Sunday, December 29, 2013

Can Free Radicals be Good for You?

This article was published in the journal Science Progress, of which I am an Editor, and to which I contribute a quarterly Current Commentary, on some pertinent and contemporary aspect of science or technology. This time I discuss how toxic free radicals really are, and whether taking antioxidants and other dietary supplements can "protect" us from them, or indeed if they are actually beneficial to us under some circumstances.

A pdf version of the article can be downloaded from this link On here it seems to work ok if you set the "page size" to 100%.

Free Radicals – the Bad Guys.
It is widely held1 that free radicals are involved in the initiation and propagation of many and various illnesses, including cancer, heart disease, stroke, rheumatoid arthritis, diabetes, and multiple sclerosis (MS). The list runs on, and even the process of ageing itself is believed to be driven by free radicals, also called Reactive Oxygen Species (ROS) or Reactive Oxygen Intermediates (ROI). Now, the species classified as ROS or ROI are derived from molecular oxygen (O2) which obviously we need to breathe to stay alive. In the main, ROS are the superoxide radical anion (O2−•), its conjugate acid, the hydroperoxyl radical (HOO), the hydroxyl radical (HO), organic peroxyl radicals (ROO), alkoxyl radicals (RO) as bona fide free radical (unpaired electron) molecules, but also included on the list are molecular (especially, singlet) oxygen (O2), organic hydroperoxides, ROOH and hydrogen peroxide itself, H2O2. It can be said that all oxygen free radicals are ROS/ROI but not all ROS/ROI are free radicals. As respired O2 enters living cells it is metabolised e.g. by the mitochondria to O2−•, which is not in itself strongly oxidising, but it provides a source of other ROS. To avoid living cells being overwhelmed by O2−•, they contain the enzyme superoxide dismutase which catalyses the reaction (equation 1):

2O2−• + 2H+ → H2O2 + O2                                         (1)

Now H2O2 is not harmless in cells since it can provide a source of HO radicals, particularly if there is free iron present, which promotes the Fenton Reaction (equation 2):

Fe2+ + H2O2 → Fe3+ + HO + OH                           (2)

HO radicals can attack sensitive molecules in cells, including membrane lipids, carbohydrates and proteins, and if they are formed in the cell nucleus, DNA bases too, potentially leading to strand-breaks and cell mutations. The attack of HO and other kinds of radicals on lipids can initiate the process known as lipid peroxidation, which is responsible for the rancidification of foodstuffs including meat. That our human “meat” does not become rancid while we remain alive is due to the fact that living cells contain antioxidants, In particular, catalase which is a common enzyme found in nearly all living organisms that are exposed to oxygen. Catalase is able to catalyse the decomposition of hydrogen peroxide to water and oxygen, and has one of the highest turnover numbers of all enzymes - one catalase molecule can convert 40 million molecules of hydrogen peroxide to water and oxygen per second. Glutathione peroxidise also catalyses the decomposition of H2O2 via the reaction by coupling its reduction to water with oxidation of reduced glutathione (GSH), a thiol-containing tripeptide (glu-cys-gly) (equation 3):

H2O2 + 2GSH → GSSG + 2H2O                             (3)

The product, oxidized glutathione (GSSG), contains a disulphide bridge, and can be converted back to GSH by glutathione reductase enzymes. It is now thought that peroxiredoxins may be even more important2 in removing H2O2 from cells in animals, bacteria, and probably plants. There are at least three classes of these enzymes, but in the function of all of them an cys-SH group present on the peroxiredoxin is oxidised by H2O2 to a sulfenic acid, cys-SOH. The interception of ROS is not perfect and around 1% of respired O2 ends-up as ROS. Over a year this amounts to 1.7 kg of ROS, since humans are fairly large animals and breathe substantial amounts of oxygen. To cope with what ROS remain, there are both intrinsic and extrinsic antioxidants present in cells, the latter being brought into the living organism and hence its cells by ingestion, i.e. in our food and in the form of deliberately taken dietary supplements. The effectiveness of latter is debatable, however, as shall shortly become evident. Many molecules that are designated as antioxidants possess phenolic groups, e.g. the vitamin-E series and compounds present in green tea, principally epigallocatechin gallate (EGCG). It is thought that such materials can act as chain-breaking antioxidants, in which the chain of free radical propagation is “broken” by transfer of an H-atom from a phenolic OH moiety to an ROO radical (equation 4):

ArOH + ROO → ArO + ROOH                               (4)

This effectively deactivates the ROO radical from abstracting an H-atom from a lipid unit to give a carbon-centred radical, which by the addition of O2 would form another ROO radical to propagate the autoxidation process (equation 5):

ROO + RH → ROOH + R                                       (5)

The door to the field of free-radical toxicology was set open in the proposal by Gerschman et al. in 19543 that oxygen poisoning and the effect of X-irradiation on animals had a common mechanism which involved the formation of free radicals. Two years later, Denham Harman suggested that the ageing process too was mediated by free radicals.4 The abstracts of these two classic papers are as follows:

Abstract: A consideration of various isolated reports in the literature has led us to the hypothesis that oxygen poisoning and radiation injury have at least one common basis of action, possibly through the formation of oxidizing free radicals. This article reviews the pertinent material that led to this hypothesis and also presents the supporting evidence obtained from (i) experiments on the protective action against oxygen poisoning by substances of varied chemical nature known to increase resistance to irradiation, and (ii) experiments on the survival in oxygen of mice irradiated and exposed to high oxygen tensions simultaneously or at different intervals.3

Abstract: This paper describes a theory about mechanisms of aging that is based on free radical chemistry: "Aging and the degenerative diseases associated with it are attributed basically to the deleterious side attacks of free radicals on cell constituents and on the connective tissues. The free radicals probably arise largely through reactions involving molecular oxygen catalyzed in the cell by oxidative enzymes and in the connective tissues by traces of metals such as iron, cobalt, and manganese.4

These ideas and their broader ramifications underwent a gestation period, with periodic mention, leading to a seminal paper by Trevor Slater and his colleagues in which an explanation for the toxicity of carbon tetrachloride (CCl4), principally to the liver, was advanced in terms of a free-radical mechanism.5 For those chronically exposed to “carbon tet” over lengthly periods, damage to the liver was not infrequent and in some cases, liver failure occurred, in addition to neurotoxic effects of CCl4, and potential links to liver cancer and kidney cancer. CCl4 used to be widely employed in the dry cleaning industry and was also commonly used as an organic solvent, but due to its toxicity has been largely superseded by safer materials. The mechanism of activation involves a reductive elimination of Cl from CCl4, (e.g. by cytochrome P450 enzymes) which forms a CCl3 radical. The CCl3 radicals can then add O2 to form CCl3OO radicals, which are particularly reactive versions of peroxyl radicals. This enhanced reactivity can be viewed in terms of the limiting canonical structures: CCl3OO <--> CCl3O+•O which for common ROO radicals, normally contribute around 50:50 to the overall structure. However, the three strongly electron withdrawing Cl-atoms tend to disfavour the second structure, with the positive charge on the O-atom adjacent to the CCl3-group, and so the unpaired electron becomes increasingly localised onto the terminal O-atom according to an increased weighting of the limiting structure CCl3OO.6 An increased localisation or “exposure” of the unaired electron tends to engender a more reactive radical character and so the H-atom abstraction reaction (equation 5) is facilitated. Thus the lipid peroxidation process overall is encouraged, causing severe damage to the liver cells so that the organ becomes cirrhotic and ultimately fails.

Good Free Radicals?
Recent research7 published from King’s College in London indicates that mice deliberately bred to possess more of an enzyme (NADPH oxidase-4) that actually produces ROS, including free radicals, suffered less heart disease than animals in which the enzyme had been “deleted”. This rather runs counter to the prevailing argument espoused above but it is thought that exposure to ROS can actually “toughen-up” an organism, so that it becomes more resistant to certain conditions like cardiovascular disease. It is well known that ROS, including superoxide, can act as cell-messengers, and so in concentrations that do not overwhelm the protective antioxidative capacity of the organism may be beneficial. Some of the ROS may act as signalling agents to operate protective pathways, for example in enhancing myocardial angiogenesis, which is the physiological process involving the growth of new blood vessels from pre-existing vessels. The latter is a critical determinant of cardiac adaptation to overload stress. Several years ago, another group of London researchers, this time from University College (UCL), reported that the basic theory underlying the toxicity of oxygen radicals is flawed.8 White blood cells, or leukocytes (also spelled "leucocytes", leuco- Ancient Greek "white"), are cells of the immune system that participate in defending the body against infectious diseases and xenobiotics (foreign agents). Five different kinds of leukocytes are known, all of them stemming from a multipotent cell termed a haematopoietic stem cell, which exists in bone marrow. Leukocytes are found throughout the body, and are present in the blood and lymphatic system, with a typical lifetime of 3 – 4 days. Leukocytes comprise ca 1% of the blood of a healthy adult, and the leukocyte count is often an indicator of disease, being raised (leukocytosis) above the normal levels of 4×109 - 1.1×1010 white blood cells/litre. The name "white blood cell" derives from the observation that after a blood sample has been centrifuged, the white cells are found in the buffy coat, a thin layer of nucleated cells between the sedimented red blood cells and the blood plasma, which is normally white in appearance.

