Monthly Archives: July 2019

Blockchain made physical: BlocKit

Caption: Parts of BlocKit Credit: Irni Khairuddin

I’m always on the lookout for something that helps make blockchain and cryptocurrency more understandable. (For the uninitiated or anyone like me who needed to refresh their memories, I have links to good essays on the topic further down in this posting.)

A July 10, 2019 news item on ScienceDaily announces a new approach to understanding blockchain technology,

A kit made from everyday objects is bringing the blockchain into the physical world.

The ‘BlocKit’, which includes items such as plastic tubs, clay discs, padlocks, envelopes, sticky notes and battery-powered candles, is aimed to help people understand how digital blockchains work and can also be used by innovators designing new systems and services around blockchain.

A team of computer scientists from Lancaster University, the University of Edinburgh in the UK, and the Universiti Teknologi MARA, in Malaysia, created the prototype BlocKit because blockchain — the decentralised digital infrastructure that is used to organise the cryptocurrency Bitcoin and holds promise to revolutionise many other sectors from finance, supply-chain and healthcare — is so difficult for people to comprehend.

A July 10, 2019 Lancaster University press release (also on EurekAlert), which originated the news item, expands on the theme,

“Despite growing interest in its potential, the blockchain is so novel, disruptive and complex, it is hard for most people to understand how these systems work,” said Professor Corina Sas of Lancaster University’s School of Computing and Communications. “We have created a prototype kit consisting of physical objects that fulfil the roles of different parts of the blockchain. The kit really helps people visualise the different component parts of blockchain, and how they all interact.

“Having tangible physical objects, such as a transparent plastic box for a Bitcoin wallet, clay discs for Bitcoins, padlocks for passwords and candles representing miners’ computational power, makes thinking around processes and systems much easier to comprehend.”

The BlocKit consisted of physical items that represented 11 key aspects of blockchain infrastructure and it was used to explore key characteristics of blockchain, such as trust – an important challenge for Bitcoin users. The kit was evaluated as part of a study involving 15 experienced Bitcoin users.

“We received very positive feedback from the people who used the kit in our study and, interestingly, we found that the BlocKit can also be used by designers looking to develop new services based around blockchain – such as managing patients’ health records for example.”

I will be providing a link to and a citation for the paper but first, I’m excerpting a few bits,

We report on a workshop with 15 bitcoin experts, [emphasis mine] 12 males, 3 females, (mean age 29, range 21-39). All participants had at least 2 years of engaging in bitcoin transactions: 9 had between 2 and 3 years, 4 had between 4 and 5 years, 2had more than 6 years. All participants have at least graduate education, i.e., 6 BSc, 7 MScs, and 2 Ph.D. Participants were recruited through the mailing lists of two universities,and through a local Bitcoins meetup group. [p. 3]

A striking finding was the overwhelmingly positive experience supported by BlocKit. Findings show that 10 participants deeply enjoyed physically touching [emphasis mine] its objects and enacting their movement in space while talking about blockchain processes: “there is going to be other transactions from other people essentially, so let’s put a few bitcoins in that box. I love this stuff, this is amazing” [P12]. Participants suggested that BlocKit could be a valuable tool for learning about blockchain: “I think this all makes sense and would be fine to explain to the novices. It is cool, this is really an interesting kit”[P7]. Other participants suggested leveraging gamification principles for learning about blockchain: “It’s almost like you could turn this into some kind of cool game like a monopoly”[P5] [p. 5]

A significant finding is the value of the kit in supporting experts to materialize and reflect on their understanding of blockchain infrastructure and its inner working. We argue that through its materiality, the kit allows bringing the mental models into question, which in turn helps experts confirm their understandings, develop more nuanced understandings, or even revise some previously held, less accurate assumptions. [emphasis mine]

Even experts are still learning about bitcoin and blockchain according to this research sample. it’s also interesting to note that the workshop participants enjoyed the physicality. I don’t see too many mentions of it in my wanderings but I can’t help wondering if all this digitization is going to leave people starved for touch.

Getting back to blockchain, here’s the link and citation I promised,

BlocKit: A Physical Kit for Materializing and Designing for Blockchain Infrastructure by Irni Eliana Khairuddin, Corina Sas, and Chris Speed.presented at Designing Interactive Systems (DIS) 2019
ACM International Conference Series [downloaded from https://eprints.lancs.ac.uk/id/eprint/132467/1/Design_Kit_DIS_28.pdf]

This paper is open access, as for BlocKit, it exists only as a prototype according to the July 10, 2019 Lancaster University press release.

Introductory essays for blockchain and cryptocurrency

Here are two of my favourites. First, there’s this February 6, 2018 essay (part ii of a series) by Tim Schneider on artnet.com explaining it all by using the art world and art market as examples,

… the fraught relationship between art and value lies at the molten core of several pieces made using blockchain technology. Part one of this series addressed how, in theory, the blockchain strengthens the markets for new media by introducing the concept of digital scarcity. This innovation means that works as simple as an “original” JPG or GIF could be made as rare as Francis Bacon paintings. (This fact leads to a host of business implications that will be covered in Part III.

However, a handful of forward-looking artists is using the blockchain to do more than reset the market’s perception of supply and demand. The technology, their work proves, is more than new software—it’s also a new medium.

The description of how artists using blockchain as a medium provides some of the best descriptions of cryptocurrency and blockchain that I’ve been able to find.

The other essay, a January 5, 2018 article for Slate.com by Joshua Oliver, provides some detail I haven’t seen anywhere else (Note: A link has been removed),

Already, blockchain has been hailed as likely to revolutionize … well … everything. Banks, health care, voting, supply chains, fantasy football, Airbnb, coffee: Nothing is beyond the hypothetical reach of blockchain as a revolutionary force. These predictions are easy to sell because blockchain is still little-understood. If you don’t quite know what blockchain is, it’s easier to imagine that it is whatever you want it to be. But before we can begin to search for the real potential amid the mass of blockchain conjecture and hype, we need to clear up what exactly we mean when we say blockchain.

