You need to read “The Very Lonely Firefly,” a story book delighting children of all ages by Eric Carle (1) to get the answer. In the mean time, you can read this article to have better insight into the enchanting world of the firefly. Are they just a pleasure to our eyes, during their short lives in the summer, or do they live on in children’s books?

Fireflies, or lightning bugs, belong to the Lampyridae family. There are thousands of firefly species all over the world and none of them are actually flies. Then what are they? Well, they are beetles, who get the names “firefly” and “lightning bug” because of the flashes of light emanating from their bodies, a process called bioluminescence (2). This “cold light” does not heat up or burn its producer through infrared or ultraviolet frequencies, and is formed by the action of an enzyme called luciferase in the lower abdomen of the firefly. It may be yellow, green, or pale red, with wavelengths from 510 to 670 nanometers. The enzyme luciferase acts on the luciferin, in the presence of magnesium ions, ATP, and oxygen to produce light (3). According to Vieira et al., 2012, in the Journal of Photochemistry and Photobiology, the firefly’s luciferase is the most important and studied bioluminescence system in scientific research(4). The firefly luciferase was cloned and isolated for the purpose of constructing bioassay systems in the late 1980s (5). Since then, due to very interesting characteristics, this system has been used in numerous biomedical, pharmaceutical and bioanalytical applications (4).

In biomedical research, the ability to visualize a biological process is very important because it offers the most direct method to support or disprove any scientific claim (6). Therefore, firefly luciferase is very desirable as a reporter in this area. Typically, the luciferase gene is cloned with a DNA sequence of interest into cells and then the cells are assayed by measuring its bioluminescence. Fusing a protein with luciferase is like putting a reflective vest on a cyclist in the dark to be able to watch him. Because the firefly luciferase lights up, it helps screening for chemical biology and drug discovery applications in academia and the pharmaceutical industry (5). For example, the firefly luciferase gene was used as a reporter to screen tumor-specific promoters in lung cancer (7). Another example showing how beneficial the firefly is for scientific research is a rapid in vivo (Latin for within the living) assessment of drug efficacy against Mycobacterium tuberculosis, which is the causative agent of most cases of tuberculosis, using an improved firefly luciferase (8). In this study, Andreu et al., 2013, used a Mycobacterium tuberculosis strain carrying a red-shifted derivative of the firefly luciferase gene to infect mice, and they monitored disease progression in living animals by bioluminescence imaging before and after treatment with a frontline anti-tuberculosis drug. Furthermore, firefly luciferase was used in a research about anti-malaria drugs, an illness which affects about 5% of the world’s population and brings a death toll of 0.5–2.5 million each year (9).

Firefly luciferase is not only used in biomedical research, but also in molecular plant biology. In the early ’90s, plant scientists were already able to show the bioluminescence of a promoter fragment fused to the firefly luciferase gene and its regulation by phytochrome (a pigment that plants use to detect light) and the circadian clock (a roughly 24 hour cycle in the physiological processes of living beings) (10) in plants. Some examples for the great usage of this system among many others include a firefly luciferase complementation assay that was used to reveal the interacting partners of Open Stomata 1 protein, which is critical for plant drought responses in Brassica oleracea (cabbage) (11) and the characterization of the promoter region of an important gene encoding a copper chaperone for the copper/zinc superoxide dismutase that is involved in oxidative stress protection of the potato plant (12).

Scientists have found many ways to use the firefly light, but what is the function of it for its real owner? Marc Branham, an assistant professor in the department of entomology and nematology at the University of Florida, explains. “Fireflies seem to flash light for a variety of reasons. The larvae produce short glows and are primarily active at night, even though many species are subterranean (underground) or semi-aquatic. Fireflies produce defensive steroids in their bodies that make them unpalatable to predators. Larvae use their glows as warning displays to communicate their distastefulness. As adults, many fireflies have flash patterns distinctive to their species and use them to identify other members of their species as well as to discriminate between members of the opposite sex. Several studies have shown that female fireflies choose mates depending upon specific male flash pattern characteristics. Higher male flash rates, as well as increased flash intensity, have been shown to be more attractive to females in two different firefly species (13).”

