Protein-rich diet may help soothe inflamed gut

Immune cells patrol the gut to ensure that harmful microbes hidden in the food we eat don't sneak into the body. Cells that are capable of triggering inflammation are balanced by cells that promote tolerance, protecting the body without damaging sensitive tissues. When the balance tilts too far toward inflammation, inflammatory bowel disease can result.

Now, researchers at Washington University School of Medicine in St. Louis have found that a kind of tolerance-promoting immune cell appears in mice that carry a specific bacterium in their guts. Further, the bacterium needs tryptophan - one of the building blocks of proteins - to trigger the cells' appearance.

"We established a link between one bacterial species - Lactobacillus reuteri - that is a normal part of the gut microbiome, and the development of a population of cells that promote tolerance," said Marco Colonna, MD, the Robert Rock Belliveau MD Professor of Pathology and the study's senior author. "The more tryptophan the mice had in their diet, the more of these immune cells they had."

If such findings hold true for people, it would suggest that the combination of L. reuteri and a tryptophan-rich diet may foster a more tolerant, less inflammatory gut environment, which could mean relief for the million or more Americans living with the abdominal pain and diarrhea of inflammatory bowel disease.

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. By AzaToth (self made based on PDB entry) [Public domain], via Wikimedia Commons

Postdoctoral researcher Luisa Cervantes-Barragan, PhD, was studying a kind of immune cell that promotes tolerance when she discovered that one group of study mice had such cells, while a second group of study mice that were the same strain of mice but were housed far apart from the first group did not have such cells.

The mice were genetically identical but had been born and raised separately, indicating that an environmental factor influenced whether the immune cells developed.

She suspected the difference had to do with the mice's gut microbiomes - the community of bacteria, viruses and fungi that normally live within the gastrointestinal tract.

Cervantes-Barragan collaborated with Chyi-Song Hsieh, MD, PhD, the Alan A. and Edith L. Wolff Distinguished Professor of Medicine, to sequence DNA from the intestines of the two groups of mice. They found six bacterial species present in the mice with the immune cells but absent from the mice without them.

With the help of Jeffrey I. Gordon, MD, the Dr. Robert J. Glaser Distinguished University Professor, the researchers turned to mice that had lived under sterile conditions since birth to identify which of the six species was involved in inducing the immune cells. Such mice lack a gut microbiome and do not develop this kind of immune cell. When L. reuteri was introduced to the germ-free mice, the immune cells arose.

To understand how the bacteria affected the immune system, the researchers grew L. reuteri in liquid and then transferred small amounts of the liquid - without bacteria - to immature immune cells isolated from mice. The immune cells developed into the tolerance-promoting cells. When the active component was purified from the liquid, it turned out to be a byproduct of tryptophan metabolism known as indole-3-lactic acid.

Tryptophan - commonly associated with turkey - is a normal part of the mouse and the human diet. Protein-rich foods contain appreciable amounts: nuts, eggs, seeds, beans, poultry, yogurt, cheese, even chocolate.

When the researchers doubled the amount of tryptophan in the mice's feed, the number of such cells rose by about 50 percent. When tryptophan levels were halved, the number of cells dropped by half.

People have the same tolerance-promoting cells as mice, and most of us shelter L. reuteri in our gastrointestinal tracts. It is not known whether tryptophan byproducts from L. reuteri induce the cells to develop in people as they do in mice, but defects in genes related to tryptophan have been found in people with inflammatory bowel disease.

"The development of these cells is probably something we want to encourage since these cells control inflammation on the inner surface of the intestines," Cervantes-Barragan said. "Potentially, high levels of tryptophan in the presence of L. reuteri may induce expansion of this population."

For more information visit:-

https://www.sciencedaily.com/releases/2017/08/170803141045.htm

https://en.wikipedia.org/wiki/Protein

http://www.prlabs.co.uk/lab-supplies.php?N=300l-msia-darts-protein-a&Id=19590

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.

For more information visit:-

http://www.compoundchem.com/2014/09/16/aminoacids/

https://en.wikipedia.org/wiki/Amino_acid

http://www.prlabs.co.uk/lab-supplies.php?N=l-arginine-for-biochemistry&Id=22533

On this day in science history: polyethylene was discovered

Polyethylene was first synthesized by the German chemist Hans von Pechmann, who prepared it by accident in 1898 while investigating diazomethane. When his colleagues Eugen Bamberger and Friedrich Tschirner characterized the white, waxy substance that he had created, they recognized that it contained long –CH2– chains and termed it polymethylene.