Leukocytes produce oxygen ROS, and the process by which they do so is vital for killing microbes efficiently. In some people, the process is defective, rendering them liable to chronic, severe and often fatal infections. Accordingly, the inference has been drawn that the ROS are themselves highly toxic, and must be harmful to human tissues if they are sufficiently virulent to kill organisms as robust as bacteria and fungi. In contrast, the UCL group found that it was not ROS that made white blood cells so destructive but the release of enzymes (proteases) with the power to digest foreign invading species. The enzymes are triggered by a flow of K+ cations within the cell. When the process was blocked using iberiotoxin (derived from scorpion venom) and paxilline (a fungal mycotoxin), the cells were no longer able to combat pathogens, demonstrating that the ROS are not as toxic as previously thought.8 The paper concludes: “These data have significance beyond the inherent value of defining the precise molecular mechanisms involved in a physiological process of paramount importance to survival. The perception that neutrophils kill microbes through toxic oxygen radicals and their metabolites provided much of the biological basis for the theories relating the toxicity of oxygen radicals to the pathogenesis of a wide variety of human diseases, and the development of antioxidant drugs for their treatment. These theories and treatment merit re-evaluation.”

Noteworthy too is a study9 by researchers at McGill’s Department of Biology, who tested the accepted “free radical theory of ageing” by creating mutant worms with an increased production of ROS in their bodies. It was found that in contrast to the expected outcome, the worms lived longer than regular worms. Even more significantly, when the mutant worms were treated with antioxidants, e.g Vitamin C, their lifetimes were shortened. The researchers then sought to mimic the apparent beneficial effect of the free radicals by treating regular, wild worms with Paraquat, a herbicide that generates superoxide and hence other ROS, by redox-cycling. Paraquat is so toxic to humans and animals that it is banned in the European Union and its use is restricted in many other parts of the world. Remarkably, they discovered that the worms lived longer after being exposed to paraquat. It is thought that in the genetically modified worms, the production of ROS can help to trigger the body’s general protective and repair mechanisms, thus acting to preserve life. Whether one can extrapolate these results for worms to far more complex organisms such as humans is a moot point, of course.

Antioxidant Supplements.
It is widely held that a “Mediterranean Diet” is very healthy since the incidences of cancer and cardiovascular diseases in the Mediterranean are lower than in the colder northern countries. This is the basis of the “five a day” diet, in which it is recommended that we consume five 80g portions of fruit and vegetables daily. An explanation for this, which has entered the public consciousness, is that a diet rich in fresh fruit and vegetables is full of antioxidants and by mopping-up free radicals is protective against these particular maladies. This must be qualified by a recent European study which found a relatively small reduction in the overall cancer rate according to their intake of fruit and vegetables in a sample of almost half a million people.10 However, in an extension of this line of thinking, a massive multi-billion dollar industry has uprisen which supplies pure antioxidant compounds in the form of pills and capsules to be taken as dietary supplements. In the U.S. alone, more than half of all adults take some form of vitamin or mineral supplement, at a cost of £23 billion/year.11 Now, not only is there precious little hard scientific evidence that taking these compounds additionally and above what is present in the diet actually does any good, it is quite possible that in too high a dose some of them can have adverse effects. The pioneer protagonist of such dietary supplementation was Linus Pauling who recommended taking Vitamin C (L-ascorbic acid) in large amounts. He did live to be 93.

L-ascorbic acid (or L-ascorbate) is an essential nutrient for humans and certain other animal species.12 In living organisms ascorbate is thought to act as an antioxidant by protecting the body against oxidative stress. Ascorbate is a cofactor in at least eight enzyme catalysed reactions, including a number involved in collagen synthesis, and when they do not function properly the disease known as scurvy arises. In animals these reactions are especially important in wound-healing and in preventing bleeding from capillaries. The nickname given by Americans to the English, “Limeys”, derives from the practice of taking lime-fruits on board ships in the British Navy so that sailors could drink the juice (which is now known to contain Vitamin C) and offset the symptoms of scurvy which had formerly beset them on long sea voyages. While the daily recommended dose of 40 – 95 mg/day is sufficient for the needs of a human adult, doses of 10 -100 times this amount have been advocated by some practitioners. There is, however, no clinical evidence that such megadoses protect against developing cancer, coronary disease or the common cold, and indeed might be harmful, e.g. in promoting kidney failure.12 Most of the excess Vitamin C is simply excreted from the body (occasioning diarrhoea) so it is unlikely to do much good.

The most infamous case of a dietary supplement proving actually harmful is the Beta-Carotene and Retinol Efficacy Trial (CARET) in which daily β-carotene (30 mg) and retinyl palmitate (25 000 IU) were given to 18,314 participants who were at high risk for lung cancer because of a history of smoking or asbestos exposure.13 The study was stopped ahead of schedule in January 1996 because participants who were randomly assigned to receive the active intervention were found to have a 28% increase in incidence of lung cancer, a 17% higher death-rate and a higher rate of death from cardiovascular disease compared with participants in the placebo group. The notion that beta-carotene could be protective against cancer stemmed from the observation made in the 1970s that people who ate a lot of carrots had a lower cancer rate than the average. I seem to remember that drinking carrot-juice was quite popular at this time, and that some people who overdid their consumption of it found their skin turned orange in places! However, there are many other substances present in actual plant material, which might act in some as yet unknown fashion in regard to inhibiting the development of cancer. In the early 1990s, trials of Vitamin E looked to be a resounding success in regard to preventing heart disease. In two studies involving over 127,000 people, it was found that those who consumed a diet rich in Vitamin E had a significantly (40%) lower incidence of cardiovascular disease than those who didn’t. It was found that the addition of Vitamin E to blood samples in vitro seemed to protect LDLs against oxidation, which was believed to be a central modality in the development of heart disease. Sales of Vitamin E soared, with 23 million Americans taking it by the end of the decade, and yet the results of various studies on Vitamin E supplements rather than as present naturally in the diet, are inconsistent in terms of overall health benefits.11,14

The Alpha-Tocopherol, Beta-Carotene (ATBC) Trial14 was a cancer prevention study conducted by the U.S. National Cancer Institute (NCI) and the National Public Health Institute of Finland from 1985 to 1993. It’s aim was to determine whether certain vitamin supplements would prevent lung cancer and other cancers in a group of 29,133 male smokers in Finland. The participants (aged 50-69) took a pill daily over a period of 5-8 years containing either: 50 milligrams (mg) alpha-tocopherol (a form of Vitamin E), 20 mg of beta-carotene (a precursor of vitamin A), both, or a placebo. The main results were as follows, and might be described as “mixed” in their benefits:
•  Men who took beta-carotene had an 18% increased incidence of lung cancer and an overall death rate of 8%. Vitamin E had no effect on the incidence of lung cancer or overall mortality. Similar results were found for taking both supplements to those taking beta-carotene alone.
 •  The effects of beta-carotene appeared more adverse in men with a relatively modest alcohol intake (more than 11 grams per day; 15 grams of alcohol is equivalent to one drink) and in those smoking at least 20 cigarettes daily.
•  Those taking vitamin E had 32% fewer cases of prostate cancer and the death-rate from prostate cancer was reduced by 41%. However, death from hemorrhagic stroke was increased by 50% in men taking alpha-tocopherol supplements, primarily among those with high blood pressure.
 •  The results of both the trial and post-trial follow-up of the ATBC Study, in conjunction with results from the CARET Study (Beta-Carotene and Retinol Efficacy Trial) completed in 1996, continue to support the recommendation that beta-carotene supplementation should be avoided by smokers. The possible preventive effects of alpha-tocopherol on prostate cancer require confirmation in other ongoing trials.14

Can Vitamin Supplements Cut the Benefits of Exercise?
To explore the possibility that antioxidants might interfere with the beneficial effects of ROS in preventing cellular damage after exercise, Michael Ristow9 at the University of Jena in Germany and his colleagues recruited 40 volunteers, and asked half of them to take 1000 milligrams of vitamin C and 400 international units of vitamin E per day. These quantities are equivalent to the amounts present in some vitamin supplements. The volunteers were also asked to exercise for 85 minutes a day, five days a week, for four weeks. The results from muscle biopsies showed a two-fold increase in a marker of ROS called TBARS (thiobarbituric acid-reactive substances) in those volunteers who didn't take antioxidants, but no increase in those who did take the supplements, in line with the accepted picture that ROS are generated during exercise and that antioxidants intercept them.

