The genera Escherichia is thought to have emerged around 102 million years ago and is known as a gram-negative pathogenic bacteria mostly found in the intestines of warm blooded animals [1]. German pediatrician and bacteriologist Theodor Escherich discovered E. coli in 1885, and for many years the bacterium was simply considered to be a commensal organism of the large intestine. It was not until 1935 that a strain of E. coli was shown to be the cause of an outbreak of diarrhea among infants [2]. The reason its pathogenic properties were discovered so late is that many of its strains are harmless. However, virulent strains of E. coli can cause various diseases in humans and in domestic animals, and are also sometimes responsible for product recalls due to contamination. Gastroenteritis, urinary tract infections, and neonatal meningitis are the most commonly observed diseases in humans, and in rare cases virulent strains are also responsible for haemolytic-uremic syndrome, peritonitis, mastitis, septicaemia and Gram-negative pneumonia [2]. Various outbreaks all around the world have been caused by E. coli, causing millions of deaths and sick people and billions of dollars have been spent fighting it. Even though death rates have decreased with the evolution of modern medicine and the discovery of antibiotics, the outbreaks are still a major concern for all countries, such as the recent outbreak in Germany in 2011 affecting 3,950 people and killing 53 [3].

Its reputation has not been one of great dignity, and it has ruined the reputation of many. You may recall in 1993, the fast food chain restaurant “Jack in the Box” suffered a major corporate crisis involving E. coli O157:H7 bacteria. Four children died of hemolytic uremic syndrome and 600 others were reported sick after eating undercooked patties contaminated with fecal material containing the bacteria at locations in Seattle and the Pacific Northwest, USA. The chain was faced with several lawsuits, each of which was quickly settled but left the chain nearly bankrupt and losing customers.

But don’t these creatures have any properties to be appreciated, I wonder…

Compared to eukaryotic cells, bacteria have a pretty basic mechanism of functioning. They don’t have sophisticated organelles, and they do not have a cell nucleus where their DNA is stored. Everything is floating along all together in the cell cytoplasm (which shocks me when I reflect upon how such a small and simple organism can cause such severe pain on “highly evolved modern humanity”). It has the basic metabolic tools for survival. And even though, at first sight, it is tempting to look down on its simplicity, today we know that it is this simplicity that gives us space for making many modifications and experiments on it, whereas in more complicated cells, like animal cells, the moment a modification is made, the entire system reacts to that and causes much trouble in the process.

The turning point of E.coli making a huge impact on our lives was in 1973, when Stanley Cohen and Herbert Boyer discovered the “Recombinant DNA Technology.” This technology allowed specific genes to be isolated from one organism and cloned to another organism by the help of bacterial plasmids. The first commercial product to be synthesized by this technology was human insulin, which is used for the treatment of diabetes [4]. This brought an amazing amount of recognition and appreciation for the technology, as the practical aspect of the technology was now proven to be commercially profitable. For the insulin to be produced, the DNA sequence that encodes human insulin was synthesized and transplanted into a plasmid that could be maintained in a non-pathogenic strain of E.coli [4]. Now the bacterial host cells acted as biological factories for the production of the two peptide chains of human insulin, which, after being combined, could be purified and used to treat diabetics who were allergic to the commercially available porcine (pig) insulin, or for diabetics from certain religious groups who abstain from pork products such as Muslims, Jews, some Christian groups, and many more who have similar concerns.

This was only the start of an incredible new technology which used bacteria to produce different proteins or enzymes to cure human diseases. Today more than 200 new drugs have been produced by recombinant DNA technology and have been used to treat over 300 million people for diseases such as cancer, multiple sclerosis, cystic fibrosis, and stroke, and to provide protection from other infectious diseases. Over 400 new drugs are in the process of being tested in human trials to treat such diseases as Alzheimer disease and heart disease (to name only two) [4].

