Tag Archives: arsenic

‘Hunting’ pharmaceuticals and removing them from water

Pharmaceuticals are not the first pollutants people think of when discussing water pollution but, for those who don’t know, it’s a big issue and scientists at the University of Surrey (UK) have developed a technology they believe will help to relieve the contamination. From an April 10, 2017 University of Surrey press release (also on EurekAlert),

The research involves the detection and removal of pharmaceuticals in or from water, as contamination from pharmaceuticals can enter the aquatic environment as a result of their use for the treatment of humans and animals. This contamination can be excreted unchanged, as metabolites, as unused discharge or by drug manufacturers.

The research has found that a new type of ‘supermolecule’, calix[4], actively seeks certain pharmaceuticals and removes them from water.

Contamination of water is a serious concern for environmental scientists around the world, as substances include hormones from the contraceptive pill, and pesticides and herbicides from allotments. Contamination can also include toxic metals such as mercury, arsenic, or cadmium, which was previously used in paint, or substances that endanger vital species such as bees.

Professor Danil de Namor, University of Surrey Emeritus Professor and leader of the research, said: “Preliminary extraction data are encouraging as far as the use of this receptor for the selective removal of these drugs from water and the possibility of constructing a calix[4]-based sensing devices.

“From here, we can design receptors so that they can bind selectively with pollutants in the water so the pollutants can be effectively removed. This research will allow us to know exactly what is in the water, and from here it will be tested in industrial water supplies, so there will be cleaner water for everyone.

“The research also creates the possibility of using these materials for on-site monitoring of water, without having to transport samples to the laboratory.”

Dr Brendan Howlin, University of Surrey co-investigator, said: “This study allows us to visualise the specific receptor-drug interactions leading to the selective behaviour of the receptor. As well as the health benefits of this research, molecular simulation is a powerful technique that is applicable to a wide range of materials.

“We were very proud that the work was carried out with PhD students and a final year project student, and research activities are already taking place with the Department of Chemical and Processing Engineering (CPI) and the Advanced Technology Institute (ATI).

“We are also very pleased to see that as soon as the paper was published online by the European Journal of Pharmaceutical Sciences, we received invitations to give keynote lectures at two international conferences on pharmaceuticals in Europe later this year.”

That last paragraph is intriguing and it marks the first time I’ve seen that claim in a press release announcing the publication of a piece of research.

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

A calix[4]arene derivative and its selective interaction with drugs (clofibric acid, diclofenac and aspirin) by Angela F Danil de Namor, Maan Al Nuaim, Jose A Villanueva Salas, Sophie Bryant, Brendan Howlin. European Journal of Pharmaceutical Sciences Volume 100, 30 March 2017, Pages 1–8 https://doi.org/10.1016/j.ejps.2016.12.027

This paper is behind a paywall.

Molecular robots (nanobots/nanorobots): a promising start at Oxford University

‘Baby steps’ is how they are describing the motion and the breakthrough in functional molecular robots at the University of Oxford. From a Dec. 11, 2014 news item on phys.org,

A walking molecule, so small that it cannot be observed directly with a microscope, has been recorded taking its first nanometre-sized steps.

It’s the first time that anyone has shown in real time that such a tiny object – termed a ‘small molecule walker’ – has taken a series of steps. The breakthrough, made by Oxford University chemists, is a significant milestone on the long road towards developing ‘nanorobots’.

‘In the future we can imagine tiny machines that could fetch and carry cargo the size of individual molecules, which can be used as building blocks of more complicated molecular machines; imagine tiny tweezers operating inside cells,’ said Dr Gokce Su Pulcu of Oxford University’s Department of Chemistry. ‘The ultimate goal is to use molecular walkers to form nanotransport networks,’ she says.

A Dec. 10, 2014 University of Oxford science blog post by Pete Wilton, which originated the news item, describes one of the problem with nanorobots,

However, before nanorobots can run they first have to walk. As Su explains, proving this is no easy task.

For years now researchers have shown that moving machines and walkers can be built out of DNA. But, relatively speaking, DNA is much larger than small molecule walkers and DNA machines only work in water.

