When science goes Captain Planet for conservation

Studying the effects of habitat fragmentation on diversity of wildlife...

In the hearts of forests and jungles around the world there exist members of a feral strain of scientist who grew up on a steady diet of the Captain Planet cartoons. They’ve swapped lab coats for khaki shirts, plastic shoe covers for walking boots, and safety goggles for binoculars in order to study and help protect the creatures surviving in the most biodiverse, but threatened, habitats in the world. Rumours of spandex-wearing are entirely unfounded though.In between the Amazon basin, the hot eastern Brazilian savannahs and the temperate grasslands of Argentina lies the Atlantic Forest. It is home to a diversity of plants and animals to rival that of the famous Amazon Rainforest itself, including a number of species found nowhere else such as the golden lion tamarin, the maned three-toed sloth, and the woolly spider monkey. The forest once stretched along one third of the coast of South America, inland as far as Paraguay. However, today the Atlantic Forest has the dubious status of being one of the most devastated habitats in the world. Shockingly, just 7% remains. What makes this statistic even worse is that the forest consists not of one continuous stretch of woodland but instead thousands of small fragments separated by huge crop and cattle farms.Deforestation of the Atlantic Forest, like in many places around the world, has had a directly detrimental effect on many species of animals by destroying their habitats. However, in all of these ecosystems across the world the wildlife that remains – even in pristine, untouched habitat – are under threat due to the effects of fragmentation.Habitat fragmentation spells very bad news for wildlife for many reasons. Firstly, small fragments don’t have the volume of fruit and other vegetation to support complex ecosystems. Low volumes of fruit and vegetation means few plant matter-eating animals, and even fewer large animals that prey on them. Secondly, large animals require not just large territories but also access to the territories of other populations of their species. This helps to avoid inbreeding and instead maintain a healthy level of genetic diversity. Unfortunately for many species of land animal, a fragment half a mile away on the other side of a cattle farm may as well be on the other side of the world.Finally, fragmentation means that more of the habitat is bordering against agricultural land. This degrades the quality of the habitat along its edges because farming has an effect on the soil, amount of shade and the temperature. This ‘Edge Effect’ is revealed in poor tree growth and the absence of many animal species up to 100 metres in from the forest edge. Additionally, more bordering against human land means more encroachment by hunters and by agricultural development, so fragments get replaced by crop fields and cattle ranches much faster than large areas do – it’s like the way a teaspoon of sugar into your tea dissolves faster than a sugar cube.There are lots of reasons that biologists may find themselves working in a jungle, savannah or swamp, other than wishing they were Steve Irwin. But one of the key concerns of ecology and conservation biologists is to document what level of biodiversity – that is, the variety of different animal and plant species – that an area can support. Biodiversity is an important indicator of how healthy an ecosystem is – decreases can reflect the detrimental effects of deforestation, disease or hunting, and increases can reflect progress of efforts to protect habitats. For example, biodiversity may be lower, i.e. there are fewer different species, in a small fragment of the Atlantic Forest compared to a much larger fragment. Often it is the biggest species that are absent in small habitat fragments – hefty grazing mammals that need a lot of land and vegetation like elephants, giraffes or tapir, or large animals at the top of their food chain like jaguars, caiman or anaconda. However, small animals are also vulnerable, especially if they have very specific dietary or shelter needs. Indeed, many of the most endangered species in the world are small animals that live a fragile existence.Assessing biodiversity starts with trying to work out how many species there are in an area, and estimating how many individuals there are of each species based on how many you find. Unluckily for scientists and ecotourists alike, habitats are rarely like safari parks, where animals are pretty much always visible and easy to observe. Biologists and conservationists don’t lament this fact though –wildlife’s fear of humans is ideal for avoiding hunters. But between animals being rare, well-hidden, fast, living in impenetrable habitat such as thick forest, or spread over a huge area, it can be difficult or even impossible to find a species. That’s why assessing a location’s biodiversity uses a wide range of different scientific techniques. These techniques range from a very simple bucket dug into the ground, to complex DNA analysis techniques in the lab. The technique you use depends on the kind of habitat you are assessing and the kind of animals you’re looking for.The most basic method is to simply walk through a habitat and keep your eyes and ears open for the animals themselves or signs of them. This works for conspicuous, noisy animals such as apes, or birds with identifiable nests, or creatures with predictable hiding habits such as some snakes
Despite being simple, this technique does need careful consideration – timing and location are everything.
Trapping methods are useful for a wide range of different animals that are harder to spot. Small, ground-dwelling animals such as rodents, scorpions, tarantulas, flightless insects, frogs, lizards and small snakes can all be assessed with drift fences and pitfall traps: they bump into a temporary fence (usually a long sheet of plastic) and in trying to get around it fall into buckets dug into the ground. With a layer of soil and shelter at the bottom, these buckets house the animals until they can be checked, recorded and released. Bigger, trigger-mechanism traps can be used to trap mammals and lizards of various sizes, often using bait to entice them in. Bats and low-flying birds can be trapped using fine nets called mist nets.For spotting cautious and elusive animals, such as jaguar or snow leopards, a camera trap is a wonderful piece of equipment. A weather-proof camera with a motion sensor can be strapped to a tree trunk or rock and left for days or sometimes weeks to digitally capture any animal that happens to pass by. They can be expensive, but they’re worth it: camera traps often provide the only picture or video of a species in an area.For those animals that can be caught, small microchips can be swiftly injected under the skin so it can be identified if caught again – calculating how many captures are actually ‘recaptures’ provides an estimate of how many of that species there are in total. For those animals that are elusive and more difficult to trap, camera traps are great for determining the presence of that species but are unlikely to be able to provide a good estimate of the number of individuals in a population.This is where laboratory science comes back into the picture. Genetic analysis is now one of the most useful and widespread tools in conservation science – and usually involves poo! Faeces give us a whole host of information – not only can it help to identify the diet and diseases of a species, the DNA of the ‘donor’ can be extracted and amplified in order to determine the individual’s identity, gender and family heritage. Obtaining the genetic code of just a few individuals can provide enough information to estimate the population number and determine the level of genetic diversity.In short, both field and lab techniques combine to help us determine if an ecosystem fragment is large enough, and has sufficient access to other fragments, to maintain healthy populations of its resident species. With this information, conservationists can go about providing these animals with what they need in order to survive well into the future. In fact, Captain Planet probably did some of his best work in a lab coat...

Measurements [Physics]

Physical quantities

those quantities which can be measured accurately are called physical quantities

The fundation of physics rest upon physical quantities

for exemple mass length thime velocity force density temperature electricalcurrent etc

Base Quantities:

these are the minimum number of those quantities in term of which other quantities can be defined

Derived Quantities 

those quantities whos definations are based on other physical quantities called as derived quantities
"the measurement of a base quantities"

involves following two steps:

1) the choice of standered 

2)estblishment of a procedure for comparing the quantity to be measured with the standerd 

An Ideal Standerd has two characteristics

a) It is accessible,

b) it is invariable.

international system of unit

In 1960, an international committee agreed on a set of definations and standered to descirbe the physical quantities this system is called the system internation [SI]
this system is based up on 

a)Base quantities

b)supplimenteary unit 

c)derived unit

A) base unit:-

the unit defined arbitrarily for the measurement of seven base quantities in comparison with them are called base quantities

the name of base quantiirs and symbols are given below:

sr.no           physical quantitites      Si unit         symbols

1                      length                       meter             m

2                      mass                          kilogram       kg

3                      time                           second           s

4                       electrical current    ampere         a

5                       Temperature           kelvin            k

6                       light intancity         candela         cd

7                       amount of substance          mole              mol

Basics of physics part 1

Our first is related to the physics in which we'll discuss different principals and method of physics
first of all we must familier with the physics

Science:

 Ever since man has started to observe , think and reason he has been wondering about the world around him. He tried to find ways to organize the disorder prevailing in the observed facts about the natural phenomenon and things in an orderly manner.

His attempts resulted in the birth of single discipline Science called as Natural Phenomenon after it when he gets huge knowledge he divides natural phenomenon into the different branches named as physics, chemistry, mathematics, biology,astronomy and many more...

Introduction to physics:

Physics is the branch of science which deals the study of matter energy and their interactions
also can be said The study of inanimated world is called Physics
Physics has hundreds of branches which will discuss in future in this blog

Physics has three frontiers 1st , 2nd, and 3rd

1st frontier

first the world of extremely large, universe it self
2nd frontier

the world of extremely small, as nucleus of an atom

3rd frontier

third one is middle sized thing as sun and earth

 some branches of physics

nuclear physics; it deals with the nuclei, particle physics which is concerned with the ultimate particles by which matter is composed,relstive mechanics which deals with the velocites approcheing within speed of light

in next post we'll read measurements

Notification

As you all are familiar that I mostly upload complex material, previous days I receive some complains that my data is hard to understand most of viewers don't have any idea about basics of bio, chemistry and physics...
that's why firstly I'll post basics concepts of sciences...
feel free to feedback

The Louisiana Wetlands: An Introduction

Science Tales from the Red Stick

A growing human presence interrupts the natural beauty and vastness of Louisiana’s coastline. Beyond the wetlands and outside the bayous are oil platforms and it seems everywhere there are warning markers of underground oil pipes. Still, the most dramatic change these wetlands are undergoing is the inundation of saltwater and the loss of land. Since the early 1930s, it is estimated that Louisiana has lost almost 5,000 square kilometers of wetlands. In fact, some say an area the size of a tennis court disappears every thirteen seconds. The wetlands are turning into water.