Are there other creatures like fireflies producing light? “Besides fireflies, many other organisms, especially marine creatures, use bioluminescence for sexual selection, attracting prey and as a means of camouflage, and it has been estimated that about 90 percent of deep-sea animals are bioluminescent, according to the Scripps Institution of Oceanography,” says Remy Melina, a staff writer for “Life’s Little Mysteries.”(14)

A firefly’s glow is a theme of summer nights, romantic poems, and childhood adventures and books. However, when you enjoy a firework show done by fireflies next time, please look at them more carefully by thinking that they have more than that to offer humanity, including thrilling scientific inventions done with just a single protein from them. Who knows what else they have waiting to be discovered by us? How amazing it is that, like everything else created on earth, a firefly is also a very precious art piece decorated with intricate features, and even though it is very tiny, its service to humanity is, in many ways, enormous.

References

http://www.barnesandnoble.com/sample/read/9780399227745
National Wildlife Federation
http://en.wikipedia.org/wiki/Firefly
Vieira J, Pinto da Silva L, Esteves da Silva JC (2012) Advances in the knowledge of light emission by firefly luciferin and oxyluciferin. J Photochem Photobiol B. 117:33-9.
Thorne N, Inglese J, Auld DS (2010) Illuminating insights into firefly luciferase and other bioluminescent reporters used in chemical biology. Chem Biol. 17(6):646-57>
Brogan J, Li F, Li W, He Z, Huang Q, Li CY (2012) Imaging molecular pathways: reporter genes Radiat Res. 177(4):508-13.
Xu R, Guo LJ, Xin J, Li WM, Gao Y, Zheng YX, Guo YH, Lin YJ, Xie YH, Wu YQ, Xu RA (2013) Luciferase assay to screen tumour-specific promoters in lung cancer.Asian Pac J Cancer Prev. 14(11):6557-62.
Andreu N, Zelmer A, Sampson SL, Ikeh M, Bancroft GJ, Schaible UE, Wiles S, Robertson BD (2013) Rapid in vivo assessment of drug efficacy against Mycobacterium tuberculosis using an improved firefly luciferase. J Antimicrob Chemother. 68(9):2118-27.
Che P, Cui L, Kutsch O, Cui L, Li Q (2012) Validating a firefly luciferase-based high-throughput screening assay for antimalarial drug discovery. Assay Drug Dev Technol. 10(1):61-8.
Millar AJ, Short SR, Chua NH, Kay SA (1992) A novel circadian phenotype based on firefly luciferase expression in transgenic plants. Plant Cell.4(9):1075-87.
Wang M, Yuan F, Hao H, Zhang Y, Zhao H, Guo A, Hu J, Zhou X, Xie CG (2013) BolOST1, an ortholog of Open Stomata 1 with alternative splicing products in Brassica oleracea, positively modulates drought responses in plants. Biochem Biophys Res Commun. 442(3-4):214-20.
Trindade LM, Horvath BM, Bergervoet MJ, Visser RG (2003) Isolation of a gene encoding a copper chaperone for the copper/zinc superoxide dismutase and characterization of its promoter in potato. Plant Physiol. 133(2):618-29.
http://www.scientificamerican.com/article/how-and-why-do-fireflies/
http://www.livescience.com/32677-what-makes-fireflies-light-up.html

Basal ganglia subcircuits distinctively encode the parsing and concatenation of action sequences.
Jin et al. Nature Neuroscience, Jan 2014.

When we learn to play a musical instrument – say the guitar – first, we have to learn notes, scales and chords; only then we will be able to play a song. The very same rule applies to our basic functions. For example, when we learn how to read, we first learn the alphabet and the rules of grammar, and then we start making sense of sentences. Neuroscientists have been intrigued by this process for many years and they have wanted to understand how our brains efficiently perform complex cognitive functions by connecting separate elements to produce a unique meaningful sequence. A recent study shed some light on this very important question. Scientists found that a specific area of the brain, the basal ganglia, can signal the integration of individual elements into a behavioral sequence. Scientists designed an experiment where they first trained mice to perform gradually faster sequences of lever presses. This behavioral test is very similar to a person learning to play a guitar solo at an increasingly faster pace. Then, they recorded the neural activity in the basal ganglia of mice performing the task and discovered that basal ganglia neurons treat a whole sequence of actions as a single behavior. This mechanism is called “chunking,” which allows the brain to efficiently organize memories and actions by integrating individual sequences. It seems like the basal ganglia implement the “chunking.” The basal ganglia are known to include two major pathways, the direct and the indirect. Scientists found that these two pathways show similar activities during the initiation of movement, but show differential activations during the execution of behavioral sequences. Interestingly, basal ganglia circuits are implicated in Parkinson’s and Huntington’s disorders, in which learning of sequences are compromised. Further studies will reveal a more mechanistic understanding of sequence integration in the brain and potential interventions to enhance it in neurological disorders.

