Tag Archives: Rice University

Vitamin C helps gold nanowires grow

This research gives new meaning to ‘Take your vitamin C’ as can be seen in a February 19, 2019 news item on Nanowerk,

A boost of vitamin C helped Rice University scientists turn small gold nanorods into fine gold nanowires.

Common, mild ascorbic acid is the not-so-secret sauce that helped the Rice lab of chemist Eugene Zubarev grow pure batches of nanowires from stumpy nanorods without the drawbacks of previous techniques.

“There’s no novelty per se in using vitamin C to make gold nanostructures because there are many previous examples,” Zubarev said. “But the slow and controlled reduction achieved by vitamin C is surprisingly suitable for this type of chemistry in producing extra-long nanowires.”

A February 19, 2019 Rice University news release (also on EurekAlert), which originated the news item, provides more technical detail about the research

The Rice lab’s nanorods are about 25 nanometers thick at the start of the process – and remain that way while their length grows to become long nanowires. Above 1,000 nanometers in length, the objects are considered nanowires, and that matters. The wires’ aspect ratio – length over width – dictates how they absorb and emit light and how they conduct electrons. Combined with gold’s inherent metallic properties, that could enhance their value for sensing, diagnostic, imaging and therapeutic applications.

Zubarev and lead author Bishnu Khanal, a Rice chemistry alumnus, succeeded in making their particles go far beyond the transition from nanorod to nanowire, theoretically to unlimited length.

The researchers also showed the process is fully controllable and reversible. That makes it possible to produce nanowires of any desired length, and thus the desired configuration for electronic or light-manipulating applications, especially those that involve plasmons, the light-triggered oscillation of electrons on a metal’s surface.

The nanowires’ plasmonic response can be tuned to emit light from visible to infrared and theoretically far beyond, depending on their aspect ratios.

The process is slow, so it takes hours to grow a micron-long nanowire. “In this paper, we only reported structures up to 4 to 5 microns in length,” Zubarev said. “But we’re working to make much longer nanowires.”

The growth process only appeared to work with pentahedrally twinned gold nanorods, which contain five linked crystals. These five-sided rods — “Think of a pencil, but with five sides instead of six,” Zubarev said — are stable along the flat surfaces, but not at the tips.

“The tips also have five faces, but they have a different arrangement of atoms,” he said. “The energy of those atoms is slightly lower, and when new atoms are deposited there, they don’t migrate anywhere else.”

That keeps the growing wires from gaining girth. Every added atom increases the wire’s length, and thus the aspect ratio.

The nanorods’ reactive tips get help from a surfactant, CTAB, that covers the flat surfaces of nanorods. “The surfactant forms a very dense, tight bilayer on the sides, but it cannot cover the tips effectively,” Zubarev said.

That leaves the tips open to an oxidation or reduction reaction. The ascorbic acid provides electrons that combine with gold ions and settle at the tips in the form of gold atoms. And unlike carbon nanotubes in a solution that easily aggregate, the nanowires keep their distance from one another.

“The most valuable feature is that it is truly one-dimensional elongation of nanorods to nanowires,” Zubarev said. “It does not change the diameter, so in principal we can take small rods with an aspect ratio of maybe two or three and elongate them to 100 times the length.”
He said the process should apply to other metal nanorods, including silver.

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

Chemical Transformation of Nanorods to Nanowires: Reversible Growth and Dissolution of Anisotropic Gold Nanostructures by Bishnu P. Khanal and Eugene R. Zubarev. ACS Nano, 2019, 13 (2), pp 2370–2378 DOI: 10.1021/acsnano.8b09203 Publication Date (Web): February 12, 2019

Copyright © 2019 American Chemical Society

This paper is behind a paywall. Below you’ll find an image fo what I believe to be the vitamin C-enhanced gold nanowires.

Caption: Gold nanowires grown in the Rice University lab of chemist Eugene Zubarev promise to provide tunable plasmonic properties for optical and electronic applications. The wires can be controllably grown from nanorods, or reduced. Credit: Zubarev Research Group/Rice University

Let them (Rice University scientists) show you how to restore oil-soaked soil

I did not want to cash in (so to speak) on someone else’s fun headline so I played with it. Hre is the original head, which was likely written by either David Ruth or Mike Williams at Rice University (Texas, US), “Lettuce show you how to restore oil-soaked soil.”

A February 1, 2019 news item on ScienceDaily on the science behind lettuce and oil-soaked soil,

Rice University engineers have figured out how soil contaminated by heavy oil can not only be cleaned but made fertile again.

How do they know it works? They grew lettuce.

Rice engineers Kyriacos Zygourakis and Pedro Alvarez and their colleagues have fine-tuned their method to remove petroleum contaminants from soil through the age-old process of pyrolysis. The technique gently heats soil while keeping oxygen out, which avoids the damage usually done to fertile soil when burning hydrocarbons cause temperature spikes.

Lettuce growing in once oil-contaminated soil revived by a process developed by Rice University engineers. The Rice team determined that pyrolyzing oil-soaked soil for 15 minutes at 420 degrees Celsius is sufficient to eliminate contaminants while preserving the soil’s fertility. The lettuce plants shown here, in treated and fertilized soil, showed robust growth over 14 days. Photo by Wen Song

A February 1, 2019 Rice University news release (also on EurekAlert), which originated the news item, explains more about the work,

While large-volume marine spills get most of the attention, 98 percent of oil spills occur on land, Alvarez points out, with more than 25,000 spills a year reported to the Environmental Protection Agency. That makes the need for cost-effective remediation clear, he said.

“We saw an opportunity to convert a liability, contaminated soil, into a commodity, fertile soil,” Alvarez said.

The key to retaining fertility is to preserve the soil’s essential clays, Zygourakis said. “Clays retain water, and if you raise the temperature too high, you basically destroy them,” he said. “If you exceed 500 degrees Celsius (900 degrees Fahrenheit), dehydration is irreversible.

The researchers put soil samples from Hearne, Texas, contaminated in the lab with heavy crude, into a kiln to see what temperature best eliminated the most oil, and how long it took.

Their results showed heating samples in the rotating drum at 420 C (788 F) for 15 minutes eliminated 99.9 percent of total petroleum hydrocarbons (TPH) and 94.5 percent of polycyclic aromatic hydrocarbons (PAH), leaving the treated soils with roughly the same pollutant levels found in natural, uncontaminated soil.

The paper appears in the American Chemical Society journal Environmental Science and Technology. It follows several papers by the same group that detailed the mechanism by which pyrolysis removes contaminants and turns some of the unwanted hydrocarbons into char, while leaving behind soil almost as fertile as the original. “While heating soil to clean it isn’t a new process,” Zygourakis said, “we’ve proved we can do it quickly in a continuous reactor to remove TPH, and we’ve learned how to optimize the pyrolysis conditions to maximize contaminant removal while minimizing soil damage and loss of fertility.

“We also learned we can do it with less energy than other methods, and we have detoxified the soil so that we can safely put it back,” he said.

Heating the soil to about 420 C represents the sweet spot for treatment, Zygourakis said. Heating it to 470 C (878 F) did a marginally better job in removing contaminants, but used more energy and, more importantly, decreased the soil’s fertility to the degree that it could not be reused.

“Between 200 and 300 C (392-572 F), the light volatile compounds evaporate,” he said. “When you get to 350 to 400 C (662-752 F), you start breaking first the heteroatom bonds, and then carbon-carbon and carbon-hydrogen bonds triggering a sequence of radical reactions that convert heavier hydrocarbons to stable, low-reactivity char.”

The true test of the pilot program came when the researchers grew Simpson black-seeded lettuce, a variety for which petroleum is highly toxic, on the original clean soil, some contaminated soil and several pyrolyzed soils. While plants in the treated soils were a bit slower to start, they found that after 21 days, plants grown in pyrolyzed soil with fertilizer or simply water showed the same germination rates and had the same weight as those grown in clean soil.

“We knew we had a process that effectively cleans up oil-contaminated soil and restores its fertility,” Zygourakis said. “But, had we truly detoxified the soil?”

To answer this final question, the Rice team turned to Bhagavatula Moorthy, a professor of neonatology at Baylor College of Medicine, who studies the effects of airborne contaminants on neonatal development. Moorthy and his lab found that extracts taken from oil-contaminated soils were toxic to human lung cells, while exposing the same cell lines to extracts from treated soils had no adverse effects. The study eased concerns that pyrolyzed soil could release airborne dust particles laced with highly toxic pollutants like PAHs.