One cause of confusion is the phrase the blockchain, which makes it sound like blockchain is one specific thing. In reality, the word blockchain is commonly used to describe two broad types of computer systems. [emphases mine] Both use similar underlying protocols, but they have other important differences. Bitcoin represents one approach to using blockchain, one wedded to principles of radical decentralization. The second approach—pioneered by more business-minded players—puts blockchain to use without adopting bitcoin’s revolutionary, decentralized governance. Both of these designs are short-handed as blockchains, so it’s easy to miss the crucial differences. Without grasping these differences, it’s hard to understand where we are today in the development of this promising technology, which blockchain ventures are worth your attention, and what might happen next.

That’s all I’ve got for now.

Controlling agricultural pests with CRISPR-based technology

CRISPR (clustered regularly interspaced short palindromic repeats) technology is often touted as being ‘precise’, which as far as I can tell, is not exactly the case (see my Nov. 28, 2018 posting about the CRISPR babies [scroll down about 30% of the way for the first hint that CRISPR isn’t]). So, it’s a bit odd to see the word ‘precise’ used as part of a new CRISPR-based technology’s name (from a January 8, 2019 news item on ScienceDaily,

Using the CRISPR gene editing tool, Nikolay Kandul, Omar Akbari and their colleagues at UC San Diego [UC is University of California] and UC Berkeley devised a method of altering key genes that control insect sex determination and fertility.

A description of the new “precision-guided sterile insect technique,” [emphasis mine] or pgSIT, is published Jan. 8 [2019] in the journal Nature Communications.

A January 8, 209 UCSD press release (also on EurekAlert) by Mario Aguilera, which originated the news item, delves further into the research,

When pgSIT-derived eggs are introduced into targeted populations, the researchers report, only adult sterile males emerge, resulting in a novel, environmentally friendly and relatively low-cost method of controlling pest populations in the future.

“CRISPR technology has empowered our team to innovate a new, effective, species-specific, self-limiting, safe and scalable genetic population control technology with remarkable potential to be developed and utilized in a plethora of insect pests and disease vectors,” said Akbari, an assistant professor in UC San Diego’s Division of Biological Sciences. “In the future, we strongly believe this technology will be safely used in the field to suppress and even eradicate target species locally, thereby revolutionizing how insects are managed and controlled going forward.”

Since the 1930s, agricultural researchers have used select methods to release sterile male insects into the wild to control and eradicate pest populations. In the 1950s, a method using irradiated males was implemented in the United States to eliminate the pest species known as the New World Screwworm fly, which consumes animal flesh and causes extensive damage to livestock. Such radiation-based methods were later used in Mexico and parts of Central America and continue today.

Instead of radiation, the new pgSIT (precision-guided sterile insect technique), developed over the past year-and-a-half by Kandul and Akbari in the fruit fly Drosophila, uses CRISPR to simultaneously disrupt key genes that control female viability and male fertility in pest species. pgSIT, the researchers say, results in sterile male progeny with 100 percent efficiency. Because the targeted genes are common to a vast cross-section of insects, the researchers are confident the technology can be applied to a range of insects, including disease-spreading mosquitoes.

The researchers envision a system in which scientists genetically alter and produce eggs of a targeted pest species. The eggs are then shipped to a pest location virtually anywhere in the world, circumventing the need for a production facility on-site. Once the eggs are deployed at the pest location, the researchers say, the newly born sterile males will mate with females in the wild and be incapable of producing offspring, driving down the population.

“This is a novel twist of a very old technology,” said Kandul, an assistant project scientist in UC San Diego’s Division of Biological Sciences. “That novel twist makes it extremely portable from one species to another species to suppress populations of mosquitoes or agricultural pests, for example those that feed on valuable wine grapes.”

The new technology is distinct from continuously self-propagating “gene drive” systems that propagate genetic alterations from generation to generation. Instead, pgSIT is considered a “dead end” since male sterility effectively closes the door on future generations.

“The sterile insect technique is an environmentally safe and proven technology,” [emphasis mine] the researchers note in the paper. “We aimed to develop a novel, safe, controllable, non-invasive genetic CRISPR-based technology that could be transferred across species and implemented worldwide in the short-term to combat wild populations.”

With pgSIT proven in fruit flies, the scientists are hoping to develop the technology in Aedes aegypti, the mosquito species responsible for transmitting dengue fever, Zika, yellow fever and other diseases to millions of people.

“The extension of this work to other insect pests could prove to be a general and very useful strategy to deal with many vector-borne diseases that plague humanity and wreak havoc an agriculture globally,” said Suresh Subramani, global director of the Tata Institute for Genetics and Society.

I have one comment about the ‘safety’ of the sterile insect technique. It’s been safe up until now but, assuming this technique works as described: What happens as this new and more powerful technique is more widely deployed possibly eliminating whole species of insects? Might these ‘pests’ have a heretofore unknown beneficial effect somewhere in the food chain or in an ecosystem? Or, there may be other unintended consequences.

Moving on, here’s a link to and a citation for the paper,

Transforming insect population control with precision guided sterile males with demonstration in flies by Nikolay P. Kandul, Junru Liu, Hector M. Sanchez C., Sean L. Wu, John M. Marshall, & Omar S. Akbari. Nature Communications volume 10, Article number: 84 (2019) DOI: https://doi.org/10.1038/s41467-018-07964-7 Published 08 January 2019

This paper is open access.

The researchers have made this illustrative image available,

Caption: This is a schematic of the new precision-guided sterile insect technique (pgSIT), which uses components of the CRISPR/Cas9 system to disrupt key genes that control female viability and male fertility, resulting in sterile male progeny. Credit: Nikolay Kandul, Akbari Lab, UC San Diego

Desalination and toxic brine

Have you ever wondered about the possible effects and impact of desalinating large amounts of ocean water? It seems that some United Nations University (UNU) researchers have asked and are beginning to answer that question. The following table illustrates the rise in desalination plants and processes,


Today 15,906 operational desalination plants are found in 177 countries. Almost half of the global desalination capacity is located in the Middle East and North Africa region (48 percent), with Saudi Arabia (15.5 percent), the United Arab Emirates (10.1 percent) and Kuwait (3.7 percent) being both the major producers in the region and globally. Credit: UNU-INWEH [downloaded from http://inweh.unu.edu/un-warns-of-rising-levels-of-toxic-brine-as-desalination-plants-meet-growing-water-needs/]

A January 14, 2019 news item on phys.org highlights the study on desalination from the UNU,

The fast-rising number of desalination plants worldwide—now almost 16,000, with capacity concentrated in the Middle East and North Africa—quench a growing thirst for freshwater but create a salty dilemma as well: how to deal with all the chemical-laden leftover brine.