The big problem is that microscopes can only detect moving objects down to the level of 10–20 nanometres. This means that small molecule walkers, whose strides are 1 nanometre long, can only be detected after taking around 10 or 15 steps. It would therefore be impossible to tell with a microscope whether a walker had ‘jumped’ or ‘floated’ to a new location rather than taken all the intermediate steps.

The post then describes how the researchers solved the problem,

… Su and her colleagues at Oxford’s Bayley Group took a new approach to detecting a walker’s every step in real time. Their solution? To build a walker from an arsenic-containing molecule and detect its motion on a track built inside a nanopore.

Nanopores are already the foundation of pioneering DNA sequencing technology developed by the Bayley Group and spinout company Oxford Nanopore Technologies. Here, tiny protein pores detect molecules passing through them. Each base disrupts an electric current passed through the nanopore by a different amount so that the DNA base ‘letters’ (A, C, G or T) can be read.

In this new research, they used a nanopore containing a track formed of five ‘footholds’ to detect how a walker was moving across it.

‘We can’t ‘see’ the walker moving, but by mapping changes in the ionic current flowing through the pore as the molecule moves from foothold to foothold we are able to chart how it is stepping from one to the other and back again,’ Su explains.

To ensure that the walker doesn’t float away, they designed it to have ‘feet’ that stick to the track by making and breaking chemical bonds. Su says: ‘It’s a bit like stepping on a carpet with glue under your shoes: with each step the walker’s foot sticks and then unsticks so that it can move to the next foothold.’ This approach could make it possible to design a machine that can walk on a variety of surfaces.

There is a video illustrating the molecular walker’s motion, (courtesy University of Oxford),

There is as noted in Wilton’s post, more work to do,

It’s quite an achievement for such a tiny machine but, as Su is the first to admit, there are many more challenges to be overcome before programmable nanorobots are a reality.

‘At the moment we don’t have much control over which direction the walker moves in; it moves pretty randomly,’ Su tells me. ‘The protein track is a bit like a mountain slope; there’s a direction that’s easier to walk in so walkers will tend to go this way. We hope to be able to harness this preference to build tracks that direct a walker where we want it to go.’

The next challenge after that will be for a walker to make itself useful by, for instance, carrying a cargo: there’s already space for it to carry a molecule on its ‘head’ that it could then take to a desired location to accomplish a task.

Su comments: ‘We should be able to engineer a surface where we can control the movement of these walkers and observe them under a microscope through the way they interact with a very thin fluorescent layer. This would make it possible to design chips with different stations with walkers ferrying cargo between these stations; so the beginnings of a nanotransport system.’

These are the first tentative baby steps of a new technology, but they promise that there could be much bigger strides to come.

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

Continuous observation of the stochastic motion of an individual small-molecule walker by Gökçe Su Pulcu, Ellina Mikhailova, Lai-Sheung Choi, & Hagan Bayley. Nature Nanotechnology (2014) doi:10.1038/nnano.2014.264 Published online 08 December 2014

This paper is behind a paywall.

Phyto-mining and environmental remediation flower in the United Kingdom

Researchers on a £3 million research programme called “Cleaning Land for Wealth” (CL4W) are confident they’ll be able to use flowers and plants to clean soil of poisonous materials (environmental remediation) and to recover platinum (phyto-mining). From the Nov. 21, 2012 news item on Nanowerk,

A consortium of researchers led by WMG (Warwick Manufacturing Group) at the University of Warwick are to embark on a £3 million research programme called “Cleaning Land for Wealth” (CL4W), that will use a common class of flower to restore poisoned soils while at the same time producing perfectly sized and shaped nano sized platinum and arsenic nanoparticles for use in catalytic convertors, cancer treatments and a range of other applications.

