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Tuesday, 17 January 2017

Simple fats, amino acids to explain how life began

Life is a process that originated 3.5 billion years ago. It emerged when the basic components of the cells that we know today, in other words, inanimate chemical molecules, gradually joined, merged, assembled themselves and interacted. At a given moment they became alive, or what amounts to the same thing, they turned into autonomous systems. As the years passed they gradually evolved until achieving their current complexity and diversity. A piece of research by the UPV/EHU is working on the start of this trajectory by studying how the chemical molecules assembled themselves so that life could begin.

A section of DNA. Zephyris at the English language Wikipedia [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons
DNA, RNA, proteins, membranes, sugars, …cells are made up of all kinds of components. In biology, and in the studies dealing with the origin of life specifically, it is very common to focus on one of these molecules and put forward hypotheses on how life originated by analysing the specific mechanisms related to it. "Basically, these studies are looking for the 'molecule of life', in other words, they set out to establish which was the most important molecule in making this milestone happen," said Kepa Ruiz-Mirazo, researcher in the Biophysics Unit and of the UPV/EHU's Department of Logic and Philosophy of Science. However, bearing in mind that "life involves activity among a huge variety of molecules and components, a change of approach has been taking place in recent years and research that takes into account various molecules at the same time is gaining strength," he added.

Besides emerging in favour of this fresh approach, Ruiz-Mirazo's group, in collaboration with the University of Montpellier, through an internship of the UPV/EHU PhD student Sara Murillo-Sánchez, has been able to show that interaction exists between some molecules and others. "Our group has expertise in research into membranes that are created in prebiotic environments, in other words, in the study of the dynamics that fatty acids, the precursors of current lipids, may have had. 

The Montpellier group for its part specialises in the synthesis of the first peptides. So when the knowledge of each group is put together, and when we experimentally blended the fatty acids and the amino acids, we could see that there was a strong synergy between them."

As they were able to see, the catalysis of the reaction took place when the fatty acids formed compartments. As they are in an aqueous medium, and due to the hydrophobic nature of lipids, they tend to join with each other and form closed compartments; in other words, they take on the function of a membrane; "at that time the membranes obviously weren't biological but chemical ones," explained Ruiz-Mirazo. In their experiments they were able to see that the conditions offered by these membranes are favourable for amino acids. "The Montpellier group had the prebiotic reactions of the formation of dipeptides very well characterised, so they were able to see that this reaction took place more efficiently in the presence of fatty acids," he added.

Besides demonstrating the synergy between fatty acids and amino acids, Ruiz-Mirazo believes it is very important to have conducted the study using basic chemical components, in other words, molecular precursors. "Life emerged out of these basic molecules; therefore, to study its origin we cannot start from the complex phospholipids that are found in today's membranes. We have demonstrated the formation of the first coming together and formation of chains on the basis of molecular precursors. Or to put it another way, we have demonstrated that it is possible to achieve diversity and complexity in biology by starting from chemistry."

In his studies, in addition to the experimental work, Ruiz-Mirazo is working in another two spheres so in the end he is studying the origin of life from three pillars or perspectives: "firstly, we have the experimental field; another is based on theoretical models and computational simulations, which we use to analyse the results obtained in the experiments, and the third is a little broader, because we are studying from the philosophical viewpoint what life is, the influence that the conception held about life exerts on the experimental field, since each conception leads you to carry out a specific type of experiment," he explained. "These three methodologies mutually feed each other: an idea that may emerge in the philosophical analysis leads you to carry out a new simulation, and the results of the simulations mark out the path for designing the experiments. Or the other way round. Most likely we will never manage to find the answer to how life began, but we are working on it: all of us living beings on Earth have the same origin and we want to know how it happened."

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Tuesday, 10 January 2017

The chemistry of the environmental effects of fireworks

Who doesn’t love fireworks at New Year? Yet whilst fireworks are undoubtedly a spectacle, they can also have a negative effect on the environment. Take a look at the graphic below, to discover some of the issues that they can cause.

Source: Compound Interest
So that’s the science, but what about the history? Who first invented the firework?