In a UN-backed paper, experts estimate the freshwater output capacity of desalination plants at 95 million cubic meters per day—equal to almost half the average flow over Niagara Falls.
For every litre of freshwater output, however, desalination plants produce on average 1.5 litres of brine (though values vary dramatically, depending on the feedwater salinity and desalination technology used, and local conditions). Globally, plants now discharge 142 million cubic meters of hypersaline brine every day (a 50% increase on previous assessments).

That’s enough in a year (51.8 billion cubic meters) to cover Florida under 30.5 cm (1 foot) of brine.

The authors, from UN University’s Canadian-based Institute for Water, Environment and Health [at McMaster University], Wageningen University, The Netherlands, and the Gwangju Institute of Science and Technology, Republic of Korea, analyzed a newly-updated dataset—the most complete ever compiled—to revise the world’s badly outdated statistics on desalination plants.

And they call for improved brine management strategies to meet a fast-growing challenge, noting predictions of a dramatic rise in the number of desalination plants, and hence the volume of brine produced, worldwide.

A January 14, 2017 UNU press release, which originated the news item, details the findings,

The paper found that 55% of global brine is produced in just four countries: Saudi Arabia (22%), UAE (20.2%), Kuwait (6.6%) and Qatar (5.8%). Middle Eastern plants, which largely operate using seawater and thermal desalination technologies, typically produce four times as much brine per cubic meter of clean water as plants where river water membrane processes dominate, such as in the US.

The paper says brine disposal methods are largely dictated by geography but traditionally include direct discharge into oceans, surface water or sewers, deep well injection and brine evaporation ponds.

Desalination plants near the ocean (almost 80% of brine is produced within 10km of a coastline) most often discharge untreated waste brine directly back into the marine environment.

The authors cite major risks to ocean life and marine ecosystems posed by brine greatly raising the salinity of the receiving seawater, and by polluting the oceans with toxic chemicals used as anti-scalants and anti-foulants in the desalination process (copper and chlorine are of major concern).

“Brine underflows deplete dissolved oxygen in the receiving waters,” says lead author Edward Jones, who worked at UNU-INWEH, and is now at Wageningen University, The Netherlands. “High salinity and reduced dissolved oxygen levels can have profound impacts on benthic organisms, which can translate into ecological effects observable throughout the food chain.”

Meanwhile, the paper highlights economic opportunities to use brine in aquaculture, to irrigate salt tolerant species, to generate electricity, and by recovering the salt and metals contained in brine — including magnesium, gypsum, sodium chloride, calcium, potassium, chlorine, bromine and lithium.

With better technology, a large number of metals and salts in desalination plant effluent could be mined. These include sodium, magnesium, calcium, potassium, bromine, boron, strontium, lithium, rubidium and uranium, all used by industry, in products, and in agriculture. The needed technologies are immature, however; recovery of these resources is economically uncompetitive today.

“There is a need to translate such research and convert an environmental problem into an economic opportunity,” says author Dr. Manzoor Qadir, Assistant Director of UNU-INWEH. “This is particularly important in countries producing large volumes of brine with relatively low efficiencies, such as Saudi Arabia, UAE, Kuwait and Qatar.”

“Using saline drainage water offers potential commercial, social and environmental gains. Reject brine has been used for aquaculture, with increases in fish biomass of 300% achieved. It has also been successfully used to cultivate the dietary supplement Spirulina, and to irrigate forage shrubs and crops (although this latter use can cause progressive land salinization).”

“Around 1.5 to 2 billion people currently live in areas of physical water scarcity, where water resources are insufficient to meet water demands, at least during part of the year. Around half a billion people experience water scarcity year round,” says Dr. Vladimir Smakhtin, a co-author of the paper and the Director of UNU-INWEH, whose institute is actively pursuing research related to a variety of unconventional water sources.

“There is an urgent need to make desalination technologies more affordable and extend them to low-income and lower-middle income countries. At the same time, though, we have to address potentially severe downsides of desalination — the harm of brine and chemical pollution to the marine environment and human health.”

“The good news is that efforts have been made in recent years and, with continuing technology refinement and improving economic affordability, we see a positive and promising outlook.”

¹The authors use the term “brine” to refer to all concentrate discharged from desalination plants, as the vast majority of concentrate (>95%) originates from seawater and highly brackish groundwater sources.

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

The state of desalination and brine production: A global outlook by Edward Jones, Manzoor Qadir, Michelle T.H.van Vliet, Vladimir Smakhtin, Seong-mu Kang. Science of The Total Environment Volume 657, 20 March 2019, Pages 1343-1356 DOI: https://doi.org/10.1016/j.scitotenv.2018.12.076 Available online 7 December 2018

Surprisingly (to me anyway), this paper is behind a paywall.

There’s no ‘I’ in team: coaching scientists to work together

While it’s true enough in English where you don’t spell the word team with the letter ‘I’, that’s not the case in French where the word is ‘equipe’. it makes me wonder how many other languages in the world have an ‘I’ in team.

Moving on. This English language saying is true enough in its way but there is no team unless you have a group of ‘I’s’ and the trick is getting them to work together as a July 18, 2019 Northwestern University news release (received via email) about a new online training tool notes,

Coaching scientists to play well together

Free tool shows how to avoid fights over data and authorship conflicts   

‘You stole my idea’ or ‘I’m not getting credit for my work’ are common disputes
Only tool validated by research to help scientists collaborate smoothly
Many NSF [US National Science Foundation] and NIH [US National Institutes of Health] grants now require applicants to show readiness for team science
Scientists can’t do it on their own

CHICAGO — When scientists from different disciplines collaborate – as is increasingly necessary to confront the complexity of challenging research problems – interpersonal tussles often arise. One scientist may accuse another of stealing her ideas. Or, a researcher may feel he is not getting credit for his work or doesn’t have access to important data. 
 
“Interdisciplinary team science is now the state of the art across all branches of science and engineering,” said Bonnie Spring, professor of preventive medicine at Northwestern University Feinberg School of Medicine. “But very few scientists have been trained to work with others outside of their own disciplinary silo.”
 
The skill is critical because many National Institute[s] of Health and National Science Foundationgrants require applicants to show readiness for team science.
 
