Chemistry Blog

Nov 10

How LCDs work


A little video I put together to explain how liquid crystal displays work, using pasta, stair gates, wool, a hair dryer and some polarizing filters.

Nov 03

How the infamous Yellow Rain investigation has foresaw a drug delivery innovation


By Mark Lorch, University of Hull

The history of science is full of episodes when a seemingly ludicrous theory is ridiculed, but then slowly gathers evidence and support to move from the fringes to the heart of the scientific consensus. Examples include Darwin’s theory of evolution by natural selection, the theory of plate tectonics that control the movement of Earth’s crust and, most recently, the Big Bang theory of the birth of our universe.

All these theories, even though initially mocked, came from respectable academics. It is rare for someone from outside the relevant scientific circles to make a wild stab in the dark and hit upon something that just happens to have a thread of truth to it. But one of these occasions involved a US intelligence officer.

Strange weather

In September 1981 Alexander Haig, the then US secretary of state, made a stunning allegation. He claimed to have evidence that Soviet-backed forces in Vietnam and Laos had been waging chemical warfare on villagers in those countries. A dossier, released shortly after, documented eye-witness accounts – dating back to 1977 – of aircraft spraying areas with a substance that left vegetation littered with small yellow spots. Far worse were reports of horrific symptoms in the exposed populations: people who suffered stomach cramps and vomiting, before dying. This, according to a lab the US government employed, was due to deadly trichothecene toxins present in the yellow material that rained down on the villagers.

The seriousness of the allegations – with the US accusing the Soviets of breaching the Geneva Protocol on the use of chemical weapons – warranted the corroboration of evidence. So samples of the yellow substance were re-tested in labs throughout the world. First military scientists at UK’s Porton Down – and then others – found something surprising: the “yellow rain” contained, primarily, pollen.

Stranger still, the pollen was not complete. It had been stripped of its proteins and contents, leaving a largely empty shell.

Faced with this unexpected finding, Sharon Watson, a US intelligence agent, proposed an explanation for the role of pollen in the mix: that it had been added to aid the dispersal and delivery of the toxins.

As Watson told a Washington press briefing in 1982: the agent initially came down wet, where it was first exposed to the skin. As the toxins were dissolved in a solvent, they were absorbed by the skin very quickly. But as the agent dried, Watson said, “a second aerosol effect” was created from kicking up the particle-sized pollen-like dust, which then lodged in the bronchii of the lung.

Watson told the briefing:

We’ve shown in studies with animals that the internasal LD-50 [the dose lethal to 50% of an exposed population] for the trichothecenes is much lower than we would have expected, and that the trichothecenes, if they come in contact with the mucous membrane, were very rapidly absorbed and are very toxic by this route.

So if you could bring the compound into contact with the mucous membranes of the bronchii, then it’s a very effective way of getting it across. So there are two different ways that the compound is absorbed. It’s [a] very clever, clever mixture.

In short, the intelligence service thought using pollen made the poison a lot more effective.

Local produce

But where did it come from? The cause of the yellow rain turned out to be something much more mundane – honey bee faeces.

Closer inspection showed that the pollen matched that from the flora in the area it was collected and was indistinguishable from local bee poo. The hollowing out of the pollen and lack of proteins was due to the bees having digested the pollen, before it was defecated and left on the leaves. The heavy yellow rain was explained by bees emerging from hives en masse, as they are inclined to do after inclement weather, and defecating (they never do this in their hives).

Meanwhile, the same labs that identified the pollen also failed to find any trace of trichothecence mixed with the pollen, which left the US theory that the yellow rain was a diabolical means of delivering chemical weapons in tatters. Whatever trichothecene was detected may have been naturally occurring, because the fungi that produce it were common in South-East Asia. Some eye witnesses still insist that chemical attacks did occur, but evidence doesn’t seem to support the use of pollen-based warfare as means of delivering those chemicals. Despite this, however, the US government hasn’t retracted its allegations, stating that the issue hasn’t been fully resolved.

The grain of truth

I always found this story with its scientific and political twists quite appealing. Little did I know that I would find myself working on Watson’s crazy idea about delivering chemicals using pollens. It turns out there was a grain of truth in it.

My colleagues and I have been stripping pollen spores down to leave the indigestible shell – to bees and man alike – called an exine. These exines are incredibly tough. They have even been found intact, along with fossils, in sedimentary rock.

We have loaded these empty pollen shells with a variety of compounds including drugs, edible oils and medical imaging agents to see if they can provide a new way of delivering these chemicals to places of interest in the human body.

Our results show that pollen capsules can indeed be used to trap chemicals and deliver them into the body. Exines provide chemical and physical protection to their surrogate cargoes. What’s more interesting is that exine shells appear to assist in the absorption of their contents across a mucous membrane. Just as Watson had suggested they might. The result, then, is a potential drug-delivery device, which was conceived by one US intelligence agent.