”One important lesson we learned is that different treatment objectives for regulatory compliance, detoxification and soil-fertility restoration need not be mutually exclusive and can be simultaneously achieved,” Alvarez said.

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

Pilot-Scale Pyrolytic Remediation of Crude-Oil-Contaminated Soil in a Continuously-Fed Reactor: Treatment Intensity Trade-Offs by Wen Song, Julia E. Vidonish, Roopa Kamath, Pingfeng Yu, Chun Chu, Bhagavatula Moorthy, Baoyu Gao, Kyriacos Zygourakis, and Pedro J. J. Alvarez. Environ. Sci. Technol., 2019, 53 (4), pp 2045–2053 DOI: 10.1021/acs.est.8b05825 Publication Date (Web): January 25, 2019

Copyright © 2019 American Chemical Society

This paper is behind a paywall.

Lifesaving moths and nanomagnets

Rice University bioengineers use a magnetic field to activate nanoparticle-attached baculoviruses in a tissue. The viruses, which normally infect alfalfa looper moths, are modified to deliver gene-editing DNA code only to cells that are targeted with magnetic field-induced local transduction. Courtesy of the Laboratory of Biomolecular Engineering and Nanomedicine

Kudos to whomever put that diagram together! That’s a lot of well conveyed information.

Now for the details about how this technology might save lives. From a November 13, 2018 news item on Nanowerk,

A new technology that relies on a moth-infecting virus and nanomagnets could be used to edit defective genes that give rise to diseases like sickle cell, muscular dystrophy and cystic fibrosis.

Rice University bioengineer Gang Bao has combined magnetic nanoparticles with a viral container drawn from a particular species of moth to deliver CRISPR/Cas9 payloads that modify genes in a specific tissue or organ with spatial control.

A November 12, 2018 Rice University news release (also on EurekAlert published on November 13, 2018), which originated the news item, provides detail,

Because magnetic fields are simple to manipulate and, unlike light, pass easily through tissue, Bao and his colleagues want to use them to control the expression of viral payloads in target tissues by activating the virus that is otherwise inactivated in blood.

The research appears in Nature Biomedical Engineering. In nature, CRISPR/Cas9 bolsters microbes’ immune systems by recording the DNA of invaders. That gives microbes the ability to recognize and attack returning invaders, but scientists have been racing to adapt CRISPR/Cas9 to repair mutations that cause genetic diseases and to manipulate DNA in laboratory experiments.

CRISPR/Cas9 has the potential to halt hereditary disease – if scientists can get the genome-editing machinery to the right cells inside the body. But roadblocks remain, especially in delivering the gene-editing payloads with high efficiency.

Bao said it will be necessary to edit cells in the body to treat many diseases. “But efficiently delivering genome-editing machinery into target tissue in the body with spatial control remains a major challenge,” Bao said. “Even if you inject the viral vector locally, it can leak to other tissues and organs, and that could be dangerous.”

The delivery vehicle developed by Bao’s group is based on a virus that infects Autographa californica, aka the alfalfa looper, a moth native to North America. The cylindrical baculovirus vector (BV), the payload-carrying part of the virus, is considered large at up to 60 nanometers in diameter and 200-300 nanometers in length. That’s big enough to transport more than 38,000 base pairs of DNA, which is enough to supply multiple gene-editing units to a target cell, Bao said.

He said the inspiration to combine BV and magnetic nanoparticles came from discussions with Rice postdoctoral researcher and co-lead author Haibao Zhu, who learned about the virus during a postdoctoral stint in Singapore but knew nothing about magnetic nanoparticles until he joined the Bao lab. The Rice team had previous experience using iron oxide nanoparticles and an applied magnetic field to open blood vessel walls just enough to let large-molecule drugs pass through.

“We really didn’t know if this would work for gene editing or not, but we thought, ‘worth a shot,'” Bao said.

The researchers use the magnetic nanoparticles to activate BV and deliver gene-editing payloads only where they’re needed. To do this, they take advantage of an immune-system protein called C3 that normally inactivates baculoviruses.

“If we combine BV with magnetic nanoparticles, we can overcome this deactivation by applying the magnetic field,” Bao said. “The beauty is that when we deliver it, gene editing occurs only at the tissue, or the part of the tissue, where we apply the magnetic field.”

Application of the magnetic field allows BV transduction, the payload-delivery process that introduces gene-editing cargo into the target cell. The payload is also DNA, which encodes both a reporter gene and the CRISPR/Cas9 system.

In tests, the BV was loaded with green fluorescent proteins or firefly luciferase. Cells with the protein glowed brightly under a microscope, and experiments showed the magnets were highly effective at targeted delivery of BV cargoes in both cell cultures and lab animals.

Bao noted his and other labs are working on the delivery of CRISPR/Cas9 with adeno-associated viruses (AAV), but he said BV’s capacity for therapeutic cargo is roughly eight times larger. “However, it is necessary to make BV transduction into target cells more efficient,” he said.

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

Spatial control of in vivo CRISPR–Cas9 genome editing via nanomagnets by Haibao Zhu, Linlin Zhang, Sheng Tong, Ciaran M. Lee, Harshavardhan Deshmukh, & Gang Bao. Nature Biomedical Engineering (2018) DOI: https://doi.org/10.1038/s41551-018-0318-7 Published: 12 November 2018

This paper is behind a paywall.

Where do I stand? a graphene artwork

A May 2,2019 news item on Nanowerk describes some graphene-based artwork being created at Rice University (Texas, US), Note: A link has been removed,

When you read about electrifying art, “electrifying” isn’t usually a verb. But an artist working with a Rice University lab is in fact making artwork that can deliver a jolt.

The Rice lab of chemist James Tour introduced laser-induced graphene (LIG) to the world in 2014, and now the researchers are making art with the technique, which involves converting carbon in a common polymer or other material into microscopic flakes of graphene.

The “ink” in “Where Do I Stand?” by artist Joseph Cohen is actually laser-induced graphene (LIG). The design shows Cohen’s impression of what LIG looks like at the microscopic level. The work was produced in the Rice University lab where the technique of creating LIG was invented. Photo by Jeff Fitlow
A detail from “Where Do I Stand?” by artist Joseph Cohen, who created the work at Rice University using laser-induced graphene as the medium. Photo by Jeff Fitlow

A May 2, 2019 Rice university news release (also received via email), which originated the news item, describes laser-induced graphene (LIG) and the art in more detail (Note: Links have been removed),

LIG is metallic and conducts electricity. The interconnected flakes are effectively a wire that could empower electronic artworks.

The paper in the American Chemical Society journal ACS Applied Nano Materials – simply titled “Graphene Art” – lays out how the lab and Houston artist and co-author Joseph Cohen generated LIG portraits and prints, including a graphene-inspired landscape called “Where Do I Stand?”

While the work isn’t electrified, Cohen said it lays the groundwork for future possibilities.

“That’s what I would like to do,” he said. “Not make it kitsch or play off the novelty, but to have it have some true functionality that allows greater awareness about the material and opens up the experience.”

Cohen created the design in an illustration program and sent it directly to the industrial engraving laser Tour’s lab uses to create LIG on a variety of materials. The laser burned the artist’s fine lines into the substrate, in this case archive-quality paper treated with fire retardant.

The piece, which was part of Cohen’s exhibit at Rice’s BioScience Research Collaborative last year, peers into the depths of what a viewer shrunken to nanoscale might see when facing a field of LIG, with overlapping hexagons – the basic lattice of atom-thick graphene – disappearing into the distance.

“You’re looking at this image of a 3D foam matrix of laser-induced graphene and it’s actually made of LIG,” he said. “I didn’t base it on anything; I was just thinking about what it would look like. When I shared it with Jim, he said, ‘Wow, that’s what it would look like if you could really blow this up.’”

Cohen said his art is about media specificity.

“In terms of the artistic application, you’re not looking at a representation of something, as traditionally we would in the history of art,” he said. “Each piece is 100% original. That’s the key.”

He developed an interest in nanomaterials as media for his art when he began work with Rice alumnus Daniel Heller, a bioengineer at Memorial Sloan Kettering Cancer Center in New York who established an artist-in-residency position in his lab.

After two years of creating with carbon nanotube-infused paint, Cohen attended an Electrochemical Society conference and met Tour, who in turn introduced him to Rice chemists Bruce Weisman and Paul Cherukuri, who further inspired his investigation of nanotechnology.

The rest is art history.

It would be incorrect to think of the process as “printing,” Tour said. Instead of adding a substance to the treated paper, substance is burned away as the laser turns the surface into foamlike flakes of interconnected graphene.