It is well known that exercise can promote a reduction in insulin resistance, which is a precursor condition to type 2 diabetes. However, when Ristow's team measured the effects of exercise on insulin sensitivity, they found no reduction in those volunteers who were taking antioxidants, but a significant decrease in those not taking them. Thus it might be concluded that antioxidants are preventing the health effects of exercise, though it should be noted that not all vitamin supplements contain such high doses of vitamin C and E, which are also far higher than would be obtained from eating the recommended amount of fruit and vegetables.  The positive effect on health from eating fruit and vegetables may be because they contain other protective compounds, and taking vitamin supplements is no substitute for them. Malcolm Jackson at the University of Liverpool is reported as commenting9: "These data are fully in accord with recent work on the actions of ROS in cells, although clearly at odds with the popular concept that dietary antioxidants are inevitably beneficial."

Antioxidant Therapies?
The issue of antioxidants acting as defenders of the body against ROS has been extended to their use in medical therapies.15 If antioxidants present in the diet can protect against damage to the organism by ROS and the development of various diseases, it might be plausible to treat various illnesses with antioxidants. This at least goes the line of reasoning, which is similar to the case for taking dietary antioxidant supplements, although as we have seen this is a fairly weak case at best. However, few antioxidants including edaravone (to treat ischaemic stroke in Japan) have found accepted clinical use. Moreover, many well-known substances including antioxidant vitamins (A, C and E), and more recently developed materials like nitrones (also used as spin-traps for radicals in Electron Spin Resonance investigations16) have not unanimously passed the scrutiny of clinical trials that they are effective in the prevention and treatment of various diseases. To date, there have been several large (>7,000 participants) clinical trials aimed to test the effectiveness of antioxidants as cancer prevention agents specifically, none of which have been convincing.17 A recent review18 emphasises the complexity of cancer and its development and the importance of eliminating as far as possible exposure to environmental carcinogens including carcinogenic metals, concluding that “prevention, as in all threatening aspects of life, being better than cure.”

Positive Roles for ROS?
As noted, antioxidant defences are not 100% effective, since oxidative damage to DNA, proteins, and lipids can be proven to occur in all aerobes under ambient levels of O2. A simple explanation for why nature has not developed a means to soak-up all ROS is that they perform important roles. It is likely that evolution had to evolve a compromise of antioxidant defences that allow such roles to be played while minimizing oxidative damage.  ROS production in animals by phagocytes and by other cells in the gastrointestinal and respiratory tracts act to defend against microorganisms. It is well-established2 that cellular processes are regulated by phosphorylation and dephosphorylation of enzymes and transcription factors, and as has become clear more lately, such regulation by oxidation and reduction (redox regulation) is just as important. Moreover, the two systems cross talk, i.e. the redox state of the cell influences phosphorylation, and vice versa. Binding of ligands to growth factor receptors on animal cells activates protein kinases that then phosphorylate and activate subsequent proteins in the signal cascade. Frequently and simultaneously, cellular ROS levels increase and aid the signalling mechanism. ROS tend not to stimulate phosphorylation directly but rather they increase net phosphorylation by inhibiting protein dephosphorylation. Protein phosphatase enzymes function in cells, but can be inactivated by attack from ROS. The ligand binding increases kinase activity, and the ROS assist by transiently inactivating phosphatases. As a source of ROS, the ligand may increase O2•– production, e.g. by activating suproxide-producing NADPH oxidase enzymes. These were originally described in phagocytes, but are now known to be widespread in animal and plant cells. When cells are exposed to additional amounts of H2O2 such as at a site of injury or inflammation or when NADPH oxidase enzymes are activated, the peroxiredoxins are partially inactivated to allow signalling. The cell smartly makes more peroxiredoxin, and reactivates the inactive form, so that the extra H2O2 can be removed once it has served its purpose.2 Rather than being a consequence of a leakage of electrons, mitochondrial H2O2 production may provide a signal to the cytoplasm and nucleus of mitochondrial activity, leading to changes in nuclear gene transcription via redox regulation and phosphorylation of transcription factors.

Humans have evolved in an atmosphere containing 21% O2, and derived therefrom, ROS are ubiquitous in ourselves and other animals, and in plants and aerobic bacteria.  Over the long human lifespan, continual and accumulated damage by ROS may contribute to the age-related development of cancer, neurodegenerative diseases, and many other disorders which ultimately urge our decline and demise. As we age, the repair of this damage seems to become less efficient. It is interesting that the concentration of oxidised protein taken from different human tissues and from rats and flies, creatures of far shorter longevity than humans, is almost constant up to about half the life-span of the species, whereupon it accumulates rapidly, and dramatically so during the last third of the lifespan.19 In terms of a human lifespan it would seem that after around the age of 40 we oxidise profoundly and inexorably. Whether this is a cause or a consequence of ageing is arguable, since as we have seen that elevated levels of ROS appeared to extend the lives of worms while treatment with antioxidants shortened them.  It is likely that ROS act as agents to kill microbes and protect us against infection, although we have noted one study that showed it was the release of proteolytic enzymes rather than ROS from white blood cells that enabled them to combat pathogens.8 ROS also play an essential and exquisite role in cell signalling mechanisms. Thus ROS may help to preserve us until our own reproductive years are concluded and the next generation has reached maturity, i.e. after the age when severe oxidation sets-in at around 40. Evolution is thoroughly pragmatic and unsentimental about such matters. The evidence is poor20,21 that taking vitamin supplements unequivocally protects us against diseases and that therapies against cancer and other diseases using antioxidants is effective. Indeed, smokers should be very careful about taking some supplements, particularly beta-carotene, which appears to increase the incidence of lung-cancer.13,14 When people are actually deficient in a vitamin, giving them extra quantities up to the recommended daily amount appears beneficial, but this may have nothing to do with the antioxidant activity of the compound which may serve a variety of biological functions.

Although there is convincing evidence from a study of nearly 500,000 subjects that consuming more than 200g of fruit and vegetables per day does protect us against developing cancer, the effect is quite small (3%).10 This, nonetheless, translates into around 7,200 cancer cases each year just in the U.K. which if prevented represents a considerable saving to the N.H.S. especially in these stringent times. It is possible that the effect of eating a diet rich in fruit and vegetables may offer some protection against cancer by some other means than the antioxidant content of these foods.20,21 Moreover, perhaps it is the “Mediterranean Lifestyle” overall that matters, and not only the diet. It is notable that much higher intakes of ca 600g/day appeared to give a protection of as much as 11% against developing cancer.10 However, the sample was much smaller and it seems likely that the lifestyle of anyone with such eating patterns differed in other respects too: less smoking and less drinking alcohol, less meat and less saturated fat, less body fat, higher dietary fibre, more exercise, and possibly a less stressful approach to life. It is likely that the human body has been adapted by evolution to adjust the balance between ROS and antioxidants so finely that the intake of additional antioxidants has but a minor influence, and so the degree of oxidative damage is little reduced. In a way, it is reminiscent of the concept of “inbuilt obsolescence”, that we cannot live forever and are designed not too, to make way for the newer and fresher generation on whom we may place our hopes.

(1) Halliwell, B. and Gutteridge, J.M.C. (2007), Free Radicals in Biology and Medicine, 4th Edition, Oxford University Press U.S.A.
(2) Halliwell, B. (2006) Reactive Species and Antioxidants. Redox Biology Is a Fundamental Theme of Aerobic Life. Plant Physiology 141, 312-322.
(3) R. Gerschman, D. L. Gilbert, S. W. Nye, P. Dwyer, W. O. Fenn, Oxygen Poisoning and X-irradiation: A Mechanism in Common. Science 119, 623-626 (1954).
(4) Denham Harman, Aging: A Theory Based on Free Radical and Radiation Chemistry. J. Gerontol. 11, 298-300 (1956).
(5) Slater, T.F. (1966) In vitro effects of carbon tetrachloride on rat-liver microsomes. Biochem. J. 101, 16p.
(6) Rhodes, C.J. and Dintinger, T.C. (1999) ESR Studies of Lipids, in Spectral Analysis of Lipids, R.Hamilton and J.Cast, eds., Sheffield Academic Press, Sheffield.
(7) Zhang, M. et al. (2010) NADPH oxidase-4 mediates protection against chronic overload load-induced stress on mouse hearts by enhancing angiogenesis. PNAS, 107, 18121-18126.
(8) Ahluwalla, J et al. (2004) The large-conductance Ca2+-activated K+ channel is essential for innate immunity. Nature, 427, 853-857.
(9) Free Radicals Good For You? Banned Herbicide Makes Worms Live Longer.
(10) Boffetta, P. et al. (2010), Fruit and Vegetable Intake and Overall Cancer Risk in the European Prospective Investigation Into cancer and Nutrition. JNCI, 102, 529-437.
(11) Melton, L. (2006) The antioxidant myth: a medical fairy tale. New Scientist, August 5th, 40-43.
 (15) Firuzi, O. et al. (2011) Antioxidant Therapy: Current Status and Future Prospects. Curr. Med. Chem., 18, in press.
(16) Rhodes, C.J. (2011) Electron spin resonance. Part one: A diagnostic method in the biomedical sciences. Sci. Prog., 94, 16-96.
(17) Goodman, M. et al. (2011) Clinical trials of antioxidants as cancer prevention agents: past, present and future. Free Rad. Biol. Med., 51, 1068-1084.
(18) Valko, M. et al. (2006) Free radicals, metals and antioxidants in oxidative stress-induced cancer. Chemico-Biological Interactions, 160, 1-40.
(19) Levine, R.L. and Stadtman, E.R. (2001) Oxidative modification of proteins during aging. Experimental Gerontology, 36, 1495-1502.
(20) Halliwell, B. (2007) Dietary polyphenols: Good, bad, or indifferent to your health? Cardiovscular Research, 73, 341-347.
(21) Gutteridge, J.M.C and Halliwell, B. (2010) Antioxidants: Molecules, medicines and myths. Biochem. Biophys. Res. Comm., 393, 561-56

Sunday, December 22, 2013

How to Cut Home Energy Use by One Quarter: "Transition Lifestyles".