A free, online training tool developed by Northwestern — teamscience.net — has been been proven to help scientists develop skills to work with other scientists outside their own discipline. 
 
A new study led by Spring showed scientists who completed the program’s modules – called COALESCE – significantly boosted their knowledge about team science and increased their self-confidence about being able to successfully work in scientific teams. Most people who completed one or more modules (84%) said that the experience of taking the modules was very likely to positively impact their future research.
 
The study will be published July 18 [2019] in the Journal of Clinical and Translational Science.
 
There are few training resources to teach scientists how to collaborate, and the ones that are available don’t have evidence of their effectiveness. Teamscience.net is the only free, validated-by-research tool available to anyone at any time. 
 
Almost 1,000 of the COALESCE users opted voluntarily to respond to questions about the learning modules, providing information about how taking each module influenced team science knowledge, skills and attitudes.
 
‘You stole my idea’
 
The most common area of dispute among collaborating scientists is authorship concerns, such as accusations that one person stole ideas from another or that a contributor was not getting credit for his or her work, the study authors said. Other disputes arise around access to and analysis of data, utilization of materials or resources and the general direction of the research itself. Underlying all of these issues is a common failure to prepare for working collaboratively with other scientists. 
 
“Preparing in advance before starting to collaborate, often through the creation of a formal collaboration agreement document, is the best way to head off these types of disputes,” said Angela Pfammatter, assistant professor of preventive medicine at Feinberg and a coauthor on the paper.
  
Spring suggested “having scientists discuss their expectations of one another and the collaboration to prevent acrimonious conflicts.” 
 
Skills to play well together
 
These skills are critical to a successful scientific team, the authors said: 

The ability to choose team members who have the right mix of expertise, temperament and accessibility to round out a team. 
The ability to anticipate what could go wrong and to develop contingency plans in advance. 
The ability to manage conflict within the team 

The teamscience.net modules help scientists acquire these skills by letting them interact with different problem scenarios that can arise in team-based research. Scientists can try out different solutions and learn from mistakes in a safe, online environment. 
 
More than 16,000 people have accessed the resource in the past six years.  Demand for team science training is expected to increase as interdisciplinary teams set out to tackle some of science’s most challenging problems. 
 
Other Northwestern authors on the paper are Ekaterina Klyachko, Phillip Rak, H. Gene McFadden, Juned Siddique and Leland Bardsley. 
 
Funding support for COALESCE is from the National Institutes of Health, National Center for Advancing Translational Sciences grants 3UL1RR025741 and UL1TR001422 and its Office of Behavioral and Social Sciences Research.

i once got caught here on this blog between two warring scientists. My August 24, 2015 posting was a pretty standard one for me. Initially, it was one of my more minimalistic pieces with a copy of the text from a university news release announcing the research and a link to the academic paper. I can’t remember if the problem was which scientist was listed first and which was listed last but one of them took exception and contacted me explaining how it was wrong. (Note: These decisions are not made by me.) I did my best to fix whatever the problem was and then the other scientist contacted me. After the dust settled, I ended up with a dog’s breakfast for my posting and a new policy.

Getting back to COALESCE: I wish the Northwestern University researchers all the best as they look for ways to help scientists work together more smoothly and cooperatively.

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

Online, cross-disciplinary team science training for health and medical professionals: Evaluation of COALESCE (teamscience.net) by Bonnie Spring, Ekaterina A. Klyachko, Phillip W. Rak, H. Gene McFadden, Donald Hedeker, Juned Siddique, Leland R. Bardsley, and Angela Fidler Pfammatter. Jurnal of Clinical and Translational Science DOI: https://doi.org/10.1017/cts.2019.383 Published online by Cambridge University Press: 18 July 2019

This paper is open access.

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.

Nanoflowers for better drug delivery; researchers looking for commercial partners

Caption: Schematic representation of the movement of the flower-like particle as it makes its way through a cellular trap to deliver therapeutic genes. Credit: WSU [Washington State University]

It looks more like a swimming pool with pool toys to me but I imagine that nobody wants to say that they’re sending ‘pool toys’ through your bloodstream. Nanoflowers or flower-shaped nanoparticles sounds nicer.

From a January 10, 2019 news item on Nanowerk,

Washington State University [WSU] researchers have developed a novel way to deliver drugs and therapies into cells at the nanoscale without causing toxic effects that have stymied other such efforts.

The work could someday lead to more effective therapies and diagnostics for cancer and other illnesses.

Led by Yuehe Lin, professor in WSU’s School of Mechanical and Materials Engineering, and Chunlong Chen, senior scientist at the Department of Energy’s Pacific Northwest National Laboratory (PNNL), the research team developed biologically inspired materials at the nanoscale that were able to effectively deliver model therapeutic genes into tumor cells. …

A January 10, 2019 WSU news release (also on EurekAlert) by Tina Hilding, which originated the news item, describes the work in greater detail,

Researchers have been working to develop nanomaterials that can effectively carry therapeutic genes directly into the cells for the treatment of diseases such as cancer. The key issues for gene delivery using nanomaterials are their low delivery efficiency of medicine and potential toxicity.

“To develop nanotechnology for medical purposes, the first thing to consider is toxicity — That is the first concern for doctors,” said Lin.

The flower-like particle the WSU and PNNL team developed is about 150 nanometers in size, or about one thousand times smaller than the width of a piece of paper. It is made of sheets of peptoids, which are similar to natural peptides that make up proteins. The peptoids make for a good drug delivery particle because they’re fairly easy to synthesize and, because they’re similar to natural biological materials, work well in biological systems.

The researchers added fluorescent probes in their peptoid nanoflowers, so they could trace them as they made their way through cells, and they added the element fluorine, which helped the nanoflowers more easily escape from tricky cellular traps that often impede drug delivery.

The flower-like particles loaded with therapeutic genes were able to make their way smoothly out of the predicted cellular trap, enter the heart of the cell, and release their drug there.

“The nanoflowers successfully and rapidly escaped (the cell trap) and exhibited minimal cytotoxicity,” said Lin.

After their initial testing with model drug molecules, the researchers hope to conduct further studies using real medicines.

“This paves a new way for us to develop nanocargoes that can efficiently deliver drug molecules into the cell and offers new opportunities for targeted gene therapies,” he said.

The WSU and PNNL team have filed a patent application for the new technology, and they are seeking industrial partners for further development.

