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.

Wilhelm Röntgen, by 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 accident.

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 (http://creativecommons.org/licenses/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 sediment."

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 discoveries."

"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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The Chemistry of Pumpkins

We eat them, we carve them, but do we really know what’s behind them? Here, we look at the chemistry of pumpkins.

Source: http://cen.acs.org/articles/93/i40/Periodic-Graphics-Chemistry-Pumpkins.html

Pumpkins are grown all around the world for a variety of reasons ranging from agricultural purposes (such as animal feed) to commercial and ornamental sales. Of the seven continents, only Antarctica is unable to produce pumpkins; the biggest international producers of pumpkins include the United States, Canada, Mexico, India, and China. The traditional American pumpkin used for jack-o-lanterns is the Connecticut Field variety.

As one of the most popular crops in the United States, 1.5 billion pounds (680,000,000 kilograms or 680,000 tonnes) of pumpkins are produced each year. The top pumpkin-producing states include Illinois, Indiana, Ohio, Pennsylvania, and California.

Pumpkins are a warm-weather crop that is usually planted in early July. The specific conditions necessary for growing pumpkins require that soil temperatures three inches (7.6 cm) deep are at least 60 °F (15.5 °C) and soil that holds water well. Pumpkin crops may suffer if there is a lack of water or because of cold temperatures (in this case, below 65 °F (18.3 °C); frost can be detrimental), and sandy soil with poor water retention or poorly drained soils that become waterlogged after heavy rain. Pumpkins are, however, rather hardy, and even if many leaves and portions of the vine are removed or damaged, the plant can very quickly re-grow secondary vines to replace what was removed.

Pumpkins produce both a male and female flower; honeybees play a significant role in fertilization. Pumpkins have historically been pollinated by the native squash bee Peponapis pruinosa, but this bee has declined, probably at least in part to pesticide sensitivity, and today most commercial plantings are pollinated by honeybees. One hive per acre (4,000 m² per hive) is recommended by the U.S. Department of Agriculture. If there are inadequate bees for pollination, gardeners often have to hand pollinate. Inadequately pollinated pumpkins usually start growing but abort before full development.

"Giant pumpkins" are a large squash (within the group of common squash Cucurbita maxima) that can exceed 1 ton (2,000 pounds) in weight. The variety arose from the large squash of Chile after 1500 A.D through the efforts of botanical societies and enthusiast farmers.

Such germplasm is commercially provocative, and in 1986 the United States extended protection for the giant squash. This protection was limited to small specimens of a very specific parameters, being a weight of 175 pounds, oblong shape, etc. In 2004, the restriction expired except for the requirement of indefinite use of the pseudonym "Dill's Atlantic Giant" for squash fitting the specific parameters or the seeds thereof.

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On this day in science history: Jupiter orbiter Galileo launched

In 1989, the Galileo space orbiter was released from the STS 34 flight of the Atlantis orbiter. Then the orbiter's inertial upper stage rocket pushed it into a course through the inner solar system. The craft gained speed from gravity assists in encounters with Venus and Earth before heading outward to Jupiter. During its six year journey to Jupiter, Galileo's instruments made interplanetary studies, using its dust detector, magnetometer, and various plasma and particles detectors. It also made close-up studies of two asteroids, Gaspra and Ida in the asteroid belt. The Galileo orbiter's primary mission was to study Jupiter, its satellites, and its magnetosphere for two years. It released an atmospheric probe into Jupiter's atmosphere on 7 Dec 1995.

Jupiter and its shrunken great red spot. By NASA, ESA, and A. Simon (Goddard Space Flight Center) [Public domain], via Wikimedia Commons

Jupiter's mass is 2.5 times that of all the other planets in the Solar System combined—this is so massive that its barycenter with the Sun lies above the Sun's surface at 1.068 solar radii from the Sun's center. Jupiter is much larger than Earth and considerably less dense: its volume is that of about 1,321 Earths, but it is only 318 times as massive. Jupiter's radius is about 1/10 the radius of the Sun, and its mass is 0.001 times the mass of the Sun, so the densities of the two bodies are similar. A "Jupiter mass" (MJ or MJup) is often used as a unit to describe masses of other objects, particularly extrasolar planets and brown dwarfs. So, for example, the extrasolar planet HD 209458 b has a mass of 0.69 MJ, while Kappa Andromedae b has a mass of 12.8 MJ.