The art itself can be much more than eye candy, given LIG’s potential for electronic applications like sensors or as triboelectric generators that turn mechanical actions into current.

“You could put LIG on your back and have it flash LEDs with every step you take,” Tour said.

The fact that graphene is a conductor — unlike paint, ink or graphite from a pencil — makes it particularly appealing to Cohen, who expects to take advantage of that capability in future works.

“It’s art with a capital A that is trying to do the most that it can with advancements in science and technology,” he said. “If we look back historically, from the Renaissance to today, the highest forms of art push the limits of human understanding.”

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

Graphene Art by Yieu Chyan, Joseph Cohen, Winston Wang, Chenhao Zhang, and James M. Tour. ACS Appl. Nano Mater., Article ASAP DOI: 10.1021/acsanm.9b00391 Publication Date (Web): April 23, 2019

Copyright © 2019 American Chemical Society

This paper appears to be open access.

Because I can’t resist the delight beaming from these faces,

maging with laser-induced graphene (LIG) was taken to a new level in a Rice University lab. From left, chemist James Tour, holding a portrait of himself in LIG; artist Joseph Cohen, holding his work “Where Do I Stand?”; and Yieu Chyan, a Rice graduate student and lead author of a new paper detailing the process used to create the art. Photo by Jeff Fitlow

Probing the physical limits of plasmons in organic molecules with fewer than 50 atoms

A Sept. 5, 2018  news item on ScienceDaily introduces the work,

Rice University [Texas, US] researchers are probing the physical limits of excited electronic states called plasmons by studying them in organic molecules with fewer than 50 atoms.

A Sept. 4, 2018 Rice University news release (also on EurekAlert published on Sept. 5, 2018), which originated the news item, explains what plasmons are and why this research is being undertaken,

Plasmons are oscillations in the plasma of free electrons that constantly swirl across the surface of conductive materials like metals. In some nanomaterials, a specific color of light can resonate with the plasma and cause the electrons inside it to lose their individual identities and move as one, in rhythmic waves. Rice’s Laboratory for Nanophotonics (LANP) has pioneered a growing list of plasmonic technologies for applications as diverse as color-changing glass, molecular sensing, cancer diagnosis and treatment, optoelectronics, solar energy collection and photocatalysis.

Reporting online in the Proceedings of the National Academy of Sciences, LANP scientists detailed the results of a two-year experimental and theoretical study of plasmons in three different polycyclic aromatic hydrocarbons (PAHs). Unlike the plasmons in relatively large metal nanoparticles, which can typically be described with classical electromagnetic theory like Maxwell’s [James Clerk Maxwell] equations, the paucity of atoms in the PAHs produces plasmons that can only be understood in terms of quantum mechanics, said study co-author and co-designer Naomi Halas, the director of LANP and the lead researcher on the project.

“These PAHs are essentially scraps of graphene that contain five or six fused benzene rings surrounded by a perimeter of hydrogen atoms,” Halas said. “There are so few atoms in each that adding or removing even a single electron dramatically changes their electronic behavior.”

Halas’ team had experimentally verified the existence of molecular plasmons in several previous studies. But an investigation that combined side by side theoretical and experimental perspectives was needed, said study co-author Luca Bursi, a postdoctoral research associate and theoretical physicist in the research group of study co-designer and co-author Peter Nordlander.

“Molecular excitations are a ubiquity in nature and very well studied, especially for neutral PAHs, which have been considered as the standard of non-plasmonic excitations in the past,” Bursi said. “Given how much is already known about PAHs, they were an ideal choice for further investigation of the properties of plasmonic excitations in systems as small as actual molecules, which represent a frontier of plasmonics.”

Lead co-author Kyle Chapkin, a Ph.D. student in applied physics in the Halas research group, said, “Molecular plasmonics is a new area at the interface between plasmonics and molecular chemistry, which is rapidly evolving. When plasmonics reach the molecular scale, we lose any sharp distinction of what constitutes a plasmon and what doesn’t. We need to find a new rationale to explain this regime, which was one of the main motivations for this study.”

In their native state, the PAHs that were studied — anthanthrene, benzo[ghi]perylene and perylene — are charge-neutral and cannot be excited into a plasmonic state by the visible wavelengths of light used in Chapkin’s experiments. In their anionic form, the molecules contain an additional electron, which alters their “ground state” and makes them plasmonically active in the visible spectrum. By exciting both the native and anionic forms of the molecules and comparing precisely how they behaved as they relaxed back to their ground states, Chapkin and Bursi built a solid case that the anionic forms do support molecular plasmons in the visible spectrum.

The key, Chapkin said, was identifying a number of similarities between the behavior of known plasmonic particles and the anionic PAHs. By matching both the timescales and modes for relaxation behaviors, the LANP team built up a picture of a characteristic dynamics of low-energy plasmonic excitations in the anionic PAHs.

“In molecules, all excitations are molecular excitations, but select excited states show some characteristics that allow us to draw a parallel with the well-established plasmonic excitations in metal nanostructures,” Bursi said.

“This study offers a window on the sometimes surprising behavior of collective excitations in few-atom quantum systems,” Halas said. “What we’ve learned here will aid our lab and others in developing quantum-plasmonic approaches for ultrafast color-changing glass, molecular-scale optoelectronics and nonlinear plasmon-mediated optics.”

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

Lifetime dynamics of plasmons in the few-atom limit by Kyle D. Chapkin, Luca Bursi, Grant J. Stec, Adam Lauchner, Nathaniel J. Hogan, Yao Cui, Peter Nordlander, and Naomi J. Halas. PNAS September 11, 2018 115 (37) 9134-9139; published ahead of print August 27, 2018 DOI: https://doi.org/10.1073/pnas.1805357115

This paper is behind a paywall.

Change the shape of water with nanotubes

An August 24, 2018 news item on ScienceDaily describes a ‘shapeshifting’ water technique,

First, according to Rice University engineers, get a nanotube hole. Then insert water. If the nanotube is just the right width, the water molecules will align into a square rod.

Rice materials scientist Rouzbeh Shahsavari and his team used molecular models to demonstrate their theory that weak van der Waals forces between the inner surface of the nanotube and the water molecules are strong enough to snap the oxygen and hydrogen atoms into place.

Shahsavari referred to the contents as two-dimensional “ice,” because the molecules freeze regardless of the temperature. He said the research provides valuable insight on ways to leverage atomic interactions between nanotubes and water molecules to fabricate nanochannels and energy-storing nanocapacitors.

An August 24, 2018 Rice University news release (also on EurekAlert and received via email), which originated the news item, delves further,

Shahsavari and his colleagues built molecular models of carbon and boron nitride nanotubes with adjustable widths. They discovered boron nitride is best at constraining the shape of water when the nanotubes are 10.5 angstroms wide. (One angstrom is one hundred-millionth of a centimeter.)

The researchers already knew that hydrogen atoms in tightly confined water take on interesting structural properties. Recent experiments by other labs showed strong evidence for the formation of nanotube ice and prompted the researchers to build density functional theory models to analyze the forces responsible.

Shahsavari’s team modeled water molecules, which are about 3 angstroms wide, inside carbon and boron nitride nanotubes of various chiralities (the angles of their atomic lattices) and between 8 and 12 angstroms in diameter. They discovered that nanotubes in the middle diameters had the most impact on the balance between molecular interactions and van der Waals pressure that prompted the transition from a square water tube to ice.

“If the nanotube is too small and you can only fit one water molecule, you can’t judge much,” Shahsavari said. “If it’s too large, the water keeps its amorphous shape. But at about 8 angstroms, the nanotubes’ van der Waals force [if you’re not familiar with the term, see below the link and citation for my brief explanation] starts to push water molecules into organized square shapes.”

He said the strongest interactions were found in boron nitride nanotubes due to the particular polarization of their atoms.

Shahsavari said nanotube ice could find use in molecular machines or as nanoscale capillaries, or foster ways to deliver a few molecules of water or sequestered drugs to targeted cells, like a nanoscale syringe.

Lead author Farzaneh Shayeganfar, a former visiting scholar at Rice, is an instructor at Shahid Rajaee Teacher Training University in Tehran, Iran. Co-principal investigator Javad Beheshtian is a professor at Amirkabir University, Tehran.

Supercomputer resources were provided with support from the [US] National Institutes of Health and an IBM Shared Rice University Research grant.