The Nov. 20, 2012 University of Warwick news release, which originated the news item, describes both how CL4W came together and how it produced an unintended project benefit,

A “Sandpit” exercise organised by the Engineering and Physical Sciences Research Council (EPSRC) allowed researchers from WMG (Warwick Manufacturing group) at the University of Warwick, Newcastle University, The University of Birmingham, Cranfield University and the University of Edinburgh to come together and share technologies and skills to come up with an innovative multidisciplinary research project that could help solve major technological and environmental challenges.

The researchers pooled their knowledge of how to use plants and bacteria to soak up particular elements and chemicals and how to subsequently harvest, process and collect that material. They have devised an approach to demonstrate the feasibility in which they are confident that they can use common classes of flower and plants (such as Alyssum), to remove poisonous chemicals such as arsenic and platinum from polluted land and water courses potentially allowing that land to be reclaimed and reused.

That in itself would be a significant achievement, but as the sandpit progressed the researchers found that jointly they had the knowledge to achieve much more than just cleaning up the land.

As lead researcher on the project Professor Kerry Kirwan from WMG at the University of Warwick explained:

“The processes we are developing will not only remove poisons such as arsenic and platinum from contaminated land and water courses, we are also confident that we can develop suitable biology and biorefining processes (or biofactories as we are calling them) that can tailor the shapes and sizes of the metallic nanoparticles they will make. This would give manufacturers of catalytic convertors, developers of cancer treatments and other applicable technologies exactly the right shape, size and functionality they need without subsequent refinement. We are also expecting to recover other high value materials such as fine chemicals, pharmaceuticals, anti-oxidants etc. from the crops during the same biorefining process.”

I last mentioned phyto-mining in my Sept. 26, 2012 post with regard to an international project being led by researchers at the University of York (UK).  The biorefining processes (biofactories) mentioned by Kirwan takes the idea of recovering platinum, etc. one step beyond phyto-mining recovery.

Here’s a picture of the flower (Alyssum) mentioned in the news release,

Alyssum montanum photographed by myself in 1988, Unterfranken, Germany [http://en.wikipedia.org/wiki/Alyssum]

From the Wikipedia essay (Note: I have removed links],

Alyssum is a genus of about 100–170 species of flowering plants in the family Brassicaceae, native to Europe, Asia, and northern Africa, with the highest species diversity in the Mediterranean region. The genus comprises annual and perennial herbaceous plants or (rarely) small shrubs, growing to 10–100 cm tall, with oblong-oval leaves and yellow or white flowers (pink to purple in a few species).

Rosie Redfield talks #arseniclife at Vancouver’s Café Scientifique tonight (April 24, 2012)

Rose Redfield seems to be everywhere in Vancouver these days. Last week (April 19, 2012) she spoke at the first ScienceOnline Vancouver Event and tonight she’s at Café Scientifique at the Railway Club, 579 Dunsmuir St. (second floor) at 7:30 pm.

Here’s the event description straight from the news release,

Our speaker for the evening will be Dr. Rosie Redfield, the biologist from UBC who was recently named one of the “10 People Who Mattered” in 2011 by Nature magazine. (http://www.nature.com/news/365-days-nature-s-10-1.9678 ).

The title and abstract for her café is:

#arseniclife and Open Science
The #arseniclife story started with a bang in late 2010, when NASA proudly announced the discovery that some bacteria could synthesize their DNA with arsenic in the backbone in place of phosphorus. But within a few days it all fell apart, as scientists used blogs and Twitter to conduct impromptu ‘post-publication peer review’. (‘#arseniclife’ is the Twitter hashtag used to identify relevant tweets.) Working with collaborators at Princeton, my lab has now shown that the key results cannot be replicated. This debacle has implications for many aspects of science, from how personal biases and funding sources affect scientific judgment to the increasing roles of social media in both the practice and public communication of science.

I hope she’s addressed that problem with overmodulation that I described in my comments about last week’s ScienceOnline Vancouver event (my April 20, 2012 posting) because she’s very interesting.

For anyone not familiar with the #arseniclife story, here’s my Dec. 8, 2012 apology  posting about it (with links to other more informed writing) and my blooper Dec. 6, 2010 posting.