Today E.coli is frequently used as a model organism for all kinds of microbiological experiments. In the lab, E. Coli. is one of the first micro-organisms that is thought of for testing a biological experiment. The reason is that E.coli cells are cheap to purchase and to sustain. They grow easily and rapidly in lab conditions and have non-pathogenic strains, so they are not dangerous for the researches doing the experiment. Whereas purchasing more complicated cells such as cancer cells or stem cells may be very costly, and moreover, may need special lab conditions to be sustained; so before more complicated cells are purchased, the experiments are usually tried out with E.coli or some other kind of model organism. More importantly, E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K12 was published by Science in 1997 [5]. Other areas in which modified E.coli has helped humanity are vaccine development, bioremediation (fighting pollution), and production of immobilised enzymes [6].

One specific example of the benefit of recombinant DNA technology for the environment is its use in the paper industry. Before the 1970’s, when there wasn’t much environmental awareness in the paper producing industry, poisonous chlorine compounds were conventionally used to achieve pulp brightness of a high order in the manufacture of high-quality paper products [7]. This chemical bleaching technique precipitated a tremendous environmental concern considering the magnitude of the industry. Plants treated with elemental chlorine produced significant amounts of dioxins. Dioxins are highly toxic, and their health effects on humans include reproductive, developmental, immune and hormonal problems. They are also known to be carcinogenic. Over 90% of human exposure is through food, primarily meat, dairy, fish and shellfish, as dioxins accumulate in the food chain in the fatty tissue of animals [7]. One alternative for these chemical bleaching processes is the use of the enzyme “xylanase,” which degrades the linear polysaccharide beta-1,4-xylan into xylose, thus breaking down hemicellulose, one of the major components of plant cell walls. Even though the use of xylanases in this industry has increased significantly with the discovery of Viikarri et al. (1986), the enzyme needs further improvements for it to be commercially acceptable [6]. To ensure the commercial utilization of hemicellulosic residues in the pulp and paper industries, the production of higher xylanase yields at low capital cost is required [6]. Such studies are ongoing with the purpose of partially mutating the amino acid sequence for the purpose of especially increasing the thermal stability of the enzyme and also increasing its metabolic activity. The gene mutation and gene expressions are generally done in either E.coli or yeast cells. Davoodi et al. has mutated the enzyme up to the point where the transition temperature increased 12 0C by introducing disulfate bonds in the enzyme [8]. The wonders this enzyme can do for the health of the environment is breathtaking, and is an area which should be further studied until finding the commercially viable kind that will eliminate chemicals from the paper industry during bleaching.

Even though some controversy remains on gene transferring, its tremendous positive impact on humanity cannot be denied. I personally think that it does need constraints and strict regulations, but this technique is one of the most remarkable techniques discovered in modern times, and E.coli has no doubt played a great role in the availability of this technology.

Even though condemning E.coli and stating its “evilness” seems like the most obvious path, we all ought to appreciate the variety and uniqueness of these creatures which also allow us to produce such large varieties of drugs. We ought to appreciate its simplicity, which allows it to have a chance of producing such sophistication. We ought to reflect upon the fact that something can be classified as “good” or “bad” only by the means in which we perceive it, and the reality of it may be completely opposite of what we had thought initially.

McPen is a freelance writer in natural sciences, Montana, US.

References

1. Battistuzzi FU, Feijao A, Hedges SB. 2004. “A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land”. BMC Evol. Biol.
2. Todar, K. “Pathogenic E. coli”. Online Textbook of Bacteriology. University of Wisconsin–Madison Department of Bacteriology.
3. “German-grown food named likely culprit in deadly outbreak”. CNN. (5 June 2010).
4. Glick, Bernard, Jack Pasternak, and Cheryl Patten. 2010. “MOLECULAR BIOTECHNOLOGY Principles and Applications of Recombinant DNA . 4th Edition.” Washington,DC: ASM Press, pp. 3-13.
5. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (September 1997). “The complete genome sequence of Escherichia coli K-12”. Science 277 (5331): 1453–62.
6. Cornelis P. 2000. “Expressing genes in different Escherichia coli compartments”. Curr. Opin. Biotechnol. 11 (5): 450–454.
7. Beg, Q.K., M. Kapoor, L. Mahajan, and G.S. Hoondal. 2001. “Microbial xylanases and their industrial applications: a review.” Springer.
8. Davoodi J., Wakarchuk W.W., Carey P.R., Surewicz W.K. 2007. “Mechanism of stabilization of Bacillus circulans xylanase upon the introduction of disulfide bonds.” Biophysical Chemistry, 125 (2-3) , pp. 453-461.

