scientists aboard the Alucia, Tsunemi Kubodera of Japan’s National Museum of Nature and Science, has been hunting giant squid in these waters for years. He managed to capture some still images of one giant squid and video of another after it was caught and brought to the surface. But none of that could compare to video of the animal alive in the deep, a view that would finally allow scientists to begin to understand the mysterious animal.

The expedition has not released expense figures, but it must have cost millions. When Chung, a graduate student at the University of Queensland, brought Widder into the lab and started fast-forwarding through the video, the scientists were already a week into a six-week expedition with nothing significant to show. Producer-types were growing tense.

Apparently, giant squid have a good sense of drama,

Now Widder is the first person to capture footage of a giant squid in its natural habitat. But even she admits that the grainy black-and-white footage, by itself, would have been a little unsatisfying. Some high-def footage would be the ultimate satisfaction. The drama-savvy squid would come through again.

Seven days after the first Medusa footage of a giant squid, Kubodera was in the clear sphere of a Triton submersible with pilot Jim Harris and NHK cameraman Tatsuhiko “Magic Man” Sugita when it happened. Kubodera was exploiting a different hypothesis: that the elusive squid find their prey by looking up with those huge eyes to see the faint silhouette of prey.

On Kubodera’s dives, the team tied a smaller, diamondback squid to the front of the sub and wrapped the bait around foam so that it would sink slower. Up and down, up and down the sub had gone for hours, using another low-light camera.

A giant squid latched on at 2,000 feet. As it drifted down, Harris matched the descent to keep the squid in full camera view. After the first few minutes they had flipped on the big lights, thinking the squid would flee, but it was committed to the bait. The sub’s maximum safe depth is 3,300 feet. Had the squid held on that far, Harris would have had to hit the brakes and the squid would have dropped out of view. But instead, at the last minute—3,000 feet—the squid swam off, so they got the entire encounter on film.

“I’ll never forget how beautiful it was,” says Harris. “It looked like it was covered in gold leaf.” That was a surprise to everyone because the dead ones certainly hadn’t looked like that. They were pasty. Kubodera says it was like seeing an entirely different animal.

Once Schrope has established the adventure aspect and revealed a giant squid covered in gold while, incidentally, establishing Widder’s credentials as a scientist and lover of marine life, there’s this,

For Widder, deep exploration remains a delight, but it’s no longer the primary focus of her career. In 2005, she left her longtime research post at the Harbor Branch Oceanographic Institution to found the Ocean Research and Conservation Association [ORCA], headquartered in a scenic old Coast Guard station on the Fort Pierce inlet. She wanted to take a step away from academia, where scientists are expected to stay relatively quiet in public and avoid anything that smacks of activism.

Widder had been growing increasingly overwhelmed by the environmental decline she was seeing, particularly pollution in coastal waters and estuaries, which are plagued by the polluted runoff of a Florida lifestyle dependent on constant growth and lots of fertilizer.

It gets better,

… She wants to wipe away the fallacy that pollution is an amorphous, intractable problem by gathering the information needed to pinpoint key problems. [emphasis mine] The group wants to create the aquatic equivalent of weather maps. Red shows polluted waters, blue the areas in the best shape. If people know the spot their kids swim in is in the red, they’ll take much more notice, she reasons. Perhaps more importantly, tourists would gravitate to cleaner waters if they could, creating a strong motivation for improvements.

Already the project has had success. [emphasis mine] Mapping the pollution in a stretch of Indian River Lagoon—Widder’s home and her office are both on the lagoon—she was surprised to find that two canals came up blue in a field of red. After some checking, the team learned that the golf course on those canals had switched to better environmental practices. They were preventing mowed grass clippings and runoff from the course from making it into the water. It was the perfect example for the local government, and in short order, a new fertilizer ordinance was passed.