The earliest documentation of fireworks dates back to 7th century China (time of the Tang Dynasty), where they were invented. The fireworks were used to accompany many festivities. It is thus a part of the culture of China and had its origin there; eventually it spread to other cultures and societies.

The art and science of firework making has developed into an independent profession. In China, pyrotechnicians were respected for their knowledge of complex techniques in mounting firework displays. Chinese people originally believed that the fireworks could expel evil spirits and bring about luck and happiness.

During the Song Dynasty (960–1279), many of the common people could purchase various kinds of fireworks from market vendors, and grand displays of fireworks were also known to be held. In 1110, a large fireworks display in a martial demonstration was held to entertain Emperor Huizong of Song (r. 1100–1125) and his court. A record from 1264 states that a rocket-propelled firework went off near the Empress Dowager Gong Sheng and startled her during a feast held in her honor by her son Emperor Lizong of Song (r. 1224–1264). 

Rocket propulsion was common in warfare, as evidenced by the Huolongjing compiled by Liu Bowen (1311–1375) and Jiao Yu (fl. c. 1350–1412). In 1240 the Arabs acquired knowledge of gunpowder and its uses from China. A Syrian named Hasan al-Rammah wrote of rockets, fireworks, and other incendiaries, using terms that suggested he derived his knowledge from Chinese sources, such as his references to fireworks as "Chinese flowers".

With the development of chinoiserie in Europe, Chinese fireworks began to gain popularity around the mid-17th century. Lev Izmailov, ambassador of Peter the Great, once reported from China: "They make such fireworks that no one in Europe has ever seen." In 1758, the Jesuit missionary Pierre Nicolas le Chéron d'Incarville, living in Beijing, wrote about the methods and composition on how to make many types of Chinese fireworks to the Paris Academy of Sciences, which revealed and published the account five years later. His writings would be translated in 1765, resulting in the popularization of fireworks and further attempts to uncover the secrets of Chinese fireworks.

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Wednesday, 4 January 2017

Zinc eaten at levels found in biofortified crops reduces 'wear and tear' on DNA

A new study by researchers from the UCSF Benioff Children's Hospital Research Institute (CHORI) shows that a modest 4 milligrams of extra zinc a day in the diet can have a profound, positive impact on cellular health that helps fight infections and diseases. This amount of zinc is equivalent to what biofortified crops like zinc rice and zinc wheat can add to the diet of vulnerable, nutrient deficient populations.

The study, published in the American Journal of Clinical Nutrition, was led by CHORI Senior Scientist Janet King, PhD. King and her team are the first to show that a modest increase in dietary zinc reduces oxidative stress and damage to DNA.

Zinc Acetate. By Chemical interest (Own work (Original text: self-made)) [Public domain], via Wikimedia Commons
"We were pleasantly surprised to see that just a small increase in dietary zinc can have such a significant impact on how metabolism is carried out throughout the body," says King. "These results present a new strategy for measuring the impact of zinc on health and reinforce the evidence that food-based interventions can improve micronutrient deficiencies worldwide."

Zinc is ubiquitous in our body and facilitates many functions that are essential for preserving life. It plays a vital role in maintaining optimal childhood growth, and in ensuring a healthy immune system. Zinc also helps limit inflammation and oxidative stress in our body, which are associated with the onset of chronic cardiovascular diseases and cancers.

Around much of the world, many households eat polished white rice or highly refined wheat or maize flours, which provide energy but do not provide enough essential micronutrients such as zinc. Zinc is an essential part of nearly 3,000 different proteins, and it impacts how these proteins regulate every cell in our body. In the absence of sufficient zinc, our ability to repair everyday wear and tear on our DNA is compromised.

In the randomized, controlled, six-week study the scientists measured the impact of zinc on human metabolism by counting DNA strand breaks. They used the parameter of DNA damage to examine the influence of a moderate amount of zinc on healthy living. This was a novel approach, different from the commonly used method of looking at zinc in the blood or using stunting and morbidity for assessing zinc status.