A wetland can be defined in many ways but most definitions include three distinguishing features: water, either at the surface or within the root zone, soil conditions unique to this wet environment, and vegetation known as hydrophytes that is adapted to these conditions. Wetlands can be fresh or salt water and in Louisiana there are both and they're equally in danger of disappearing.
According to the United States Geological Survey (USGS) and the Louisiana Department of Fish and Wildlife (LDWF) Louisiana has about 3,560 square kilometers of fresh water wetland and 6,600 square kilometers of tidal (salt water) wetland. That’s an area equivalent to two states of Rhode Island or almost 14 Isle of Mans. Wetlands include landscape features you are familiar with such as marshes, bogs, and swamps.
The wetlands I grew up with were small. You could easily walk across them and you could always see the edge. This is not the case in Louisiana. Here the wetlands stretch to the horizon. They are dotted with small fishing camps and telephone poles that sit at weird angles due to the shifting ground. Often flooded roads and abandoned houses blot the landscape. Despite this I had only to spend a single day out there accompanying two scientists on their monthly monitoring trip to Barataria Bay southwest of New Orleans, to be hooked.
We loaded our small boat early in the morning and headed to the southern most sampling station closest to the Gulf of Mexico. The plan was to work our way north collecting water samples for phytoplankton (microscopic plants), zooplankton (microscopic animals) and bacteria counts, nutrient analyses, and other water characteristics (temperature, salinity, dissolved oxygen, light attenuation). Regular monitoring is part of larger effort to understand the changes occurring along Louisiana’s coastline.
On this day, we wound our way up and down narrow passages surprising fish and sneaking up on alligators. The sky was grey and ominous. Because it is so flat you can see thunderstorms well in the distance - the rain and lightening drumming the water. Twin storms merged into one and chased us all the way to our last sampling station. From there, we headed into a bayou. A bayou is a secondary extension of a larger waterway – in this case – the Mississippi River. Thick with dark green vegetation and monstrous plants, this bayou had a prehistoric and deeply wild feel. Alligator eyes rose just above the surface and brilliant blue horse flies, the size of small birds, buzzed overhead. The water was slow moving and brown, hiding whatever it was that might be waiting underneath. What the bayou’s future holds is more readily detectable.
The coast of Louisiana is a deltaic system built of sediment transported from all over the United States by the Mississippi River. The Mississippi River drains 41% of the contiguous states of the US and is fed by the Missouri, Arkansas, and Ohio Rivers.  The river carries this sediment load to the coast where it settles out and forms sediment lobes or land. Typically, as silt and clay clog the natural path of the river, it switches course finding a more direct and quicker route to the coast. This process is called delta switching and it occurs approximately once every one thousand years.
But as the population grew, and with the establishment of the Port of New Orleans, it became necessary to control the Mississippi River. Levees were constructed to maintain its path and the natural delta switching that occurred for thousands of years was interrupted. Gone then was the sediment distribution and ultimately the land building. Now the Gulf of Mexico can encroach, un-impeded by the River. Sometimes wetlands can keep up with sea level rise through sediment trapping and soil building but not here. These factors combine with land subsidence, the compaction of sediment, to augment the drowning of these wetlands. While subsidence can be a natural geologic process, human activities may also be the cause. Fluid (i.e. oil, gas, groundwater) extraction from underneath the marshes and/or artificial drainage systems have been blamed for high rates of subsidence in Louisiana. The final straw is shipping channels that have been cut and the pipelines that have been laid beneath the marshes. While this has increased navigation abilities it has also allowed saltwater inundation of the many freshwater marshes. For example, the cypress forests that once characterized this area are quickly vanishing because they cannot tolerate saltwater.
The disappearance of these wetlands has innumerable consequences. The coastal landscape is an important habitat for animals and migrating birds while the marsh provides an essential nursery ground for fish. According to Louisiana State University’s Agricultural Center, 95% of commercial fish landings for the Gulf of Mexico depend on the coastal wetlands and 25% of all seafood consumed in the US originates from Louisiana. The bountiful harvest of oysters and crawfish (crayfish) that once drove the local economy is threatened too. Many people have relocated or constructed their houses on stilts to protect them from the encroaching water. On a national scale almost 30% of the oil and gas consumed in the US passes through ports and pipes of South Louisiana. But without these wetlands more than 48,000 km of pipelines would be exposed to open water and waves. On an even larger scale, hurricanes that have struck Louisiana have even provoked increases in global oil prices.
But I am most interested in the loss of wetlands for another reason. Wetlands are areas rich in organic matter and can be important areas for nutrient cycling. Specifically, I am interested in the cycling of nitrogen and a process called denitrification. Denitrification is bacterial process that converts usable forms of nitrogen to unusable forms. It is therefore a natural cleansing process which can remove man-made nitrogen (such as fertilisers) from the environment. As the water from the Mississippi River drains the US it not only brings sediment for land building but high concentrations of nutrients (such as nitrates and phosphates). Most of these nutrients originate from agricultural practices high in the watershed. When the nutrients reach the coast they can stimulate the growth of phytoplankton which can be good for the growing fish. But, like all things, too many nutrients and too much phytoplankton growth can lead to negative consequences. Most notably in this case, when the phytoplankton die they sink to the bottom and decompose, which leads to the water becoming oxygen depleted, killing shellfish and finfish. One striking example of this is the Dead Zone in the Gulf of Mexico. The Dead Zone is a 13,000 - 21,000 square km area of oxygen-depleted water devoid of most forms of life. While many factors contribute to its size and duration, the high concentration of nutrients entering from the Mississippi River is thought to be the main cause.

So here is our dilemma – how do we build land and yet decrease the amount of nutrients entering the Gulf of Mexico? The answer may just lie in sustaining healthy wetlands. One option is to allow more water from the Mississippi River to be directed into the wetlands. By doing this, as it flowed to the coast the river would once again distribute sediment and the wetland might act like a giant filter and remove contaminating nitrogen. Working with colleagues here at LSU I hope to improve our understanding of how much nutrient cycling can occur in these systems and how these processes might change with temperature and water flow.
Beauty-wise, Louisiana’s coast rivals the icecaps of the Antarctic, the rolling waves of the Pacific and the tropical beaches of the Caribbean. But protecting these wetlands is about more than preserving a magnificent landscape. We should all feel a great sense of urgency to guard a culture, an economy, and a natural wonder teeming with life...
References:
- Mitsch, W.J. and Gosselink, J.G. (1993). Wetlands. Van Nostrand Reinhold, New York, N.Y.
- Dunne, M. (2005). America’s Wetland: Louisiana’s vanishing coast. Louisiana State University Press. Baton Rouge, LA
- America’s Wetland Foundation - www.americaswetland.com

 

Protein Origami: Pop-up Books & Nature's Polymers

...the science of studying protein folding

Have you ever had one of those really complicated pop-up books where the dinosaur leaps out of the page towards you in 3-dimensions with every tooth and scale separately attached in perfect and horrifying detail? polymers - the protein.

