Monthly Archives: November 2016

How sand ‘holds its breath’

Researchers in Australia have made an important discovery about how sand ‘holds its breath’ – specifically, how diatoms survive in the ever-changing environmental conditions of a beach. The finding has major implications for the biofuels industry.

Sand. By Siim Sepp (Own work), via Wikimedia Commons
The popular Middle Park beach in Melbourne is under the international spotlight following a world-first study by Monash University chemists who have discovered how sand ‘holds its breath’.

The discovery, published in Nature Geoscience, has major implications and potential uses in the biofuels industry, according to lead authors Associate Professor Perran Cook and PhD student Michael Bourke from the Water Studies Centre, School of Chemistry.

Sand is full of algae called diatoms, but this environment is mixed about continuously so these organisms might get light one minute then be buried in the sediment with no oxygen the next.

“This is a new mechanism by which this type of algae survive under these conditions,” said Associate Professor Cook.

“Our work has found that they ferment, like yeast ferments sugar to alcohol.
“In this case, the products are hydrogen and ‘fats’, for example, oleate, which is a component of olive oil.”

Sand often has high concentrations of algae, which are highly productive and an important food source for food webs in the bay.

It is important to understand how these organisms survive in the harsh environment in which they live.

In this work, scientists present the first study of the importance of anoxic micro-algal metabolism through fermentation in permeable sediments.

They combined flow-through reactor experiments with microbiological approaches to determine the dominant contributors and pathways of dissolved inorganic carbon production in permeable sediments.

They show that micro-algal dark fermentation is the dominant metabolic pathway, which is the first time this has been documented in an environmental setting.

“The finding that hydrogen is a by-product of this metabolism has important implications for the types of bacteria present in the sediment,” said Associate Professor Cook.

“It is well known that bacteria in the sediment can ‘eat’ hydrogen, however, these hydrogen eating bacteria may be more common than we previously thought.”

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Why Lithium-ion Batteries Catch Fire

Why have some of Samsung’s phones been catching fire? Check
out the infographic below to find out.

Source: Compound Interest 

So, who invented the lithium battery? 

Lithium batteries were
proposed by M Stanley Whittingham, now at Binghamton University, while working
for Exxon in the 1970s. Whittingham used titanium(IV) sulfide and lithium metal
as the electrodes. However, this rechargeable lithium battery could never be
made practical. Titanium disulfide was a poor choice, since it has to be
synthesized under completely sealed conditions. This is extremely expensive
(it cost $1000 per kilo for titanium disulfide raw material in the 1970s).

When exposed to air, titanium disulfide reacts to form
hydrogen sulfide compounds, which have an unpleasant odour. For this, and other
reasons, Exxon discontinued development of Whittingham’s lithium-titanium
disulfide battery. Batteries with metallic lithium electrodes presented safety issues,
as lithium is a highly reactive element; it burns in normal atmospheric
conditions because of the presence of water and oxygen. As a result, research
moved to develop batteries where, instead of metallic lithium, only lithium
compounds are present, being capable of accepting and releasing lithium ions.

Reversible intercalation in graphite and intercalation into
cathodic oxides was discovered in the 1970s by J. O. Besenhard at TU Munich.
Besenhard proposed its application in lithium cells. Electrolyte decomposition
and solvent co-intercalation into graphite were severe early drawbacks for
battery life.

There were two main trends in the research and development
of electrode materials for lithium ion rechargeable batteries. One was the
approach from the field of electrochemistry centering on graphite intercalation
compounds, and the other was the approach from the field of new
nano-carbonaceous materials.

History described above is based on the former stand point.
On the other hand, in the recent interview article concerning the first stage
of scientific research activity directly related to the LIB developments, it is
stated that looking at the major streams in research development, the
negative-electrode of today’s lithium ion rechargeable battery has its origins
in PAS (polyacenic semiconductive material) discovered by Professor Tokio
Yamabe and later Shjzukuni Yata at the beginning of 1980’s. The seed of this
technology, furthermore, was the discovery of conductive polymers by Professor
Hideki Shirakawa and his group, and it could also be seen as having started
from the polyacetylene lithium ion battery developed by MacDiarmid and Heeger
et al.

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What molecules you leave on your phone reveal about your lifestyle

We leave behind trace chemicals, molecules and microbes on every object we touch. By sampling the molecules on cell phones, researchers at University of California San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences were able to construct lifestyle sketches for each phone’s owner, including diet, preferred hygiene products, health status and locations visited. This proof-of-concept study, published November 14 by Proceedings of the National Academy of Sciences, could have a number of applications, including criminal profiling, airport screening, medication adherence monitoring, clinical trial participant stratification and environmental exposure studies.

“You can imagine a scenario where a crime scene investigator comes across a personal object – like a phone, pen or key – without fingerprints or DNA, or with prints or DNA not found in the database. They would have nothing to go on to determine who that belongs to,” said senior author Pieter Dorrestein, PhD, professor in UC San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences. “So we thought – what if we take advantage of left-behind skin chemistry to tell us what kind of lifestyle this person has?”