Comments on ScienceOnline Vancouver’s first event

Bravo to the organizers, Catherine Anderson, Sarah Chow, and Peter Newberry of Vancouver’s (Canada) first ScienceOnline event last night (Thursday, April 19, 2012 first mentioned my April 4, 2012 posting). They attracted, by my count,  a crowd of about 75-80 people. A free event held at Science World, there were three speakers Rosie Redfield, Lisa Johnson, and Anthony Floyd. Here’s a bit more about them from the event description page,

  • Rosie Redfield – Named Nature’s most influential person of 2011, this associate professor of microbiology at UBC [University of British Columbia] hit science fame through her blog RRResearch disputing NASA’s claim life exists in arsenic.
  • Lisa Johnson – Multiplatform journalist with a keen interest in environment and science stories. She enjoys digging, storytelling, and finding context in breaking news.
  • Anthony Floyd – aerospace research engineer with a PhD in Civil Engineering from UBC. Although strictly a digital immigrant, Anthony grew up with technology as technology grew up. He is quite active in social media. Anthony’s a proud dad to two boys, year-round bike commuter, opinionated political observer, and Maritimer-in-exile.

The event was titled, Where do you get your science? It was the third event I attended yesterday so maybe I was a little less tolerant than I can be. I was expecting a lively discussion about finding science what I got was Redfield and Johnson talking about the arsenic life story and their roles in that story locally and, in Redfield’s case, internationally. The only one who really talked about finding science online was Floyd.

I’m not sure if the organizers were hoping that the ‘arsenic life’ stories would somehow tie into the topic or if the two speakers just went off on their own tangents.

Redfield gave an ‘ignite’ talk, which is five minutes long with 20 slides in a timed slideshow where the speaker has to keep time with the slides. I’m sorry to say she overmodulated (used the storytime voice usually aimed at an audience of five-year olds)  for much of the talk. Johnson made the point several times that it wasn’t her fault that the story was wrong. She did admit at one point that she could have dug more deeply and, in fact, someone suggested that she talk to Rosie Redfield for advice about this story at very early stage, something she failed to do. Most valuable to me was the reminder of the constraints that journalists are under.

Note: I, too,  got caught up with my Dec. 6, 2010 posting and I subsequently apologized, Dec. 8, 2010 posting.

Floyd, as I noted earlier, did address the question, Where do you get your science?, although he did ask his audience to make a bit of a leap when he used a story about searching for information about bicycle helmets and bylaws to illustrate one of his points.

I wasn’t able to stay for the more informal discussion after the speakers finished but the organizers  did manage a good icebreaker exercise at the beginning. The audience seemed mostly to be mostly in their 20s and 30s.

It was a very technology-heavy event in that there was livestreaming, multiple computers and screens, references to tweeting and Storify, etc.

Aside: All three of the events I attended yesterday had technology issues of one kind or another. I’m not especially happy when almost all of the attention is on the technology while the live audience is left waiting or is interrupted during question period to accommodate a tweet or has to endure feedback.

I did mention Storify, the ScienceOnline Vancouver Storify ‘story’ is here and you can check #sovan on Twitter for other responses to last night’s event.

All in all, it was a very promising start, despite my nitpicks.

My apologies for arsenic blooper

I made a mistake when reporting on NASA and the ‘arsenic’ bacterium. Apparently, the research methodology was problematic and the conclusion that the bacterium can substitute arsenic for phosphorus in its DNA is not supported by the evidence as presented.

Martin Robbins at the Lay Scientist blog (one of The Guardian’s science blogs) has posted an analysis of how this ‘media storm’ occurred. The article which started it all was in a well respected,  peer-reviewed journal, Science (which is published by the American Association for the Advancement of Science).  From Robbins’s Dec. 8, 2010 posting,

Should the paper have been published in the first place? Carl Zimmer’s blog post for Slate collects the responses of numerous scientists to the work, including the University of Colorado’s Shelley Copley declaring that: “This paper should not have been published.”

There are two distinct questions here to tease apart: ‘should the paper have been published?’ and ‘should it have been published in Science?’