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

First Principles Study of Water Nanotubes Captured Inside Carbon/Boron Nitride Nanotubes by Farzaneh Shayeganfar, Javad Beheshtian, and Rouzbeh Shahsavari. Langmuir, DOI: 10.1021/acs.langmuir.8b00856 Publication Date (Web): August 23, 2018

Copyright © 2018 American Chemical Society

This paper is behind a paywall.

For the purposes of the posting, van der Waals force(s) are weak adhesive forces measured at the nanoscale. Humans don’t feel them (we’re too big) but gecko lizards can exploit those forces which is why they are able to hang from the ceiling by a single toe.  There’s a more informed description here in the van der Waals force entry on Wikipedia.

First CRISPR gene-edited babies? Ethics and the science story

Scientists, He Jiankui and Michael Deem, may have created the first human babies born after being subjected to CRISPR (clustered regularly interspaced short palindromic repeats) gene editing.  At this point, no one is entirely certain that these babies  as described actually exist since the information was made public in a rather unusual (for scientists) fashion.

The news broke on Sunday, November 25, 2018 through a number of media outlets none of which included journals associated with gene editing or high impact journals such as Cell, Nature, or Science.The news broke in MIT Technology Review and in Associated Press. Plus, this all happened just before the Second International Summit on Human Genome Editing (Nov. 27 – 29, 2018) in Hong Kong. He Jiankui was scheduled to speak today, Nov. 27, 2018.

Predictably, this news has caused quite a tizzy.

Breaking news

Antonio Regalado broke the news in a November 25, 2018  article for MIT [Massachusetts Institute of Technology] Technology Review (Note: Links have been removed),

According to Chinese medical documents posted online this month (here and here), a team at the Southern University of Science and Technology, in Shenzhen, has been recruiting couples in an effort to create the first gene-edited babies. They planned to eliminate a gene called CCR5 in hopes of rendering the offspring resistant to HIV, smallpox, and cholera.

The clinical trial documents describe a study in which CRISPR is employed to modify human embryos before they are transferred into women’s uteruses.

The scientist behind the effort, He Jiankui, did not reply to a list of questions about whether the undertaking had produced a live birth. Reached by telephone, he declined to comment.

However, data submitted as part of the trial listing shows that genetic tests have been carried out on fetuses as late as 24 weeks, or six months. It’s not known if those pregnancies were terminated, carried to term, or are ongoing.

Apparently He changed his mind because Marilynn Marchione in a November 26, 2018 article for the Associated Press confirms the news,

A Chinese researcher claims that he helped make the world’s first genetically edited babies — twin girls born this month whose DNA he said he altered with a powerful new tool capable of rewriting the very blueprint of life.

If true, it would be a profound leap of science and ethics.

A U.S. scientist [Dr. Michael Deem] said he took part in the work in China, but this kind of gene editing is banned in the United States because the DNA changes can pass to future generations and it risks harming other genes.

Many mainstream scientists think it’s too unsafe to try, and some denounced the Chinese report as human experimentation.

There is no independent confirmation of He’s claim, and it has not been published in a journal, where it would be vetted by other experts. He revealed it Monday [November 26, 2018] in Hong Kong to one of the organizers of an international conference on gene editing that is set to begin Tuesday [November 27, 2018], and earlier in exclusive interviews with The Associated Press.

“I feel a strong responsibility that it’s not just to make a first, but also make it an example,” He told the AP. “Society will decide what to do next” in terms of allowing or forbidding such science.

Some scientists were astounded to hear of the claim and strongly condemned it.

It’s “unconscionable … an experiment on human beings that is not morally or ethically defensible,” said Dr. Kiran Musunuru, a University of Pennsylvania gene editing expert and editor of a genetics journal.

“This is far too premature,” said Dr. Eric Topol, who heads the Scripps Research Translational Institute in California. “We’re dealing with the operating instructions of a human being. It’s a big deal.”

However, one famed geneticist, Harvard University’s George Church, defended attempting gene editing for HIV, which he called “a major and growing public health threat.”

“I think this is justifiable,” Church said of that goal.

h/t Cale Guthrie Weissman’s Nov. 26, 2018 article for Fast Company.

Diving into more detail

Ed Yong in a November 26, 2018 article for The Atlantic provides more details about the claims (Note: Links have been removed),

… “Two beautiful little Chinese girls, Lulu and Nana, came crying into the world as healthy as any other babies a few weeks ago,” He said in the first of five videos, posted yesterday {Nov. 25, 2018] to YouTube [link provided at the end of this section of the post]. “The girls are home now with their mom, Grace, and dad, Mark.” The claim has yet to be formally verified, but if true, it represents a landmark in the continuing ethical and scientific debate around gene editing.

Late last year, He reportedly enrolled seven couples in a clinical trial, and used their eggs and sperm to create embryos through in vitro fertilization. His team then used CRISPR to deactivate a single gene called CCR5 in the embryos, six of which they then implanted into mothers. CCR5 is a protein that the HIV virus uses to gain entry into human cells; by deactivating it, the team could theoretically reduce the risk of infection. Indeed, the fathers in all eight couples were HIV-positive.

Whether the experiment was successful or not, it’s intensely controversial. Scientists have already begun using CRISPR and other gene-editing technologies to alter human cells, in attempts to treat cancers, genetic disorders, and more. But in these cases, the affected cells stay within a person’s body. Editing an embryo [it’s often called, germline editing] is very different: It changes every cell in the body of the resulting person, including the sperm or eggs that would pass those changes to future generations. Such work is banned in many European countries, and prohibited in the United States. “I understand my work will be controversial, but I believe families need this technology and I’m willing to take the criticism for them,” He said.

“Was this a reasonable thing to do? I would say emphatically no,” says Paula Cannon of the University of Southern California. She and others have worked on gene editing, and particularly on trials that knock out CCR5 as a way to treat HIV. But those were attempts to treat people who were definitively sick and had run out of other options. That wasn’t the case with Nana and Lulu.

“The idea that being born HIV-susceptible, which is what the vast majority of humans are, is somehow a disease state that requires the extraordinary intervention of gene editing blows my mind,” says Cannon. “I feel like he’s appropriating this potentially valuable therapy as a shortcut to doing something in the sphere of gene editing. He’s either very naive or very cynical.”

“I want someone to make sure that it has happened,” says Hank Greely, an ethicist at Stanford University. If it hasn’t, that “would be a pretty bald-faced fraud,” but such deceptions have happened in the past. “If it is true, I’m disappointed. It’s reckless on safety grounds, and imprudent and stupid on social grounds.” He notes that a landmark summit in 2015 (which included Chinese researchers) and a subsequent major report from the National Academies of Science, Engineering, and Medicine both argued that “public participation should precede any heritable germ-line editing.” That is: Society needs to work out how it feels about making gene-edited babies before any babies are edited. Absent that consensus, He’s work is “waving a red flag in front of a bull,” says Greely. “It provokes not just the regular bio-Luddites, but also reasonable people who just wanted to talk it out.”

Societally, the creation of CRISPR-edited babies is a binary moment—a Rubicon that has been crossed. But scientifically, the devil is in the details, and most of those are still unknown.

CRISPR is still inefficient. [emphasis mine] The Chinese teams who first used it to edit human embryos only did so successfully in a small proportion of cases, and even then, they found worrying levels of “off-target mutations,” where they had erroneously cut parts of the genome outside their targeted gene. He, in his video, claimed that his team had thoroughly sequenced Nana and Lulu’s genomes and found no changes in genes other than CCR5.

That claim is impossible to verify in the absence of a peer-reviewed paper, or even published data of any kind. “The paper is where we see whether the CCR5 gene was properly edited, what effect it had at the cellular level, and whether [there were] any off-target effects,” said Eric Topol of the Scripps Research Institute. “It’s not just ‘it worked’ as a binary declaration.”

In the video, He said that using CRISPR for human enhancement, such as enhancing IQ or selecting eye color, “should be banned.” Speaking about Nana and Lulu’s parents, he said that they “don’t want a designer baby, just a child who won’t suffer from a disease that medicine can now prevent.”

But his rationale is questionable. Huang [Junjiu Huang of Sun Yat-sen University ], the first Chinese researcher to use CRISPR on human embryos, targeted the faulty gene behind an inherited disease called beta thalassemia. Mitalipov, likewise, tried to edit a gene called MYBPC3, whose faulty versions cause another inherited disease called hypertrophic cardiomyopathy (HCM). Such uses are still controversial, but they rank among the more acceptable applications for embryonic gene editing as ways of treating inherited disorders for which treatments are either difficult or nonexistent.