Mobile phone evolution. By Anders (Own work) , via Wikimedia Commons
In a 2015 study, Dorrestein’s team constructed 3D models to illustrate the molecules and microbes found at hundreds of locations on the bodies of two healthy adult volunteers. Despite a three-day moratorium on personal hygiene products before the samples were collected, the researchers were surprised to find that the most abundant molecular features in the skin swabs still came from hygiene and beauty products, such as sunscreen.

“All of these chemical traces on our bodies can transfer to objects,” Dorrestein said. “So we realized we could probably come up with a profile of a person’s lifestyle based on chemistries we can detect on objects they frequently use.”

Thirty-nine healthy adult volunteers participated in Dorrestein’s latest study. The team swabbed four spots on each person’s cell phone – an object we tend to spend a lot of time touching – and eight spots on each person’s right hand, for a total of nearly 500 samples. Then they used a technique called mass spectrometry to detect molecules from the samples. They identified as many molecules as possible by comparing them to reference structures in the GNPS database, a crowdsourced mass spectrometry knowledge repository and annotation website developed by Dorrestein and co-author Nuno Bandeira, PhD, associate professor at the Jacobs School of Engineering and Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego.

With this information, the researchers developed a personalized lifestyle “read-out” from each phone. Some of the medications they detected on phones included anti-inflammatory and anti-fungal skin creams, hair loss treatments, anti-depressants and eye drops. Food molecules included citrus, caffeine, herbs and spices. Sunscreen ingredients and DEET mosquito repellant were detected on phones even months after they had last been used by the phone owners, suggesting these objects can provide long-term composite lifestyle sketches.

“By analyzing the molecules they’ve left behind on their phones, we could tell if a person is likely female, uses high-end cosmetics, dyes her hair, drinks coffee, prefers beer over wine, likes spicy food, is being treated for depression, wears sunscreen and bug spray – and therefore likely spends a lot of time outdoors – all kinds of things,” said first author Amina Bouslimani, PhD, an assistant project scientist in Dorrestein’s lab. “This is the kind of information that could help an investigator narrow down the search for an object’s owner.”

There are limitations, Dorrestein said. First of all, these molecular read-outs provide a general profile of person’s lifestyle, but they are not meant to be a one-to-one match, like a fingerprint. To develop more precise profiles and for this method to be more useful, he said more molecules are needed in the reference database, particularly for the most common foods people eat, clothing materials, carpets, wall paints and anything else people come into contact with. He’d like to see a trace molecule database on the scale of the fingerprint database, but it’s a large-scale effort that no single lab will be able to do alone.

Moving forward, Dorrestein and Bouslimani have already begun extending their study with an additional 80 people and samples from other personal objects, such as wallets and keys. They also hope to soon begin gathering another layer of information from each sample – identities of the many bacteria and other microbes that cover our skin and objects. In a 2010 study, their collaborator and co-author, Rob Knight, PhD, professor in the UC San Diego School of Medicine and Jacobs School of Engineering and director of the Center for Microbiome Innovation at UC San Diego, contributed to a study in which his team found they could usually match a computer keyboard to its owner just based on the unique populations of microbes the person left on it. At that time, they could make the match with a fair amount of accuracy, though not yet precisely enough for use in an investigation.

Beyond forensics, Dorrestein and Bouslimani imagine trace molecular read-outs could also be used in medical and environmental studies. For example, perhaps one day physicians could assess how well a patient is sticking with a medication regimen by monitoring metabolites on his or her skin. Similarly, patients participating in a clinical trial could be divided into subgroups based on how they metabolize the medication under investigation, as revealed by skin metabolites – then the medication could be given only to those patients who can metabolize it appropriately. Skin molecule read-outs might also provide useful information about a person’s exposure to environmental pollutants and chemical hazards, such as in a high-risk workplace or a community living near a potential pollution source.

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On this day in science history: the first X-rays were observed

In 1895, Wilhelm Röntgen first observed X-rays during an experiment at Würzburg University. After further investigation, on 1 Jan 1896, he notified other scientists of his discovery of this new radiation that would become known as X-rays. He sent copies of his manuscript and some of his X-ray photographs to several renowned physicists and friends, including Lord Kelvin in Glasgow and in Paris. On 5 Jan 1896, Die Presse published the news in a front-page article which described his investigations and suggested new methods of medical diagnoses might be made with this new kind of radiation.

Röntgen, b
y Nobel foundation [Public domain or Public domain], via Wikimedia Commons

So, what are the properties of X-Rays? 

X-ray photons carry enough energy to ionize atoms and disrupt molecular bonds. This makes it a type of ionizing radiation, and therefore harmful to living tissue. A very high radiation dose over a short period of time causes radiation sickness, while lower doses can give an increased risk of radiation-induced cancer. In medical imaging this increased cancer risk is generally greatly outweighed by the benefits of the examination. The ionizing capability of X-rays can be utilized in cancer treatment to kill malignant cells using radiation therapy. It is also used for material characterization using X-ray spectroscopy.