Theoretical models indicate that if Jupiter had much more mass than it does at present, it would shrink. For small changes in mass, the radius would not change appreciably, and above about 500 M⊕ (1.6 Jupiter masses) the interior would become so much more compressed under the increased pressure that its volume would decrease despite the increasing amount of matter. As a result, Jupiter is thought to have about as large a diameter as a planet of its composition and evolutionary history can achieve. The process of further shrinkage with increasing mass would continue until appreciable stellar ignition is achieved as in high-mass brown dwarfs having around 50 Jupiter masses.

Although Jupiter would need to be about 75 times as massive to fuse hydrogen and become a star, the smallest red dwarf is only about 30 percent larger in radius than Jupiter. Despite this, Jupiter still radiates more heat than it receives from the Sun; the amount of heat produced inside it is similar to the total solar radiation it receives. This additional heat is generated by the Kelvin–Helmholtz mechanism through contraction. This process causes Jupiter to shrink by about 2 cm each year.  When it was first formed, Jupiter was much hotter and was about twice its current diameter.

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Methane muted: How did early Earth stay warm?

For at least a billion years of the distant past, planet Earth should have been frozen over but wasn't. Scientists thought they knew why, but a new modeling study from the Alternative Earths team of the NASA Astrobiology Institute has fired the lead actor in that long-accepted scenario.

Humans worry about greenhouse gases, but between 1.8 billion and 800 million years ago, microscopic ocean dwellers really needed them. The sun was 10 to 15 percent dimmer than it is today - too weak to warm the planet on its own. Earth required a potent mix of heat-trapping gases to keep the oceans liquid and livable.

For decades, atmospheric scientists cast methane in the leading role. The thinking was that methane, with 34 times the heat-trapping capacity of carbon dioxide, could have reigned supreme for most of the first 3.5 billion years of Earth history, when oxygen was absent initially and little more than a whiff later on. (Nowadays oxygen is one-fifth of the air we breathe, and it destroys methane in a matter of years.)

Full structural formula of the methane molecule

"A proper accounting of biogeochemical cycles in the oceans reveals that methane has a much more powerful foe than oxygen," said Stephanie Olson, a graduate student at the University of California, Riverside, a member of the Alternative Earths team and lead author of the new study published September 26 in the Proceedings of the National Academy of Sciences. "You can't get significant methane out of the ocean once there is sulfate."

Sulfate wasn't a factor until oxygen appeared in the atmosphere and triggered oxidative weathering of rocks on land. The breakdown of minerals such as pyrite produces sulfate, which then flows down rivers to the oceans. Less oxygen means less sulfate, but even 1 percent of the modern abundance is sufficient to kill methane, Olson said.

Olson and her Alternative Earths coauthors, Chris Reinhard, an assistant professor of earth and atmospheric sciences at Georgia Tech University, and Timothy Lyons, a distinguished professor of biogeochemistry at UC Riverside, assert that during the billion years they assessed, sulfate in the ocean limited atmospheric methane to only 1 to 10 parts per million - a tiny fraction of the copious 300 parts per million touted by some previous models.

The fatal flaw of those past climate models and their predictions for atmospheric composition, Olson said, is that they ignore what happens in the oceans, where most methane originates as specialized bacteria decompose organic matter.

Seawater sulfate is a problem for methane in two ways: Sulfate destroys methane directly, which limits how much of the gas can escape the oceans and accumulate in the atmosphere. Sulfate also limits the production of methane. Life can extract more energy by reducing sulfate than it can by making methane, so sulfate consumption dominates over methane production in nearly all marine environments.