I have, and if you're like me then you've probably also taken a peek behind the dinosaur to find out how the pop-up works. Peering between the pages like this is similar to the work that goes on in labs around the world where scientists are trying to understand the workings of one of Nature's most powerful
Proteins are massive molecules that are crucial for keeping the cells in our bodies in working order. For instance they provide the rails and the motor for microscopic cellular ‘trains’ that move biochemical cargos from one end of a cell to another, they act as molecular messengers allowing cells to communicate with each other and they package DNA so that the regions of the genome that aren’t being used are tidily coiled away. They also monitor what the cell is doing, and when something causes trouble, they get rid of it, which might even involve killing the cell. And just as the pop-up book is made from pieces of card glued to the page in the right order, proteins are made from molecular cards called amino acids, which are linked together in the right order.
If this gluing is done correctly, the protein spontaneously folds to take up its completed 3D shape. And just like opening a pop-up book, most of the time the protein folding works smoothly, but occasionally things can go wrong. A mutation in the DNA sequence coding for a certain protein can lead to the inclusion of the wrong amino acid, which is akin to inserting a wrongly shaped piece of card in the pop-up book. This causes the mature protein to go out of shape or "mis-fold", so it cannot carry out its intended role correctly. In fact an amazing 80% of human disease-causing mutations affect proteins in this way.
Proteins recognise and interact with each other according to their shape, so having the correct structure is critical for a protein to work effectively. If it fails in this role the results can be fatal. For instance some proteins do the job of killing malfunctioning cells, such as cells that have become malignant, and under these circumstances a failure in the process can mean cancer.
But while many people have been working on ways to treat diseases by correcting the function of affected proteins, my research looks at the fundamental question of how proteins fold when they are working properly. If we want to understand complicated diseases, we first need to understand how things work normally.  A lot of the questions I’m asking are just the same as those you might ask about the pop-up book. What does the folded protein look like? What does the unfolded one look like? Is there a preferred order or logic to the self-assembly?
The proteins I study are 100 million times smaller than the pop-ups in a book, and a hundred times smaller than even a light microscope can see. The result is that I can't just watch what happens - instead I have to infer it by measuring other things. For example, by measuring the speed at which a protein folds and then substituting one amino acid building block for another before repeating the measurement, I can find out which parts fold first. Then, by comparing the results for similar proteins, it's possible to work out how small differences in amino acid sequence affect the way the protein folds.
At the moment, if we design a new protein we can only guess what the final shape will be – but it is the final shape that dictates what the protein can or cannot do! Making new proteins is a bit like knowing what you want the pop-up to look like, but clumsily sticking pieces of card onto the book without really understanding how the process works.
But there are ways around this: if you take a protein similar to the product you want, you can make small changes and slowly build up something useful. It's a bit like changing the pop-up dinosaur into a dragon, although making it into a Volkswagon Beetle would be much harder. My hope is that one day we will fully understand the rules of our pop-up books – not only to understand disease but also to treat it by designing protein drugs that will do exactly what we choose.

 

How Climate Change is Choking Marine Ecosystems

Why warmer weather means bad news for the estuarine nitrogen cycle

Quick, when I say "ocean" what are the images that come to mind? Humpback whales breaking through blue water or maybe miles of coral reef guarded by brightly colored fish. But what if I told you that the smallest things, those that can’t be seen with the un-aided eye, are also worthy of exploration. In the water running seaward and in the sand and mud at your toes – there is life. Life that is responsible for the recycling of nutrients and sometimes the cleansing of water.

It turns out that microscopic forms of life living in marine sediments play a crucial role in regulating the amount of nutrients (nitrogen and phosphorus) in the water column. We care about the amount and kinds of nutrients in the water because they feed microscopic plants (phytoplankton) that form the basis of the food web. When it comes to marine systems we are primarily concerned with nitrogen. Nitrogen has the most profound impact on coastal systems because it is the limiting nutrient. That is, it is often the least abundant relative to the amount required to form life, so phytoplankton growth is restricted by the supply of that nutrient.

Nevertheless, while nitrogen is necessary for plant growth, too much of it released into the marine environment can have dramatic negative affects. Excess nitrogen can trigger unusually large phytoplankton blooms that shade the water and make it impossible for other aquatic plants, such as eel grass, to survive. And when the phytoplankton bloom dies and sinks to the bottom, the decomposition process uses up the available oxygen, which kills fish, shellfish, and other bottom-dwelling organisms. Unfortunately, humans introduce nitrogen into the environment in many ways, including burning fossil fuels, fertilizing fields and lawns, and through human waste.

The nitrogen cycle is complex and many processes work to keep nitrogen within a system. Only one process, known as denitrification, permanently removes nitrogen. It occurs in land, freshwater and marine ecosystems and is a form of bacterial respiration that converts biologically usable forms of nitrogen (i.e. nitrites, nitrates, and ammonium salts) to an unusable form, chiefly nitrogen gas, N₂.

This is an example of a sediment core collected from the estuary. The silver you see at the top is part of the corer. The grey base you see hold the sediment in the core tube. In this sediment core you can see a moon snail in the middle.

Denitrification is important because it is the dominant nitrogen removal route in estuaries and the continental shelf. It occurs naturally and can remove a substantial portion of the total nitrogen load to the estuary. In a sense, it is nature’s cleanser for the estuary – removing the nitrogen and therefore combating the negative effects mentioned above. Because denitrification is so important, estuaries have been described as "filters" or "sinks."

We set out to measure this process in a temperate estuary called Narragansett Bay along the northeast coast of the United States. We began by collecting sediments throughout the estuary and bringing them back to the lab. Once in the lab we sealed the sediments and the overlying water together in a gas tight container and over time extracted water samples. We then used an instrument that can precisely measure dissolved gases in water called a membrane inlet mass spectrometer.

In 2005, we learned that the rate of denitrification had decreased substantially since it was first measured here in the late 1970s. The cleansing process that is so vital for maintaining the estuary had slowed. We continued to sample through 2006 and we discovered a remarkable change. Instead of producing nitrogen gas through denitrification, the sediments began to do the opposite. That is, they were instead fixing nitrogen.

The membrane inlet mass spectrometer, otherwise referred to as MIMS, requires a small size and no sample preparation. In addition the instrument can process water samples for dissolved gas concentrations quickly (about 20 to 30 an hour) and very precisely.

During nitrogen fixation bacteria in the sediment take nitrogen gas and turn it into a biologically usable form of nitrogen (for example nitrate or ammonium). To visualize this change - imagine the sediments breathing. When denitrification dominates the sediments are exhaling – cleansing the water of excess nitrogen. But, when nitrogen fixation occurs the sediments inhale – bringing more nitrogen into the system. In fact, we found that the sediments added more than 1.5 times the amount of nitrogen from the land and atmosphere combined in the summer of 2006. This is a major shift from the estuary acting as a nitrogen "filter or sink" to acting as a nitrogen "source".

Finding nitrogen fixation in the sediments was surprising and also a bit worrisome. Most organisms cannot fix nitrogen and it has long been thought that this process was generally not important in marine sediments. What would cause this dramatic shift? And what might it mean for estuaries and the global ocean?

To answer these questions we began exploring other ecological changes that have occurred in the bay. In the thirty years since denitrification was first measured the average annual water temperature has increased by 1.5ºC and finfish have been replaced by crabs and lobsters. Most dramatic of all has been the shift in the timing and magnitude of the winter-spring phytoplankton bloom that once characterized this bay. The amount of phytoplankton in the water column has decreased by almost 40%. This decrease is important because in coastal systems the phytoplankton fall to the bottom and feed the organisms that live in the sediment. Without this pulse of food or organic matter the organisms cannot survive.

The sediment cores, sealed with a gas tight lid, in a water bath. The water bath allows us to maintain the field temperature for the sediment cores. The whole set up is placed in an environmental chamber – again allowing us to control the temperature so we may look at seasonal changes in sediment nutrient cycling. When we extract a sample for analysis we replace the water from the two large white containers that holds filtered site water. The large grey circle in the middle has a motor that turns high powered magnets attached to a plastic plate. In each of the sediment cores there is magnet attached to the lid. As the plastic plate moves it causes the magnets inside the sediment cores to move too. This helps us keep the water above the sediment constantly stirred to mimic real environmental conditions.

We thought that this decrease in organic matter might also be responsible for the flip from denitrification to nitrogen fixation. So we designed a series of experiments that would test our hypothesis. We added varying amounts of organic matter to individual sediment cores as well as large four square meter sediment plots. The sediments that received the fresh organic matter were all denitrification dominated and the sediments with no organic matter were all fixing nitrogen. So now we think we know what caused the switch - the bacteria responsible for denitrification need fresh organic matter. We also think we know why the phytoplankton production has decreased.

The decrease in phytoplankton production over the last thirty years has been increasingly linked to changes in climate. There are two main working hypotheses and it is important to note that both might be responsible. The first is that the warming waters of the bay allow zooplankton, which are microscopic animals, to feed or graze down the phytoplankton earlier and longer. If this is the case, the phytoplankton never reach "bloom" capacity because the zooplankton eat them too quickly.

The other hypothesis is that warmer winters have more cloudy days and conversely colder winters have more sunny days. Lots of research, here in Narragansett Bay and in other regions such as the Gulf of Maine and the Baltic, has shown that the onset of the winter-spring phytoplankton bloom is determined by the amount of light the phytoplankton receive. If the phytoplankton get less light then this could also decrease the overall amount of phytoplankton growth.

The long term effects of what we observed last summer still need to be explored. The next step is to determine how much of the fixed nitrogen is recycled into the water column. This will help us to determine if the fixed nitrogen can affect other ecological processes in the bay. We also need to see if nitrogen fixation is taking place in other estuaries and along the continental shelf. Since these areas are hot spots for nitrogen removal through denitrification, should they switch to nitrogen fixation, it could have important consequences for the open ocean.

Why Don't Woodpeckers Get Brain Damage?

Beating your head against a hard surface can be a sign of frustration, yet for a woodpecker it’s a fact of life...

In the late 70's, a study carried out by Philip May, Joaquin Fuster, Jochen Haber and Ada Hirschman, using high-speed photography (capable of taking 2000 frames a second), revealed that the impact deceleration, when a woodpecker's beak travelling at 7 metres per second slams into a tree trunk, can exceed one thousand times the force of gravity (1200g).