Polythylene balls, by Lluis tgn (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons

The first industrially practical polyethylene synthesis (diazomethane is a notoriously unstable substance that is generally avoided in industrial application) was discovered in 1933 by Eric Fawcett and Reginald Gibson, again by accident, at the Imperial Chemical Industries (ICI) works in Northwich, England.  Upon applying extremely high pressure (several hundred atmospheres) to a mixture of ethylene and benzaldehyde they again produced a white, waxy material. Because the reaction had been initiated by trace oxygen contamination in their apparatus, the experiment was, at first, difficult to reproduce. It was not until 1935 that another ICI chemist, Michael Perrin, developed this accident into a reproducible high-pressure synthesis for polyethylene that became the basis for industrial LDPE production beginning in 1939. Because polyethylene was found to have very low-loss properties at very high frequency radio waves, commercial distribution in Britain was suspended on the outbreak of World War II, secrecy imposed, and the new process was used to produce insulation for UHF and SHF coaxial cables of radar sets. During World War II, further research was done on the ICI process and in 1944 Bakelite Corporation at Sabine, Texas, and Du Pont at Charleston, West Virginia, began large-scale commercial production under license from ICI.

The breakthrough landmark in the commercial production of polyethylene began with the development of catalyst that promote the polymerization at mild temperatures and pressures. The first of these was a chromium trioxide–based catalyst discovered in 1951 by Robert Banks and J. Paul Hogan at Phillips Petroleum. In 1953 the German chemist Karl Ziegler developed a catalytic system based on titanium halides and organoaluminium compounds that worked at even milder conditions than the Phillips catalyst. The Phillips catalyst is less expensive and easier to work with, however, and both methods are heavily used industrially. By the end of the 1950s both the Phillips- and Ziegler-type catalysts were being used for HDPE production. In the 1970s, the Ziegler system was improved by the incorporation of magnesium chloride. Catalytic systems based on soluble catalysts, the metallocenes, were reported in 1976 by Walter Kaminsky and Hansjörg Sinn. The Ziegler- and metallocene-based catalysts families have proven to be very flexible at copolymerizing ethylene with other olefins and have become the basis for the wide range of polyethylene resins available today, including very low density polyethylene and linear low-density polyethylene. Such resins, in the form of UHMWPE fibers, have (as of 2005) begun to replace aramids in many high-strength applications.

One of the main problems of polyethylene is that without special treatment it's not readily biodegradable, and thus accumulates. In Japan, getting rid of plastics in an environmentally friendly way was the major problem discussed until the Fukushima disaster in 2011. It was listed as a $90 billion market for solutions. Since 2008, Japan has rapidly increased the recycling of plastics, but still has a large amount of plastic wrapping which goes to waste.

In May 2008, Daniel Burd, a 16-year-old Canadian, won the Canada-Wide Science Fair in Ottawa after discovering that Pseudomonas fluorescens, with the help of Sphingomonas, can degrade over 40% of the weight of plastic bags in less than three months.

The thermophilic bacterium Brevibacillus borstelensis (strain 707) was isolated from a soil sample and found to use low-density polyethylene as a sole carbon source when incubated together at 50°C. Biodegradation increased with time exposed to ultraviolet radiation.

In 2010, a Japanese researcher, Akinori Ito, released the prototype of a machine which creates oil from polyethylene using a small, self-contained vapor distillation process.

In 2014, a Chinese researcher discovered that Indian mealmoth larvae could metabolize polyethylene from observing that plastic bags at his home had small holes in them. Deducing that the hungry larvae must have digested the plastic somehow, he and his team analyzed their gut bacteria and found a few that could use plastic as their only carbon source. Not only could the bacteria from the guts of the Plodia interpunctella moth larvae metabolize polyethylene, they degraded it significantly, dropping its tensile strength by 50%, its mass by 10% and the molecular weights of its polymeric chains by 13%.

For more information visit:-

https://todayinsci.com/3/3_27.htm

https://en.wikipedia.org/wiki/Polyethylene

http://www.prlabs.co.uk/lab-supplies.php?N=ethylene-oxide-monitor&Id=41684

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."

For more information visit:-

https://www.sciencedaily.com/releases/2016/11/161128131328.htm

http://www.prlabs.co.uk/lab-supplies.php?N=sand-fontainebleau&Id=58829

Breast milk protein could be used in fight against antibiotic resistance

An antibiotic developed from human breast milk could combat certain drug-resistant bacteria, British scientists have found.