Single Gene Separates Queen from Workers

Ubx promotes corbicular development in Apis mellifera
Medved V. et al. Biology Letters, Jan 2014

In a hive of honey bees, the queen and worker bees have very different jobs. A new study shows that a single gene called Ultrbithrox (Ubx) separates a queen from worker bees. The Ubx gene was previously known to control leg and hindquarter development in bees. Interestingly, researchers now identified three functions for Ubx specific to worker bees. First, Ubx promotes the development of a smooth spot on the hind legs where the “pollen baskets” are located. Second, Ubx directs the formation of eleven perfectly spaced bristles on the section of the leg called the “pollen comb.” Third, Ubx mediates the formation of the “pollen press” which is a protrusion that helps pack and transport pollen back to the hive. Essentially, the Ubx gene promotes the development of three different physical structures on worker bees so that they can collect and transport pollen. Researchers confirmed these findings by silencing the Ubx gene genetically in worker bees and found that specialized leg features, including pollen combs and pollen presses, completely disappeared in the absence of the Ubx gene. Moreover, analyses of other bee species in the region revealed that the size and complexity of pollen baskets are directly correlated with the social behaviors of the particular bee species, suggesting that pollen baskets have yet-to-be-identified roles on the social behaviors of bees. Furthermore, the pollination of 35 percent of the world’s crops (with a $216 billion market value) depends on bees carrying pollen from one flower to another. This study might help us to develop new genetic approaches to make bees better, more efficient pollinators and to ultimately combat the worldwide pollination problem.

Molecular Switch in Aging Blood Cells Discovered

A canonical to non-canonical Wnt signaling switch in haematopoietic stem-cell ageing
Florian MC et al. Nature, October2013

Every single cell in our body ages over time. The aging of a cell is typically characterized by the progressive loss of physiological function and increased vulnerability to death. The aging of our cells/tissues/organs is the primary risk factor for any human diseases. One critical cell type that dramatically changes its properties during aging are blood stem cells, aka Hematopoietic Stem Cells (HSCs). Young HSCs have the capacity to differentiate into the diverse lineages of erythroid, lymphoid, and myeloid cells. Young HSCs are polarized (asymmetrical) cells, in which distinct cytoskeletal proteins (also called the “polarity complex”) are asymmetrically distributed within. However, the aged HSCs are mostly apolarized (symmetrical) cells and they differentiate only into lineages of myeloid cells (including, red blood cells, macrophages and monocytes) rather than lymphocytes (white blood cells in the immune system). The molecular changes in aging HSCs have largely been unknown. A recent study published in Nature shed some light onto the molecular identity of the ageing HSCs. Scientists showed that ageing HSCs have higher levels of a secreted protein called WNT5a, whereas the young HSCs have almost no WNT5a protein expressed in the cell. Moreover, the increased levels of WNT5a are found to attenuate the levels of the “polarity complex” proteins in HSCs and thus result in apolarized cells, which resemble the aging HSCs. Furthermore, transplantation studies revealed that increased WNT5a levels cause aging-related phenotypes and low Wnt5a levels promote a rejuvenation process in mice. These findings show that Wnt5a is the key molecule that controls the shift between young and old HSCs. Therapeutic approaches using antagonists of the Wnt5a molecule could potentially alleviate aging-related pathologies in the patients with a variety of blood diseases.

If we consider human nature as a book, the encoded information contained within, together with all the elements of inner and outer environments (bio-psycho-socio-cultural), becomes meaningful and functional. This is because each book has a visible structure composed of letters (semiotic DNA sequence) and a manifested meaning (semantic web) in a particular environment. From this point of view, genes should not be seen as mandatory codes, but should be considered as similar to the art of marbling (or ebru, which is the making of different patterns on a fluid by small vibrations of the ink droplets), for they are created by the united effect of various dynamic forces, and can only be understood accordingly. Human willpower and responsibility will also gain meaning and value when they are analyzed within the framework of the reaction intervals presented within the motifs of human nature which are shaped by the mutual effects genes and cultural factors have on each other. In this sense, human nature and culture should be evaluated together. We can organize the factors that determine human behavior and manners under three main titles – genetic, physicochemical environment, and psycho-socio-cultural factors. We can only speculate statistically as to how large or small a role each factor plays in development.