The Conversation

Mark Lorch does not work for, consult to, own shares in or receive funding from any company or organisation that would benefit from this article, and has no relevant affiliations.

This article was originally published on The Conversation.
Read the original article.

Oct 01

Peer Reviewed Play List


It’s probably no news to most of use that puns, quotes and lyrics crop  up on a fairly regular bases in titles of research papers. But scientists making humorous and cultural references in their published work does appear to be news in some quarters. A group of Swedish scientist have caught the medias with their 17 year long quest to plant Bob Dylan’s lyrics into their papers. For example who can forget the classic Nature Medicine hit Nitric Oxide and inflammation: The answer is blowing in the wind and or the epic ballad of neuroscience told in  Blood on the Tracks: A Simple Twist of Fate? .

But to really appreciate the research surely you have to listen to the inspiring lyrics whilst reading the papers. So clearly we need a ‘Peer Reviewed Play List‘ to link the science and the music.

So starting with the Dylan tracks and the papers that his lyrics featured in, here’s the play-list and a link to the same on Spotify. Feel free to add any lyrical papers you come across in the comments and I’ll put them on the play-list. Or tweet them using #PeerReviewLyrics.

 

The biological role of nitrate and nitrite: The times they are a-changin’  (Time’s they are a-changin’  tops the charts with 112 publications listed in Scopus).

Blood on the Tracks: A Simple Twist of Fate?

Nitric Oxide and inflammation: The answer is blowing in the wind 

Dietary nitrate – a slow train coming

Tangled up in Blue : Molecular Cardiology in the Postmolecular era.

Finding MyoD with a little help from my Friends

Another Brick in the Wall: RNAi Screens Identify New Barriers in iPSC Reprogramming

CDK versus GSK-3 Inhibition: A Purple Haze No Longer?

Stairway to heaven: Evaluating levels of biological organization correlated with the successful ascent of natural waterfalls in the hawaiian stream goby sicyopterus stimpsoni 

Take five – Type VII secretion systems of Mycobacteria

Sep 26

The Minecraft Chemistry Challenge


Minecraft is an truly awesome game. Think of it as digital lego set in a infinitely explorable world. But its real draw is that is encourages creativity on so many level. Players can build what they like, but also the code is open source, allowing creative coders to fiddle with rules and resources in the game. The result is a multitude of modifications (or mods in Minecraft parlance).

L5mDx

There are mods for every taste, including those who favour a spot of virtual  chemistry, in the form of Minechem. It allows for some surprisingly sophisticated chemistry. With a range of devises and tools everything in the world can be broken down into elements, and then reacted together to yield an incredible array of compounds.

As fun as Minechem is, my favourite mod of the moment is Printcraft. This allows the player to output anything they have built to a file that can be read by a 3D printer. And given that I have just assembled one of these wonderful contraptions (or ‘plastic tat generators’ as my better half prefers to call it), combined with my son’s Minecraft addiction means that my house is now slowly being invaded by virtual buildings turned real.

So I think I need something more meaningful to do with it. And so over to you. Build me something! Build me something original that’s related to the chemical sciences, be it useful, interesting or just plain cool. And I’ll 3D print (and send the designer) the best ones.

So here are the rules:

1) Construct something related to the chemical sciences in Minecraft, using the official printcraft server (use Minecraft 1.7.8)

Alternatively you can download the sever and run it locally or use the one I’ve set up (connect to IP 54.68.24.135:25565 using Minecraft 1.6.4)

2) Upload the STL file ,that printcraft spits out, to Thingiverse and tag it with 3DMineChem.

3) Add a link to your Thingiverse file in the comments below.

Lets see what we can come up with shall we?

P.S My ulterior motive is that I’m trying to come up with an Minecraft/chemistry workshop for school children and I need some inspiration and some beta-testers of my server.

Sep 23

First Friday: Ask a Scientist


Soon after moving to Tallahassee my wife (Debbie) and I were encouraged to check out First Friday, an eclectic, once-a-month gathering of local musicians, artists, food trucks, and performers. Located in a lumber yard-turned-art park known as Railroad Square, First Friday is a wonderful opportunity to see locals celebrating their hobbies and personal interests. Following this spirit, Debbie and I, along with my colleague Greg Dudley, decided to contribute as well – and our Ask a Scientist (AaS) booth was born. We gather 4-5 scientists–predominantly FSU faculty—from across disciplines like chemistry, physics, engineering, psychology, medicine and biology and stand by a tent with a sign proclaiming Ask a Scientist. What follows is ~3 hours each month spent drinking beer and talking science with people passing by.