The pièce de résistance,

They seem a world apart, but to Widder, the deep-sea exploration for fantastic creatures and the coastal environmental work guided by microbes are intimately tied. Not just because it’s all one big sea. Attention from the higher profile deep-sea work gives her a bully pulpit for focusing attention on things people don’t want to hear about, like water pollution. “I don’t want to hear about that stuff either,” she says. “But we’ve got to deal with it.” …

Too often in environmental stories writers and activists, in an attempt to communicate the seriousness of the issues,  project a sense of doom. Necessary in the early days, the time has come to change the tone otherwise there’s a risk of inculcating hopelessness (some might say it’s already happening), which is the last thing we need. As Widder says, ” … we’ve got to deal with it.”

Very nicely done Mr. Schrope and Dr. Widder!

You can find more about ORCA here, by the way, the story has videos of the giant squid, and Discovery Channel (which broadcast the documentary on Jan. 27, 2013) also has information about the giant squid. Canadians are not allowed to view the video on the US website, we are required to visit the .ca website.

ETA Mar. 20, 2013: Danish scientists have determined that all giant squid no matter where they are found are related as per a Mar. 19, 2013 news item on ScienceDaily,

The giant squid is one of the most enigmatic animals on the planet. It is extremely rarely seen, except as the remains of animals that have been washed ashore, and placed in the formalin or ethanol collections of museums. But now, researchers at the University of Copenhagen leading an international team, have discovered that no matter where in the world they are found, the fabled animals are so closely related at the genetic level that they represent a single, global population, and thus despite previous statements to the contrary, a single species worldwide.

Brains in the US Congress

Tomorrow, May 24, 2012, Jean Paul Allain, associate professor of nuclear engineering at Purdue University (Illinois) will be speaking to members of the US Congress about repairing brain injuries using nanotechnology-enabled bioactive coatings for stents. From the May 21, 2012 news item on Nanowerk,

“Stents coated with a bioactive coating might be inserted at the site of an aneurism to help heal the inside lining of the blood vessel,” said Jean Paul Allain, an associate professor of nuclear engineering. “Aneurisms are saclike bulges in blood vessels caused by weakening of artery walls. We’re talking about using a regenerative approach, attracting cells to reconstruct the arterial wall.”

He will speak before Congress on Thursday (May 24) during the first Brain Mapping Day to discuss the promise of nanotechnology in treating brain injury and disease.

The May 21, 2012 news release (by Emil Venere) for Purdue University offers insight into some of the difficulties of dealing with aneurysms using today’s technologies,

Currently, aneurisms are treated either by performing brain surgery, opening the skull and clipping the sac, or by inserting a catheter through an artery into the brain and implanting a metallic coil into the balloon-like sac.

Both procedures risk major complications, including massive bleeding or the formation of potentially fatal blood clots.

“The survival rate is about 50/50 or worse, and those who do survive could be impaired,” said Allain, who holds a courtesy appointment with materials engineering and is affiliated with the Birck Nanotechnology Center in Purdue’s Discovery Park.

Allain goes on to explain how his team’s research addresses these issues (from the May 21, 2012 Purdue University news release),

Cells needed to repair blood vessels are influenced by both the surface texture – features such as bumps and irregular shapes as tiny as 10 nanometers wide – as well as the surface chemistry of the stent materials.

“We are learning how to regulate cell proliferation and growth by tailoring both the function of surface chemistry and topology,” Allain said. “There is correlation between surface chemistry and how cells send signals back and forth for proliferation. So the surface needs to be tailored to promote regenerative healing.”

The facility being used to irradiate the stents – the Radiation Surface Science and Engineering Laboratory in Purdue’s School of Nuclear Engineering – also is used for work aimed at developing linings for experimental nuclear fusion reactors for power generation.

Irradiating materials with the ion beams causes surface features to “self-organize” and also influences the surface chemistry, Allain said.

The stents are made of nonmagnetic materials, such as stainless steel and an alloy of nickel and titanium. Only a certain part of the stents is rendered magnetic to precisely direct the proliferation of cells to repair a blood vessel where it begins bulging to form the aneurism.