Should you and your company be interested in partnering with the researchers, contact:

  • Yuehe Lin, professor, School of Mechanical and Materials Engineering, 509‑335‑8523, yuehe.lin@wsu.edu
  • Tina Hilding, communications director, Voiland College of Engineering and Architecture, 509‑335‑5095, thilding@wsu.edu

For those who’d like more information, here’s a link to and a citation for the paper,

Efficient Cytosolic Delivery Using Crystalline Nanoflowers Assembled from Fluorinated Peptoids by Yang Song, Mingming Wang, Suiqiong Li, Haibao Jin, Xiaoli Cai, Dan Du, He Li, Chun‐Long Chen, Yuehe Lin. Small DOI: https://doi.org/10.1002/smll.201803544 First published: 22 November 2018

This paper is behind a paywall.

Searchable database for hazardous nanomaterials and a Graphene Verification Programme

I have two relatively recent news bits about nanomaterials, the second being entirely focused on graphene.

Searchable database

A July 9, 2019 news item on Nanowerk announces a means of finding out what hazards may be associated with 300 different nanomaterials (Note: A Link has been removed),

A new search tool for nanomaterials has been published on the European Union Observatory for Nanomaterials (EUON) website. It will enable regulators to form a better view of available data and give consumers access to chemicals safety information.

The tool combines data submitted by companies in their REACH registrations [Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) ], data collected about nanomaterials used as ingredients in cosmetic products under the Cosmetics Regulation and data from the public national nanomaterial inventories of Belgium and France.

A July 3, 2019 EUON press release, which originated the news item, provides a bit more detail,

The EUON’s search brings data from these sources together in one place, allowing users to easily search for nanomaterials that are currently on the EU market. The results are linked to ECHA’s [European Chemicals Agency] database of chemicals registered in the EU and, for the first time, summarised information about the substances, their properties as well as detailed safety and characterisation data can be easily found.

Background

While there are over 300 nanomaterials on the EU market, 37 are currently covered by an existing registration under REACH. The information requirements for REACH were revised last year with explicit obligations for nanomaterials manufactured in or imported to the EU. The new requirements enter into force in January 2020 and will result in more publicly available information.

The EUON aims to increase the transparency of information available to the public on the safety and markets of nanomaterials in the EU. A key aim of the observatory is to create a one-stop shop for information, where EU citizens and stakeholders including NGOs, industry, and regulators can all easily find accessible and relevant safety information on nanomaterials on the EU market.

Here’s the searchable database.

Graphene verification

There was a bit of a scandal about fake graphene in the Fall of 2018 (my May 28, 2019 posting gives details). Dexter Johnson provides additional insight and information about the launch of a new graphene verification programme and news of a slightly older graphene verification programme in his July 9, 2019 article for the Nanoclast blog on the IEEE (Institute of Electrical and Electronics Engineers) website (Note: Links have been removed),

Last year [2018], the graphene community was rocked by a series of critical articles that appeared in some high-profile journals. First there was an Advanced Material’s article with the rather innocuously title: “The Worldwide Graphene Flake Production”. It was perhaps the follow-up article that appeared in the journal Nature that really shook things up with its incendiary title: “The war on fake graphene”.

In these two articles it was revealed that material that had been claimed to be high-quality (and high-priced) graphene was little more than graphite powder. Boosted by their appearance in high-impact journals, these articles threatened the foundations of the graphene marketplace.

But while these articles triggered a lot of hand wringing among the buyers and sellers of graphene, it’s not clear that their impact extended much beyond the supply chain of graphene. Whether or not graphene has aggregated back to being graphite is one question. An even bigger one is whether or not consumers are actually being sold a better product on the basis that it incorporates graphene.

Dexter details some of the issues from the consumer’s perspective (Note: Links have been removed),

Consumer products featuring graphene today include everything from headphones to light bulbs. Consequently, there is already confusion among buyers about the tangible benefits graphene is supposed to provide. And of course the situation becomes even worse if the graphene sold to make products may not even be graphene: how are consumers supposed to determine whether graphene infuses their products with anything other than a buzzword?

Another source of confusion arises because when graphene is incorporated into a product it is effectively a different animal from graphene in isolation. There is ample scientific evidence that graphene when included in a material matrix, like a polymer or even paper, can impart new properties to the materials. “You can transfer some very useful properties of graphene into other materials by adding graphene, but just because the resultant material contains graphene it does not mean it will behave like free-standing graphene, explains Tom Eldridge, of UK-based Fullerex, a consultancy that provides companies with information on how to include graphene in a material matrix

The rest of Dexter’s posting goes on to mention two new graphene verification progammes (producer and product) available through The Graphene Council. As for what the council is, there’s this from council’s About webpage,

The Graphene Council was founded in 2013 with a mission to serve the global community of graphene professionals. Today, The Graphene Council is the largest community in the world for graphene researchers, academics, producers, developers, investors, nanotechnologists, regulatory agencies, research institutes, material science specialists and even the general public. We reach more than 50,000 people with an interest in this amazing material. 

Interestingly the council’s offices are located in the US state of North Carolina. (I would have guessed that its headquarters would be in the UK, given the ‘ownership’ the UK has been attempting to establish over graphene Let me clarify, by ownership I mean the Brits want to be recognized as dominant or preeminent in graphene research and commercialization.)

The council’s first verified graphene producer is a company based in the UK as can be seen in an April 1, 2019 posting by council director Terrance Barkan on the council’s blog,

The Graphene Council is pleased to announce that Versarien plc is the first graphene company in the world to successfully complete the Verified Graphene Producer™ program, an independent, third party verification system that involves a physical inspection of the production facilities, a review of the entire production process, a random sample of product material and rigorous characterization and testing by a first class, international materials laboratory.

The Verified Graphene Producer™ program is an important step to bring transparency and clarity to a rapidly changing and opaque market for graphene materials, providing graphene customers with a level of confidence that has not existed before.

“We are pleased to have worked with the National Physical Laboratory (NPL) in the UK, regarded as one of the absolute top facilities for metrology and graphene characterization in the world.
 
They have provided outstanding analytical expertise for the materials testing portion of the program including Raman Spectroscopy, XPS, AFM and SEM testing services.” stated Terrance Barkan CAE, Executive Director of The Graphene Council.
 