Since joining Transition Town Reading, a couple of years ago, we have begun to think carefully about how much energy we use at home. The mandatory installation of a smart-meter has proved a useful aid, as rather like a traffic light system, it goes from green, which is more or less the stand-by situation, through a warning amber, e.g. when we switch the electric kettle on, to red for danger, when the kettle, washing machine and the electric immersion heater have all cut-in together. The price is shown too, which certainly brings home how much of our resources are being consumed at particular moments in time, and by which devices. The figures are given below, so that a comparison can be made for the final two quarters of last year (2012) and this one (2013).

Some figures from our electricity bills:

2013 Q4    Usage 708 kWh cost £105.98
2012 Q4    Usage 942 kWh cost £133.72

2013 Q3    Usage 646 kWh cost £101.06
2012 Q3    Usage 839 kWh cost £121.55

The way electricity is priced can appear to have a somewhat nebulous quality, and so it is more meaningful to look at the kWh figures directly, rather than to try and use cost as a gauge of energy usage. As a matter of fact, we changed tariff in July/August, and while the current tariff includes a standing charge, the previous one did not. Our current tariff charges 12.39p/kWh. The previous tariff charged one price for the first 25% of the electricity used and a different one for the remainder. In price terms, the differential is 20.7% and 16.9%, respectively, for the third and fourth quarters of the years 2012/2013, or an average of 19%, and so we can say that we have knocked a fifth off our electricity bill, which is no mean feat. Yet more strikingly, the kWh figures reveal decreases of 24.8% for the final quarter and 23.0% for the penultimate quarter, and thus we have reduced our actual electricity use by about a quarter, and without experiencing any particular discomfort. So, how have we done it?

As noted, the smart-meter gives a visual alarm of when we are really getting through the juice. Probably this triggers a psychological response to simply switch things off! We have also efficiently draught-proofed the house, putting draught-excluder around the external doors, and closing full-length curtains across the doorways. Another saving is that whereas we used to run the washing machine every day, with just small loads, now we pile it all up and do a (twice) weekly wash, in fact much as folk used to, certainly when we were kids!

We have introduced a "shredded-paper box" which is based on the "hay-box" principle, and we often cook a meal (a stew, say), by getting it started by simmering it on the hob for half an hour, then covering the pot with its lid and putting the whole into the box, which contains shredded paper as an insulating material. The food then cooks (usually overnight) for maybe 12 hours, by which time meat is really tender, and the pot is still warm from the initial input of energy. This is a very efficient way of cooking. Also only one "cook" is involved, it being necessary to merely warm up portions for meals over the next few days, or whenever we want to eat it.

One other deliberate innovation is that, while we used to keep the immersion heater on all the time, now we heat up a tank-full of water and then switch the heater off. The present tank is very well insulated, and will keep water hot for three days or so, by which time we have used most of it anyway. We were alerted to the fact that this tank, which we had installed about a year ago, was much better insulated, and hence gave out much less warmth than its predecessor, when the cat moved out of the airing cupboard. The animal used to spend its winter days asleep in there, kept warm by the water tank, and its energy losses, but now has had to find warmer quarters elsewhere in this domicile.

The main reason for turning the water heater off as much as possible was not to save energy (I have heard the argument that to keep the heater switched on, so that the amount of energy being drawn is regulated by the thermostat, actually uses less energy, but I am not convinced this is true) but rather that since this is a hard-water area, the hot element encourages the lime-scale to precipitate from the water, and onto the element itself. Thus has been the demise of several immersion elements and a few hot water tanks over the past twenty odd years! Only time will tell if this strategy is sound for prolonging the life of the element, which has normally needed replacing every 3 years or so.

The final contribution to using less energy is serendipitous, since we suddenly realised that we no longer (or only rarely) needed to run the dehumidifier. Until about 7 years ago, we had only single-glazing. The result was that when the weather was cold, the moisture from the air used to condense on the window panes overnight, and by morning the windowsills were practically covered by pools of water, which we used to simply mop up with a cloth and wring out into a sink. Then, we had double-glazing installed to provide better insulation. Naturally enough, this worked wonderfully, and to the extent that there was no longer any condensation via the windows, but plenty in the kitchen and especially the bathroom, where mould began to thrive. Thus, for the first time in our many years living here, we bought a dehumidifier, which seemed irksomely ironic, since we were now using more electricity, to cure a problem that we had created by implementing an intended energy-saving strategy in the first place.

On the advice of a local energy consultant and former builder, Dr Tony Cowling, whom we know through being members of Transition Town Reading, each morning, we now open all the windows for about an hour. Although it is counter-intuitive to the uninitiated (as we were) - i.e. thinking that you want to keep the wet, moist air out of the house, especially during the cold, wet, snowy winter period - in fact the air inside the house is always far more humid than that outside. So, open the windows and out it goes! The outcome is that we no longer have mould growing, and there is no need to run the dehumidifier, which saves on electricity.

All in all, this represents an appreciable saving both of energy and money, and really with precious little effort or inconvenience.

What about gas?

As an update (14-4-14) to this article, our gas bill has just arrived for the first quarter of 2014, which compares with the same quarter of the previous year (2013) as follows:

2014 Q1   Usage 1,307.25 kWh  cost £72.39
2013 Q1   Usage 1,927.57 kWh  cost £97.34

Hence, our usage is down 32% on the same period last year which is hardly surprising since we've had mild weather compared with the same period last year. But last year's was slightly down on the previous year as well.

Jumpers and cardigans rule - OK!!!

Friday, December 13, 2013

"University Shambles" Wins Authors Show 2013 Contest.

Winner of the 2013 The Authors Show contest: the novel "University Shambles".


Write-up of a Lecture to the Ethical Society, given at Conway Hall, Sunday 3rd of March (2013), 11.00: "How to Ruin the Best University System in the World." Given by Professor Chris Rhodes: author of the novel "University Shambles" (a black comedy).

(First published in the Ethical Record - The Proceedings of the Conway Hall Ethical Society. April 2013, p12-15). 

Tony Blair, shortly after his inauguration in 1997 as Prime Minister of Great Britain famously said that we needed, “Education, Education, Education”, and that 50% of our young people should attend university. It is not clear exactly what analysis produced this proportion exactly, but currently, the figure is 47%, so the wish has almost been fulfilled. The expansion of the university and higher education sector began long before Mr Blair, and by the time Harold Wilson came to power as Prime Minister in 1964, a wave of new universities had already been initiated, including Sussex, York, UEA, Kent, Warwick and Essex, the so called “plate glass” universities. In 1992, shortly after Margaret Thatcher had stepped down as leader of the Conservative party and Prime Minister, with John Major assuming that role, the binary divide between the universities and the polytechnics was abolished, and the expansion of the entire university sector was urged-on in earnest, and at an unparalleled scale. It is of historical interest, and germane to this discussion, to consider the origins of the various universities, which initially were Oxford, and then Cambridge, followed by the other “ancients”, e.g. St. Andrews, Glasgow, Edinburgh and Dublin, acknowledging others, such as Durham and Manchester Victoria in the nineteenth century, with the creation of the red brick universities (Liverpool, Manchester, Bristol, Birmingham, Leeds and Sheffield) in the first decade of the 20th century.

The University of London was created in 1836, by the merger of University College and Kings College, and though with older roots, Imperial College was formally established in 1907. In the city’s East End, the educational component of the People's Palace was admitted on an initial three-year trial basis as a School of the University of London on 15 May 1907 as East London College. In 1910 the College's status in the University of London was extended for a further five years, with unlimited membership being conferred in May 1915. The polytechnics were institutions of a different kind, but some can trace their roots back to the mechanics institutes of the 1820s, and the London Polytechnic to 1838. Around 30 new polytechnics were formed in the 1960s expansion of higher education, and it was Tony Crosland - Secretary of State for Education and Science (1965‒67) – who created the “binary system”. Polytechnics focussed more on “high quality vocational work” and initially on engineering and applied science. Their awards, from B.Sc. through to Ph.D., were validated by the Council for National Academic Awards (CNAA). Among the innovations of the polytechnics were “sandwich degrees” and part-time courses, which were especially appropriate for “professions”, such as engineering, town planning, law, architecture, and for training science technicians. There was far less emphasis on research than in the universities, which tended to be “applied” and often connected to local industry.