According to King, these results are relevant to the planning and evaluation of food-based solutions for mitigating the impact of hidden hunger and malnutrition. King believes that biofortification can be a sustainable, long-term solution to zinc deficiency.

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Wednesday, 28 December 2016

On this day in science history: chewing gum was patented

In 1869, William Finley Semple of Mount Vernon, Ohio, was issued the first U.S. patent for chewing gum (No. 98,304), made of "the combination of rubber with other articles adapted to the formation of an acceptable chewing gum", but he never commercially produced gum. That was done by Thomas Adams of Staten Island, N.Y., who knew that chicle, a natural tree gum, could be chewed. His first experiments to vulcanize chicle for use as a rubber substitute were unsuccessful until he boiled a small batch of chicle in his kitchen and created the first chicle-based chewing gum. Testing sales at a local store, he found people liked his gum. In 1871, Adams patented a gum-producing machine so he could increase production.

Chewing gum stick by Lusheeta, via Wikimedia Commons

Humans have used chewing gum in some form for at least 100,000 years. Modern chewing gum today is made from butadiene-based synthetic rubber. Most chewing gums are considered polymers. Longer polymers can produce larger bubbles due to increased intermolecular forces.

Chewing gum in many forms has existed since the Neolithic period. 6,000-year-old chewing gum made from birch bark tar, with tooth imprints, has been found in Kierikki in Finland. The tar from which the gums were made is believed to have antiseptic properties and other medicinal benefits. It is chemically similar to petroleum tar and is in this way different from most other early gums. The Aztecs, as the ancient Mayans before them, used chicle as a base for making a gum-like substance and to stick objects together in everyday use. Forms of chewing gums were also chewed in Ancient Greece. The Ancient Greeks chewed mastic gum, made from the resin of the mastic tree. Mastic gum, like birch bark tar, has antiseptic properties and is believed to have been used to maintain oral health. Both chicle and mastic are tree resins. Many other cultures have chewed gum-like substances made from plants, grasses, and resins.

The American Indians chewed resin made from the sap of spruce trees. The New England settlers picked up this practice, and in 1848, John B. Curtis developed and sold the first commercial chewing gum called The State of Maine Pure Spruce Gum. In this way, the industrializing West, having forgotten about tree gums, rediscovered chewing gum through the First Americans. Around 1850 a gum made from paraffin wax, which is a petroleum product, was developed and soon exceeded the spruce gum in popularity. To sweeten these early gums the chewer would often make use of a plate of powdered sugar, which they would repeatedly dip the gum into to maintain sweetness.

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Monday, 19 December 2016

How the Antarctic Ice Sheet is affecting climate change

Scientists have known for decades that small changes in climate can have significant impacts on the massive Antarctic Ice Sheet.

Now a new study suggests the opposite also is true. An international team of researchers has concluded that the Antarctic Ice Sheet actually plays a major role in regional and global climate variability - a discovery that may also help explain why sea ice in the Southern Hemisphere has been increasing despite the warming of the rest of the Earth.

Results of the study are being published this week in the journal Nature.

View of the Riiser-Larsen Ice Shelf in Antarctica. By Ben Holt  (NASA), via Wikimedia Commons

Global climate models that look at the last several thousand years have failed to account for the amount of climate variability captured in the paleoclimate record, according to lead author Pepijn Bakker, a former post-doctoral researcher at Oregon State University now with the MARUM Center for Marine Environmental Studies at the University of Bremen in Germany.

The research team's hypothesis was that climate modelers were overlooking one crucial element in the overall climate system - an aspect of the ocean, atmosphere, biosphere or ice sheets - that might affect all parts of the system.

"One thing we determined right off the bat was that virtually all of the climate models had the Antarctic Ice Sheet as a constant entity," Bakker said. "It was a static blob of ice, just sitting there. What we discovered, however, is that the ice sheet has undergone numerous pulses of variability that have had a cascading effect on the entire climate system."

The Antarctic Ice Sheet, in fact, has demonstrated dynamic behavior over the past 8,000 years, according to Andreas Schmittner, a climate scientist in Oregon State's College of Earth, Ocean, and Atmospheric Sciences and co-author on the study.