Andrew Pollard, Science Area Leader of the Surface Technology Group, National Physical Laboratory, said: “In order to develop real-world products that can benefit from the ‘wonder material’, graphene, we first need to fully understand its properties, reliably and reproducibly.
 
“Whilst international measurement standards are currently being developed, it is critical that material characterisation is performed to the highest possible level.
 
As the UK’s National Measurement Institute (NMI) with a focus on developing the metrology of graphene and related 2D materials, we aim to be an independent third party in the testing of graphene material for companies and associations around the world, such as The Graphene Council.” 
 
Neill Ricketts, CEO of Versarien said: “We are delighted that Versarien is the first graphene producer in the world to successfully complete the Graphene Council’s Verified Graphene Producer™ programme.”
 
“This is a huge validation of our technology and will enable our partners and potential customers to have confidence that the graphene we produce meets globally accepted standards.”
 
“There are many companies that claim to be graphene producers, but to enjoy the benefits that this material can deliver requires high quality, consistent product to be supplied.  The Verified Producer programme is designed to verify that our production facilities, processes and tested material meet the stringent requirements laid down by The Graphene Council.”

“I am proud that Versarien has been independently acclaimed as a Verified Graphene Producer™ and look forward to making further progress with our collaboration partners and numerous other parties that we are in discussions with.”

James Baker CEng FIET, the CEO of Graphene@Manchester (which includes coordinating the efforts of the National Graphene Institute and the Graphene Engineering and Innovation Centre [GEIC]) stated: “We applaud The Graphene Council for promoting independent third party verification for graphene producers that is supported by world class metrology and characterization services.”

“This is an important contribution to the commercialization of graphene as an industrial material and are proud to have The Graphene Council as an Affiliate Member of the Graphene Engineering and Innovation Centre (GEIC) here in Manchester ”.

Successful commercialization of graphene materials requires not only the ability to produce graphene to a declared specification but to be able to do so at a commercial scale.
It is nearly impossible for a graphene customer to verify the type of material they are receiving without going through an expensive and time consuming process of having sample materials fully characterized by a laboratory that has the equipment and expertise to test graphene.

The Verified Graphene Producer™ program developed by The Graphene Councilprovides a level of independent inspection and verification that is not available anywhere else.

As for the “Verified Graphene Product” programme mentioned in Dexter’s article (it’s not included in the excerpts here), I can’t find any sign of it ion the council’s website.

Controlling neurons with light: no batteries or wires needed

Caption: Wireless and battery-free implant with advanced control over targeted neuron groups. Credit: Philipp Gutruf

This January 2, 2019 news item on ScienceDaily describes the object seen in the above and describes the problem it’s designed to solve,

University of Arizona biomedical engineering professor Philipp Gutruf is first author on the paper Fully implantable, optoelectronic systems for battery-free, multimodal operation in neuroscience research, published in Nature Electronics.

Optogenetics is a biological technique that uses light to turn specific neuron groups in the brain on or off. For example, researchers might use optogenetic stimulation to restore movement in case of paralysis or, in the future, to turn off the areas of the brain or spine that cause pain, eliminating the need for — and the increasing dependence on — opioids and other painkillers.

“We’re making these tools to understand how different parts of the brain work,” Gutruf said. “The advantage with optogenetics is that you have cell specificity: You can target specific groups of neurons and investigate their function and relation in the context of the whole brain.”

In optogenetics, researchers load specific neurons with proteins called opsins, which convert light to electrical potentials that make up the function of a neuron. When a researcher shines light on an area of the brain, it activates only the opsin-loaded neurons.

The first iterations of optogenetics involved sending light to the brain through optical fibers, which meant that test subjects were physically tethered to a control station. Researchers went on to develop a battery-free technique using wireless electronics, which meant subjects could move freely.

But these devices still came with their own limitations — they were bulky and often attached visibly outside the skull, they didn’t allow for precise control of the light’s frequency or intensity, and they could only stimulate one area of the brain at a time.

A Dec. 21, 2018 University of Azrizona news release (published Jan. 2, 2019 on EurekAlert), which originated the news item, discusses the work in more detail,

“With this research, we went two to three steps further,” Gutruf said. “We were able to implement digital control over intensity and frequency of the light being emitted, and the devices are very miniaturized, so they can be implanted under the scalp. We can also independently stimulate multiple places in the brain of the same subject, which also wasn’t possible before.”

The ability to control the light’s intensity is critical because it allows researchers to control exactly how much of the brain the light is affecting — the brighter the light, the farther it will reach. In addition, controlling the light’s intensity means controlling the heat generated by the light sources, and avoiding the accidental activation of neurons that are activated by heat.

The wireless, battery-free implants are powered by external oscillating magnetic fields, and, despite their advanced capabilities, are not significantly larger or heavier than past versions. In addition, a new antenna design has eliminated a problem faced by past versions of optogenetic devices, in which the strength of the signal being transmitted to the device varied depending on the angle of the brain: A subject would turn its head and the signal would weaken.

“This system has two antennas in one enclosure, which we switch the signal back and forth very rapidly so we can power the implant at any orientation,” Gutruf said. “In the future, this technique could provide battery-free implants that provide uninterrupted stimulation without the need to remove or replace the device, resulting in less invasive procedures than current pacemaker or stimulation techniques.”

Devices are implanted with a simple surgical procedure similar to surgeries in which humans are fitted with neurostimulators, or “brain pacemakers.” They cause no adverse effects to subjects, and their functionality doesn’t degrade in the body over time. This could have implications for medical devices like pacemakers, which currently need to be replaced every five to 15 years.

The paper also demonstrated that animals implanted with these devices can be safely imaged with computer tomography, or CT, and magnetic resonance imaging, or MRI, which allow for advanced insights into clinically relevant parameters such as the state of bone and tissue and the placement of the device.

This image of a combined MRI (magnetic resonance image) and CT (computer tomography) scan bookends, more or less, the picture of the device which headed this piece,

Combined image analysis with MRI and CT results superimposed on a 3D rendering of the animal implanted with the programmable bilateral multi µ-ILED device. Courtesy: University of Arizona

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

Fully implantable optoelectronic systems for battery-free, multimodal operation in neuroscience research by Philipp Gutruf, Vaishnavi Krishnamurthi, Abraham Vázquez-Guardado, Zhaoqian Xie, Anthony Banks, Chun-Ju Su, Yeshou Xu, Chad R. Haney, Emily A. Waters, Irawati Kandela, Siddharth R. Krishnan, Tyler Ray, John P. Leshock, Yonggang Huang, Debashis Chanda, & John A. Rogers. Nature Electronics volume 1, pages652–660 (2018) DOI: https://doi.org/10.1038/s41928-018-0175-0 Published 13 December 2018

This paper is behind a paywall.