The phosphate and nitrogen compounds found in the waste material that are released into the environment go through some biological processes and are transformed into nourishing salts for the phytoplankton. When there is an increase in temperature, these salts may cause some of the phytoplankton to grow and reproduce excessively. The toxic materials released by some, and the use of excessive oxygen, are harmful to other organisms.

Another example of pollution is related with algae. When the number of microbial plants called algae reaches one million per cubic decimeter (1 million/dm3) of water, the consumption of oxygen required in order to mineralize, and break-down the organic materials found in the water increases, and therefore a compound of toxins which pollute the water, such as hydrogen sulfide (H2S), are released. This pollution can cause the death of fish and other organisms which live in the water. As a result of the reduction in water quality, an increase in the type of algae called cyanobacteria occurs and the biotoxins that they produce threatens human health.

More than forty types of algae produce various toxins. Some of these toxins damage the human liver, some attack the nervous system (particularly the brain), some can cause allergic skin reactions, and some can even induce cancer. The release of domestic, industrial, and agricultural waste and the high percentage of nutrients (such as nitrogen and phosphor compounds) into the aquatic ecosystem can cause an excessive increase of algae in the waters. This algal bloom in fresh water is referred to as eutrophication. In oceans, it is referred to as red tide because the water appears to be a reddish color. Both present a significant environmental problem.

In low doses humans are exposed to these toxins by the consumption of drinking water. In Brazil in 1988, almost 2000 people developed gastroenteritis over a forty day period due to the consumption of drinking water contaminated by these toxins, and eighty-eight of them died. In South Australia, as early as 1878, many sheep, horses, dogs and other animals died as a result of drinking water from Lake Alexandrina, which was covered by scum caused by an aglal bloom called Nodularia spumigena.

Mussels, a delicacy eaten and enjoyed by many, accumulate large amounts of toxins because they feed on phytoplankton. One study found that in fresh water mussels (Mytilus galloprovincialis) that fed on cyanobacteria, almost 10.7 g toxins per gram of bodyweight was accumulated. This is also the case in marine mussels. It has been determined that these toxins in gradually increased concentrations are passed onto organisms higher on the food chain by consumption. Accordingly, we should always consider the potential risk factors before consuming shellfish.

Biotoxins are released into the water after being broken down by algae. Thus, when an algal bloom reaches high levels, there is an increase in the density of toxins in the water. As these toxins dissolve in the water, purifying the contaminated water requires not only expensive, but also advanced technology methods. Unfortunately, it is impossible to remove this waste in many of the existing refining plants. The toxin concentration in drinking and utility water should be reduced in regions where drinking water is obtained from lakes by mixing it with uncontaminated water, particularly during the spring when the algal bloom occurs. Thus, reducing the amount of biotoxins in the water to a level that will cause minimal harm to aquatic organisms should help to reduce the risks to humans.

Many types of waste released into the environment cause damage, which adversely affect humans. Polluting the environment may be easy, but purifying the environment of this pollution is a very difficult task. Indeed, humans were not created to act irresponsibly and destroy the universe in which they are mere guests. On the contrary, the human is a delicate guest with sublime duties. Protecting the natural resources provided for our needs and utilizing these resources in the most productive manner, without disturbing the balance of nature, is a duty of every human on earth.