Behaviors like an inclination to crime, having intimate feelings for same sex individuals, cognitive and sensory sharpness, a desire for excitement and risk, or an inclination to addiction cannot be described by one or two genes. For instance, there are many factors (environment, genes) involved in acts of violence. However, one missing and insufficient factor can trigger violence. For instance, the Monoamine oxidase A enzyme is encoded by the MAO-A gene; this enzyme is in charge of degrading neurotransmitter molecules such as dopamine, serotonin, norepinephrine (these enable signaling between nerve cells). Depending on the mutations or polymorphisms of this gene, if the enzyme cannot function sufficiently, these individuals display an inclination towards violence and aggressive behavior. But if the person is aware of the situation and gets educational support from others, this behavior can be controlled.

Similarly, every person has a variable degree of genes that put them at risk for cancer. If these genes are activated via environmental factors – such as smoking, poor nutrition, mutagens, carcinogens – cancer may develop. On the other hand, if a person is lacking the cancer-causing genes or has low inclination towards cancer, such a person may not get cancer, even if he or she is a smoker. Similar statements can be made for genes associated with addictions, sexual perversions, and violent tendencies. More significantly, we can produce more value and meaning out of behavior-related genes when we evaluate them according to their context, position, and other factors, along with their relations to other genes. That is to say, there is a complicated network of factors that shape behavior. That’s why a DNA sequence alone cannot determine, all by itself, the development of emotions and manners, skills, and personality. In other words, phenotype can never be predicted 100% just by the interpretation of genetic information.

Brain and personality development is a multi-faceted, exposome mystery. From the start of pregnancy, especially throughout the preschool era, everything one is exposed to, and the way those events shape one’s nature, is called exposome. This can include subconscious events, for all sorts of personal history plays a role in such development. The connections of 1011 neuron cells that exist in an average human brain are not only determined by genes. Human DNA contains 6.2 x 109 nucleotide (letter), or information. Reading and using this raw information depends on many factors. Neurons can establish new connections via internal and external stimuli, while on the other hand, the number of neuron cells and connection networks can be changed by the neurochemical substances and hormones that they synthesize. All of the information required to define fine details in the motifs and connections of brain cells is not present in the genome. Mere environmental factors are not enough to complement this missing information.

Aside from these, many factors play a role in brain development and function. When the ends of axons and dendrites extend, they do so by recognizing nanomolecules that guide them all the way to the target organ or region. They happen to make minor changes and deviations during this extension. These changes are extreme enough that this extension is part deterministic and part trial and error. They reach the target through a statistically systemic algorithm but with a certainty less than 100%. Axons that are extended from eyes to the brain have a 1% possibility of taking a wrong turn at optic chiasm, and therefore not reaching the brain or arriving at the wrong region of it. However, there are also signalization systems built in our brains that recognize and correct these errors. If axons cannot receive the correct signals from target neurons, they get degraded. And sometimes a neuron of the axon terminates itself. These observations clearly show that brain development does not take place by a molecular program that is predetermined down to the minutest details but rather through a flexible program open to changes and errors.

This flexible program is explained by materialistic philosophy as “chance,” which basically means being in the right place at the right time to encounter the right factors. The same program, in religious literature, is explained by factors known as fate, kismet, destiny, divine blessing, and grant. Aside from that, there are also certain uncontrollable activations and a genetic background in the brain that are involved before we start a conscious action. From this perspective, motifs generated by biological and genetic inclinations set the infrastructure for the freedom of decision making and self-determination. Since our thoughts, emotions, and acts are formed within the neurogenetic and neurochemical construct of the brain, the motif that is created by the background here generates inclinations for specific acts and behaviors. In other words, events that take place in our brain chemistry during the fetal period and early childhood years are significant determinants of human development. The human brain can function in a state with willpower and consciousness, but can also function automatically, without consciousness. Briefly, it is through our genes that the framework of what we can achieve, our reaction intervals and threshold values are determined, and the possibility of an act is indicated. But the boundaries of the final decision are determined via statistical possibilities as a result of a person’s interaction with their environment. Therefore the boundary is not determined in a mandatory fashion, but via external dynamics (like manners, beliefs, or moral nourishment).