Tackling antibiotic-resistant bacteria, known as superbugs, is a priority for the government. A panel set up by David Cameron forecast that they would cost 10 million lives and £700bn a year worldwide by 2050 if the problem went unchecked.

The breakthrough, by the National Physical Laboratory (NPL) and University College London, found that the minuscule fragment, less than a nanometre in width, is responsible for giving the protein its anti-microbial properties.

This is what makes breast milk so important in protecting infants from disease in their first months of life. The protein, called lactoferrin, effectively kills bacteria, fungi and even viruses on contact.

After identifying the fragment, scientists re-engineered it into a virus-like capsule that can recognise and target specific bacteria and damage them on contact, but without affecting any surrounding human cells.

The team suggested this could help the fight against antibiotic resistance by serving as “delivery vehicles” for cures. The capsules could even pave the way for treatments for previously incurable conditions such as sickle-cell disease, cystic fibrosis and Duchenne muscular dystrophy.

The Lactating Breast

When the baby sucks, a hormone called oxytoxin starts the milk flowing from the alveoli, through the ducts (milk canals) into the sacs (milk pools) behind the areola and finally into the baby's mouth.

In an interview with the Times, Dame Sally Davies, the chief medical officer for England, said governments and experts needed to do more to tackle the antibiotics issue. “We need on average 10 new antibiotics every decade. If others do not work with us, it’s not something we can sort on our own,” she said. “This is a global problem. I am optimistic about this. The science is crackable. It’s doable.”

Colin Garner, honorary professor of pharmacology at the University of York and head of the charity Antibiotic Research UK, said the situation was too urgent to wait for international consensus. “The pipeline of new drugs had dried up and the problem was on the brink of becoming intractable, he told the Times.

“My heart sinks when I hear the term ‘global initiative’. How long has it taken the world to come to a sort of consensus about climate change?” he said.

“The problem of antibiotic resistance will be at least as intractable, because each nation takes a different view of what is required.”

The NPL findings are reported in the Royal Society of Chemistry journal Chemical Science.

For more information visit:

http://www.theguardian.com/science/2016/jan/23/protein-in-breast-milk-could-be-used-to-combat-certain-bacteria-scientists-find

https://www.prlabs.co.uk/lab-supplies.php?N=protein-precipitation-kit&Id=1446

Oxygen oasis in Antarctic lake reflects Earth in distant past

At the bottom of a frigid Antarctic lake, a thin layer of green slime is generating a little oasis of oxygen, a team including UC Davis researchers has found. It's the first modern replica discovered of conditions on Earth two and a half billion years ago, before oxygen became common in the atmosphere. The discovery is reported in a paper in the journal Geology.

The switch from a planet with very little available oxygen to one with an atmosphere much like today's was one of the major events in Earth's history, and it was all because some bacteria evolved the ability to photosynthesize. By about 2.4 billion years ago, geochemical records show that oxygen was present all the way to the upper atmosphere, as ozone.

What is not clear is what happened in between, or how long the transition - called the Great Oxidation Event - lasted, said Dawn Sumner, professor and chair of earth and planetary sciences at UC Davis and an author on the paper. Scientists have speculated that here may have been "oxygen oases," local areas where was abundant before it became widespread around the planet.

The new discovery in Lake Fryxell in the McMurdo Dry Valleys could be a modern example of such an ancient oxygen oasis, and help geochemists figure out what to look for in ancient rocks, Sumner said.

Lake Fryxell. Credit: Tyler Mackey, UC Davis 

Sumner and collaborators including Ian Hawes of the University of Canterbury, New Zealand have been studying life in these ice-covered lakes for several years. The microbes that survive in these remote and harsh environments are likely similar to the first forms of life to appear on Earth, and perhaps on other planets.

The discovery occurred "a little by accident," Sumner said. Hawes and Tyler Mackey, a UC Davis graduate student working with Sumner, were helping out another research team by diving in Lake Fryxell. The lakes of the Dry Valleys typically contain oxygen in their upper layers, but are usually anoxic further down, Sumner said. Lake Fryxell is unusual because it becomes anoxic at a depth where light can still penetrate.

During their dives below the oxygen zone, Hawes and Mackey noticed some bright green bacteria that looked like they could be photosynthesizing. They took measurements and found a thin layer of oxygen, just one or two millimeters thick, being generated by the bacteria.

Something similar could have been happening billions of years ago, Sumner said.

"The thought is, that the lakes and rivers were anoxic, but there was light available, and little bits of oxygen could accumulate in the mats," she said.