In contrast, He’s team disableda normal gene in an attempt to reduce the risk of a disease that neither child had—and one that can be controlled. There are already ways of preventing fathers from passing HIV to their children. There are antiviral drugs that prevent infections. There’s safe-sex education. “This is not a plague for which we have no tools,” says Cannon.

As Marilynn Marchione of the AP reports, early tests suggest that He’s editing was incomplete [emphasis mine], and at least one of the twins is a mosaic, where some cells have silenced copies of CCR5 and others do not. If that’s true, it’s unlikely that they would be significantly protected from HIV. And in any case, deactivating CCR5 doesn’t confer complete immunity, because some HIV strains can still enter cells via a different protein called CXCR4.

Nana and Lulu might have other vulnerabilities. …

It is also unclear if the participants in He’s trial were fully aware of what they were signing up for. [emphasis mine] The team’s informed-consent document describes their work as an “AIDS vaccine development project,” and while it describes CRISPR gene editing, it does so in heavily technical language. It doesn’t mention any of the risks of disabling CCR5, and while it does note the possibility of off-target effects, it also says that the “project team is not responsible for the risk.”

He owns two genetics companies, and his collaborator, Michael Deem of Rice University,  [emphasis mine] holds a small stake in, and sits on the advisory board of, both of them. The AP’s Marchione reports, “Both men are physics experts with no experience running human clinical trials.” [emphasis mine]

Yong’s article is well worth reading in its entirety. As for YouTube, here’s The He Lab’s webpage with relevant videos.

Reactions

Gina Kolata, Sui-Lee Wee, and Pam Belluck writing in a Nov. 26, 2018 article for the New York Times chronicle some of the response to He’s announcement,

It is highly unusual for a scientist to announce a groundbreaking development without at least providing data that academic peers can review. Dr. He said he had gotten permission to do the work from the ethics board of the hospital Shenzhen Harmonicare, but the hospital, in interviews with Chinese media, denied being involved. Cheng Zhen, the general manager of Shenzhen Harmonicare, has asked the police to investigate what they suspect are “fraudulent ethical review materials,” according to the Beijing News.

The university that Dr. He is attached to, the Southern University of Science and Technology, said Dr. He has been on no-pay leave since February and that the school of biology believed that his project “is a serious violation of academic ethics and academic norms,” according to the state-run Beijing News.

In a statement late on Monday, China’s national health commission said it has asked the health commission in southern Guangdong province to investigate Mr. He’s claims.

“I think that’s completely insane,” said Shoukhrat Mitalipov, director of the Center for Embryonic Cell and Gene Therapy at Oregon Health and Science University. Dr. Mitalipov broke new ground last year by using gene editing to successfully remove a dangerous mutation from human embryos in a laboratory dish. [I wrote a three-part series about CRISPR, which included what was then the latest US news, Mitalipov’s announcement, along with a roundup of previous work in China. Links are at the end of this section.’

Dr. Mitalipov said that unlike his own work, which focuses on editing out mutations that cause serious diseases that cannot be prevented any other way, Dr. He did not do anything medically necessary. There are other ways to prevent H.I.V. infection in newborns.

Just three months ago, at a conference in late August on genome engineering at Cold Spring Harbor Laboratory in New York, Dr. He presented work on editing the CCR₅ gene in the embryos of nine couples.

At the conference, whose organizers included Jennifer Doudna, one of the inventors of Crispr technology, Dr. He gave a careful talk about something that fellow attendees considered squarely within the realm of ethically approved research. But he did not mention that some of those embryos had been implanted in a woman and could result in genetically engineered babies.

“What we now know is that as he was talking, there was a woman in China carrying twins,” said Fyodor Urnov, deputy director of the Altius Institute for Biomedical Sciences and a visiting researcher at the Innovative Genomics Institute at the University of California. “He had the opportunity to say ‘Oh and by the way, I’m just going to come out and say it, people, there’s a woman carrying twins.’”

“I would never play poker against Dr. He,” Dr. Urnov quipped.

Richard Hynes, a cancer researcher at the Massachusetts Institute of Technology, who co-led an advisory group on human gene editing for the National Academy of Sciences and the National Academy of Medicine, said that group and a similar organization in Britain had determined that if human genes were to be edited, the procedure should only be done to address “serious unmet needs in medical treatment, it had to be well monitored, it had to be well followed up, full consent has to be in place.”

It is not clear why altering genes to make people resistant to H.I.V. is “a serious unmet need.” Men with H.I.V. do not infect embryos. …

Dr. He got his Ph.D., from Rice University, in physics and his postdoctoral training, at Stanford, was with Stephen Quake, a professor of bioengineering and applied physics who works on sequencing DNA, not editing it.

Experts said that using Crispr would actually be quite easy for someone like Dr. He.

After coming to Shenzhen in 2012, Dr. He, at age 28, established a DNA sequencing company, Direct Genomics, and listed Dr. Quake on its advisory board. But, in a telephone interview on Monday, Dr. Quake said he was never associated with the company.

Deem, the US scientist who worked in China with He is currently being investigated (from a Nov. 26, 2018 article by Andrew Joseph in STAT),

Rice University said Monday that it had opened a “full investigation” into the involvement of one of its faculty members in a study that purportedly resulted in the creation of the world’s first babies born with edited DNA.

Michael Deem, a bioengineering professor at Rice, told the Associated Press in a story published Sunday that he helped work on the research in China.

Deem told the AP that he was in China when participants in the study consented to join the research. Deem also said that he had “a small stake” in and is on the scientific advisory boards of He’s two companies.

Megan Molteni in a Nov. 27, 2018 article for Wired admits she and her colleagues at the magazine may have dismissed CRISPR concerns about designer babies prematurely while shedding more light on this  latest development (Note: Links have been removed),

We said “don’t freak out,” when scientists first used Crispr to edit DNA in non-viable human embryos. When they tried it in embryos that could theoretically produce babies, we said “don’t panic.” Many years and years of boring bench science remain before anyone could even think about putting it near a woman’s uterus. Well, we might have been wrong. Permission to push the panic button granted.

Late Sunday night, a Chinese researcher stunned the world by claiming to have created the first human babies, a set of twins, with Crispr-edited DNA….

What’s perhaps most strange is not that He ignored global recommendations on conducting responsible Crispr research in humans. He also ignored his own advice to the world—guidelines that were published within hours of his transgression becoming public.

On Monday, He and his colleagues at Southern University of Science and Technology, in Shenzhen, published a set of draft ethical principles “to frame, guide, and restrict clinical applications that communities around the world can share and localize based on religious beliefs, culture, and public-health challenges.” Those principles included transparency and only performing the procedure when the risks are outweighed by serious medical need.

The piece appeared in the The Crispr Journal, a young publication dedicated to Crispr research, commentary, and debate. Rodolphe Barrangou, the journal’s editor in chief, where the peer-reviewed perspective appeared, says that the article was one of two that it had published recently addressing the ethical concerns of human germline editing, the other by a bioethicist at the University of North Carolina. Both papers’ authors had requested that their writing come out ahead of a major gene editing summit taking place this week in Hong Kong. When half-rumors of He’s covert work reached Barrangou over the weekend, his team discussed pulling the paper, but ultimately decided that there was nothing too solid to discredit it, based on the information available at the time.

Now Barrangou and his team are rethinking that decision. For one thing, He did not disclose any conflicts of interest, which is standard practice among respectable journals. It’s since become clear that not only is He at the helm of several genetics companies in China, He was actively pursuing controversial human research long before writing up a scientific and moral code to guide it.“We’re currently assessing whether the omission was a matter of ill-management or ill-intent,” says Barrangou, who added that the journal is now conducting an audit to see if a retraction might be warranted. …

“There are all sorts of questions these issues raise, but the most fundamental is the risk-benefit ratio for the babies who are going to be born,” says Hank Greely, an ethicist at Stanford University. “And the risk-benefit ratio on this stinks. Any institutional review board that approved it should be disbanded if not jailed.”

Reporting by Stat indicates that He may have just gotten in over his head and tried to cram a self-guided ethics education into a few short months. The young scientist—records indicate He is just 34—has a background in biophysics, with stints studying in the US at Rice University and in bioengineer Stephen Quake’s lab at Stanford. His resume doesn’t read like someone steeped deeply in the nuances and ethics of human research. Barrangou says that came across in the many rounds of edits He’s framework went through.