By about 1973, practically all the university posts had been filled, in many cases by protégés of the great and the good, often with no formal interview, with little demographic chance for new blood for many years to come. The 1970s saw a rise of militancy and industrial strife in Britain, which culminated in the Winter of Discontent in 1979, with rubbish piling up in the streets, bodies going unburied, and power being seized from Labour by the Conservatives, led by Margaret Thatcher, “The Iron Lady”. As part of an effort to control the trade unions, which had run amok in the previous decade, causing Britain’s competitiveness to decline, especially against the ascending Far East, the Thatcher government began to cut subsidies from industries that were deemed unprofitable, e.g. coal and steel production. The result of this was that the number of unemployed rose to 3 million, and as a countermanding measure, during the 1980s, some 2.5 million were taken from this register and placed on invalidity benefit (“on the sick”), thus setting the seeds of the current “benefits culture”, in an act of political manoeuvring but with dire social consequences. The university cuts began in 1981, with four technological universities, Salford, Bradford, Aston and Brunel, each losing >30% of their funding. This rationalisation process would continue under Sir Keith Joseph, Secretary of State for Education and Science. In 1985, Mrs Thatcher was ignominiously denied an honorary degree from her alma mater, the University of Oxford, but in the subsequent rationalisation of the universities, a substantial number of small chemistry and physics departments were closed, and now many universities have neither. Indeed, as Mrs Thatcher put it herself, in 1988: “Can an institution that has neither a physics nor a chemistry department be called a university?”

1992 was a momentous year for two reasons: (1) the binary divide between the polytechnics and the universities was abolished and, (2) the format of the later Research Assessment Exercise (RAE) was introduced. This would ultimately multiply the number of students attending “university” by nearly 400% (2010/11, 47%). However, it also created a bottom layer in a league of (now) 116 universities, while the effect of the RAE concentrated most of the research funding in the top 10. Formerly, the polytechnics received their own funding from local authorities, but along with the other universities, were funded by the HEFCE once all had been awarded university status. So, what was the real reason for re-branding the polytechnics as universities? Was it all aimed in the service of inclusiveness and greater opportunities for the nation’s youth? Not entirely. The collapse of the “old” manufacturing industry in 80s, then recession, meant that record numbers of unemployed 18–24 year olds were projected, and a huge embarrassment for a government that wants to be re-elected. In parallel, due to the decline in British industry, the polytechnics effectively lost their original role. Through the expediency of renaming the polytechnics as universities, and expanding the student population by a factor of four, vast numbers of young people were kept from the unemployment figures, being in education instead. The expansion was however not funded accordingly, and spending per student fell by 40%.

The quality of professors, in the enlarged corpus of universities, is hardly uniform, since in some (mostly new) universities, there are many “professors” with practically no published work. In some subjects, e.g. “pharmacy practice”, awarding a “professorship” is the only way candidates can be paid sufficiently to attract them from the private sector, but irrespective of their academic quality. The latter situation now applies in both the old and newer universities. With such large numbers of students to teach, the character of the job of an academic has changed immeasurably, and there are many staff now employed on teaching-only contracts. All universities have also become much more bureaucratic than they were, in part stemming from the local-authority roots of the polytechnics. It is of concern, that 36% of those graduating since 2005 were employed in sales and customer service roles in 2011, including sales assistants, cleaners, waiters, shelf-stackers, bar-staff, hotel porters and call centre staff, while 14% graduating since 2005 were unemployed in 2011. So, of those graduates who are employed, 42% are in low-skilled jobs. One in three applications for this year’s graduate vacancies are from students who had  graduated last year, or before, and while there are 10 million graduates in the U.K., there are only 9 million “graduate level” jobs. The question arises then, is it really worthwhile to incur a debt of £30,000 to end up working in a job that a school-leaver could have done? It is likely that the increase in fees from £3,000 to £9,000 in 2012, raising that debt to perhaps £50,000, will prove to be a critical element in providing an answer. Certainly, 18 year olds that I have spoken to, are not taking going to “uni” as a right of passage, but considering other options, including apprenticeships. The recent indicators are consistent with a progressive drop in the number of applications, and a declining number of applicants actually taking up university places when offered to them.

A major fault is that the system was expanded overly and too rapidly, and with scant regard to the subjects being studied. The introduction of a “bums on seats” funding policy forced universities to accept the vast additional numbers of students, but the system is now producing more graduates than there are graduate-level jobs. The polytechnics adopted the trappings of universities, but with neither the traditions nor the standards, and tragically, in so doing, good polys lost their strong vocational role in education and society and became bad universities. As noted, the bottom half of the league table of universities are all ex-polys. The quality of the system has been eroded further by a lack of proper standards being implemented over academic promotions: professorships and readerships. The universities have also been over-bureaucratised, with support staff becoming managers over the academic staff, and hence a significant shift in the power base has occurred. By way of remedial action, Professors and Readers should re-apply for their titles against proper national standards for which an independent body is necessary to validate the quality of such candidates, who should be demoted or removed, if found wanting - e.g. to be a science professor, you should be of the quality to be awarded a D.Sc. The system overall needs restructuring, with the former polytechnics in part looking to their roots, as good local colleges, providing more work-related and practical training. Professor Michael Brown, a former Vice-Chancellor of Liverpool John Moores University, stated that the current system was “not fit for purpose”, in regard to preparing graduates for the work-place, and introduced a “World of Work” “WOW” certificate. WOW runs in parallel with the student’s degree programme, and provides training in teamwork, negotiating skills, and a whole host of potentially very useful abilities. It is well regarded by the CBI and by potential employers. Professor Edith Sim, the Dean of Science at Kingston University, has stressed the importance for all universities in improving their relationships with business, but particularly those such as Kingston. Indeed, it is universities like Kingston, ex-polytechnics and mainly teaching-led, who are likely to suffer most under the government austerity cuts, removing 80% of their teaching funding, in comparison with 40% being cut from university research budgets overall.

For a while, Reading College was part of Thames Valley University, following a merger between the two institutions, but TVU has since been disbanded, and RC has gone back to its former name. RC runs apprenticeships with local businesses; catering and hospitality; travel and tourism; motor vehicles; hair and beauty; plumbing, gas and heating; bricklaying; electrical installation and design; barbering; horticulture. It is surely not necessary that every subject be taught in a university, or that it should necessarily be a degree, e.g. catering, tourism, golf-course management, and hotel management. Some degrees fare worse than others, especially in such a tough market, e.g. media and communications, for which employment is down 40% on last year. Not all courses described as apprenticeships are the same, and Michael Gove, the Education Secretary, has emphasised the necessity of raising the bar on all such schemes to ensure a common and high standard, perhaps on a par with Germany and Switzerland, nations where technical training is taken very seriously.

In respect of how our future education system and universities will be, the unseen game changer is Peak Oil, which the Canadian economist, Jeff Rubin, has described as “running out of the oil we can afford to burn” The cost of fuel will continue to rise, meaning the “kiss of death” to the global economy. The U.S. now makes little of its own steel, and instead, ore is mined in South America and brought to China, where it is turned into steel, and the steel is then transported to the U.S. Cheap labour and cheap fuel make this strategy possible, but as fuel costs rise, it will become cheaper to do the mining and processing in the U.S., thus rebuilding the U.S. steel industry, and creating hundreds of thousands of jobs in the process. Many industries could be home-grown and we will need many practically trained people, meaning a requirement for fewer universities in their present form, but more colleges. Hence universities must adapt, and are probably entering another transitional phase, no less dramatic than that which began in 1992.

Thursday, November 28, 2013

Applications of Bioremediation and Phytoremediation.

This article has been published in the journal Science Progress, which I am an Editor of. You can download a free pdf version, with figures etc. from this link:


The decontamination of soil and water from pollutants using microorganisms (bioremediators) is known as bioremediation1. There are essentially two approaches, described as in situ and ex situ. In situ methods are those in which the contaminated material is treated at the site, whereas when the material is physically removed to be treated elsewhere it is referred to as ex situ. Some technologies that are related to bioremediation include those of phytoremediation2,3, and are outlined below. It is possible for bioremediation to occur under natural conditions, or it can be stimulated, e.g. by the application of fertilizers (biostimulation), and more recently it has been shown that through the addition of matched microbe strains to the medium, the effectiveness of the resident microbe population to decompose contaminants may be enhanced. It should not be imagined that every type of contaminant can be disposed of by means of this approach, and e.g. heavy metal contaminants, such as Cd2+ and Pb2+, tend to resist interception by microorganisms, which can at best change their oxidation state so that the solubility of the cations is decreased. The better way is to physically remove heavy metals using phytoremediation, by which the toxins are bioaccumulated into the body of plants, above ground, which can then be harvested and removed. By measuring the Oxidation Reduction Potential (redox) in soil and groundwater, along with pH, temperature, O2 tension, concentrations of electron acceptors and donors, and of decomposition products, such as CO2, a measure of the bioremediation process can be obtained. Table 1 shows different biological decomposition processes, the rates of which decrease in decreasing order of the redox potential (fastest at higher potentials), although the detail of the overall bioremediation process per se is only scantly indicated by such values. To gain insight over a larger area, sufficient measurements should be made on and around the contaminated site such that contours of equal redox potential can be drawn. It is further necessary to perform analyses to ascertain that the levels of the contaminating compounds (and their products of decomposition) are below regulatory limits.
Table 14. Biodegradation processes of decreasing rate according to decreasing redox potential.
 Redox potential
(Eh in mV
O2 + 4e + 4H+ → 2H2O
600 ~ 400