With repeated trauma of this magnitude it's surprising that the bird's head remains attached to its body, never mind the risk of developing a severe headache, concussion or even brain damage. So why don’t they? Indeed, when other small birds accidentally fly into windows they often tumble to the ground and appear to be "knocked out" for a while before picking themselves up and fluttering off; so why should woodpeckers be any different?
The answer is that evolution has equipped them with a number of adaptations that make repeatedly banging your head against a hard surface 20 times per second slightly more tolerable.
Firstly, woodpeckers have relatively small brains which, in contrast to a human, are packed fairly tightly inside their skull cavity. This prevents the excessive movement of the brain inside the skull, which causes so-called 'contre-coup' injuries in humans. These occur when the brain bashes into the skull following a knock on the head. In other words the head stops, but the brain keeps on moving momentarily afterwards.
Secondly, unlike a human brain the surface of which is thrown into ridges and folds known as gyri to enable more grey matter to be packed in, the woodpecker’s brain has a smooth surface and, through its small size, a high surface area to weight ratio. This means that the impact force is spread over a much larger area, relatively speaking, compared with a human. Again, this minimises the applied trauma. The bird’s brain is also bathed in relatively little cerebrospinal fluid, which also helps to reduce the transmission of the shock waves to the brain surface.
Finally, and possibly most importantly, the woodpecker also makes sure that he minimises any side to side movement of his head, and this is where May and his colleague’s fast film footage comes in.
The team found a tame acorn woodpecker, which could be encouraged to perform for their camera by bashing out a few words on an old typewriter. They watched as the bird first took aim and delivered a number of "test taps" before unleashing a salvo of strikes, but always in a dead straight line.
This approach is crucial because it avoids placing rotational or sheering stresses on the nerve fibres in the brain. Humans involved in car and motorcycle accidents frequently develop the symptoms of 'diffuse axonal injury' (DAI) where sudden deceleration coupled with rotation literally twists the different parts of the brain off each other like a lid coming off a jar. By hammering in a dead straight line woody woodpecker avoids giving himself DAI, further minimising the risk of brain damage.
An unresolved issue however, is that the researchers noted from their photographs that their study subject also took the precaution of closing his eyes just before each strike. But whether this was to keep wood chips out, or the eyeballs in, is anyone’s guess!
Original references:
- May et al., Arch Neurol 1979 Jun; 36(6): 370-3
- May et al., Lancet 1976 Feb 28;1(7957):454-5

 

Biomimetics: Borrowing from Biology

The idea of looking to nature for inspiration is a notion perhaps most notably associated with the arts, Mother Nature isn't a muse exclusive to the artist; she can also inspire scientists, engineers and industrialists.

particularly painting and poetry. But
Nor is the concept of borrowing from biology new to us. More than 3000 years ago the Chinese craved a synthetic silk, and more recently the Wright brothers based the designs for their planes on birds' wings. George Mestral grasped the concept for his invention, Velcro, from the burrs that stuck to his dog’s coat, and the unique, super-efficient cooling system of the Eastgate Centre in Harare, Zimbabwe, is modelled on the system of ducts and passages used by termites to maintain a constant temperature in their mounds. It's on these foundations that the field of biomimetics has been built, and over the last 15 years it's gained momentum rapidly.
Also known as biomimicry and bionics, biomimetics can be defined as "the abstraction of good design from nature" and came about when engineers and medical researchers realised that many of the answers they sought were already available in nature. For example, why spend many years and colossal amounts of money trying to design a new building material from scratch when the chances are there is something in nature that can already do most of what you want? Better still it's likely to have been refined to near perfection during millions of years of evolution.
So, with a little ingenuity and some modifications, a once challenging problem can be elegantly resolved. Exploiting nature and avoiding the pitfalls that have already been ironed out by evolution is precisely what Thomas Speck of The University of Freiberg did when designing the "Technical Plant Stem", a novel material combining features from the stems of the giant reed (Arundo donax) and Dutch rush (Equisetum hyemale).
Inspired by the observation of these plants standing tall, swaying in the wind and yet never appearing to break, this new material combines both stiffness and elasticity with a resistance to breakage and has the potential to be used in the fabrication of a wide range of applications from building materials to snowboards.
This relatively new scientific field of Biomimetics is especially interesting as it brings together researchers from all disciplines to generate solutions to a vast array of problems and appears to be limited only by the imaginations of those involved.
Geckos, glue and sticky tapeGeckos are amazing creatures with the ability to walk up the smoothest of surfaces and even on ceilings, but quite how these lizards achieve their adhesive properties eluded scientists for a long time. One suggestion was that, just like cartoon villains with suction cups strapped to their hands and feet, the geckos used suction to adhere to walls. This was ruled out when these sticky little creatures were still able to cling on tightly in a vacuum. Instead, since even the smoothest of surfaces have microscopic undulations, it was suggested that the geckos used friction to climbs walls, but this couldn’t explain why they are able to walk on ceilings. Another hypothesis was that, like the cockroach, they exuded a glue-like substance from their feet, but this was not possible as their feet are dry and free from the glands required to excrete such a substance.
The answer to this conundrum came about in 2000, when Professor Full and colleagues at UC Berkley looked more closely at the toes of the Tokay Gecko (Gecko gecko). They discovered that each of the gecko’s toes were covered in thousands of tiny "nano-hairs", called setae, each less than one tenth the thickness of a human hair. At the end of each seta were hundreds to thousands of minute mushroom shaped structures called spatulae. The gecko’s super adhesive abilities are achieved because these minuscule structures allow the geckos feet to get so close to the surface, such as a wall, that the molecules of the spatulae and the surface are able to interact electrically. This generates tiny forces, known as van der Waals attractions, that lock the two surfaces together. Although individually they are extremely weak, with billions of molecules interacting with each other the combined force is more than ample for the Gecko to stick to pretty much any surface. If your own hand had the same sticking power, it would be able to hold about 40kg.
Once the mystery of the sticky footed gecko had been solved, the applications of this knowledge to technology were rapidly realised. Within three years a group of scientists from the University of Manchester, lead by Professor Geim, had produced a sticky tape that consisted of microscopic hairs of polyimide which mimicked a gecko’s toes. This sticky tape was believed to be as effective as the real thing, and the researchers were not short of offers from Spiderman wannabes who volunteered to be hung from the lab window by the tape. Unfortunately, the would-be spidys' dreams were never realised, mainly because of the lengthy and expensive process used to produce the tape.

Figure 1a: Scanning electron microscope image of a 1cm2 section of the Gecko-sticky tape.	Figure 1b: Spiderman toy hanging from a glass plate, attached using the tape with a contact area of approximately 0.5cm2.	Figure 1c: Bunching of the hairs is a problem that reduces the adhesive properties of the tape.

In 2006 BAE systems announced that they were able to generate a gecko-like adhesive using a modified version of photo-lithography, the method used to make silicon chips, that was economically viable and easy to scale-up. This super-adhesive was made using polyamide, like nylon, and like the design from Manchester consisted of mushroom shaped structures. While not as sticky as the gecko’s feet, it could quite comfortably stick an elephant to the ceiling, should you have any call to do so! However, unlike conventional adhesives, the gecko-inspired substance can be reused, easily peeling from the surface to which it was stuck, meaning that a Spiderman suit is now a possibility and no doubt likely to appear on a great number of childrens' (and adults') wish lists. The other advantage is that it doesn’t leave any sticky residues behind, so no more patches of blue fluff where something was once stuck. But there are still advances to be made, and the scientists involved hope to make this adhesive even stickier, so for now we’ll just have to wait and stick to using ladders for our window cleaning chores.

Leaves, Loos and the Lotus EffectDespite preferring to grow in muddy rivers and lakes, the leaves of the Lotus plant (Nelumbo nucifera) remain clean and free of contaminants, even after emerging from the murky waters. This self-cleaning ability is believed to be why this plant is regarded as a symbol of purity in many Asian religions and has been the inspiration for many biomimetic inventions.
Instinctively you might think that smoother surfaces would be the cleanest, as grooves and ridges would only serve to trap dirt. However, on closer inspection two German scientists, Professors Barthlott and Neinhuis, revealed that the shiny detritus-free surface of the lotus leaf is anything but smooth. Scanning electron microscope images revealed that the leaves were very rough and covered in micro-lumps and bumps of protruding epidermal (outermost) cells, which were in turn covered in wax crystals around one nanometre (1 millionth of a millimetre) in diameter. The wax crystals are hydrophobic (water hating) and so they repel water droplets and help prevent wetting of the leaf surface. The combination of these micro- and nano-scale features greatly reduces the contact area between the surface and water molecules, which is the key to the cleaning process and explains how even a light rain shower is enough to wash the leaves clean.