… China’s central government in Beijing has yet to come down one way or another. Condemnation would make He a rogue and a scientific outcast. Anything else opens the door for a Crispr IVF cottage industry to emerge in China and potentially elsewhere. “It’s hard to imagine this was the only group in the world doing this,” says Paul Knoepfler, a stem cell researcher at UC Davis who wrote a book on the future of designer babies called GMO Sapiens. “Some might say this broke the ice. Will others forge ahead and go public with their results or stop what they’re doing and see how this plays out?”

Here’s some of the very latest information with the researcher attempting to explain himself.

What does He have to say?

After He’s appearance at the Second International Summit on Human Genome Editing today, Nov. 27, 2018, David Cyranoski produced this article for Nature,

He Jiankui, the Chinese scientist who claims to have helped produce the first people born with edited genomes — twin girls — appeared today at a gene-editing summit in Hong Kong to explain his experiment. He gave his talk amid threats of legal action and mounting questions, from the scientific community and beyond, about the ethics of his work and the way in which he released the results.

He had never before presented his work publicly outside of a handful of videos he posted on YouTube. Scientists welcomed the fact that he appeared at all — but his talk left many hungry for more answers, and still not completely certain that He has achieved what he claims.

“There’s no reason not to believe him,” says Robin Lovell-Badge, a developmental biologist at the Francis Crick Institute in London. “I’m just not completely convinced.”

Lovell-Badge, like others at the conference, says that an independent body should confirm the test results by performing an in-depth comparison of the parents’ and childrens’ genes.

Many scientists faulted He for a lack of transparency and the seemingly cavalier nature in which he embarked on such a landmark, and potentially risky, project.

“I’m happy he came but I was really horrified and stunned when he described the process he used,” says Jennifer Doudna, a biochemist at the University of California, Berkeley and a pioneer of the CRISPR/Cas-9 gene-editing technique that He used. “It was so inappropriate on so many levels.”

He seemed shaky approaching the stage and nervous during the talk. “I think he was scared,” says Matthew Porteus, who researches genome-editing at Stanford University in California and co-hosted a question-and-answer session with He after his presentation. Porteus attributes this either to the legal pressures that He faces or the mounting criticism from the scientists and media he was about to address.

He’s talk leaves a host of other questions unanswered, including whether the prospective parents were properly informed of the risks; why He selected CCR5 when there are other, proven ways to prevent HIV; why he chose to do the experiment with couples in which the fathers have HIV, rather than mothers who have a higher chance of passing the virus on to their children; and whether the risks of knocking out CCR5 — a gene normally present in people, which could have necessary but still unknown functions — outweighed the benefits in this case.

In the discussion following He’s talk, one scientist asked why He proceeded with the experiments despite the clear consensus among scientists worldwide that such research shouldn’t be done. He didn’t answer the question.

He’s attempts to justify his actions mainly fell flat. In response to questions about why the science community had not been informed of the experiments before the first women were impregnated, he cited presentations that he gave last year at meetings at the University of California, Berkeley, and at the Cold Spring Harbor Laboratory in New York. But Doudna, who organized the Berkeley meeting, says He did not present anything that showed he was ready to experiment in people. She called his defence “disingenuous at best”.

He also said he discussed the human experiment with unnamed scientists in the United States. But Porteus says that’s not enough for such an extraordinary experiment: “You need feedback not from your two closest friends but from the whole community.” …

Pressure was mounting on He ahead of the presentation. On 27 November, the Chinese national health commission ordered the Guangdong health commission, in the province where He’s university is located, to investigate.

On the same day, the Chinese Academy of Sciences issued a statement condemning his work, and the Genetics Society of China and the Chinese Society for Stem Cell Research jointly issued a statement saying the experiment “violates internationally accepted ethical principles regulating human experimentation and human rights law”.

The hospital cited in China’s clinical-trial registry as the that gave ethical approval for He’s work posted a press release on 27 November saying it did not give any approval. It questioned the signatures on the approval form and said that the hospital’s medical-ethics committee never held a meeting related to He’s research. The hospital, which itself is under investigation by the Shenzhen health authorities following He’s revelations, wrote: “The Company does not condone the means of the Claimed Project, and has reservations as to the accuracy, reliability and truthfulness of its contents and results.”

He has not yet responded to requests for comment on these statements and investigations, nor on why the hospital was listed in the registry and the claim of apparent forged signatures.

Alice Park’s Nov. 26, 2018 article for Time magazine includes an embedded video of He’s Nov. 27, 2018 presentation at the summit meeting.

What about the politics?

Mara Hvistendahl’s Nov. 27, 2018 article about this research for Slate.com poses some geopolitical questions (Note: Links have been removed),

The informed consent agreement for He Jiankui’s experiment describes it as an “AIDS vaccine development project” and used highly technical language to describe the procedure that patients would undergo. If the reality for some Chinese patients is that such agreements are glossed over, densely written, or never read, the reality for some researchers working in the country is that the appeal of cutting-edge trials is too great to resist. It is not just Chinese scientists who can be blinded by the lure of quick breakthroughs. Several of the most notable breaches of informed consent on the mainland have involved Western researchers or co-authors. … When people say that the usual rules don’t apply in China, they are really referring to authoritarian science, not some alternative communitarian ethics.

For the many scientists in China who adhere to recognized international standards, the incident comes as a disgrace. He Jiankui now faces an ethics investigation from provincial health authorities, and his institution, Southern University of Science and Technology, was quick to issue a statement noting that He was on unpaid leave. …

It would seem that US [and from elsewhere]* scientists wanting to avoid pesky ethics requirements in the US have found that going to China could be the answer to their problems. I gather it’s not just big business that prefers deregulated environments.

Guillaume Levrier’s  (he’ studying for a PhD at the Universté Sorbonne Paris Cité) November 16, 2018 essay for The Conversation sheds some light on political will and its impact on science (Note: Links have been removed),

… China has entered a “genome editing” race among great scientific nations and its progress didn’t come out of nowhere. China has invested heavily in the natural-sciences sector over the past 20 years. The Ninth Five-Year Plan (1996-2001) mentioned the crucial importance of biotechnologies. The current Thirteenth Five-Year Plan is even more explicit. It contains a section dedicated to “developing efficient and advanced biotechnologies” and lists key sectors such as “genome-editing technologies” intended to “put China at the bleeding edge of biotechnology innovation and become the leader in the international competition in this sector”.

Chinese embryo research is regulated by a legal framework, the “technical norms on human-assisted reproductive technologies”, published by the Science and Health Ministries. The guidelines theoretically forbid using sperm or eggs whose genome have been manipulated for procreative purposes. However, it’s hard to know how much value is actually placed on this rule in practice, especially in China’s intricate institutional and political context.

In theory, three major actors have authority on biomedical research in China: the Science and Technology Ministry, the Health Ministry, and the Chinese Food and Drug Administration. In reality, other agents also play a significant role. Local governments interpret and enforce the ministries’ “recommendations”, and their own interpretations can lead to significant variations in what researchers can and cannot do on the ground. The Chinese National Academy of Medicine is also a powerful institution that has its own network of hospitals, universities and laboratories.

Another prime actor is involved: the health section of the People’s Liberation Army (PLA), which has its own biomedical faculties, hospitals and research labs. The PLA makes its own interpretations of the recommendations and has proven its ability to work with the private sector on gene editing projects. …

One other thing from Levrier’s essay,

… And the media timing is just a bit too perfect, …

Do read the essay; there’s a twist at the end.

Final thoughts and some links

If I read this material rightly, there are suspicions there may be more of this work being done in China and elsewhere. In short, we likely don’t have the whole story.

As for the ethical issues, this is a discussion among experts only, so far. The great unwashed (thee and me) are being left at the wayside. Sure, we’ll be invited to public consultations, one day,  after the big decisions have been made.

Anyone who’s read up on the history of science will tell you this kind of breach is very common at the beginning. Richard Holmes’  2008 book, ‘The Age of Wonder: How the Romantic Generation Discovered the Beauty and Terror of Science’ recounts stories of early scientists (European science) who did crazy things. Some died, some shortened their life spans; and, some irreversibly damaged their health.  They also experimented on other people. Informed consent had not yet been dreamed up.

In fact, I remember reading somewhere that the largest human clinical trial in history was held in Canada. The small pox vaccine was highly contested in the US but the Canadian government thought it was a good idea so they offered US scientists the option of coming here to vaccinate Canadian babies. This was in the 1950s and the vaccine seems to have been administered almost universally. That was a lot of Canadian babies. Thankfully, it seems to have worked out but it does seem mind-boggling today.