2NO3 + 10e + 12H+ → N2 + 6H2O
500 ~ 200
  Manganese(IV) reduction
  MnO2 + 2e + 4H+ → Mn2+ + 2H2O    
400 ~ 200
Iron(III) reduction
Fe(OH)3 + e + 3H+ → Fe2+ + 3H2O
300 ~ 100
Sulfate reduction
SO42− + 8e +10 H+ → H2S + 4H2O
0 ~ −150
2CH2O → CO2 + CH4
−150 ~ −220
Bioremediation can be used in locations that cannot readily be treated other than by excavation, e.g. spillages of petrol or chlorinated solvents which may contaminate groundwater. This is usually a much cheaper approach than excavating material to be disposed of elsewhere, or through other ex situ strategies, and which reduces or eliminates the need for "pump and treat", which is often employed where clean groundwater has been contaminated. The process may be enhanced by the addition of appropriate oxidising or reducing amendment agents. There is scope too for the creation of genetically modified microorganisms that are specifically tailored for bioremediation5, e.g. the most radioresistent organism known so far, the aptly named bacterium Deinococcus radiodurans has been modified to consume and digest toluene and mercury cations in the presence of high level nuclear waste6.
Some applications of microbial biodegradation.

The move toward finding “green” ways to ameliorate many environmental woes, including dealing with polluted environments, has led to a rising focus toward microbial degradation. Such methods of bioremediation and biotransformation exploit the remarkable diversity of xenobiotic metabolism by microbes. Thus, an enormous range of polluting materials may be addressed, including hydrocarbons (e.g. from oil-spills), polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclics, pharmaceutical substances, pesticides, heavy metals (e.g. Cd2+, Pb2+, Cu2+, Zn2+) and various radionuclides (e.g. Cs+, Sr2+). Detailed genomic, metagenomic, proteomic, bioinformatic and other high-throughput analytical techniques, as applied to environmentally important microorganisms, have disclosed key features of critical biodegradative pathways and the ability of such organisms to adapt to changing environmental conditions and stress factors. To achieve a truly sustainable society, it is mandatory to reduce the environmental impact of humans, and achieving this through the use of the remarkable catabolic versatility of microorganisms to degrade or convert a variety of polluting compounds is a potential “holy grail”. Through genome-based global studies, unparalleled advances are now possible from in silico (meaning, "performed on a computer, or by computer simulation") views of metabolic and regulatory networks, along with providing insight into the evolution of degradation pathways and of molecular adaptation strategies in microorganisms, at the behest of changing environmental conditions. The degradation of PAHs provides a good example of the use of these methods7.
While it was formerly considered that the mineralization of aromatic hydrocarbons and halogenated compounds is probably not possible in the absence of oxygen, the more recent discovery of previously unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria has shown that these processes do indeed occur in nature. Through an increasing application of genomics in the field of environmental microbiology, novel molecular insights into these new metabolic properties are now possible. The ~4.7 Mb genome of the facultative denitrifying Aromatoleum aromaticum strain EbN1 was the first to be determined for an anaerobic hydrocarbon degrader. The genome sequence revealed about two dozen gene clusters, which included a number of paralogs, in a coding for a complex catabolic network for anaerobic and aerobic degradation of aromatic compounds. Genomes of anaerobic hydrocarbon degrading bacteria were recently sequenced for the iron-reducing species Geobacter metallireducens (accession nr. NC_007517) and the perchlorate-reducing Dechloromonas aromatica (accession nr. NC_007298). Complete genome sequences also determined for bacteria capable of anaerobic degradation of halogenated hydrocarbons by halorespiration are: the ~1.4 Mb genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1 and the ~5.7 Mb genome of Desulfitobacterium hafniense strain Y51. All these bacteria were shown8 to contain multiple paralogous genes for reductive dehalogenases, while unprecedented insights were attained into the evolution of reductive dehalogenation and differing strategies for niche adaptation. Previously, it was demonstrated that Desulfitobacterium chlororespirans – originally evaluated for halorespiration on chlorophenols – can also use some brominated compounds, such as the herbicide bromoxynil and its major metabolite as electron acceptors for growth9. De-iodination is possible too, although the overall reductive mechanism may differ in detail9.
A complete description of Desulfitobacterium hafniense strain PCP-1 has been described, which can convert pentachlorophenol (PCP) into 3-chlorophenol, dehalogenate a number of related chloroaromatic compounds and convert tetrachloroethene to trichloroethene. Four gene loci, encoding putative chlorophenol-reductive dehalogenases (CprA2 to CprA5) were detected, and the products of two of these loci have been demonstrated to dechlorinate different chlorinated phenols. The strain PCP-1 was used at the laboratory scale to degrade PCP, as present in contaminated environments, and it is concluded therefore that Desulfitobacterium hafniense PCP-1 is an excellent candidate to exploit in the development processes for the bioremediation of organohalide compounds10. A report has appeared of the isolation of the ability of the Acetobacterium sp. Strain AG, to reductively debrominate technical mixtures of Octabrominated and Pentabrominated diphenyl ethers11. It should be noted that a critical factor in effective microbial degradation is the amount of the pollutant that is accessible to microorganisms. As an early example, O'Loughlin et al. showed12 that most soil clays and cation-exchange resins accelerated the rate of biodegradation of 2-picoline by Arthrobacter sp. strain R1, as a result of adsorption of the substrate onto the clays, an apparent exception being kaolin. The directed movement of motile organisms towards or away from chemicals in the environment (chemotaxis) is an important physiological response that may contribute to effective catabolism of molecules in the environment. In addition, mechanisms for the intracellular accumulation of aromatic molecules via various transport mechanisms are also important13.
Biodegradation of petroleum and its products.
The ecological toxicity of petroleum is well known, for which seabirds floundering in a thick black soup of crude oil are the “poster child”.  Such marine environments are especially vulnerable to oil spills since coastal regions and the open sea are not readily isolated, and for example, the implementation of boom structures, intended to confine the oil, is of limited efficacy. In addition to such human-induced environmental catastrophes as the Deepwater Horizon disaster in the Gulf of Mexico, a remarkable 250 million litres of petroleum enter the marine environment every year from natural seepages. Oil spills are almost never as long-lived as they might at first appear, however, and the environment cleans them up substantially, given enough time. Recently, some of the agents for this beneficial activity have been identified: the hydrocarbonoclastic bacteria (HCB)14, of which Alcanivorax borkumensis was the first to be completely genome-sequenced. It would appear that other components of petroleum, including heterocyclic compounds, e.g. pyridine- and quinoline- derivatives, are degraded by similar though separate mechanisms as pertain for hydrocarbons.
Optimisation of bioreactors for waste treatment.
The human species generates colossal quantities of waste, which needs to be processed to protect the environment from it. Hence, in deriving a sustainable development programme, the use of living organisms provides a “green” alternative to chemical/engineering solutions which are costly and potentially environmentally damaging in their own right. Bioreactors provide a highly controlled “contained” space in which biotreatment processes can be carried out, in the avoidance of some of the limitations of more “open” systems. Such is the versatility of these devices that a wide range of wastes can be treated under optimized conditions. However, it is necessary to consider the genomic aspects15 of the various microorganisms involved along with their expressed transcripts and proteins. Although this is laborious using conventional genomic approaches, an adaptation of high-throughput methods of analysis – originally developed for medical applications - is now available with which to evaluate biotreatment in confined environments.
Mycoremediation16 (bioremediation by fungi).
Fungi are an essential component of the soil food web, and provide nourishment for the other biota that live in the soil. In the natural ecosystem, a realm of organisms from different kingdoms make their assault on those different substrates that are present. The rate of degradation becomes maximal when there is a good supply of nutrients present, e.g. N, P, K and other essential inorganic elements. Aspergillus and other moulds are highly efficient in decomposing starches, hemicelluloses, celluloses, pectins and other sugar polymers, and some aspergilli can degrade such intractable substrates as fats, oils, chitin, and keratin. Substrates of human origin, such as paper and textiles (cotton, jute and linen) are readily degraded by these moulds, when the process is often referred to as biodeterioration. In 1969, when the Italian city of Florence (Firenza) flooded, it was found that 74% of the isolates from a damaged Ghirlandaio fresco in the Ognissanti church were Aspergillus versicolor. Fungi function through the mycelium, which exudes extracellular enzymes and acids able to decompose lignin and cellulose, the two essential components of plant fibre. In mycoremediation the correct fungal species must be selected to target a particular pollutant, and it is possible thus to degrade successfully the nerve gases VX and sarin. By inocculating a plot of soil contaminated by diesel oil, with mycelia from oyster mushrooms, it was found that after 4 weeks, 95% of many of the PAHs had been converted to non-toxic compounds. It seems that the naturally present community of microbes acts in concert with the fungi to decompose the contaminants, finally to CO2 plus H2O (full mineralisation). In 2007, a cargo ship spilled 58,000 gallons of fuel along the San Francisco shoreline. Hair mats, resembling S.O.S. pads the size of a doormat, were used as sponges to soak up spilled oil. They were then collected and layered with oyster mushroom and straw. The mushrooms broke down the oil and in several weeks the resulting soil was good enough to be used to for roadside landscaping. Wood-degrading fungi are extremely effective in decomposing toxic aromatic pollutants from petroleum and also chlorinated persistent pesticides. Mycofiltration is a similar procedure, in which mycelia are used as a filter to remove toxic materials and microorganisms from water in the soil. A major protagonist of mycoremediation is Paul Stamets, who proposes17 there should be “Mycological Response Teams”, who would employ the approach to recycle and rebuild healthy soil in the area following any incident. 