Figure 2: The Lotus Effect. Water forms droplets on the tips of the epidermal protrusions and collects pollutants, dirt and small insects as it rolls off the leaf.

Instead of sitting flat along the surface of the leaf, the water only makes contact with the leaf at the top of the lumps (figure 2),  which forces it into spherical droplets. Then, even with the slightest of angles, instead of sliding down the leaf surface the bead of water starts to roll and tumbles off the leaf picking up dirt particles and small insects as it goes. This process, called the Lotus Effect, is so efficient that even honey and water-based glues will roll straight off the leaves, leaving no trace behind.
So-well has evolution refined this system that even hydrophobic dirt particles, which would ordinarily repel water, are trapped by the rolling water droplet and washed away. This is because the particles on the leaves only make contact at the tip of the wax crystals and so do not adhere very well. This means that the energy required by the water to pick them up is much less than the energy required to stick them to the leaf and so they are washed off.
But this effective method of self-cleansing is not restricted to this sacred plant. It also operates naturally in cabbages, reeds and the wings of butterflies and dragonflies, and it has now been exploited by industry to produce several technologies including a water repellent spray developed by BASF. This agent uses nanoparticles and water resistant polymers such as polypropylene, polyethylene and wax that self assemble into tiny structures which can mimic the Lotus Effect. This spray can be effectively applied to a wide range of surfaces from masonry to textiles and leather. Other products in the same vein include Lotusan, a house paint that combines this effect with other characteristics of water-repellent paints, and a more water-efficient urinal that cleans itself using only a fraction of the water required by a regular facility.
I can't imagine many people wouldn’t be attracted by such technology: houses and windows that would clean themselves with every rain shower, shoes that no longer need polishing, clothes that shun dirt. And the technology can have a positive environmental impact too, dramatically reducing the water required to flush a toilet for example.
Blood clots, arteries and self-healing space craftNevertheless, inspirational as nature may be, not all biomimetic innovations are direct copies of their natural world counterparts. Instead, sometimes the concept provides the clue to a more advanced technological solution. Take the blood clotting system for example. When you cut yourself, it is not long before your blood clots to prevent further bleeding and a scab appears. Hidden and protected by the scab your body repairs the damage below and after a short period it is as good as new.

Figure 3a: Micro glass tubes used to contain the resin and setting agent.

So can a similar method be adopted to repair wounds in the skin of a spacecraft? Well yes and no. On the one hand a self-healing system would spare astronauts from having to attempt risky repairs in space, but a repair that worked on the relatively slow time-scale used by the body's clotting system would be of little practical benefit, so it would need to be speeded up.

With this in mind Drs Bond and Trask of Bristol University set about developing a composite material for use in space craft construction that would heal itself in the event of damage. Just as blood passes through tissues in tiny capillaries, the Bristol team have incorporated glass tubes (figure 3a), each only sixty microns (60 thousandths of a millimetre) in diameter, throughout the material (figure 3b). The tubes contain either a resin, or a chemical setting agent which triggers the resin to polymerise and set hard.

This arrangement means that if the material is stressed or cracked, the tubes will rupture, allowing the two "clotting" components to escape and mix. The resulting hard plug will block the breach and restore strength and integrity to the material. Indeed, by including a fluorescent dye to the tubes, it's possible to see the new hardened resin being deposited wherever the material was damaged (figure 3c).

Figure 3b: The glass tubes were set in the composite material in layers.

Although the inclusion of the glass "blood vessels" reduced the strength of the material by 16% and the healed section was only 87% as strong as the original, this piece of research demonstrates that the concept of self-healing materials is feasible and now research is on-going to produce stronger "healants". Also, unlike the mammalian vascular system where blood circulates and is topped up in the event of loss, the present system works only once. So the team are now looking at ways to allow circulation and re-filling of the vessels. And just as our own circulatory system plays a key role in transport and temperature regulation in the body, it may be that the vessels of the space craft could be used to serve similar purposes too, helping to keep down weight and save space.
Another feature of the mammalian response to wounding that would be useful in the vasculature of a space craft is bruising, which can indicate damage below the surface. Often fractures occur inside a composite material leaving no external sign of damage. But if a give-away "bruise" could be generated at the same time as the healant is deposited, it could be used to identify problem areas more speedily.

Figure 3b: Repairs are localised to the areas of damage as observed using a flourescent dye.

The idea of a self-healing spacecraft complete with vascular system may seem a little strange and even more advanced than many sci-fi movies, but with the speed at which these developments are being made it may not be too long before it becomes a reality.

The tip of the iceberg...Sometimes inspiration can be gleaned from the strangest of places, such as worms inspiring the development of robots that could be used to carry cameras into your intestines, traffic systems modelled on the behaviour of ants, and the skunk cabbage that is revealing secrets of how to keep warm during the winter.
Perhaps the most quirky phenomenon that sparked some research was the observation of bullet-proof pheasants. Occasionally, a pheasant can be hit with shot from a shotgun and yet escape unscathed, possibly due to its feathers absorbing the shot’s energy. This sparked an interest in understanding the properties of the feather protein keratin and its potential use in high-velocity impact protection, such as bullet-proof vests.
Other bio-inspired inventions include the sharkskin swimsuit, worn by 28 of the 33 gold medal winners at the swimming events in the 2000 Sydney Olympics. The swimsuit was designed to channel water over the body in the same way that a shark's skin does, reducing drag. Researchers have also been looking at the humble pine cone for other clothing ideas such as anti-sweat ventilation flaps that open and close in response to moisture when things get a bit sweaty. Penguins are also helping to keep polar explorers warm thanks to synthetic insulators based on their feathers; the breakthrough here is that, unlike down, they don't lose their insulating capacity when they become wet.
Where the next invention or moment of inspiration will come from, is virtually impossible to predict, but nature appears to have an inexhaustible supply of answers. All we need is a little ingenuity an open mind.

Bio-plastics: Turning Wheat And Potatoes into Plastics

he science of how "taters" can become Tupperware

In the past, fields of wheat and rows of potatoes were seldom destined for anything more than a rumbling tummy. But bio-products have come a long way since people first branched out into weaving hemp into clothes and pulping papyrus into scrolls. Today the line between Mother Nature and man made has never been more blurred. Animals are re-engineered into living drug factories, crops fuel our cars and now plants are increasingly being repackaged as the epitome of the synthetic world – plastic. Wheat, maize, vegetable oils, sugar beet and even the trusty spud are finding new life as water bottles, car fuel lines and laptops.

Wheat, maize, vegetable oils, sugar beet and even the trusty spud are finding new life as water bottles, car fuel lines and laptops.

Bio-plastics harness the natural structures found in crops or trees, such as slightly modified forms of the chains of sugars in starch or cellulose, that share the ability to be easily reshaped that has made conventional oil based plastics so useful. Bio-materials scientists are also constantly tweaking these natural structures to try and better replicate the durability and flexibility of conventional plastics.
Global business is now turning to bio-plastics for an increasing number of applications, as consumers and governments demand cleaner alternatives to petroleum based technologies and their reckless production of the greenhouse gas CO2.
Worldwide players, such as DuPont and Toyota Motor Corp, are making vast investments in new technologies and processing plants with the hope of cornering a multi-billion pound industry.
The "BC" at Bangor University in North Wales has 18-years experience of working with large companies and Non-Governmental Organisations (NGOs) to find sustainable and viable bio-based alternatives to man-made materials.
BC director Paul Fowler points out that “practically anything that you can find as polyethene you can find as a bio-plastic. You are talking about a whole range of everyday products - cups, combs and wrappers, everything you can think of is out there. There are inroads being made all the time - on the one hand there is research into trying to get biological alternatives to replicate the properties of conventional plastics and on the other hand people are looking at the natural properties of these plants and trying to find an application for them. Most of the manufacture is happening in the US and continental Europe. The UK is a producer of wheat starch and biotimber but the only major bioplastic producer is Innovia Films in Cumbria, which produces cellulose films.”
Innovia Films has an annual turnover of £400m, employing 1,200 people worldwide and producing more than 120,000 tonnes of film – used in packaging to protect food. Japan is also forging ahead, from the leading role in bioplastic production played by Toyota to its recent passing of a triumvirate of laws pushing forward environmental initiatives.
In South Korea too there is a rapid drive to replace conventional plastic packaging with polylactic acid bio-plastics.
Fowler says bio-plastics also offer an opportunity to get a double return for the energy used in their manufacture – first as a useful item and secondly as a fuel source. “My view is that we should burn them at the end of their life to recover energy, which could be then used to produce new materials,” he said. “In the first instance you have a valuable resource can use, be it as packaging or a shopping bag, and then you are also getting some energy back at the end of it. The biggest advantage of such bio-materials is the reduction of CO2 emissions in their production over petrochemical-based plastics.”
He also suggests that burning bio-plastics would also avoid the problems caused by them breaking down and producing methane, which is 25-times more potent as a greenhouse gas than CO2.
The BC is currently looking at developing naturally-derived alternatives to phthalates, which are plasticisers added to PVCs to make them more flexible in products such as electrical cable flex. It follows concerns that phthalates are metabolised in the body into substances that can mimic the body's own hormones, including those concerned with fertility. The centre is also developing bio-resins, natural alternatives to synthetic resins such as phenol and formaldehyde.
What types of bioplastic are there?
The common types of bio-plastics are based on cellulose, starch, polylactic acid (PLA), poly-3-hydroxybutyrate (PHB), and polyamide 11 (PA11). Cellulose-based plastics are usually produced from wood pulp and used to make film-based products such as wrappers and to seal in freshness in ready-made meals.
Thermoplastic starch is the most important and widely used bioplastic, accounting for about 50pc of the bio-plastics market. Pure starch’s ability to absorb humidity has led to it being widely used for the production of drug capsules in the pharmaceutical sector. Plasticisers, such as sorbitol and glycerine are added to make it more flexible and produce a range of different characteristics. It is commmonly derived from crops such as potatoes or maize.