Tapping into wound healing by harnessing the natural healing process

If you’re imagining an enhanced chakra balancing experience or more efficient digestion of your vitamin supplements, you will be a little disappointed in this latest news from the Imperial College of London (ICL). On the other hand, if you have damaged tissue, this discovery could make your recovery much easier. From a January 7, 2019 news item on phys.org,

Materials are widely used to help heal wounds: Collagen sponges help treat burns and pressure sores, and scaffold-like implants are used to repair bones. However, the process of tissue repair changes over time, so scientists are developing biomaterials that interact with tissues as healing takes place

Now, Dr. Ben Almquist and his team at Imperial College London have created a new molecule that could change the way traditional materials work with the body. Known as traction force-activated payloads (TrAPs), their method lets materials talk to the body’s natural repair systems to drive healing.

The researchers say incorporating TrAPs into existing medical materials could revolutionise the way injuries are treated. Dr. Almquist, from Imperial’s Department of Bioengineering, said: “Our technology could help launch a new generation of materials that actively work with tissues to drive healing.”

A January 7, 2019 ICL press release (also on EurekAlert) by Caroline Brogan, which originated the news item, expands on the theme,

After an injury, cells ‘crawl’ through the collagen ‘scaffolds’ found in wounds, like spiders navigating webs. As they move, they pull on the scaffold, which activates hidden healing proteins that begin to repair injured tissue.

The researchers in the study designed TrAPs as a way to recreate this natural healing method. They folded the DNA segments into three-dimensional shapes known as aptamers that cling tightly to proteins. Then, they attached a customisable ‘handle’ that cells can grab onto on one end, before attaching the opposite end to a scaffold such as collagen.

During laboratory testing of their technique, they found that cells pulled on the TrAPs as they crawled through the collagen scaffolds. The pulling made the TrAPs unravel like shoelaces to reveal and activate the healing proteins. These proteins instruct the healing cells to grow and multiply

The researchers also found that by changing the cellular ‘handle’, they can change which type of cell can grab hold and pull, letting them tailor TrAPs to release specific therapeutic proteins based on which cells are present at a given point in time. In doing so, the TrAPs produce materials that can smartly interact with the correct type of cell at the correct time during wound repair.

This is the first time scientists have activated healing proteins using differing cell types in man-made materials. The technique mimics healing methods found in nature. Dr Almquist said: “Creatures from sea sponges to humans use cell movement to activate healing. Our approach mimics this by using the different cell varieties in wounds to drive healing.””

From lab to humans

This approach is adaptable to different cell types, so could be used in a variety of injuries such as fractured bones, scar tissue after heart attacks, and damaged nerves. New techniques are also desperately needed for patients whose wounds won’t heal despite current interventions, like diabetic foot ulcers, which are the leading cause of non-traumatic lower leg amputations.

TrAPs are relatively straightforward to create and are fully man-made, meaning they are easily recreated in different labs and can be scaled up to industrial quantities. Their adaptability also means they could help scientists create new methods for laboratory studies of diseases, stem cells, and tissue development.

Aptamers are currently used as drugs, meaning they are already proven safe and optimised for clinical use. Because TrAPs take advantage of aptamers that are safe for humans, they may be able to take a shorter path to the clinic than methods that start from ground zero.

Dr Almquist said: “TrAPs provide a flexible method of actively communicating with wounds, as well as key instructions when and where they are needed. This intelligent healing is useful during every phase of the healing process, has the potential to increase the body’s chance to recover, and has far-reaching uses on many different types of wounds. This technology could serve as a conductor of wound repair, orchestrating different cells over time to work together to heal damaged tissues.”

The researchers have made available an image and a video abstract illustrating their work,

TrAPs could harness the body’s natural healing powers to repair bone. Courtesy: Imperial College of London

By the way, the video was produced by www.animateyour.science (based in Adelaide, Australia) and they have a very interesting About page,

Our story

Your research is brilliant and novel. I’m sure of it. You might even be a pioneer in your field. But ask yourself honestly, is it enough? Is it truly enough to make a difference in the world?
 
My name is Tullio Rossi, and I founded Animate Your Science on my quest to make a positive impact on society through science.
 
During my Ph.D., I found that my peer-reviewed paper alone wasn’t cutting it. If I wanted to reach my peers, let alone the general public, I needed to communicate my findings in a fun and imaginative way.
 
This realization changed everything and inspired me to create “Lost at Sea,” an award-winning video that reached the hearts and minds of thousands of people.
 
The success of this first video blew my mind. And I got to thinking, maybe other scientists are lost at sea, so to speak. Maybe others want to reach the masses with their research, but just don’t know where to start.
 
This was the day Animate Your Science was born.

Why we do it

What we really want to do is bring science into society. That’s the true value of this company and the reason we believe in it.

We love science but we believe that, if not communicated properly, science is of limited use to society.​
 
As scientists, it’s our privilege and duty to unearth these revelations and package them in a way that appeals to our peers as well as the general public.

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

Biologically Inspired, Cell‐Selective Release of Aptamer‐Trapped Growth Factors by Traction Forces by Anna Stejskalová, Nuria Oliva, Frances J. England, Benjamin D. Almquist. Advanced Materials DOI: https://doi.org/10.1002/adma.201806380 First published: 07 January 2019

This paper is open access.

Innerspace of a nanoparticle

A Jan. 3, 2019 news item on ScienceDaily touts a new means of transporting DNA-coated nanoparticles (DNA is deoxyribonucleic acid),

This holiday season, scientists at the Center for Functional Nanomaterials (CFN) — a U.S. Department of Energy Office of Science User Facility at Brookhaven National Laboratory — have wrapped a box of a different kind. Using a one-step chemical synthesis method, they engineered hollow metallic nanosized boxes with cube-shaped pores at the corners and demonstrated how these “nanowrappers” can be used to carry and release DNA-coated nanoparticles in a controlled way. The research is reported in a paper published on Dec. 12 [2018] in ACS Central Science, a journal of the American Chemical Society (ACS).