For all the indignation and shock we’re seeing, this is not the first time nor will it be the last time someone steps over a line in order to conduct scientific research. And, that is the eternal problem.

Meanwhile I think some of the real action regarding CRISPR and germline editing is taking place in the field (pun!) of agriculture:

My Nov. 27, 2018 posting titled: ‘Designer groundcherries by CRISPR (clustered regularly interspaced short palindromic repeats)‘ and a more disturbing Nov. 27, 2018 post titled: ‘Agriculture and gene editing … shades of the AquAdvantage salmon‘. That second posting features a company which is trying to sell its gene-editing services to farmers who would like cows that  never grow horns and pigs that never reach puberty.

Then there’s this ,

The Genetic Revolution‘, a documentary that offers relatively up-to-date information about gene editing, which was broadcast on Nov. 11, 2018 as part of The Nature of Things series on CBC (Canadian Broadcasting Corporation).

My July 17, 2018 posting about research suggesting that scientists hadn’t done enough research on possible effects of CRISPR editing titled: ‘The CRISPR ((clustered regularly interspaced short palindromic repeats)-CAS9 gene-editing technique may cause new genetic damage kerfuffle’.

My 2017 three-part series on CRISPR and germline editing:

CRISPR and editing the germline in the US (part 1 of 3): In the beginning

CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

CRISPR and editing the germline in the US (part 3 of 3): public discussions and pop culture

There you have it.

Added on November 30, 2018: David Cyanowski has written one final article (Nov. 30, 2018 for Nature) about He and the Second International Summit on Human Genome Editing. He did not make his second scheduled appearance at the summit, returning to China before the summit concluded. He was rebuked in a statement produced by the Summit’s organizing committee at the end of the three-day meeting. The situation with regard to his professional status in China is ambiguous. Cyanowski ends his piece with the information that the third summit will take place in London (likely in the UK) in 2021. I encourage you to read Cyanowski’s Nov. 30, 2018 article in its entirety; it’s not long.

Added on Dec. 3, 2018: The story continues. Ed Yong has written a summary of the issues to date in a Dec. 3, 2018 article for The Atlantic (even if you know the story ift’s eyeopening to see all the parts put together.

J. Benjamin Hurlbut, Associate Professor of Life Sciences at Arizona State University (ASU) and Jason Scott Robert, Director of the Lincoln Center for Applied Ethics at Arizona State University have written a provocative (and true) Dec. 3, 2018 essay titled, CRISPR babies raise an uncomfortable reality – abiding by scientific standards doesn’t guarantee ethical research, for The Conversation. h/t phys.org

*[and from elsewhere] added January 17, 2019.

Added on January 23, 2019: He has been fired by his university (Southern University of Science and Technology in Shenzhen) as announced on January 21, 2019.  David Cyranoski provides a details accounting in his January 22, 2019 article for Nature.

Boron nitride nanotubes

Most of the talk about nanotubes is focused on carbon nanotubes but there are other kinds as a May 21, 2018 Rice University news release (also received via email and on EurekAlert and in a May 21, 2018 news item on ScienceDaily), notes,

Boron nitride nanotubes are primed to become effective building blocks for next-generation composite and polymer materials based on a new discovery at Rice University – and a previous one.

Scientists at known-for-nano Rice have found a way to enhance a unique class of nanotubes using a chemical process pioneered at the university. The Rice lab of chemist Angel Martí took advantage of the Billups-Birch reaction process to enhance boron nitride nanotubes.

The work is described in the American Chemical Society journal ACS Applied Nano Materials.

Boron nitride nanotubes, like their carbon cousins, are rolled sheets of hexagonal arrays. Unlike carbon nanotubes, they’re electrically insulating hybrids made of alternating boron and nitrogen atoms.

Insulating nanotubes that can be functionalized will be a valuable building block for nanoengineering projects, Martí said. “Carbon nanotubes have outstanding properties, but you can only get them in semiconducting or metallic conducting types,” he said. “Boron nitride nanotubes are complementary materials that can fill that gap.”

Until now, these nanotubes have steadfastly resisted functionalization, the “decorating” of structures with chemical additives that allows them to be customized for applications. The very properties that give boron nitride nanotubes strength and stability, especially at high temperatures, also make them hard to modify for their use in the production of advanced materials.

But the Billups-Birch reaction developed by Rice Professor Emeritus of Chemistry Edward Billups, which frees electrons to bind with other atoms, allowed Martí and lead author Carlos de los Reyes to give the electrically inert boron nitride nanotubes a negative charge.

That, in turn, opened them up to functionalization with other small molecules, including aliphatic carbon chains.

“Functionalizing the nanotubes modifies or tunes their properties,” Martí said. “When they’re pristine they are dispersible in water, but once we attach these alkyl chains, they are extremely hydrophobic (water-avoiding). Then, if you put them in very hydrophobic solvents like those with long-chain hydrocarbons, they are more dispersible than their pristine form.

“This allows us to tune the properties of the nanotubes and will make it easier to take the next step toward composites,” he said. “For that, the materials need to be compatible.”

After he discovered the phenomenon, de los Reyes spent months trying to reproduce it reliably. “There was a period where I had to do a reaction every day to achieve reproducibility,” he said. But that turned out to be an advantage, as the process only required about a day from start to finish. “That’s the advantage over other processes to functionalize carbon nanotubes. There are some that are very effective, but they may take a few days.”

The process begins with adding pure ammonia gas to the nanotubes and cooling it to -70 degrees Celsius (-94 degrees Fahrenheit). “When it combines with sodium, lithium or potassium — we use lithium — it creates a sea of electrons,” Martí said. “When the lithium dissolves in the ammonia, it expels the electrons.”

The freed electrons quickly bind with the nanotubes and provide hooks for other molecules. De los Reyes enhanced Billups-Birch when he found that adding the alkyl chains slowly, rather than all at once, improved their ability to bind.

The researchers also discovered the process is reversible. Unlike carbon nanotubes that burn away, boron nitride nanotubes can stand the heat. Placing functionalized boron nitride tubes into a furnace at 600 degrees Celsius (1,112 degrees Fahrenheit) stripped them of the added molecules and returned them to their nearly pristine state.

“We call it defunctionalization,” Martí said. “You can functionalize them for an application and then remove the chemical groups to regain the pristine material. That’s something else the material brings that is a little different.”

The researchers have provided this pretty illustration of boron nitride nanotube,

Caption: Rice University researchers have discovered a way to ‘decorate’ electrically insulating boron nitride nanotubes with functional groups, making them more suitable for use with polymers and composite materials. Credit: Martí Research Group/Rice University

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

Chemical Decoration of Boron Nitride Nanotubes Using the Billups-Birch Reaction: Toward Enhanced Thermostable Reinforced Polymer and Ceramic Nanocomposites by Carlos A. de los Reyes, Kendahl L. Walz Mitra, Ashleigh D. Smith, Sadegh Yazdi, Axel Loredo, Frank J. Frankovsky, Emilie Ringe, Matteo Pasquali, and Angel A. Martí. ACS Appl. Nano Mater., Article ASAP DOI: 10.1021/acsanm.8b00633 Publication Date (Web): May 16, 2018

Copyright © 2018 American Chemical Society

This paper is behind a paywall.

Removing more than 99% of crude oil from ‘produced’ water (well water)

Should you have an oil well nearby (see The Urban Oil Fields of Los Angeles in an August 28, 2014 photo essay by Alan Taylor for The Atlantic for examples of oil wells in various municipalities and cities associated with LS) , this news from Texas may interest you.

From an August 15, 2018 news item on Nanowerk,

Oil and water tend to separate, but they mix well enough to form stable oil-in-water emulsions in produced water from oil reservoirs to become a problem. Rice University scientists have developed a nanoparticle-based solution that reliably removes more than 99 percent of the emulsified oil that remains after other processing is done.
The Rice lab of chemical engineer Sibani Lisa Biswal made a magnetic nanoparticle compound that efficiently separates crude oil droplets from produced water that have proven difficult to remove with current methods.

An August 15, 2018 Rice University news release (also on EurekAlert), which originated the news item, describes the work in more detail,

Produced water [emphasis mine] comes from production wells along with oil. It often includes chemicals and surfactants pumped into a reservoir to push oil to the surface from tiny pores or cracks, either natural or fractured, deep underground. Under pressure and the presence of soapy surfactants, some of the oil and water form stable emulsions that cling together all the way back to the surface.

While methods exist to separate most of the oil from the production flow, engineers at Shell Global Solutions, which sponsored the project, told Biswal and her team that the last 5 percent of oil tends to remain stubbornly emulsified with little chance to be recovered.