FOMA(TM) N701iECO phone made of PLA bioplastics reinforced with kenaf fibres developed by NEC, UNITIKA and NTTDoCoMo © Paul Fowler

PLA is a transparent plastic whose characteristics resemble common petrochemical-based plastics such as polyethylene and polpropylene. It can be processed on equipment that already exists for the production of conventional plastics. PLA is produced from the fermentation of starch from crops, most commonly corn starch or sugarcane in the US, into lactic acid that is then polymerised. Its blends are used in a wide range of applications including computer and mobile phone casings, foil, biodegradable medical implants, moulds, tins, cups, bottles and other packaging.
PHB is very similar to poylpropylene, which is used in a wide variety of fields including packaging, ropes, bank notes and car parts. It is a transparent film, which is also biodegradable. Interest in PHB is currently very high with companies worldwide aiming to expand their current production capacity. There are estimates that this could lead to a price reduction below five euros per kilogram but this would still be four times the market price of polyethylene in February 2007. The South American sugar industry has commited to producing PHB on an industrial scale.
PA 11 is derived from vegetable oil and is known under the tradename Rislan. It is prized for its thermal reistance that makes it valued for use in car fuel lines, pneumatic air brake tubing, electrical anti-termite cable sheathing and oil and gas flexible pipes and control fluid umbilicals. These are often reinforced with fibres from the kenaf plant, a member of the hibiscus family traditionally used to make paper, to increase heat resistance and durability.
At the cutting edge of bioplastic technology lie polyhydroxyalkanoate (PHA) materials. These are derived from the conversion of natural sugars and oils using microbes. They can be processed into a number of materials including moulded goods, fibre and film and are biodegradable and have even been used as water resistant coatings.
What are the benefits of bio-plastics?
- Reduced CO2 emissions.
One metric ton of bio-plastics generates between 0.8 and 3.2 fewer metric tons of carbon dioxide than one metric ton of petroleum-based plastics. Electronic giant Sony uses PLA in several of its smaller components, including one of its new walkmans, but in future hopes to use PLA-based polymers to reduce its carbon dioxide emissions by 20pc and non-renewable resource input by 55pc compared to oil-based ABS.
- Rising oil prices
Despite currently costing more to produce than conventional plastics bio-plastics are becoming more viable with increasing and instability in oil prices, which are in turn triggering spikes in conventional plastic costs, illustrated in a sharp upturn two years ago. Dwindling oil supplies means that man will eventually be forced to turn to a sustainable basis for plastics.
- Waste
Bio-plastics reduce the amount of toxic run-off generated by the oil-based alternatives but also are more commonly biodegradable. The US’s second largest biopolymer producer Metabolix, of Cambridge, Massachusetts, claims that its plastics are biodegradable in composting bins, wetlands and the oceans. On the flip side not all bio-plastics are biodegradable and there are a growing number of conventional plastics that can naturally break down. The downside of their biodegradability is the methane that can be released as the bio-plastics decompose is a powerful greenhouse gas.
- Benefit to rural economy
Prices of crops, such as maize, have risen sharply in the wake of global interest in the production of biofuels and bio-plastics, as countries across the world look for alternatives to oil to safeguard the environment and provide energy security.
- Enhanced properties
In some fields engineered bio-plastics are now beating oil-based alternatives at their own game. Multinational materials giant Arkema has produced a form of Rislan PA11 that is being used in Europe and Brazil in fuel lines to carry biofuels as it is better able to withstand the corrosive effects of biofuels than oil-based alternatives such as polyamide 12. Rislan is widely used in oilfield applications as well as automotive brake lines. Elsewhere innovations in PA11 production are helping increase car passenger safety and reduce the risk of accidents by inhibiting spark ignition in the fuel lines. US car giant General Motors has replaced its non-conductive fuel-pump modules for new North American car models as it felt it was the best material for the job. In the US chemical multinational DuPont says it has developed a bioplastic derived from corn sugar that has superior stiffness and strength to its naturally based competitors. Global electronics corporation NEC has produced a kenaf-reinforced laptop casing, made of 90pc PLA, which helps reduce overheating by conducting heat better than stainless steel coupled with high temperature resistance and increased strength.
Who are the flagwavers?
Bio-plastics are not being produced by a group of hippies brewing up in their garage. Some of the world’s largest companies including multi-billion dollar chemicals company DuPont, car manufacturer Toyota, UK-based Innovia, US food processing behemoth Cargill and electronics giants NEC and Fujitsu are pouring money into driving the technology and production forward.
NEC and its partners Unitika and NTT DoCoMo produce mobile phone and laptop casings based on plant-derived bio-plastics, mostly PLA. NEC plans to expand its green credentials by substituting more than 10pc of the oil-based plastics in its electronic products with bio-plastics by 2010.
Toyota Motor Corp uses mainly PLA bio-plastics, derived from sweet potatoes corn and sugar beet, reinforced with kenaf to produce components for its cars such as the Prius and Lexus. It hopes to grow its bio-plastics division into a four billion yen business by 2020 and capture two thirds of the global market for petroleum free plastics.
Fujitsu introduced its FMV BIBLO notebook PC series two years ago, which it has manufactured using a material called Ecodear, a combination of 50 pc PLA and an oil-based plastic. Fujitsu is now developing a castor oil derived PA 11 plastic with Arkema, which is more flexible and will help expand its use of bio-plastics in notebook computers. The material can withstand repeated bending thanks to scientists weakening the interaction of the chain molecule in PA 11 and relaxing the stereoregularity of their organisation. The improved durability means its prototypes of PC cover components consist of 60-80 percent of the new bioplastic, an unprecedented achievement to date. Fujitsu is also using high density fillers to increase strength and extend its use into notebook covers and other applications requiring high impact resistance. The new material is expected to cut carbon dioxide emissions by 42pc compared to oil-based nylon 6/6.
DuPont in particular is continuing to expand the market for bio-plastics and plans to continue to offer hybrid bio/conventional plastic materials until the market matures, which could eventually cost less than the oil-based alternatives. DuPont has teamed up with sugar giant Tate & Lyle to build the world’s largest aerobic fermentation plant in Loudon in Tennessee in the US for the production of bio-PDO, with a capacity of 45,000 metric tonnes a year.
The largest commercial producer of bioplastic in the US is NatureWorks, owned by Cargill. The company’s plant in Blair, Nebraska uses corn sugar to produce PLA plastics packaging material and its own Ingeo-brand fibres.
What lies ahead?
With US President George Bush’s recent pledge to produce 35 billion gallons of renewable and alternative fuel by 2017 - driving the price of maize up 60pc in the past two months - the farmer’s field is fast turning into a high tech bio-battleground.
Mr. Fowler warns that the still fledgling industry will have to fight for space and commercial viability as millions of hectares are given over to corn, rapeseed and sugarbeet for bio-fuel production. "There is a real tension between the use of agriculture for fodd versus plastics and other non-food uses and this whole move to produce new fuels," he said. Whereas only two years ago plant materials were at the cheap end of the market and bio-products such as straw had little value, now it is really much more costly. There would have to be a step change in the extent of the production to match oil-based plastics. The amount of bioplastics produced worldwide is less than 200,000 tonnes a year; contrast that with the more than 30 million tonnes of oil-based plastics. You can see we have a long way to go before they replace conventional plastics".

 

The Science of HIV & AIDS in the UK

The biology and impact of the world's worst pandemic

In the UK the plight of AIDS today gets much less attention from the public and the media than it did back in the 1980’s and early 1990’s. This often leads to the misconception that AIDS is no longer a problem in this country; in reality, the increasing prevalence of HIV in the UK proves that this is simply not true.