Hard X-rays can traverse relatively thick objects without being much absorbed or scattered. For this reason, X-rays are widely used to image the inside of visually opaque objects. The most often seen applications are in medical radiography and airport security scanners, but similar techniques are also important in industry (e.g. industrial radiography and industrial CT scanning) and research (e.g. small animal CT). The penetration depth varies with several orders of magnitude over the X-ray spectrum. This allows the photon energy to be adjusted for the application so as to give sufficient transmission through the object and at the same time good contrast in the image.

X-rays have much shorter wavelength than visible light, which makes it possible to probe structures much smaller than what can be seen using a normal microscope. This can be used in X-ray microscopy to acquire high resolution images, but also in X-ray crystallography to determine the positions of atoms in crystals.

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Fossilized dinosaur brain tissue identified for the first time

An unassuming brown pebble, found more than a decade ago by
a fossil hunter in Sussex, has been confirmed as the first example of
fossilised brain tissue from a dinosaur.

The fossil, most likely from a species closely related to
Iguanodon, displays distinct similarities to the brains of modern-day
crocodiles and birds. Meninges – the tough tissues surrounding the actual
brain – as well as tiny capillaries and portions of adjacent cortical tissues
have been preserved as mineralised ‘ghosts’.

The results are reported in a Special Publication of the
Geological Society of London, published in tribute to Professor Martin Brasier
of the University of Oxford, who died in 2014. Brasier and Dr David Norman from
the University of Cambridge co-ordinated the research into this particular
fossil during the years prior to Brasier’s untimely death in a road traffic

The fossilised brain, found by fossil hunter Jamie Hiscocks
near Bexhill in Sussex in 2004, is most likely from a species similar to
Iguanodon: a large herbivorous dinosaur that lived during the Early Cretaceous
Period, about 133 million years ago.

Triceratops skeleton. Source: Allie_Caulfield Derivative: User:MathKnight [CC BY-SA 3.0 (, via Wikimedia Commons
Finding fossilised soft tissue, especially brain tissue, is
very rare, which makes understanding the evolutionary history of such tissue
difficult. “The chances of preserving brain tissue are incredibly small,
so the discovery of this specimen is astonishing,” said co-author Dr Alex
Liu of Cambridge’s Department of Earth Sciences, who was one of Brasier’s PhD
students in Oxford at the time that studies of the fossil began.

According to the researchers, the reason this particular
piece of brain tissue has been so well-preserved is that the dinosaur’s brain
was essentially ‘pickled’ in a highly acidic and low-oxygen body of water – similar to a bog or swamp – shortly after its death. This allowed the soft
tissues to become mineralised before they decayed away completely, so that they
could be preserved.

“What we think happened is that this particular
dinosaur died in or near a body of water, and its head ended up partially
buried in the sediment at the bottom,” said Norman. “Since the water
had little oxygen and was very acidic, the soft tissues of the brain were
likely preserved and cast before the rest of its body was buried in the

Working with colleagues from the University of Western
Australia, the researchers used scanning electron microscope (SEM) techniques
in order to identify the tough membranes, or meninges, that surrounded the
brain itself, as well as strands of collagen and blood vessels. Structures that
could represent tissues from the brain cortex (its outer layer of neural
tissue), interwoven with delicate capillaries, also appear to be present. The
structure of the fossilised brain, and in particular that of the meninges,
shows similarities with the brains of modern-day descendants of dinosaurs,
namely birds and crocodiles.

In typical reptiles, the brain has the shape of a sausage,
surrounded by a dense region of blood vessels and thin-walled vascular chambers
(sinuses) that serve as a blood drainage system. The brain itself only takes up
about half of the space within the cranial cavity.

In contrast, the tissue in the fossilised brain appears to
have been pressed directly against the skull, raising the possibility that some
dinosaurs had large brains which filled much more of the cranial cavity.
However, the researchers caution against drawing any conclusions about the
intelligence of dinosaurs from this particular fossil, and say that it is most
likely that during death and burial the head of this dinosaur became
overturned, so that as the brain decayed, gravity caused it to collapse and
become pressed against the bony roof of the cavity.

“As we can’t see the lobes of the brain itself, we
can’t say for sure how big this dinosaur’s brain was,” said Norman.
“Of course, it’s entirely possible that dinosaurs had bigger brains than
we give them credit for, but we can’t tell from this specimen alone. What’s
truly remarkable is that conditions were just right in order to allow
preservation of the brain tissue – hopefully this is the first of many such

“I have always believed I had something special. I
noticed there was something odd about the preservation, and soft tissue
preservation did go through my mind. Martin realised its potential significance
right at the beginning, but it wasn’t until years later that its true
significance came to be realised,” said paper co-author Jamie Hiscocks,
the man who discovered the specimen. “In his initial email to me, Martin
asked if I’d ever heard of dinosaur brain cells being preserved in the fossil
record. I knew exactly what he was getting at. I was amazed to hear this coming
from a world renowned expert like him.”

The research was funded in part by the Natural Environment
Research Council (NERC) and Christ’s College, Cambridge.

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