This may be defined as the treatment of environmental problems by using plants in situ so to avoid the need to excavate the contaminant material for disposal elsewhere. Phytoremediation18,19 may be applied to the amelioration of contaminated soils, water, or air, using plants that can contain, degrade, or eliminate metals, pesticides, solvents, explosives, crude oil and its derivatives (refined fuels), and related contaminating materials. Phytoremediation has been used successfully for the restoration of abandoned metal-mine workings, and cleaning up sites where polychlorinated biphenyls have been dumped during manufacture, and for the mitigation of on-going coal mine discharges. Phytoremediation uses the natural ability of particular plants (“hyperaccumulators”, described below) to bioaccumulate, degrade, or otherwise reduce the environmental impact of contaminants in soils, water, or air. Those contaminants that have been successfully mitigated in phytoremediation projects worldwide are metals, pesticides, solvents, explosives, and crude oil and its derivatives, and the technology has become increasingly popular and has been employed at sites with soils contaminated with lead, uranium, and arsenic. A major disadvantage of phytoremediation is that it takes a relatively long time to achieve, because the process rests upon the ability of a plant to thrive in an environment that is not ideal for normal plant growth.
Advantages and limitations of phytoremediation
  • Advantages:
    • In terms of cost, phytoremediation is lower than that of traditional processes both in situ and ex situ.
    • The plants can be easily monitored.
    • There is the possibility of the recovery and re-use of valuable metals (by companies specializing in “phyto-mining”).
    • It is potentially the least harmful method because it uses naturally occurring organisms and preserves the environment in a more natural state.
    • Trees may be used in phytoremediation, since they grow on land of marginal quality, have long life-spans and a high flood tolerance. Willows and poplars are most commonly used, and can grow 6-8 feet (ca 2 metres) per year. For deep contamination, hybrid poplars with roots extending 30 feet deep have been used, which penetrate microscopically sized pores in the soil matrix and each tree can cycle 100 L of water per day, functioning almost as a solar powered and self-contained pump and treatment system.
    • Phytoscreening is possible, in which plants may be used as biosensors for particular types of contaminants, thus giving a signal of underlying contaminant plumes, e.g. trichloroethene has been detected in the trunks of trees.
    • Genetic engineering may confer improvements to phytoremediation, e.g. genes encoding a nitroreductase from a bacterium, when inserted into tobacco, increased the resistance of the plant to the toxic effects of TNT and the uptake of the material. Plants may be genetically modified to grow in soils even when the pollution levels in the soil are lethal for non-treated plants, and to absorb a greater concentration of the contaminant.
  • Limitations:
    • Phytoremediation is limited to the surface area and depth occupied by the plant roots.
    • Slow growth and low biomass require a long-term commitment.
    • Using plants, it is not possible to prevent entirely the leaching of contaminants into the groundwater (without the complete removal of the contaminated ground, which in itself does not resolve the problem of contamination).
    • The survival of the plants is affected by the toxicity of the contaminated land and the general condition of the soil.
    • Bio-accumulation of contaminants, especially metals, into the plants which then pass into the food chain, from primary level consumers upwards, or requires the safe disposal of the affected plant material, i.e. the plants might be eaten by animals.
    • The procedure is slow.
Hyperaccumulators and biotic interactions.
If a plant is able to concentrate a particular contaminant, to a given minimum concentration (> 1000 mg/kg of dry weight for nickel, copper, cobalt, chromium or lead; or > 10,000 mg/kg for zinc or manganese), it is categorized as a hyperaccumulator. This capacity for accumulation is a result of genetic adaptation over many generations in hostile environments. Metal hyperaccumulation can affect various different factors, such as protection, interferences between different species of plants, mutualism (e.g. mycorrhizae, pollen and seed dispersal), commensalism, and biofilm.
Different possible phytoremediation methods.
Various processes that are mediated by plants or algae might be used to address environmental problems:
  • Phytoextraction — uptake and concentration of substances from the environment into the plant biomass.
  • Phytostabilization — reducing the mobility of substances in the environment, for example, by limiting the leaching of substances from the soil.
  • Phytotransformation — chemical modification of environmental substances as a direct result of plant metabolism, often resulting in their inactivation, degradation (phytodegradation), or immobilization (phytostabilization).
  • Phytostimulation — enhancement of soil microbial activity for the degradation of contaminants, typically by organisms that associate with roots. This process is also known as rhizosphere degradation. Phytostimulation can also involve aquatic plants supporting active populations of microbial degraders, as in the stimulation of atrazine degradation by hornwort.
  • Phytovolatilization — removal of substances from soil or water with release into the air, sometimes as a result of phytotransformation to more volatile and/or less polluting substances.
  • Rhizofiltration — filtering water through a mass of roots to remove toxic substances or excess nutrients. The pollutants remain absorbed in or adsorbed to the roots.
In phytoextraction (or phytoaccumulation) plants or algae are used to extract contaminants from soils, sediments or water into harvestable plant biomass (those organisms that take larger-than-normal amounts of contaminants from the soil are called hyperaccumulators). Phytoextraction has been used more often for extracting heavy metals than for organic contaminants. The plants absorb contaminants through the root system which they then contain in the root biomass and/or move them into the stems and/or leaves. A living plant may continue to absorb contaminants until it is harvested. After harvest, a lower level of the contaminant will remain in the soil, so the growth/harvest cycle must usually be repeated through several crops to achieve a significant cleanup. The process can be repeated to affect further decontamination. There are two forms of phytoextraction:
  • Natural hyper-accumulation, where plants take up the contaminants in soil unassisted.
  • Induced (assisted) hyper-accumulation, in which a conditioning fluid containing a chelator or another agent is added to soil to increase metal solubility or mobilization so that the plants can absorb them more easily. In many cases natural hyperaccumulators are metallophyte plants that can tolerate and incorporate high levels of toxic metals.
Examples of phytoextraction:
  • Arsenic, using the Sunflower (Helianthus annuus), or the Chinese Brake fern (Pteris vittata), a hyperaccumulator. Chinese Brake fern stores arsenic in its leaves.
  • Cadmium, using willow (Salix viminalis): willow has a significant potential as a phytoextractor of cadmium (Cd), zinc (Zn), and copper (Cu), as willow has some specific characteristics like high transport capacity of heavy metals from root to shoot and huge amount of biomass production; can be used also for production of bioenergy in the biomass energy power plant.
  • Cadmium and zinc, using Alpine pennycress (Thlaspi caerulescens), a hyperaccumulator of these metals at levels that would be toxic to many plants, although its growth appears to be inhibited by copper.
In phytostabilization the intention is to stabilize, or contain the pollutant over the long-term. There may be a number of contributing factors to this, e.g. the reduction of wind (soil) erosion by the body of the plant, but the roots of the plant can resist water (soil) erosion, immobilize the pollutants by adsorption or accumulation, and provide a zone around the roots where the pollutant can be deposited in an immobilized form. In contrast with phytoextraction, phytostabilization aims mainly to sequester pollutants in soil around the roots but not in the plant tissues. Hence the pollutants are increasingly less bioavailable, such that exposure to livestock, wildlife, and humans is reduced. Mine tailings may be stabilized by growing a vegetative cap. 
Some plants, e.g. cannas, are able to detoxify organic pollutants - pesticides, explosives, solvents, industrial chemicals, and other xenobiotic substances  - by metabolising them. The metabolic functions of microorganisms living in association with plant roots may also metabolize these substances, as present in soil or water. Due to the complex and recalcitrant nature of many of these compounds, they cannot be broken down entirely (mineralised) to basic molecules (H2O, CO2, etc.) by plants and hence the term phytotransformation represents molecular alterations rather than the complete decomposition of the compound. Phytotransformation may be viewed18 as a "Green Liver" because plants behave analogously to the human liver in processing these xenobiotic compounds, introducing polar groups such as –OH to them. This is known as Phase I metabolism, similar to the way that the human liver increases the polarity of drugs and foreign compounds. In plants, it is enzymes such as nitroreductases which carry out these transformations, whereas in the human liver it is enzymes such as the Cytochrome P450s that perform the task. Phase II metabolism in the second step in phytotransformation, in which the polarity of the xenobiotic molecule is increased by combination with plant biomolecules such as glucose and amino-acids. This is called “conjugation”, and is once more similar to processes such as glucoronidation (addition of glucose) and glutathione addition reactions, catalysed by appropriate enzymes. The effect of the two metabolic steps may serve to detoxify the xenobiotic and aid its mobilization via aqueous channels. In Phase III metabolism, the xenobiotic becomes sequestered, by incorporation in a complex “lignin-type” structure, where it is kept apart from the normal functioning of the plant. The phytotransformation of trinitrotoluene (TNT) has been well studied, and a detailed mechanism proposed for it.