A January 3, 2018 Brookhaven National Laboratory (BNL) news release (also on EurekAlert), which originated the news item, explains the work in more detail (Note: Links have been removed),

“Imagine you have a box but you can only use the outside and not the inside,” said co-author Oleg Gang, leader of the CFN Soft and Bio Nanomaterials Group. “This is how we’ve been dealing with nanoparticles. Most nanoparticle assembly or synthesis methods produce solid nanostructures. We need methods to engineer the internal space of these structures.

“Compared to their solid counterparts, hollow nanostructures have different optical and chemical properties that we would like to use for biomedical, sensing, and catalytic applications,” added corresponding author Fang Lu, a scientist in Gang’s group. “In addition, we can introduce surface openings in the hollow structures where materials such as drugs, biological molecules, and even nanoparticles can enter and exit, depending on the surrounding environment.”

Synthetic strategies have been developed to produce hollow nanostructures with surface pores, but typically the size, shape, and location of these pores cannot be well-controlled. The pores are randomly distributed across the surface, resulting in a Swiss-cheese-like structure. A high level of control over surface openings is needed in order to use nanostructures in practical applications–for example, to load and release nanocargo

In this study, the scientists demonstrated a new pathway for chemically sculpturing gold-silver alloy nanowrappers with cube-shaped corner holes from solid nanocube particles. They used a chemical reaction known as nanoscale galvanic replacement. During this reaction, the atoms in a silver nanocube get replaced by gold ions in an aqueous solution at room temperature. The scientists added a molecule (surfactant, or surface-capping agent) to the solution to direct the leaching of silver and the deposition of gold on specific crystalline facets.

“The atoms on the faces of the cube are arranged differently from those in the corners, and thus different atomic planes are exposed, so the galvanic reaction may not proceed the same way in both areas,” explained Lu. “The surfactant we chose binds to the silver surface just enough–not too strongly or weakly–so that gold and silver can interact. Additionally, the absorption of surfactant is relatively weak on the silver cube’s corners, so the reaction is most active here. The silver gets “eaten” away from its edges, resulting in the formation of corner holes, while gold gets deposited on the rest of the surface to create a gold and silver shell.”

To capture the structural and chemical composition changes of the overall structure at the nanoscale in 3-D and at the atomic level in 2-D as the reaction proceeded over three hours, the scientists used electron microscopes at the CFN. The 2-D electron microscope images with energy-dispersive X-ray spectroscopy (EDX) elemental mapping confirmed that the cubes are hollow and composed of a gold-silver alloy. The 3-D images they obtained through electron tomography revealed that these hollow cubes feature large cube-shaped holes at the corners

“In electron tomography, 2-D images collected at different angles are combined to reconstruct an image of an object in 3-D,” said Gang. “The technique is similar to a CT [computerized tomography] scan used to image internal body structures, but it is carried out on a much smaller size scale and uses electrons instead of x-rays.”

The scientists also confirmed the transformation of nanocubes to nanowrappers through spectroscopy experiments capturing optical changes. The spectra showed that the optical absorption of the nanowrappers can be tuned depending on the reaction time. At their final state, the nanowrappers absorb infrared light.

“The absorption spectrum showed a peak at 1250 nanometers, one of the longest wavelengths reported for nanoscale gold or silver,” said Gang. “Typically, gold and silver nanostructures absorb visible light. However, for various applications, we would like those particles to absorb infrared light–for example, in biomedical applications such as phototherapy.”

Using the synthesized nanowrappers, the scientists then demonstrated how spherical gold nanoparticles of an appropriate size that are capped with DNA could be loaded into and released from the corner openings by changing the concentration of salt in the solution. DNA is negatively charged (owing to the oxygen atoms in its phosphate backbone) and changes its configuration in response to increasing or decreasing concentrations of a positively charged ion such as salt. In high salt concentrations, DNA chains contract because their repulsion is reduced by the salt ions. In low salt concentrations, DNA chains stretch because their repulsive forces push them apart.

When the DNA strands contract, the nanoparticles become small enough to fit in the openings and enter the hollow cavity. The nanoparticles can then be locked within the nanowrapper by decreasing the salt concentration. At this lower concentration, the DNA strands stretch, thereby making the nanoparticles too large to go through the pores. The nanoparticles can leave the structure through a reverse process of increasing and decreasing the salt concentration.

“Our electron microscopy and optical spectroscopy studies confirmed that the nanowrappers can be used to load and release nanoscale components,” said Lu. “In principle, they could be used to release optically or chemically active nanoparticles in particular environments, potentially by changing other parameters such as pH or temperature.”

Going forward, the scientists are interested in assembling the nanowrappers into larger-scale architectures, extending their method to other bimetallic systems, and comparing the internal and external catalytic activity of the nanowrappers.

“We did not expect to see such regular, well-defined holes,” said Gang. “Usually, this level of control is quite difficult to achieve for nanoscale objects. Thus, our discovery of this new pathway of nanoscale structure formation is very exciting. The ability to engineer nano-objects with a high level of control is important not only to understanding why certain processes are happening but also to constructing targeted nanostructures for various applications, from nanomedicine and optics to smart materials and catalysis. Our new synthesis method opens up unique opportunities in these areas.”

“This work was made possible by the world-class expertise in nanomaterial synthesis and capabilities that exist at the CFN,” said CFN Director Charles Black. “In particular, the CFN has a leading program in the synthesis of new materials by assembly of nanoscale components, and state-of-the-art electron microscopy and optical spectroscopy capabilities for studying the 3-D structure of these materials and their interaction with light. All of these characterization capabilities are available to the nanoscience research community through the CFN user program. We look forward to seeing the advances in nano-assembly that emerge as scientists across academia, industry, and government make use of the capabilities in their research.”

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

Tailoring Surface Opening of Hollow Nanocubes and Their Application as Nanocargo Carriers by Fang Lu, Huolin Xin, Weiwei Xia, Mingzhao Liu, Yugang Zhang, Weiping Cai, and Oleg Gang. ACS Cent. Sci., 2018, 4 (12), pp 1742–1750 DOI: 10.1021/acscentsci.8b00778 Publication Date (Web): December 12, 2018

Copyright © 2018 American Chemical Society

This paper is open access.