References

• Pouria S. de Andrade A. 1988. “Fatal microcystin intoxication in haemodialysis unit in Caruaru, Brazil.” Lancet 352:21-26.
• Carmichael W.W., Azevedo S.M.F.O. 2001. “Human fatalities from cyanobacteria: Chemical and biological evidence for cyanotoxins.” Environ. Health Perspect 109: 663-668.
• Codd G.A., Bell S.G., Kaya K., Ward C.J., Beattie K.A., Metcalf J.S. 1999. “Cyanobacterial toxins, exposure routes and human health.” Eur. J. Phycol. 34:405-415.

In the early 1970s, a young graduate student, Richard Blakemore, observed an interesting group of bacteria in a mud sample collected from Eel Pond in Massachusetts. These bacteria were migrating through a certain edge of the microscope slide. Rotating the slide did not affect their motion; they were still moving through north. Repeating the experiment in the dark also showed that it was not light that affected the bacteria’s swimming direction. The experiments left one possible explanation to the directed motion of the bacteria and that was a crazy one-that they were sensing the magnetic field of the earth! It wasn’t hard for Blakemore to place a magnet next to the microscope slide and to prove that the crazy idea was indeed true. The bacteria were attracted by the south pole of the magnet and repelled by the north pole of it. This was the beginning of a new field of an interdisciplinary research, which attracted many scientists from very different fields such as, microbiology, physics, geophysics and paleogeology.

To understand how magnetotactic bacteria feel the magnetic field, it would be useful to check one’s transmission electron micrograph (Figure 1). The chain of magnetite (iron oxide) crystals forming a specialized organelle, called magnetesome, can be seen easily. The length of the whole chain is around one micron and each small crystal is around 50-60 nanometers. Each small crystal can be considered as a small magnet. These small magnets are aligned in a way that they support each other and the chain becomes a strong magnet. A lipid bilayer membrane surrounds this chain and holds them together. Forming chains on a straight line is not an expected behavior for small magnetite crystals. If they are produced synthetically, they accumulate together to form an aggregate. The pathways of chain formation in magnetesome are still an open question.

Magnetotactic properties are not limited to a certain species. There are many different bacteria that have magnetotactic properties. Therefore the magnetesomes may differ in size, length and even in chemistry. Some magnetotactic bacteria have greigite (iron sulfide) minerals instead of magnetite. Alsothere are magnetotactic bacteria that have more than one magnetesomes. (Figure –2)

Magnetesomes passively align bacteria parallel to the geomagnetic field but do not exert a force on bacteria to change their speed. Aligned with the magnetic field, the bacteria decide to either move towards south or north. Interestingly, almost all magnetotactic bacteria in northern hemisphere are north seeking, almost all magnetotactic bacteria in southern hemisphere are south seeking, and magnetotactic bacteria living around the geomagnetic equator consist of almost equal number of bacteria of each magnetic polarity. The bacteria in northern and southern hemispheres may have different polarities but they have one thing in common; they both move downwards. The geomagnetic field is not exactly parallel to the earth’s surface except around the geomagnetic equator. As it may seem in figure-3, the magnetic field lines are tilted up and down respectively in southern and northern hemispheres. Therefore the north seeking bacteria in northern hemisphere end up at the bottom of the water and so do the south seeking bacteria in southern hemisphere. Most of the magnetotactic bacteria cannot survive in atmospheric oxygen levels, so sensing vertical position and moving downwards, where oxygen concentration is low, is crucial for them.

Being north seeking or down seeking, i.e. polarity, is a genetic property for magnetotactic bacteria. Almost all progenies (descendants) of a north-seeking cell are also north-seeking cells. However this requires partition of magnetesomes to each daughter cell during the division. Occasionally, daughter cells may have no magnetesomes or they maybe too small to have a magnetic moment, so they develop their own magnetesomes. When these progenies develop their own magnetesomes they may have either polarity. Therefore any natural population of magnetotactic bacteria has less than 0.5% “wrong” polarity members. Wrong is written in quotation marks because without that “mistake” magnetotactic bacteria would live only in one hemisphere of the earth.