Worldwide, accepted definitions, facts and figures on HIV and AIDS include:

• Acquired immune deficiency syndrome (AIDS) is a collection of symptoms and infections that result from specific damage to the immune system by the human immunodeficiency virus (HIV).
• HIV is transmitted through the direct contact of a mucous membrane, or the bloodstream, with a bodily fluid containing HIV.
• The late stage of the condition leaves individuals prone to opportunistic infections and tumours.
• Whilst antiretroviral treatments for AIDS and HIV exist to reduce the mortality and morbidity of HIV infection to date there is no known cure; even access to these antiretroviral treatments is not routine in all countries.
• Researchers believe that sometime in the 1930’s a form of simian immunodeficiency virus jumped to humans who butchered or ate chimpanzee bush meat in the Democratic Republic of Congo. The virus became HIV-1, the most widespread form found today.
• The world’s first known case of AIDS has been traced to a sample of blood plasma from a man who died in 1959. During the 1970’s HIV continued to spread undetected around the world and hence the pandemic began. Today an estimated 40 million people are living with HIV worldwide.
• As of January 2006, the Joint United Nations Programme on HIV/AIDS and the World Health Organization estimate that AIDS has killed more than 25 million people since it was first recognised on June 5^th, 1981.
• The stigma associated with HIV/AIDS is severe and extends to providers and volunteers involved with the care of HIV infected patients. AIDS exerts its toll also on societies, devastating their economies, decimating their labour forces and orphaning children.
• Thus, it is one of the most destructive pandemics in recorded history, surpassing even the Black Death. By 2015 it is estimated that 60 million people will have died of AIDS.
• In 2004 the global spending on AIDS was $6.1b. Estimated global AIDS spending required in 2007 for prevention and care is $20b. Less than 3% of all money spent on AIDS goes towards developing a vaccine for the disease.
• In February 2007 a study published in the Lancet showed that male circumcision could dramatically reduce the risk of HIV infection. The randomised control trial showed that circumcised men were 60% less likely to pick up HIV. This means that if all of the 2.5 million men in KwaZulu-Natal province had been circumcised, 37,000 new HIV infections could have been prevented in 2007 alone.

The history of HIV / AIDS in the UKThe first recognised case of AIDS in the UK was recorded in December 1981, when doctors at Brompton Hospital in London reported the case of a 49 year old homosexual man who had died ten days post referral. He was suffering from a rare infection that almost always occurs in individuals with severely weakened immune systems. Doctors believed that the condition might be linked to similar cases that had been occurring amongst gay men in the US.

Throughout the 1980’s the number of newly diagnosed HIV infections per year in the UK rose steadily. The figure plateaued during the 1990’s, averaging about 3,000 cases per year, but then increased dramatically after 1999. By 2005, the annual number of newly diagnosed infections was more than 7,500, and an estimated 63,500 people over 15 years of age were living with HIV in the UK, 20,100 (32%) of whom were believed to be unaware of having been infected. Since the pandemic began there have been 17,161 known UK HIV deaths.

The science bit...HIV is a retrovirus, meaning that it uses a chemical relative of DNA, called RNA (ribonucleic acid), as its genetic material. It primarily attacks components of the human immune system, including T lymphocytes and other white blood cells that carry "CD4" receptors on their surfaces. HIV enters its target cells by binding to both the CD4 molecule and a chemokine "co-receptor", of which there are two forms, CCR5 and CXCR4. Once inside the cell the virus makes a DNA copy of its genome and then uses an enzyme it carries with it, called integrase, to insert this copy into the cell’s own DNA. Either immediately, or after a period of dormancy known as latency, the virus then hijacks the cell and turns it into a virus factory. The newly produced viruses leave the infected cell, destroying it in the process, and move on to invade other CD4+ cells, which are mainly T lymphocytes. These are the cellular linchpins that help to marshall the other components of the body's immune system. As their numbers dwindle the ability of the body to mount an effective immune response to combat other invaders, including bacteria, viruses and fungi, is progressively weakened. This means that HIV kills by slowly destroying the immune system and leaving the infected individual vulnerable to infection by so called "low grade" or opportunistic bugs.

What is the natural history of HIV infection? What are the symptoms?
Most infections with HIV are initially "silent", meaning that a person may not notice that anything is wrong. Then, several weeks after infection, patients often develop a "seroconversion illness", which characteristically includes flu-like symptoms, lymphadenopathy (swollen lymph glands), fevers, loss of appetite and weight, diarrhoea and general lethargy and malaise. During this time infected individuals have very high levels of virus in the bloodstream (10 million viruses per millilitre of blood is not uncommon). The reason for this very high viral load is that the virus is able to replicate (grow) largely unchecked because the immune system has yet to mount an effective suppressive response, including the production of antibodies that can mop up viral particles. As a result the number of CD4+ T cells can fall to very low levels at this time, and the patient is highly infectious.

But then the immune system kicks in, and the virus largely retreats, hiding within lymphoid tissues and replicating only very slowly. The levels of virus in the blood stream become much lower, the patient is less infectious and feels well. Untreated, an infected individual usually remains "healthy" like this for 5 to 15 years.

Structure of the human immunodeficiency virus (HIV) viral particle.

However, the body’s immune system only has a limited ability to control HIV. The virus makes mistakes when it copies its genetic code. Roughly once in every 10,000 genetic letters that are copied the virus introduces the wrong genetic base. Since the genome contains about 9000 bases in total, almost every genome copied will contain an error. The result is that these genetic mistakes alter the appearance of the virus and so make it harder for the immune system to recognise and keep up, because it is trying to hit a moving target. Eventually, through this progressive shape-shifting, the virus takes on a form that the immune system cannot respond to, and at this point the pace of the infection begins to accelerate and the number of CD4+ T cells begins to fall.

When the CD4 count falls below a critical threshold (400 per microlitre of blood) the body is no longer able to defend itself. At this point an HIV-infected individual is said to have AIDS, and patients usually begin to develop opportunistic infections caused by organisms that would not normally affect healthy people. These include mycobaterial infections (caused by bacteria related to tuberculosis), the lung infection PCP (pneumocystis carinii pneumonia), oral and genital thrush, complications of CMV (cytomegalovirus), chronic diarrhoea and weight loss, toxoplasmosis, meningitis, dementia, and polyomavirus (JC virus), which is associated with a disease of the brain's white matter known as PML (progressive multifocal leucoencephalopathy). At this point patients are often prescribed prophylactic drugs to help ward off some of these infections including co-trimoxazole, which can slow down the progression of PCP.

Without treatment the median survival time after developing AIDS is only about 9 months. However, the rate of clinical disease progression varies widely between individuals from 2 weeks to 20 years. Many factors affect this rate of progression, including age, quality of health care and the presence of co-existing infections. An individual's genetic make-up also plays an important role because it's now becoming clear that some people are resistant to certain strains of HIV and although they become infected they do not seem to develop AIDS, or they do so only extremely slowly. There are even people who seem to be totally immune to infection with the virus. They carry a mutated cell surface marker called CCR5-delta-32, which prevents HIV from locking onto and invading their cells. Scientists hope that understanding what makes these people able to resist the virus may hold the key to future therapies to block infection amongst susceptible individuals.

TreatmentWhilst the number of people living with HIV is rising each year, the number of HIV infections that progress to AIDS has dropped dramatically since 1996. This is primarily the result of anti-retroviral therapies, which are available to slow the progress of the virus. These target essential components of the viral replication cycle and include reverse transciptase (RT) inhibitors, which interfere with the way the virus makes a complementary "cDNA" copy of its RNA genome, and protease inhibitors, which prevent the virus from cutting up the raw materials it needs to form new viral particles.

There are two types of drugs that block RT; these are known as nucleoside and non-nucleoside RT inhibitors. The nucleoside RT inhibitors are structurally very similar to normal DNA bases, but they lack a critical chemical group required to enable a DNA chain to grow. So when the viral RT inserts one of these altered bases into the copy that it's making of its genetic code, it can't finish the job because it cannot add the next genetic letter. An example of this type of agent is the drug AZT or zidovudine (azidothymidine). The non-nucleoside RT inhibitors, which include drugs like efavirenz and nevirapine, work slightly differently. They target the RT enzyme itself and bind to it, distorting its shape so that it cannot work properly. This stops the virus from replicating.

Protease inhibitors (PIs) only emerged more recently. They work by blocking the action of a protein-cutting enyzme carried by HIV, which is critical to the virus being able to assemble new infectious particles. If this enzyme is prevented from doing its job the virus cannot escape from the infected cell. An example of the PIs includes saquinavir, which is famous for being one of the first drugs produced by building a computer model of the shape of the viral enzyme and then designing a drug specifically to block it.

There are also agents known as fusion inhibitors, which are a newer type of drug that work by stopping HIV from binding with the CD4 receptors that it uses to enter cells. One being evaluated at the moment is called efurvatide.