“Injected chemicals and natural surfactants in crude oil can oftentimes chemically stabilize the oil-water interface, leading to small droplets of oil in water which are challenging to break up,” said Biswal, an associate professor of chemical and biomolecular engineering and of materials science and nanoengineering.

The Rice lab’s experience with magnetic particles and expertise in amines, courtesy of former postdoctoral researcher and lead author Qing Wang, led it to combine techniques. The researchers added amines to magnetic iron nanoparticles. Amines carry a positive charge that helps the nanoparticles find negatively charged oil droplets. Once they do, the nanoparticles bind the oil. Magnets are then able to pull the droplets and nanoparticles out of the solution.

“It’s often hard to design nanoparticles that don’t simply aggregate in the high salinities that are typically found in reservoir fluids, but these are quite stable in the produced water,” Biswal said.

The enhanced nanoparticles were tested on emulsions made in the lab with model oil as well as crude oil.

In both cases, researchers inserted nanoparticles into the emulsions, which they simply shook by hand and machine to break the oil-water bonds and create oil-nanoparticle bonds within minutes. Some of the oil floated to the top, while placing the test tube on a magnet pulled the infused nanotubes to the bottom, leaving clear water in between.

Best of all, Biswal said, the nanoparticles can be washed with a solvent and reused while the oil can be recovered. The researchers detailed six successful charge-discharge cycles of their compound and suspect it will remain effective for many more.

She said her lab is designing a flow-through reactor to process produced water in bulk and automatically recycle the nanoparticles. That would be valuable for industry and for sites like offshore oil rigs, where treated water could be returned to the ocean.

It seems to me that ‘produced water’ is another term for polluted water.I guess it’s the reverse to Shakespeare’s “a rose by any other name would smell as sweet” with polluted water by any other name seeming more palatable.

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

Recyclable amine-functionalized magnetic nanoparticles for efficient demulsification of crude oil-in-water emulsions by Qing Wang, Maura C. Puerto, Sumedh Warudkar, Jack Buehler, and Sibani L. Biswal. Environ. Sci.: Water Res. Technol., 2018, Advance Article DOI: 10.1039/C8EW00188J First published on 15 Aug 2018

This paper is behind a paywall.

Rice has included this image amongst others in their news release,

Rice University engineers have developed magnetic nanoparticles that separate the last droplets of oil from produced water at wells. The particles draw in the bulk of the oil and are then attracted to the magnet, as demonstrated here. Photo by Jeff Fitlow

There’s also this video, which, in my book, borders on magical,

‘Lilliputian’ skyscraper: white graphene for hydrogen storage

This story comes from Rice University (Texas, US). From a March 12, 2018 news item on Nanowerk,

Rice University engineers have zeroed in on the optimal architecture for storing hydrogen in “white graphene” nanomaterials — a design like a Lilliputian skyscraper with “floors” of boron nitride sitting one atop another and held precisely 5.2 angstroms apart by boron nitride pillars.

Caption Thousands of hours of calculations on Rice University’s two fastest supercomputers found that the optimal architecture for packing hydrogen into “white graphene” involves making skyscraper-like frameworks of vertical columns and one-dimensional floors that are about 5.2 angstroms apart. In this illustration, hydrogen molecules (white) sit between sheet-like floors of graphene (gray) that are supported by boron-nitride pillars (pink and blue). Researchers found that identical structures made wholly of boron-nitride had unprecedented capacity for storing readily available hydrogen. Credit Lei Tao/Rice University

A March 12, 2018 Rice University news release (also on EurekAlert), which originated the news item, goes into extensive detail about the work,

“The motivation is to create an efficient material that can take up and hold a lot of hydrogen — both by volume and weight — and that can quickly and easily release that hydrogen when it’s needed,”  [emphasis mine] said the study’s lead author, Rouzbeh Shahsavari, assistant professor of civil and environmental engineering at Rice.

Hydrogen is the lightest and most abundant element in the universe, and its energy-to-mass ratio — the amount of available energy per pound of raw material, for example — far exceeds that of fossil fuels. It’s also the cleanest way to generate electricity: The only byproduct is water. A 2017 report by market analysts at BCC Research found that global demand for hydrogen storage materials and technologies will likely reach $5.4 billion annually by 2021.

Hydrogen’s primary drawbacks relate to portability, storage and safety. While large volumes can be stored under high pressure in underground salt domes and specially designed tanks, small-scale portable tanks — the equivalent of an automobile gas tank — have so far eluded engineers.

Following months of calculations on two of Rice’s fastest supercomputers, Shahsavari and Rice graduate student Shuo Zhao found the optimal architecture for storing hydrogen in boron nitride. One form of the material, hexagonal boron nitride (hBN), consists of atom-thick sheets of boron and nitrogen and is sometimes called white graphene because the atoms are spaced exactly like carbon atoms in flat sheets of graphene.

Previous work in Shahsavari’s Multiscale Materials Lab found that hybrid materials of graphene and boron nitride could hold enough hydrogen to meet the Department of Energy’s storage targets for light-duty fuel cell vehicles.

“The choice of material is important,” he said. “Boron nitride has been shown to be better in terms of hydrogen absorption than pure graphene, carbon nanotubes or hybrids of graphene and boron nitride.

“But the spacing and arrangement of hBN sheets and pillars is also critical,” he said. “So we decided to perform an exhaustive search of all the possible geometries of hBN to see which worked best. We also expanded the calculations to include various temperatures, pressures and dopants, trace elements that can be added to the boron nitride to enhance its hydrogen storage capacity.”

Zhao and Shahsavari set up numerous “ab initio” tests, computer simulations that used first principles of physics. Shahsavari said the approach was computationally intense but worth the extra effort because it offered the most precision.

“We conducted nearly 4,000 ab initio calculations to try and find that sweet spot where the material and geometry go hand in hand and really work together to optimize hydrogen storage,” he said.

Unlike materials that store hydrogen through chemical bonding, Shahsavari said boron nitride is a sorbent that holds hydrogen through physical bonds, which are weaker than chemical bonds. That’s an advantage when it comes to getting hydrogen out of storage because sorbent materials tend to discharge more easily than their chemical cousins, Shahsavari said.

He said the choice of boron nitride sheets or tubes and the corresponding spacing between them in the superstructure were the key to maximizing capacity.

“Without pillars, the sheets sit naturally one atop the other about 3 angstroms apart, and very few hydrogen atoms can penetrate that space,” he said. “When the distance grew to 6 angstroms or more, the capacity also fell off. At 5.2 angstroms, there is a cooperative attraction from both the ceiling and floor, and the hydrogen tends to clump in the middle. Conversely, models made of purely BN tubes — not sheets — had less storage capacity.”

Shahsavari said models showed that the pure hBN tube-sheet structures could hold 8 weight percent of hydrogen. (Weight percent is a measure of concentration, similar to parts per million.) Physical experiments are needed to verify that capacity, but that the DOE’s ultimate target is 7.5 weight percent, and Shahsavari’s models suggests even more hydrogen can be stored in his structure if trace amounts of lithium are added to the hBN.

Finally, Shahsavari said, irregularities in the flat, floor-like sheets of the structure could also prove useful for engineers.

“Wrinkles form naturally in the sheets of pillared boron nitride because of the nature of the junctions between the columns and floors,” he said. “In fact, this could also be advantageous because the wrinkles can provide toughness. If the material is placed under load or impact, that buckled shape can unbuckle easily without breaking. This could add to the material’s safety, which is a big concern in hydrogen storage devices.

“Furthermore, the high thermal conductivity and flexibility of BN may provide additional opportunities to control the adsorption and release kinetics on-demand,” Shahsavari said. “For example, it may be possible to control release kinetics by applying an external voltage, heat or an electric field.”

I may be wrong but this “The motivation is to create an efficient material that can take up and hold a lot of hydrogen — both by volume and weight — and that can quickly and easily release that hydrogen when it’s needed, …”  sounds like a supercapacitor. One other comment, this research appears to be ‘in silico’, i.e., all the testing has been done as computer simulations and the proposed materials themselves have yet to be tested.

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

Merger of Energetic Affinity and Optimal Geometry Provides New Class of Boron Nitride Based Sorbents with Unprecedented Hydrogen Storage Capacity by Rouzbeh Shahsavari and Shuo Zhao. Small Vol. 14 Issue 10 DOI: 10.1002/smll.201702863 Version of Record online: 8 MAR 2018

© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.