Magnetotactic bacteria are not the only creatures that can sense geomagnetic field. For example birds, also, can sense geomagnetic field and find their direction while they are migrating. However, birds use other factors such as sun and the horizon to find their direction and their body is much more complex. Also they do not sense magnetic field in a mechanical way like magnetotactic bacteria do, but probably they have some complex chemical ways of magnetic reception. That is another research field by itself and this article’s volume is not enough to go into it.

Everything, every entity that we see around us calls us to reflect upon their Creator. The ones that we see with electron microscopes or high-tech tools are not exceptions. Magnetotactic bacteria synthesizes magnetite crystals from scratch and then puts them in an order like beads hitched on a string. Could it be possible for them to manage this incredible task on their own accord and without acting in the name of God? To this day we cannot even understand the basic principles of that process to its complete degree in order to mimic it. In fact, the more we understand the more we esteem and at awe we become from the great craft of Supreme Artist.

Auroras (northern lights), with their beautiful colors, make long winter nights more bearable in Arctic Circle. They are emitted by charged particles, something very harmful for living creatures if ever reached to earth’s surface and trapped in earth’s geomagnetic field. (Figure-4) While thinking about magnetotactic bacteria I remember those beautiful scenes I had seen in pictures that had caught my awe and wonder and can’t help but express deep gratitude once more to the Creator and Sustainer of it all, of us all, who guides the tiny little cells to more livable environments with the very same geomagnetic field that He protects us from harmful solar winds. Extraordinary is the ordinaries we are surrounded by!

Ahmet Uysal is a PhD candidate in Physics at Northwestern University, Evanston, IL.

References

1. Richard P. Blakemore, 1982, “Magnetotactic bacteria”. Ann. Rev. Micrbiol. 36:217-238
2. Dirk Schüler, 2008, “Genetics and cell biology of magnetesome formation in magnetotactic bacteria”. FEMS Microbiol. Rev., 32:654-672
3. Arash Komeili, 2007, “Molecular mechanisms of magnetesome formation”. Annu. Rev. Biochem. 76:351-366
4. Thorsten Ritz, Salih Adem, and Klaus Schulten, 2000, “A model for photoreceptor-based magnetoreception in birds”. Biophysical Journal. 78:707-718
5. http://www.birdgeo.com/images/CTE1810.jpg
6. http://solar-center.stanford.edu/images/solar-wind-magfield_b.gif

As this news spread throughout the world, people began to ask if one day a human being could be cloned. Certainly, at least in theory, it seemed possible. Some people even claimed that it would be a good idea to clone such geniuses as Einstein and others who had passed away. On the other hand, others argued that such knowledge could lead to cloning such people as Hitler, and that this was reason enough never to open the door to this potentially dangerous technology. 

The role of environment

But is DNA everything? Is DNA the only item that makes us human? Case studies of same egg twins’ show that there is more to us than DNA. Researchers have noticed that such twins, despite having the same DNA and being brought up mainly in the same environment and the same manner, somehow follow different paths, acquire unique personalities, and show evidence of different characteristics, although they may show similarities during childhood. Thus we can see that environment is an important factor on human behavior.

Used in this context, environment refers to the surrounding society, culture, belief, and moral values in other words, that which separates human beings from animals. DNA, the acronym used for a person’s genetic code, plays the key role in the beginning of any biological life form. This key molecule functions similarly in both animals and plants to produce living cells.

Human beings have a special life-giving feature: the soul. Although its nature remains a mystery, its existence is felt deeply in the conscience and gives us a distinct nature that is not shared by non-human life forms. Although a person’s first biological body is evident in the DNA even before it assumes an identity, it is the soul that determines his or her character and temper. Another shaping factor that should not be underestimated is the surrounding society (e.g., family, school, and economy) that unites with the soul and contours the body.