Doctors have also recently been testing a new agent called raltegravir, which is an "integrase inhibitor". This prevents the virus from inserting a copy of its genetic material into the host cell genome. In a recent trial published in the Lancet doctors randomly allocated 179 patients with end-stage HIV / AIDS to receive either the active drug or a placebo. After 6 months the patients receiving raltegravir showed a 98% drop in the levels of virus in the bloodstream, compared with only 45% in the placebo group. The next step will be to test raltegravir in combination with other HAART regimen drugs in healthier patients who are not approaching the end-stages of their disease. It may make a considerable difference to the rate of disease progression.

So there are lots of drugs with which we can now combat HIV; but there's a problem. Because the virus frequently makes mistakes when it copies its genetic material it rapidly develops forms of the virus that are resistant to the action of these drugs. To slow down the rate at which this happens, rather than use them singly, a cocktail of drugs is used, often one from each of the three classes (nucleoside RT inhibitors, non-nucleoside RT inhibitors and protease inhibitors). This is known as HAART or Highly Active Antiretroviral Therapy (HAART) and it has dramatically reduced the evolution of viral resistance and prolonged the time during which an HIV-infected individual remains healthy and symptom free. However, it's worth emphasising that, whilst drugs help to control the spread of HIV to uninfected cells, unfortunately there is no treatment available at present that can eradicate HIV once integrated into a host.

Side effects...
This means that individuals using HAART have to take medication every day for the rest of their lives, and this often causes severe side effects. When individuals first start treatment they may suffer headaches, hypertension or general malaise (feeling unwell), although these usually improve or disappear with time. Other side effects can include diarrhoea, nausea, fatigue, anaemia, lipodystrophy, skin problems, neuropathy, mitochondrial toxicity, dyslipidaemia and bone problems. Whilst most people who take anti-HIV medications have some side effects it must not be assumed that everyone gets every side effect that has ever been written down.
Another problem with combating HIV is that a number of different strains of the virus can arise due to differences in selection pressures as the virus encounters different individuals, different drugs and different routes of spread. This can result in resistance to multiple anti-retrovirals and frequently occurs through a process called recombination. It occurs because each HIV virion carries two complete RNA genomic strands, meaning that homologous recombination can occur when a cell is coinfected with two different but related strains. The two strains may then exchange genetic material, including drug resistance traits. The process of recombination also therefore poses theoretical problems for the development of a safe vaccine against HIV.
The situation is also made worse by the fact that increasing numbers of patients are found to be carrying resistant forms of the virus at diagnosis, even before any drug therapy has been administered. Indeed, in 2004 an estimated 9% of new HIV diagnoses were found to be drug resistant strains, presumably acquired from individuals who had already received treatment. If patients then acquire additional strains of the virus with different resistance profiles the process of recombination can yield multiply-resistant viruses. In a case described recently in the Lancet this resulted in an individual producing a strain of the virus that was resistant to every available anti-retroviral agent. The patient in question also progressed to AIDS and died within six months of becoming infected.

The main ways HIV is transmitted in the UKThe three main transmission routes of HIV are sexual contact, exposure to infected body fluids or tissues and from mother to foetus or child during the perinatal period. It is possible to find HIV in the saliva, tears and urine of infected individuals but there are no recorded cases of infection by these secretions and the risk of infection is negligible. Breast milk, however, is known to be a significant risk factor for mother to child transmission of HIV. Studies have shown that if no anti-infection precautions are taken then 15-20% of new born babies will be infected, but if they are also breast-fed this proportion rises to over 50%. As a result HIV-positive mothers are advised not to breastfeed their babies.

A reported 754 HIV-infected children had been born in the UK to infected mothers as of the end of December 2006. Aware of the increasing risk posed by HIV to newborns and care-workers, in 1999 the UK Government introduced routine antenatal testing for HIV amongst all pregnant women. In those found to be positive, the use of antiretroviral treatment can greatly reduce the chances of a mother passing the infection to her baby. Since 1996 the increased use of such treatment has caused the rate of mother-to-child transmission to fall substantially.

Early media coverage of AIDS in the UK focused on injecting drug users. During the early 1980’s it was a big problem, but in 1986 needle exchanges began to operate across the UK, providing clean needles and giving drug users information and support. These schemes were largely effective in reducing the prevalence of HIV among certain members of this population. However, while they account for a small proportion of people living with HIV in the UK, the prevalence of HIV among injecting drug users has risen significantly in recent years (from 1:110, in 2002, to 1:62, in 2006). This rise has been attributed to an increase in the use of drugs outside of London where needle exchange schemes and information about HIV are harder to access.

Government policy in the UKAccording to the latest Government legislation, NHS treatment for HIV is free to everyone who is living in the UK legally. This means that people who are living in the UK without due authority (such as illegal immigrants and failed asylum seekers) must pay for any HIV treatment they receive.

This measure aimed to tackle health tourism, the process whereby people migrate to a country in order to take advantage of better healthcare services there. However, denial of treatment to people in these situations can effectively be a death sentence, especially if they are then deported to countries where no treatment is available.

There are certain 'notifiable diseases', for which a person will always receive treatment in the UK regardless of their legal status, in order to prevent the rapid spread of epidemics. HIV, however is not on the notifiable diseases list. If a woman has no legal right to be in the UK then she will only receive medication to stop her baby being born HIV positive if doctors decide it is an 'emergency'.

Financial costs to the UK health system

• The cost of managing a patient with HIV is around £16,000 a year.
• The total cost of treatment and care in 2002/03 was estimated to be £345m.
• In 2000 it was estimated that the average lifetime treatment cost for an HIV positive person was between £135k and £181k.

Why is HIV / AIDS still on the increase in the UK?There is currently no vaccine or cure for HIV or AIDS. The only known methods of prevention are based on avoiding exposure to the virus, male circumcision which is discussed below, and antiretroviral treatment administered directly after a highly significant exposure. This is known as post exposure prophylaxis (PEP) and comprises a 4 week drug schedule, the side effects of which are very unpleasant.

Another reason people are still dying of AIDS is due to many being diagnosed with HIV at a late stage of infection. In 2005 more than one third of adults diagnosed with HIV had a CD4 count lower than the recommended threshold for starting treatment. At this stage treatment is much less likely to work. This late diagnosis is alarmingly common, highlighting the need for greater awareness and for people to access testing services as soon as possible if they think they may have been exposed to HIV.

What is next?Billions of pounds are spent every year worldwide on caring for and treating individuals with HIV/AIDS and on resources to prevent further spreading of the virus. However, ultimately it is a cure that is required to combat this pandemic. A vaccine to prevent HIV infection, as an alternative method to current therapies, may still be many years away. Not only might such a vaccine have to prime antibodies to attack HIV (the way most vaccines work) but it might also need to increase T cell production. Vaccine trials have been undertaken in South Africa, Kenya, the USA and Thailand, though most have yet to yield promising results. Controversial vaccines made from the blood of HIV carriers have been tested in Nigeria and Thailand. Other developing avenues for treatment of HIV positive individuals include gene therapy, targeted radiation therapy and nanotube technology to block the invasion of HIV into target cells. In April 2007 researchers even identified a component naturally present in human blood (a protein derived from alpha-1-antitrypsin) that can block HIV entry into cells.

In the absence of a vaccine researchers have turned to other approaches to try to combat the virus. A promising discovery, confirmed earlier in 2007, was that male circumcision can dramatically reduce, by 60%, the chances of acquiring HIV. The first clues that circumcision might be beneficial in halting the spread of HIV came after researchers noticed much lower prevalences of HIV infection amongst communities in which males were routinely circumcised. This hypothesis was tested recently in a series of randomised control trials in which HIV-negative volunteers seeking the procedure were randomly assigned either to undergo circumcision immediately or to wait for a period of time first. The patients were then followed up with regular HIV tests. The trial had to be stopped prematurely on ethical grounds when a large excess of HIV cases were found in the group of individuals asked to wait before undergoing the procedure. Scientists think that the foreskin represents a significant portal of entry for the virus because it is relatively enriched in cell types targeted by HIV, it provides an environment in which the virus can persist for an extended period thus maximising the risk of infection, and the mucosa of the foreskin can develop tiny fissures during intercourse and these facilitate viral entry and infection.

In response to these findings, the WHO / UNAIDS have recommended that it should be considered as an effective preventative measure. According to Kevin de Cock, director of the World Health Organisation's AIDS department, "This is an extraordinary development...Circumcision is the most potent intervention in HIV prevention that has been described". And according to Marie-Louise Newell of the University of KwaZulu-Natal in South Africa and Till Barnighausen of the Harvard School of Public Health "if all of the 2.5 million men in KwaZulu-Natal province had been circumcised, 37,000 new infections could have been prevented in 2007".

But none of these strategies can be effective without education, particularly about safe sex. One in ten girls aged 16-19 in the UK is infected with chlamydia, which can only have been acquired through unsafe sex. This is clear evidence that large numbers of young people are placing  themselves at direct risk of HIV, probably because they are from a generation who never saw the "grim reaper" television adverts of the 1980s when AIDS first hit the headlines. HIV is a very real threat and still very much a life sentence. Unless people can be made aware of this then the problem will only continue to get worse.