The researchers now want to know more about the chemical reactions between the "oxygen oasis" and the anoxic water immediately above it and sediments below. Is the oxygen absorbed? What reactions occur with minerals in the water?

Understanding how this oxygen oasis reacts with the environment around it could help identify chemical signatures preserved in rocks. Researchers could then go looking for similar signatures in rocks from ancient lake beds to find "whiffs of oxygen" prior to the Great Oxidation Event.

For more information visit:-

http://www.sciencedaily.com/releases/2015/09/150901140759.htm

https://www.prlabs.co.uk/lab-supplies.php?N=oxygen-emptied-cylinder&Id=60499

The smell of the earth!

Ever wondered what the smell of the earth is?  Maybe you've visited the countryside while farmers have been ploughing their fields and smelled it.  The smell is caused by Geosmin which is an organic compound with a distinct earthy aroma produced by a type of Actinobacteria.

Geosmin is produced by the bacteria Streptomyces, a genus of Actinobacteria and released when these microorganisms die.

Geosmin is a colourless liquid, with a boiling point of 270°C.  The human nose is extremely sensitive to geosmin and is able to detect it at concentrations as low as 5 parts per trillion.  It is the smell after a rainstorm when the ground is wet.

Geosmin is often responsible for unpleasant tastes in water supplies. Cyanobacteria (blue-green algae) and actinobacteria release geosmin when they die, and this can be absorbed by bottom-feeding freshwater fish such as carp and catfish. Geosmin combines with 2-methylisoborneol, which concentrates in the fatty skin and dark muscle tissues. Geosmin breaks down in acid conditions; hence, vinegar, lemon and other acidic ingredients are used in fish recipes to help reduce the muddy flavour.

Geosmin can sometimes be tasted in wine or drinking water.

It has also been suggested that camels can detect the smell of geosmin that had been released by Streptomyces miles away in wet ground, and track the geosmin to find an oasis; in return the camel could carry away and disperse the spores of the Streptomyces bacterium.

Soil is considered to be the "skin of the earth" and consists of a solid phase (minerals and organic matter) as well as a porous phase that holds gases and water.  It carries essential nutrients for plantlife and is a habitat for organisms that take part in decomposition of organic matter and the creation of a habitat for new organisms.

For more information visit:-
http://web.expasy.org/spotlight/back_issues/035/
http://en.wikipedia.org/wiki/Soil

The Petri Dish!

Google is commemorating today the achievements of the scientist Julius Richard Petri with a Google Doodle that shows his invention - the Petri dish - in action.

Today would have been the German bacteriologist's 160th birthday. In the animation on the Google homepage, the word "Google" is replaced with a series of the dishes in the Google colours. A hand appears, swabbing each of them, then you can watch as the bacteria grow.

 

Julius Richard Petri (May 31, 1852 – December 20, 1921) was a German microbiologist who is generally credited with inventing the Petri dish while working as assistant to pioneering bacteriologist Robert Koch.

 

Petri dishes are often used to make plates that are used for microbiology studies. The dish is partially filled with warm liquid containing agar, and a mixture of specific ingredients that may include nutrients, blood, salts, carbohydrates, dyes, indicators, amino acids and antibiotics. After the agar cools and solidifies, the dish is ready to receive a microbe-laden sample in a process known as inoculation or "plating." For virus or phage cultures, a two-step inoculation is needed: bacteria are grown first to provide hosts for the viral inoculum.

Often, the bacterial sample is diluted on the plate by a process called "streaking": a sterile plastic stick, or a wire loop which has been sterilized by heating is used to take the first sample, and make a streak on the agar dish. Then a fresh stick, or a newly-sterilized loop, passes through that initial streak, and spreads the plated bacteria onto the dish. This is repeated a third, and sometimes a fourth time, resulting in individual bacterial cells that are isolated on the plate, which then divide and grow into single "clonal" bacterial colonies.
Petri plates are sometimes incubated upside down (agar on top) to lessen the risk of contamination from settling airborne particles and to prevent water condensation from accumulating and disturbing the cultured microbes.

P&R Labpak supply a wide range of petri dishes - glass and disposable plastic in various diameters.  If you need any, why not contact us?

We also supply various agars and media from all leading brands.

 

For more information visit:-

http://en.wikipedia.org/wiki/Julius_Richard_Petri

http://www.independent.co.uk/life-style/gadgets-and-tech/news/google-doodle-celebrates-work-of-julius-richard-petri--the-scientist-widely-credited-with-inventing-the-petri-dish-8638084.html