The era in which one lives also has a role in determining one’s character. Given that a society is made up of individuals, it is subject to changes in moral values over time. Thus it is quite likely that if Einstein or Hitler were cloned, the resulting person would be an ordinary contemporary man who is obsessed with sports cars and the Internet, and a man who carries his cellular phone wherever he goes.

What made Hitler a monster was the era and society in which he lived, not his genes. What made Einstein a genius was the chance to explore and use his own capabilities and intelligence. It is quite certain that genes are the sole parameters that affect a person’s intelligence and other intellectual features. In addition, the wonderful and unknown nature of a human being would be more conclusive and understandable if the complex interactions between the spiritual properties and cultural effects were taken together as a whole.

The role of the soul

People can be cloned. In fact, clones that are biologically similar and yet behaviorally unique would be the best proof of the soul’s existence. Since the soul cannot be cloned, as it issues from a different world, cloning a person’s body may not be that dangerous. But it also would not make any sense. Moreover, the cloned individual could end up as a dangerous animal.

Consider the following example of inter-species breeding: When a horse and a donkey are mated, the resulting animal is a non-fertile hybrid. If a female horse and a male donkey are mated, the result is a non-fertile mule. If a male horse and a female donkey are mated, the result is a smaller and weaker animala hinny. But since half of the DNA comes from each animal and thus each hybrid offspring has the same DNA, how can this difference be explained? Obviously, the DNA contained within the mitochondria of the female horse’s egg cell makes a huge difference.

Other issues

The patent dilemma: The patent (copyright) system prevents any illegal copying and imitating and ensures that the actual researcher and inventor is rewarded. Drugs and chemical substances are the most patented items in medicine. After a large portion of the human DNA puzzle was solved, the issue of how to patent this information was put on the American agenda.

President Clinton declared that most parts of human DNA had been determined. However, such information was not to be placed in the hands of humanity at large, for the pharmaceutical companies had spent vast sums of money to produce this information. Also, it would be a serious violation of basic commercial sense for the companies to just give this information to the general public for free.

In addition, paying for the copyrights to acquire the technology does not mean that you are totally free to with it what you want, for these same copyrights limit the usage of that particular technology. This means that if cures are found for AIDS, cancer, and other currently incurable diseases, only the wealthy will be able to afford them.

Determining does not mean understanding: DNA consists of exons and introns. Exons form the meaningful parts of DNA by uniting with each other. We call the result genes. Introns are the non-meaningful parts of DNA. What is interesting here is that these non-meaningful introns make up 97 percent of all DNA. One wonders if they have functions, other than protecting and shielding the meaningful parts from external radiation and ultraviolet light, that are unknown to contemporary scientists? For example, each human cell contains about 4 meters of DNA chain in its nucleus. Surprisingly, introns and exons are represented by the same symbolic letters (A, C, G, and T), so determining the DNA chain is nothing more than a new beginning. The more important task is to identify the genes made of exons, which are non-trivially embedded into the introns.

The exact number of human genes remains unknown. According to some scientists, this number is either 25,000 or 32,000. Determining the DNA chain written with a four-letter alphabet is like trying to determine the meaning of an ancient inscription. Just seeing what it looks like does not mean that one can read it, for the latter is far more difficult than the former. This suggests that just determining the DNA chain is not enough, and that truly understanding the genes and their exact locations requires more time.

Conclusion

Human DNA has been determined, but we must remember that there are as many combinations as there are people. Also, the claim that DNA has been determined’ is true only for a select group of people. Human DNA differs from race to race, society to society, and even from disease to disease. Thus it will take more time to develop a full comparative table of human DNA. It would be great if our current technology somehow could devise a single formula to represent the gene map of every individual.

References

• Anderson, Kenneth N. (ed.), Lois E. Anderson (ed.), and Walter D. Glanze. Mosby’s Medical Dictionary. 5th ed. Mosby Year Book, Inc.: 1997.
• Erturk, Hikmet, DNA Her Sey mi?’ Siziniti, no. 269 (June 2001): 228-29. Translated by Emrah Altunkaya.