Researchers will study the stents using blood from pigs during the first phase in collaboration with the Walter Reed National Military Medical Center.

The stent coating’s surface is “functionalized” so that it interacts properly with the blood-vessel tissue. Some of the cells are magnetic naturally, and “magnetic nanoparticles” would be injected into the bloodstream to speed tissue regeneration. Researchers also are aiming to engineer the stents so that they show up in medical imaging to reveal how the coatings hold up in the bloodstream.

The research is led by Allain and co-principal investigator Lisa Reece of the Birck Nanotechnology Center. This effort has spawned new collaborations with researchers around the world including those at Universidad de Antioquía, University of Queensland. The research also involves doctoral students Ravi Kempaiah and Emily Walker.

The work is funded with a three-year, $1.5 million grant from the U.S. Army. Cells needed to repair blood vessels are influenced by both the surface texture – features such as bumps and irregular shapes as tiny as 10 nanometers wide – as well as the surface chemistry of the stent materials.

As I find the international flavour to the pursuit of science quite engaging, I want to highlight this bit in the May 21, 2012 news item on Nanowerk which mentions a few other collaborators on this project,

Purdue researchers are working with Col. Rocco Armonda, Dr. Teodoro Tigno and other neurosurgeons at Walter Reed National Military Medical Center in Bethesda, Md. Collaborations also are planned with research scientists from the University of Queensland in Australia, Universidad de Antioquía and Universidad de Los Andes, both in Colombia.

The US Congress is not the only place to hear about this work, Allain will also be speaking in Toronto at the 9th Annual World Congress of Society for Brain Mapping & Therapeutics (SBMT) being held June 2 – 4, 2012.

Robot ethics at Vancouver’s next Café Scientifique

AJung Moon, a mechanical engineering researcher at the University of British Columbia, will be giving a talk: Roboethics – A discussion on how robots are impacting our society on Tuesday, May 31, 2011, 7:30 pm at the Railway Club,579 Dunsmuir St., Vancouver, BC. From the announcement,

From vacuuming houses to befriending older persons at care facilities, robots are starting to provide convenient and efficient solutions at homes, hospitals, and schools. For decades, numerous works in science fiction have imaginatively warned us that robots can bring catastrophic ethical, legal, and social issues into our society. But is today’s robotics technology advanced enough to the point that we should take these fictional speculations seriously? Roboticists, philosophers, and policymakers agree that we won’t see Terminator or Transformers type robots any time soon, but they also agree that the technology is bringing forth ethical issues needing serious discussions today. In this talk, we will highlight some of the ways robots are already impacting our society, and how the study of human-robot interaction can help put ethics into its design.

Moon has a blog called Roboethic info DataBase, where she posts the latest about robots and ethics.

Here’s a picture of her,

AJung Moon (downloaded from her Roboethics info DataBase blog)

I wonder what she makes of the RoboEarth project where robots will uploading information to something which is the equivalent of the internet and wikipedia (my Feb. 14, 2011 posting, scroll down a few paragraphs) or the lingodroids project where robots are creating a language. From the May 17, 2011 article by Katie Gatto (originally written for the IEEE [Institute of Electrical and Electronics Engineers) on physorg.com,

Communication is a vital part of any task that has to be done by more than one individual. That is why humans in every corner of the world have created their own complex languages that help us share the goal. As it turns out, we are not alone in that need, or in our ability to create a language of our own.

Researchers at the University of Queensland and Queensland University of Technology have created a pair of robots who are creating their own language. The bots, which are being taught how to speak but not given specific languages, are learning to create a lexicon of their own.

The researchers have named these bots, lingodroids and you can read the paper here,

Research paper: Schulz, R., Wyeth, G., & Wiles, J. (In Press) Are we there yet? Grounding temporal concepts in shared journeys, IEEE Transactions on Autonomous Mental Development [PDF]

I hope to get to the talk on Tuesday, May 31, 2011. Meanwhile, Happy Weekend (and for Canadians it’s a long weekend)!