The numerical model used in this study calculated sulfate reduction, methane production, and a broad array of other biogeochemical cycles in the ocean for the billion years between 1.8 billion and 800 million years ago. This model, which divides the ocean into nearly 15,000 three-dimensional regions and calculates the cycles for each region, is by far the highest resolution model ever applied to the ancient Earth. By comparison, other biogeochemical models divide the entire ocean into a two-dimensional grid of no more than five regions.

"Free oxygen [O2] in the atmosphere is required to form a protective layer of ozone [O3], which can shield methane from photochemical destruction," Reinhard said. When the researchers ran their model with the lower oxygen estimates, the ozone shield never formed, leaving the modest puffs of methane that escaped the oceans at the mercy of destructive photochemistry.

With methane demoted, scientists face a serious new challenge to determine the greenhouse cocktail that explains our planet's climate and life story, including a billion years devoid of glaciers, Lyons said. Knowing the right combination other warming agents, such as water vapor, nitrous oxide, and carbon dioxide, will also help us assess habitability of the hundreds of billions of other Earth-like planets estimated to reside in our galaxy.

"If we detect methane on an exoplanet, it is one of our best candidates as a biosignature, and methane dominates many conversations in the search for life on Mars," Lyons said. "Yet methane almost certainly would not have been detected by an alien civilization looking at our planet a billion years ago - despite the likelihood of its biological production over most of Earth history."

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The chemistry behind the aroma of coffee

The Aroma of Coffee (Compound Interest) 

What is it about that delicious smell of coffee? Or, more specifically, what lies behind it? The graphic above takes a look at a selection of the chemical compounds behind this aroma. 

So that's the chemistry, but what about the biology of coffee?

Several species of shrub of the genus Coffea produce the berries from which coffee is extracted. The two main species commercially cultivated are Coffea canephora (predominantly a form known as 'robusta') and C. arabica. C. arabica, the most highly regarded species, is native to the southwestern highlands of Ethiopia and the Boma Plateau in southeastern Sudan and possibly Mount Marsabit in northern Kenya. C. canephora is native to western and central Subsaharan Africa, from Guinea to Uganda and southern Sudan. Less popular species are C. liberica, C. stenophylla, C. mauritiana, and C. racemosa.

All coffee plants are classified in the large family Rubiaceae. They are evergreen shrubs or trees that may grow 5 m (15 ft) tall when unpruned. The leaves are dark green and glossy, usually 10–15 cm (4–6 in) long and 6 cm (2.4 in) wide, simple, entire, and opposite. Petioles of opposite leaves fuse at base to form interpetiolar stipules, characteristic of Rubiaceae. The flowers are axillary, and clusters of fragrant white flowers bloom simultaneously. Gynoecium consists of inferior ovary, also characteristic of Rubiaceae. The flowers are followed by oval berries of about 1.5 cm (0.6 in). When immature they are green, and they ripen to yellow, then crimson, before turning black on drying. Each berry usually contains two seeds, but 5–10% of the berries have only one; these are called peaberries. 

Arabica berries ripen in six to eight months, while robusta take nine to eleven months.

Coffea arabica is predominantly self-pollinating, and as a result the seedlings are generally uniform and vary little from their parents. In contrast, Coffea canephora, and C. liberica are self-incompatible and require outcrossing. This means that useful forms and hybrids must be propagated vegetatively. Cuttings, grafting, and budding are the usual methods of vegetative propagation. On the other hand, there is great scope for experimentation in search of potential new strains.

In 2016, Oregon State University entomologist George Poinar, Jr. announced the discovery of a new plant species that's a 45-million-year-old relative of coffee found in amber. Named Strychnos electri, after the Greek word for amber (electron), the flowers represent the first-ever fossils of an asterid, which is a family of flowering plants that not only later gave us coffee, but also sunflowers, peppers, potatoes, mint — and deadly poisons.

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