Human willpower is our capacity and strength to make free decisions and selections under the effects of spiritual, genetic, and environmental frameworks (endophenotype). The decisions and selections cannot take place independently from the sources nourishing one’s metaphysical world, cultural circles, or from the impact of neurochemicals in the brain and our hormones. “God burdens no soul except within its capacity” (2:286) is a sign of mercy and compassion from the Qur’an, indicating that the field of action and boundaries of the human willpower are determined based on multiple factors and wise causes. Producing customized religious rulings according to one’s natural strengths and weaknesses is also a very meaningful legal action in Islamic law. It is, in a sense, an acknowledgement that everyone has trials and experiences that are different than others’.

Humans have responsibilities within defined, limited conditions, and they can only make decisions within those permissible intervals of conditions and the constraints of their natural dispositions. If we can analyze human actions in a model that looks into their dispositions, cultural environments, genetic inclinations, and spiritual and moral nourishment, then we can attain better results in the education and character development of human beings.

Each factor mentioned above affects the child’s sexual separation and differentiation to various degrees. Misbehaviors during sexual development may emerge as a result of a complex mosaic of biological, psychological, sociocultural factors. There is not a complete consensus around the main reasons for this, yet each researcher favors one factor in the light of their expertise and ideological choices. However, objective observations and research point out that the quality of relationship between the parents and children is very influential in this matter. The display of unhealthy sexual inclinations stems from a negative background where there is not enough parent-child relationships to help the child develop. In families of children with strange sexual behaviors, a suppressive, excessively controlling model of mother and a distant, aggressive model of a father who resorts to violence are often found to exist. That is why many problems with intimacy and sex that occur later in life can be viewed as a developmental ailment and a problem of insufficient parental communication rather than a mandatory genetic phenomenon.

Various problems can arise when healthy differentiation and separation do not take place during a child’s development. A child, in the beginning, is like a part of the mother. If differentiated by detachment from the mother, and from her compassion and care, a child struggles to develop a healthy sense of ego. Such a child becomes inclined to develop a personality that is dependent, passive, and lacking sufficient confidence.

Research clearly states that each child is born with different inclinations and threshold values that are determined genetically and hormonally for each of his or her possible characters and behaviors. These potential inclinations and threshold values can surface depending on internal and external stimuli and educational styles. Even though both genders carry hormones belonging to each other naturally, during development one steps forward upon expression of encoded gender genes. When it comes to displaying sexual abnormalities, everybody is, genetically speaking, a dry log or a wet log. A dry log can easily catch fire, a wet one does not. However, it is the responsibility of society and parents to provide a spark-free environment for the dry log. Spiritual and biological nourishment during the developmental process are found to be significantly influential in diseases and aging, in disorders of character development, and in anomalies in sexual behaviors. When proper measures are taken timely, via suitable environments and educational modes, the possible surfacing of behavioral pathologies may be prevented or reduced for children potentially at risk. Through correct guidance and education, the expression and regulation of genes can be altered and managed, controlling these naturally present inclinations.

Cezmi Aydin is a freelance writer in natural sciences.

References

• Alper, Joseph S. (1998). “Genes, free will, and criminal responsibility.” Soc. Sci. Med. Vol. 46, No. 12, pp. 1599 1611
• Meyer, Lia Midori Nascimento, Gilberto Cafezeiro Bomfim, Charbel Nino El-Hani. 2011. “How to Understand the Gene in the Twenty-First Century?” Sci & Educ. DOI 10.1007/s11191-011-9390-z
• Levitt, Mairi and Neil Manson. 2007. “My Genes Made Me Do It? The Implications of Behavioural Genetics for Responsibility and Blame.” Health Care Anal. 15, pp. 33–40.
• Richardson, Brian. 2011. “What’s wrong with me? Coming to terms with same sex attraction.” Nursing Children 24 and Young People. October 2011. Volume 23. Number 8. pp. 22-24.
• William J. Jenkins. 2010. “Can Anyone Tell Me Why I’m Gay? What Research Suggests Regarding The Origins of Sexual Orientation.” North American Journal of Psychology, 2010, Vol. 12, No. 2. pp. 279-296.
• Botz-Bornstein, