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Monday, 22 May 2017

A guide to the twenty common amino acids

Have you ever thought about what makes up your body? Only 20 amino acids! Take a look at the graphic below, to discover the structure of each of these, plus information on the notation used to represent them.

Source: Compound Interest. Click to enlarge.

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, although other elements are found in the side chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.

In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent known as a "side chain"); often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins. These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics. 

Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids. The other two ("non-standard" or "non-canonical") are selenocysteine (present in many noneukaryotes as well as most eukaryotes, but not coded directly by DNA), and pyrrolysine (found only in some archea and one bacterium). Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts) is generally considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids.

Many important proteinogenic and non-proteinogenic amino acids have biological functions. For example, in the human brain, glutamate (standard glutamic acid) and gamma-amino-butyric acid ("GABA", non-standard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters. Hydroxyproline, a major component of the connective tissue collagen, is synthesised from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells. Carnitine is used in lipid transport.

Nine proteinogenic amino acids are called "essential" for humans because they cannot be created from other compounds by the human body and so must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species.

Because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, and chiral catalysts.

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Tuesday, 16 May 2017

Diesels pollute more than lab tests detect

Because of testing inefficiencies, maintenance inadequacies and other factors, cars, trucks and buses worldwide emit 4.6 million tons more harmful nitrogen oxide (NOx) than standards allow, according to a new study co-authored by University of Colorado Boulder researchers.

The study, published in Nature, shows these excess emissions alone lead to 38,000 premature deaths annually worldwide, including 1,100 deaths in the United States.

The findings reveal major inconsistencies between what vehicles emit during testing and what they emit in the real world - a problem that's far more severe, said the researchers, than the incident in 2015, when federal regulators discovered Volkswagen had been fitting millions of new diesel cars with "defeat devices."

Red Diesel Tank, by Meena Kadri [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
The devices sense when a vehicle is undergoing testing and reduce emissions to comply with government standards. Excess emissions from defeat devices have been linked to about 50 to 100 U.S. deaths per year, studies show.

"A lot of attention has been paid to defeat devices, but our work emphasizes the existence of a much larger problem," said Daven Henze, an associate professor of mechanical engineering at CU Boulder who, along with postdoctoral researcher Forrest Lacey, contributed to the study. "It shows that in addition to tightening emissions standards, we need to be attaining the standards that already exist in real-world driving conditions."

The research was conducted in partnership with the International Council on Clean Transportation, a Washington, D.C.-based nonprofit organization, and Environmental Health Analytics LLC.

For the paper, the researchers assessed 30 studies of vehicle emissions under real-world driving conditions in 11 major vehicle markets representing 80 percent of new diesel vehicle sales in 2015. Those markets include Australia, Brazil, Canada, China, the European Union, India, Japan, Mexico, Russia, South Korea and the United States.

They found that in 2015, diesel vehicles emitted 13.1 million tons of NOx, a chemical precursor to particulate matter and ozone. Exposure in humans can lead to heart disease, stroke, lung cancer and other health problems. Had the emissions met standards, the vehicles would have emitted closer to 8.6 million tons of NOx.

Heavy-duty vehicles, such as commercial trucks and buses, were by far the largest contributor worldwide, accounting for 76 percent of the total excess NOx emissions.

Henze used computer modeling and NASA satellite data to simulate how particulate matter and ozone levels are, and will be, impacted by excess NOx levels in specific locations. The team then computed the impacts on health, crops and climate.

"The consequences of excess diesel NOx emissions for public health are striking," said Susan Anenberg, co-lead author of the study and co-founder of Environmental Health Analytics LLC.

China suffers the greatest health impact with 31,400 deaths annually attributed to diesel NOx pollution, with 10,700 of those deaths linked to excess NOx emissions beyond certification limits. In Europe, where diesel-passenger cars are common, 28,500 deaths annually are attributed to diesel NOx pollution, with 11,500 of those deaths linked to excess emissions.

The study projects that by 2040, 183,600 people will die prematurely each year due to diesel vehicle NOx emissions unless governments act.

The authors say emission certification tests, both prior to sale and by vehicle owners, could be more accurate if they were to simulate a broader variety of speeds, driving styles and ambient temperatures. Some European countries now use portable testing devices that track emissions of a car in motion.

"Tighter vehicle emission standards coupled with measures to improve real-world compliance could prevent hundreds of thousands of early deaths from air pollution-related diseases each year," said Anenberg.

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Tuesday, 9 May 2017

On this day in science history: the Hindenburg Zeppelin arrived at Lakehurst, New Jersey, USA

In 1936, the Hindenburg Zeppelin arrived at Lakehurst, New Jersey, USA, from Germany marking the beginning of a regular transatlantic passenger service. The flight, carrying 51 passengers and 56 crew, took 61 hours.

Hindenburg at Lakehurst, by U.S. Department of the Navy. Bureau of Aeronautics. Naval Aircraft Factory, Philadelphia, Pennsylvania (USA). [Public domain], via Wikimedia Commons
The Hindenburg was a large German commercial passenger-carrying rigid airship, the lead ship of the Hindenburg class, the longest class of flying machine and the largest airship by envelope volume. It was designed and built by the Zeppelin Company (Luftschiffbau Zeppelin GmbH) on the shores of Lake Constance in Friedrichshafen and was operated by the German Zeppelin Airline Company (Deutsche Zeppelin-Reederei). The Hindenburg had a duralumin structure, incorporating 15 Ferris wheel-like bulkheads along its length, with 16 cotton gas bags fitted between them. The bulkheads were braced to each other by longitudinal girders placed around their circumferences. The airship's outer skin was of cotton doped with a mixture of reflective materials intended to protect the gas bags within from radiation, both ultraviolet (which would damage them) and infrared (which might cause them to overheat). The gas cells were made by a new method pioneered by Goodyear using multiple layers of gelatinized latex rather than the previous goldbeater's skins. In 1931 the Zeppelin Company purchased 5,000 kg (11,000 lb) of duralumin salvaged from the wreckage of the October 1930 crash of the British airship R101, which might have been re-cast and used in the construction of the Hindenburg.

The interior furnishings of the Hindenburg were designed by Fritz August Breuhaus, whose design experience included Pullman coaches, ocean liners, and warships of the German Navy. The upper "A" Deck contained small passenger quarters in the middle flanked by large public rooms: a dining room to port and a lounge and writing room to starboard. Paintings on the dining room walls portrayed the Graf Zeppelin's trips to South America. A stylized world map covered the wall of the lounge. Long slanted windows ran the length of both decks. The passengers were expected to spend most of their time in the public areas, rather than their cramped cabins.

The lower "B" Deck contained washrooms, a mess hall for the crew, and a smoking lounge. Harold G. Dick, an American representative from the Goodyear Zeppelin Company, recalled "The only entrance to the smoking room, which was pressurized to prevent the admission of any leaking hydrogen, was via the bar, which had a swiveling air lock door, and all departing passengers were scrutinized by the bar steward to make sure they were not carrying out a lit cigarette or pipe."

Helium was initially selected for the Hindenburg’s lifting gas because it was the safest to use in airships, as it is not flammable. One proposed measure to save helium was to make double-gas cells for 14 of the 16 gas cells; an inner hydrogen cell would be protected by an outer cell filled with helium, with vertical ducting to the dorsal area of the envelope to permit separate filling and venting of the inner hydrogen cells. At the time, however, helium was also relatively rare and extremely expensive as the gas was only available in industrial quantities from distillation plants at certain oil fields in the United States. Hydrogen, by comparison, could be cheaply produced by any industrialized nation and being lighter than helium also provided more lift. Because of its expense and rarity, American rigid airships using helium were forced to conserve the gas at all costs and this hampered their operation.

Despite a U.S. ban on the export of helium under the Helium Control Act of 1927, the Germans designed the airship to use the far safer gas in the belief that they could convince the US government to license its export. When the designers learned that the National Munitions Control Board would refuse to lift the export ban, they were forced to re-engineer the Hindenburg to use hydrogen for lift. Despite the danger of using flammable hydrogen, no alternative lighter-than-air gases could provide sufficient lift. One beneficial side effect of employing hydrogen was that more passenger cabins could be added. The Germans' long history of flying hydrogen-filled passenger airships without a single injury or fatality engendered a widely held belief they had mastered the safe use of hydrogen. The Hindenburg's first season performance appeared to demonstrate this, however the airship was destroyed by fire 14 months later on May 6, 1937, at the end of the first North American transatlantic journey of its second season of service. Thirty-six people died in the accident, which occurred while landing at Lakehurst. This was the last of the great airship disasters; it was preceded by the crashes of the British R38 in 1921 (44 dead), the US airship Roma in 1922 (34 dead), the French Dixmude in 1923 (52 dead), the British R101 in 1930 (48 dead), and the US Akron in 1933 (73 dead).


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Tuesday, 2 May 2017

Mice with missing lipid-modifying enzyme heal better after heart attack

Two immune responses are important for recovery after a heart attack - an acute inflammatory response that attracts leukocyte immune cells to remove dead tissue, followed by a resolving response that allows healing.

The human heart by Patrick J. Lynch, medical illustrator (Patrick J. Lynch, medical illustrator) [CC BY 2.5 (http://creativecommons.org/licenses/by/2.5)], via Wikimedia Commons
Failure of the resolving response can allow a persistent, low-grade nonresolving inflammation, which can lead to progressive acute or chronic heart failure. Despite medical advances, 2 to 17 percent of patients die within one year after a heart attack due to failure to resolve inflammation. More than 50 percent die within five years.

Using a mouse heart attack model, Ganesh Halade, Ph.D., and his University of Alabama at Birmingham colleagues have shown that knocking out one particular lipid-modifying enzyme, along with a short-term dietary excess of a certain lipid, can improve post-heart attack healing and clear inflammation. Halade, an assistant professor in the UAB Department of Medicine, hopes that future physicians will be able to use knowledge from studies like his to boost healing in patients after heart attacks and prevent heart failure.

"Our goal is healing, and we are reaching that goal," he said of efforts in the UAB Division of Cardiovascular Medicine.

Why are lipids and lipid-modifying enzymes important in inflammation and resolving inflammation? Three key lipid modifying enzymes in the body change the lipids into various signaling agents. Some of these signaling agents regulate the triggering of inflammation, and others promote the reparative pathway.

The lipids modified by the enzymes are two types of essential fatty acids that come from food, since mammals cannot synthesize them. One is n-6 or omega-6 fatty acids, and the other type is n-3 or omega-3 fatty acids. The balance of these two types is important.

The Mediterranean diet, with a near balance of omega-3 and omega-6 fatty acids, promotes heart health. The Western diet, with large amounts of omega-6 fatty acids that greatly exceed the levels of omega-3 fatty acids, can lead to heart disease.

The three main lipid-modifying enzymes compete with each other to modify whatever fatty acids are available from the diet. So, Halade and colleagues asked, what will happen if we knock out one of the key enzymes, the 12/15 lipoxygenase?

They reasoned that this would increase the metabolites produced by the other two main enzymes, cyclooxygenase and cytochrome P450 because they no longer had to compete with 12/15 lipoxygenase for lipids to modify. This might be a benefit because those signaling lipids produced through the cyclooxygenase and cytochrome P450 pathways were already known to lead to major resolution promotion factors for post-heart attack healing.

The UAB researchers found that knocking out the 12/15 lipoxygenase and feeding the mice a short-term excess of polyunsaturated fatty acids led to increased leukocyte clearance after experimental heart attack, meaning less chronic inflammation. It also improved heart function, increased the levels of bioactive lipids during the reparative phase of healing, and led to higher levels of reparative cytokine markers. Additionally, the heart muscle showed less of the fibrosis that is a factor in heart failure.

Besides congestive heart failure, persistent inflammation aggravates a vicious cycle in many cardiovascular diseases, including atherogenesis, atheroprogression, atherosclerosis and peripheral artery disease.

Halade says further mechanistic studies are warranted to develop novel targets for treatment and to find therapies that support the onset of left ventricle healing and prevent heart failure pathology.

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Tuesday, 25 April 2017

On this day in science history: Pioneer 10 crossed the orbit of Pluto

In 1983, Pioneer 10, an American space probe, crossed the orbit of Pluto, the outermost planet, to continue its voyage into the universe beyond our solar system. This space exploration project was conducted by the NASA Ames Research Center in California, and the space probe was manufactured by TRW Inc.

Pioneer 10 was launched on March 2, 1972, by an Atlas-Centaur expendable vehicle from Cape Canaveral, Florida. Between July 15, 1972, and February 15, 1973, it became the first spacecraft to traverse the asteroid belt. Photography of Jupiter began on November 6, 1973, at a range of 25,000,000 kilometres (16,000,000 mi), and a total of about 500 images were transmitted. The closest approach to the planet was on December 4, 1973, at a range of 132,252 kilometres (82,178 mi). During the mission, the on-board instruments were used to study the asteroid belt, the environment around Jupiter, the solar wind, cosmic rays, and eventually the far reaches of the Solar System and heliosphere.

Artist's impression of Pioneer 10's flyby of Jupiter, by Rick Guidice [Public domain], via Wikimedia Commons
So, what do we know about Jupiter?

Jupiter is the fifth planet from the Sun and the largest in the Solar System. It is a giant planet with a mass one-thousandth that of the Sun, but two and a half times that of all the other planets in the Solar System combined. Jupiter and Saturn are gas giants; the other two giant planets, Uranus and Neptune are ice giants. Jupiter has been known to astronomers since antiquity. The Romans named it after their god Jupiter. When viewed from Earth, Jupiter can reach an apparent magnitude of −2.94, bright enough for its reflected light to cast shadows, and making it on average the third-brightest object in the night sky after the Moon and Venus.

Jupiter is primarily composed of hydrogen with a quarter of its mass being helium, though helium comprises only about a tenth of the number of molecules. It may also have a rocky core of heavier elements, but like the other giant planets, Jupiter lacks a well-defined solid surface. Because of its rapid rotation, the planet's shape is that of an oblate spheroid (it has a slight but noticeable bulge around the equator). The outer atmosphere is visibly segregated into several bands at different latitudes, resulting in turbulence and storms along their interacting boundaries. A prominent result is the Great Red Spot, a giant storm that is known to have existed since at least the 17th century when it was first seen by telescope. Surrounding Jupiter is a faint planetary ring system and a powerful magnetosphere. Jupiter has at least 67 moons, including the four large Galilean moons discovered by Galileo Galilei in 1610. Ganymede, the largest of these, has a diameter greater than that of the planet Mercury.

Radio communications were lost with Pioneer 10 on January 23, 2003, because of the loss of electric power for its radio transmitter, with the probe at a distance of 12 billion kilometers (80 AU) from Earth.

Jupiter has been explored on several other occasions by robotic spacecraft, such as the Voyager flyby missions and later, the Galileo orbiter. In late February 2007, Jupiter was visited by the New Horizons probe, which used Jupiter's gravity to increase its speed and bend its trajectory en route to Pluto. The latest probe to visit the planet is Juno, which entered into orbit around Jupiter on July 4, 2016. Future targets for exploration in the Jupiter system include the probable ice-covered liquid ocean of its moon Europa.

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Tuesday, 18 April 2017

Mission control: salty diet makes you hungry, not thirsty

We've all heard it: eating salty foods makes you thirstier. But what sounds like good nutritional advice turns out to be an old-wives' tale. In a study carried out during a simulated mission to Mars, an international group of scientists has found exactly the opposite to be true. "Cosmonauts" who ate more salt retained more water, weren't as thirsty, and needed more energy.

Salt shaker, by Dubravko Sorić SoraZG on Flickr [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
For some reason, no one had ever carried out a long-term study to determine the relationship between the amount of salt in a person's diet and his drinking habits. Scientists have known that increasing a person's salt intake stimulates the production of more urine - it has simply been assumed that the extra fluid comes from drinking. Not so fast! say researchers from the German Aerospace Center (DLR), the Max Delbrück Center for Molecular Medicine (MDC), Vanderbilt University and colleagues around the world. Recently they took advantage of a simulated mission to Mars to put the old adage to the test. Their conclusions appear in two papers in the current issue of The Journal of Clinical Investigation.

What does salt have to do with Mars? Nothing, really, except that on a long space voyage conserving every drop of water might be crucial. A connection between salt intake and drinking could affect your calculations - you wouldn't want an interplanetary traveler to die because he liked an occasional pinch of salt on his food. The real interest in the simulation, however, was that it provided an environment in which every aspect of a person's nutrition, water consumption, and salt intake could be controlled and measured.

The studies were carried out by Natalia Rakova (MD, PhD) of the Charité and MDC and her colleagues. The subjects were two groups of 10 male volunteers sealed into a mock spaceship for two simulated flights to Mars. The first group was examined for 105 days; the second over 205 days. They had identical diets except that over periods lasting several weeks, they were given three different levels of salt in their food.

The results confirmed that eating more salt led to a higher salt content in urine - no surprise there. Nor was there any surprise in a correlation between amounts of salt and overall quantity of urine. But the increase wasn't due to more drinking - in fact, a salty diet caused the subjects to drink less. Salt was triggering a mechanism to conserve water in the kidneys.

Before the study, the prevailing hypothesis had been that the charged sodium and chloride ions in salt grabbed onto water molecules and dragged them into the urine. The new results showed something different: salt stayed in the urine, while water moved back into the kidney and body. This was completely puzzling to Prof. Jens Titze, MD of the University of Erlangen and Vanderbilt University Medical Center and his colleagues. "What alternative driving force could make water move back?" Titze asked.

Experiments in mice hinted that urea might be involved. This substance is formed in muscles and the liver as a way of shedding nitrogen. In mice, urea was accumulating in the kidney, where it counteracts the water-drawing force of sodium and chloride. But synthesizing urea takes a lot of energy, which explains why mice on a high-salt diet were eating more. Higher salt didn't increase their thirst, but it did make them hungrier. Also the human "cosmonauts" receiving a salty diet complained about being hungry.

The project revises scientists' view of the function of urea in our bodies. "It's not solely a waste product, as has been assumed," Prof. Friedrich C. Luft, MD of the Charité and MDC says. "Instead, it turns out to be a very important osmolyte - a compound that binds to water and helps transport it. Its function is to keep water in when our bodies get rid of salt. Nature has apparently found a way to conserve water that would otherwise be carried away into the urine by salt."

The new findings change the way scientists have thought about the process by which the body achieves water homeostasis - maintaining a proper amount and balance. That must happen whether a body is being sent to Mars or not. "We now have to see this process as a concerted activity of the liver, muscle and kidney," says Jens Titze.

"While we didn't directly address blood pressure and other aspects of the cardiovascular system, it's also clear that their functions are tightly connected to water homeostasis and energy metabolism."

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Monday, 10 April 2017

The chemistry behind the new one pound coin

We all know that money makes the world go around, but do you know what goes into it? The new pound coin arrived on 28th March, largely as a preventative measure against counterfeiting.  Take a look at the graphic below for more information about its composition.

Source: Compound Interest

Why the new coin is harder to counterfeit:
  1. 12-sided - its distinctive shape means it stands out by sight and by touch
  2. Bimetallic - The outer ring is gold coloured (nickel-brass) and the inner ring is silver coloured (nickel-plated alloy)
  3. Latent image - it has an image like a hologram that changes from a '£' symbol to the number '1' when the coin is seen from different angles
  4. Micro-lettering - around the rim on the heads side of the coin tiny lettering reads: ONE POUND. On the tails side you can find the year the coin was produced
  5. Milled edges - it has grooves on alternate sides
  6. Hidden high security feature - an additional security feature is built into the coin to protect it from counterfeiting but details have not been revealed

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