Below is a time-lapse of our August AaS event. The evening featured the following scientists: David Meckes (virology and biomedical sciences), Brian Miller (biochemistry), Tom Albrecht-Schmitt (nuclear chemistry), and myself (Ken Hanson, energy/material chemistry). We try to rotate a new batch of scientists every month.

There are four types of common interactions/questions:

1) Most people are genuinely excited to ask questions, many which are prompted by current events. Our virologist was asked about Ebola in August and our paleontologist was asked about the colossal dinosaur in September. Other examples of general questions include: How are memories formed? How accurate is the chemistry in Breaking Bad? And my personal favorite as a photophysical chemist: Why is the sky blue?

2) Some people interpret our “Ask a Scientist” prompt as, “Stump a Scientist.” At best these questions come from fellow scientists who good-naturedly know what is difficult to answer (like how do you cure x?). At worst, these questions come with sarcasm or a prepared (dare I say egotistical) lecture on what our answer missed.

3) The third type of question is political: How do you feel about fracking? Is global warming real? These questions usually lead to long conversations.

4) The final type of question seeks to understand who we are and why we created the booth: Who is coordinating this event?” Who is sponsoring this? When we share that we’re unsponsored and just having fun the response is usually something along the lines of, “This is very cool” or “Keep up the good work.”

So, if you happen to be in Tallahassee during the first Friday of any month, please stop by Railroad Square and our AaS booth. We’re always happy to say ‘hello’ and talk science. We also try to post ‘example questions’ each month to help prompt participation. So I welcome any accessible, general science questions you’ve heard as well.

Sep 16

Hack your inkjet printer and turn it into a lab robot


If you stop and think about it for a moment, you will realise what an astonishing feat of precision engineering your colour printer is. It can take the primary colours – cyan, yellow, magenta and black – and mix them together carefully enough to achieve more than a million different hues and shades. Not only that but the drops of colour are mere nanolitres (billionths of a litre) in volume, each of which is then placed on the paper – assuming its not jammed in the feeder tray – with better than pinpoint accuracy.

Now a group of enterprising chemists from Tsinghua University are exploiting that precision engineering, which normally results in high-resolution colour prints, to screen millions of different chemical reactions. Their results have been published in the journal Chemical Communications.

Yifei Zhang and colleagues have been trying to understand reaction pathways in living things. Every chemical process that goes on in living organisms is controlled by a cascade of reactions. The steps in a cascade are mediated by protein molecules called enzymes. Each enzyme makes a small chemical alteration, like workers on a production line, to a molecule before passing its product onto the next enzyme. In this way, for example, plants build sugars from carbon dioxide and your food gets broken down and then reconstructed into other useful chemicals for your body.

The problem is that to understand these complicated processes by reconstructing them outside of a living cell is difficult. The concentrations of an enzyme relative to the next in the line is key. Get this wrong and bottle necks are formed in the production line, as one enzyme works faster than the next.

To figure out what are the right conditions to replicate a living cell’s workings, chemists must set up and monitor a vast number of reactions. Screening large numbers of reactions like this is often done using “96-well plates”, which are 96 tiny containers with a unique combination of chemicals in each. These reactions might be set up manually or, if the lab is well-funded, by an expensive robot. But even with the best robots available it can still be a slow process.

Colour printers are a lot cheaper than robots. And if the inks are replaced by solutions of enzymes then suddenly you have a device that has the potential to dispense more than a million different reaction mixtures.

That is just want Yifei and colleagues have done. Their printers were loaded with a series of enzymes that, when they work together in the correct ratios, produce coloured reaction products. These were printed directly onto paper where it was immediately obvious, from the intensity of a coloured dot, which reaction mixtures worked best.

In the test cases reactions were deliberately chosen that resulted in colour changes. This made for a nice quick visual indication of whether the system worked well. So for example one test started with glucose and a chemical called ABTS in the magenta cartridge, then the enzymes glucose oxidase (GOx) and horse-radish peroxidase (HRP) in the yellow and cyan cartridges. When they are mixed together the GOx removes a hydrogen from the glucose and adds it to oxygen, producing hydrogen peroxide. Next the HRP reacts this with the ABTS, which results in a green chemical.

The potential applications for these printer-based mixtures extend beyond curiosity-driven research on biological pathways. Yifei and colleagues have already shown that by loading the printer cartridges with the right enzymes they can use the set up to indicate the presence of glucose in a sample. Glucose in urine is a indication of diabetes, so their printer-based chemistry already has the potential to diagnose diabetes.

The result then could be a future where a trip to the doctors results in a printout of, quite literally, your urine and some enzymes alongside, after 30 seconds or so, a diagnosis and the prescription.

The Conversation

Mark Lorch does not work for, consult to, own shares in or receive funding from any company or organisation that would benefit from this article, and has no relevant affiliations.

This article was originally published on The Conversation.
Read the original article.

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