To the first question I would say ‘yes’. Peer review isn’t supposed to be about declaring whether a paper is definitely right and therefore fit for publication on that basis. The purpose of publishing paper is to submit ideas for further discussion and debate, with peer review serving as a fairly loose filter to weed out some of the utter crap. The contribution a paper makes to science goes far beyond such trivialities as whether or not it’s actually right.

Wolfe-Simon et al’s paper might be wrong, but it has also sparked an interesting and useful debate on the evidence and methodology required to make claims about this sort of thing, and the next paper on this subject that comes along with hopefully be a lot stronger as a result of this public criticism. You could argue on that basis that its publication is useful.

I would argue that the real bone of contention is whether it should have been published in Science – after all, if it had appeared in the Journal of Speculative Biological Hypotheses (and not been hyped) nobody would have given a crap. On this I’m not really qualified to comment, but what I can say is that given the wealth of scientists coming forward to criticize the work, it’s remarkable that the journal found three willing to pass it.

Robbins goes on to analyze the impact that the embargo (story is considered confidential until a prescribed date) that Science applied to the story about the article had on mainstream and other media. He also notes the impact that bloggers had on the story,

The quality, accuracy and context of material available on leading blogs exceeded that of much of mainstream media reporting by light years. While newspapers ran away with the story, it was left to bloggers like Ed Yong, Carl Zimmer, Lewis Dartnell and Phil Plait to put things into perspective.

But more importantly it turns out that peer review is being done on blogs. John Hawks and Alex Bradley – both scientists with relevant expertise – found methodological problems. Rosie Redfield, a microbiology professor a the University of British Colombia [sic], wrote an extensive and detailed take-down of the paper on her blog that morphed into a letter to Science, which I sincerely hope they publish.

Robbins does not suggest that the blogosophere is the perfect place for peer review only that it played an important role regarding this research. There is much more to the posting and I do encourage you to read it.

I did look at Rosie Redfield’s postings about the papers. I found her Dec. 4, 2010 posting to provide the most accessible analysis of the methodological issues of the two. Her Dec. 8, 2010 posting is her submission to Science about the matter.

I do apologize for getting caught up in the frenzy.

Elemental difference: a bacterium that lives on arsenic

[ETA Dec. 8, 2010: The ‘arsenic bacterium’ story noted has been corrected in my Dec. 8, 2010 posting. The conclusions first reported do not seem to be supported by the evidence in the article.] There’s a podcast over at The Guardian science blogs that features last week’s story from NASA (US National Aeronautics and Space Administration) about a bacterium, living deep in a California Lake, that uses arsenic instead of phosphorus in its molecular makeup. From the Dec. 2, 2010 article by Alok Jha for The Guardian newspaper,

A bacterium discovered in a Californian lake appears to be able to use arsenic in its molecular make-up instead of phosphorus – even incorporating the toxic chemical into its DNA. That’s significant because it goes against the general rule that all terrestrial life depends on six elements: oxygen, hydrogen, carbon, nitrogen, sulphur and phosphorus.  These are needed to build DNA, proteins and fats and are some of the biological signatures of life that scientists look for on other planets. [emphases mine]

Christened GFAJ-1, the microbe lends weight to the notion held by some astrobiologists that there might be “weird” forms of life on Earth, as yet undiscovered, that use elements other than the basic six in their metabolism. Among those who have speculated is Prof Paul Davies, a cosmologist at Arizona State University and an author on the latest research.

“This organism has dual capability – it can grow with either phosphorus or arsenic,” said Davies. “That makes it very peculiar, though it falls short of being some form of truly ‘alien’ life belonging to a different tree of life with a separate origin. However, GFAJ-1 may be a pointer to even weirder organisms. The holy grail would be a microbe that contained no phosphorus at all.”

As the pundits note, this changes some fundamental ideas we have about life on this planet and elsewhere.

Getting back to the podcast, the hosts also cover stories about the neanderthals and the [UK] Natural History Museum’s new approach to telling the story of evolution using a ‘kid-proof iPad’.