"There is a natural variability in the deeper part of the ocean adjacent to the Antarctic Ice Sheet - similar to the Pacific Decadal Oscillation, or El Niño/La Niña but on a time scale of centuries - that causes small but significant changes in temperatures," Schmittner said. "When the ocean temperatures warm, it causes more direct melting of the ice sheet below the surface, and it increases the number of icebergs that calve off the ice sheet."

Those two factors combine to provide an influx of fresh water into the Southern Ocean during these warm regimes, according to Peter Clark, a paleoclimatologist in OSU's College of Earth, Ocean, and Atmospheric Sciences and co-author on the study.

"The introduction of that cold, fresh water lessens the salinity and cools the surface temperatures, at the same time, stratifying the layers of water," Clark said. "The cold, fresh water freezes more easily, creating additional sea ice despite warmer temperatures that are down hundreds of meters below the surface."

The discovery may help explain why sea ice has expanded in the Southern Ocean despite global warming, the researchers say. The same phenomenon doesn't occur in the Northern Hemisphere with the Greenland Ice Sheet because it is more landlocked and not subject to the same current shifts that affect the Antarctic Ice Sheet.

"One message that comes out of this study is that the Antarctic Ice Sheet is very sensitive to small changes in ocean temperatures, and humans are making the Earth a lot warmer than it has been," Bakker said.

Sediment cores from the sea floor around Antarctica contain sand grains delivered there by icebergs calving off the ice sheet. The researchers analyzed sediments from the last 8,000 years, which showed evidence that many more icebergs calved off the ice sheet in some centuries than in others. Using sophisticated computer modeling, the researchers traced the variability in iceberg calving to small changes in ocean temperatures.

The Antarctic Ice Sheet covers an area of more than 5 million square miles and is estimated to hold some 60 percent of all the fresh water on Earth. The east part of the ice sheet rests on a major land mass, but in West Antarctica, the ice sheet rests on bedrock that extends into the ocean at depths of more than 2,500 meters, or more than 8,000 feet, making it vulnerable to disintegration.

Scientists estimate that if the entire Antarctic Ice Sheet were to melt, global sea levels would rise some 200 feet.

Other authors on the study include Nicholas Golledge of Victoria University of Wellington in New Zealand and Michael Weber of the University of Bonn in Germany.

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Tuesday, 13 December 2016

The Chemistry of Mummification

These days, when we think of the preservation of bodies, we think of cryogenics, but as we all know, the Ancient Egyptians were as fascinated with life after death as we are. Click on the infographic below to find out more about the chemistry of mummification.


It takes about 70 days to completely mummify a dead body and in Ancient Egypt there were no restrictions on who could be mummified, as long as you could pay! The Egyptians believed that when they died they would make a journey to another world where they would lead a new life. They would need all the things they had used when they were alive so their family would put those things in their grave. Egyptians paid vast amounts of money to have their bodies properly preserved. 

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Wednesday, 7 December 2016

On this day in science history - Galileo spacecraft orbits Jupiter

In 1995, the Galileo spacecraft arrived at Jupiter and entered orbit after 6 years of travel including a flyby of Venus and two asteroids, Gaspra and Ida. The orbiter had also carried an atmospheric probe with scientific instruments, which it had released from the main spacecraft in July 1995, five months before reaching Jupiter. Galileo then spent a further 8 years examining Jupiter and its moons Io and Europa. 

Jupiter. By NASA, ESA, and A. Simon (Goddard Space Flight Center) [Public domain], via Wikimedia Commons
In 1994, the Galileo orbiter was present to watch the fragments of comet Shoemaker-Levy 9 crash into Jupiter. Its mission was concluded 21 September 2003 by sending the orbiter into Jupiter's atmosphere at a speed of nearly 50 km/sec, destroying it to avoid any chance of it contaminating local moons with bacteria from Earth.

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 is a gas giant, along with Saturn, with the other two giant planets, Uranus and Neptune, being ice giants. Jupiter was known to astronomers of ancient times. 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.

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