Phytostimulation and rhizoremediation.

This term identifies the process where compounds released from plant roots enhance microbial activity in the rhizosphere, which is the narrow region of soil around the roots of plants, and associated soil microorganisms. Soil which is not part of the rhizosphere is known as bulk soil. In rhizoremediation, microorganisms degrade soil contaminants in the rhizosphere. It is usual that those soil pollutants which are remediated by this method are highly hydrophobic organic xenobiotics that are hence unable to enter the plant. Rather than the plant being a main protagonist in this process, it creates a haven in which microorganisms in the rhizosphere are able to perform the degradation. The plant acts as a solar-powered pump, which draws in both water and the xenobiotic agent, simultaneously producing substrates (e.g. root exudates and root turnover) that assist the growth of the microbes which act as pollutant degrading agents. Microbial activity is stimulated in the rhizosphere through a number of different routes: (i) exudates, e.g. sugars, carbohydrates, amino acids, acetates, and enzymes, nourish indigenous microbe populations; (ii) root systems bring oxygen into the rhizosphere, meaning that aerobic transformations are supported; (3) the available organic carbon is enhanced through the growth of fine-root biomass; (4) mycorrhizae fungi, which are an essential component of the rhizosphere, provide unique enzymatic pathways lending the capacity to degrade pollutant molecules that would not be degraded by bacteria alone; and (5) the presence of plants (and their roots) creates a domain for microbial populations, which are activated in the rhizosphere. There have been five enzyme systems identified in soils: (i) dehalogenase (which acts in dechlorination reactions of chlorinated hydrocarbons); (ii) nitroreductase (essential for the initial step of nitroaromatic degradation); (iii) peroxidase (a critical catalyst for oxidation reactions); (iv) laccase (able to begin the decomposition of otherwise robust aromatic ring structures); (v) nitrilase (another key factor in oxidation processes). The method is limited in that when there are high concentrations of pollutants present, the plants may be overwhelmed and die. The successful use of phytostimulation has been demonstrated in the remediation of chlorinated solvents from groundwater, petroleum hydrocarbons from soil and groundwater and PAHs from soil.

Probably, this is the most controversial of the phytoremediation technologies, since it involves the release of contaminants either directly, or in a metabolically modified form, into the atmosphere. Phytovolatilization20 has been used principally for the removal of Hg2+ ions which are transformed into less toxic elemental mercury21. Tritium (3H), a radioactive isotope of hydrogen with a half-life of about 12 years, decaying to helium, has also been removed by phytovolatilization22. A good deal more research is necessary before this strategy becomes mainstream, since there are various negative features to be addressed. For example, mercury that is released into the atmosphere from plants is likely to be recycled by precipitation and thus returned the ecosystem, and the method is restricted both to sites where the concentration of contaminants is toward the low side, and where the contamination is no deeper than the roots of the plants being used. 
Rhizofiltration23 involves filtering contaminated water through a mass of roots for the extraction of contaminants, or excess nutrients, e.g. phosphorus. The contaminated water can either be collected from a waste site and taken to where plants are being hydroponically cultivated, or the plants may be planted in the area directly. In both cases, the roots draw up the water and its associated contaminants. This process is very similar to phytoextraction in that the contaminants become sequestered in the form of harvestable plant biomass. Then new plants are grown and harvested until a satisfactory degree of decontamination is achieved. It is the concentration and precipitation of heavy metals that is sought principally. While noting these similarities, the fundamental difference between the two approaches is that rhizofiltration is used in aquatic environments, while phytoextraction is applied to the decontamination of soils. There are limitations to rhizofiltration. As usual in phytoremediation methods, any contaminant that is below the rooting depth will not be extracted, and if the level of contamination is too high the plants will not grow. Depending on the type of plant and contaminant, the process may need to be continued over a protracted period, before regulatory levels are achieved. It is generally true that many different kinds of contaminants will be present – in some cases a mixture of organics and heavy metals – and thus the use of rhizofiltration alone is unlikely to succeed. Importantly, the plants chosen should be non-fodder crop to minimize poisoning animals, which might eat them in contaminated form.  That noted, the effective removal of heavy metal cations, e.g. Cu2+, Cd2+, Cr6+, Ni2+, Pb2+, and Zn2+ from aqueous solutions has been demonstrated24, and the removal of low-level radionuclides, from liquid streams25. In that latter application, a “feeder layer” of soil is suspended above the stream through which plants grow, from which the plant roots extend downward into the water. In this way, fertilizer can be used to help the plants to grow, while avoiding adding to the contamination of the stream, while the latter is cleansed of heavy metal cations26. Rhizofiltration is cost-effective when large volumes of water must be treated containing low concentrations of contaminants. Inclusive of the costs of the capital outlay and final waste disposal, the cost of removing radionuclides from water using sunflowers was reckoned (at 1996 prices) at $2─6 per thousand gallons of water treated27.

(4) Meagher, R.B. (2000). "Phytoremediation of toxic elemental and organic pollutants." Current Opinion in Plant Biology 3, 153.
(5) Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology (1st ed.). Caister Academic Press.
(6) Brim, H. et al. (2000) "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments." Nature Biotechnology 18, 85.
(8) Heider, J. and Rabus, R. (2008) "Genomic Insights in the Anaerobic Biodegradation of Organic Pollutants." Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2.
(9) Cupples, A. M., Sanford, R.A. and Sims, G.K. (2005) “Dehalogenation of Bromoxynil (3,5-Dibromo-4-Hydroxybenzonitrile) and Ioxynil (3,5-Diiodino-4-Hydroxybenzonitrile) by Desulfitobacterium chlororespirans.” Appl. Env. Micro. 71, 3741.
(10) Villemur, R. (2013) “The pentachlorophenol-dehalogenating Desulfitobacterium hafniense strain PCP-1.” Phil. Trans. Roy. Soc. B. 368, 1616.
(11) Ding, C., Chow, W.L., Lee,L.K. and He,J.(2013)”Isolation of Acetobacterium sp. 
Strain AG, Which Reductively Debrominates Octa- and Pentabrominated Diphenyl Ether 
Technical Mixtures.” J. Appl. Environ. Microbiol. 79,1110.
(12) O'Loughlin, E. J, Traina, S.J. and Sims, G.K. (2000) “Effects of sorption on the 
biodegradation of 2-methylpyridine in aqueous suspensions of reference clay minerals.” 
Environ. Toxicol. and Chem. 19, 2168.
(13) Parales, R.E. et al. (2008). "Bioavailability, Chemotaxis, and Transport of Organic 
Pollutants." Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic 
Press. ISBN 978-1-904455-17-2.
(15) Dracopoulos, D.C., and Piccoli, R. (2010) “Bioreactor control by genetic programming”, Parallel Problem Solving from Nature, PPSN XI Lecture Notes in Computer Science, 6239, 181.
(18) Burken, J.G. (2004), "2. Uptake and Metabolism of Organic Compounds: Green-Liver Model", in McCutcheon, S.C.; Schnoor, J.L. (Eds.), Phytoremediation: Transformation and Control of Contaminants, A Wiley-Interscience Series of Texts and Monographs, Hoboken, NJ: John Wiley, p. 59, doi:10.1002/047127304X.ch2, ISBN 0-471-39435-1
(22) Dushenkov, S. (2003) “Trends in phytoremediation or radionuclides.” Plant and Soil, 249, 167.
(24) EPA, (1998) “A Citizen's Guide to Phytoremediation,.” U.S. Environmental Protection Agency, Office of Solid Waste and Emergency Response,” EPA 542-F-98-011, August.
(25) Dushenkov, V., Motto, H., Raskin, I. and Nanda Kumar, P.B.A. (1995) "Rhizofiltration: the Use of Plants to Remove Heavy Metals From Aqueous Streams." Environmental Science Technology 30, 1239.
(26) Raskin, I., Smith, R.D. and Salt, D.E. (1997) "Phytoremediation of Metals: Using Plants to Remove Pollutants from the Environment." Current Opinion in Biotechnology. 8, 221.
(27) Cooney, C. M. (1996) "Sunflowers Remove Radionuclides From Water in Ongoing Phytoremediation Field Tests." Environmental Science and Technology 30, 194.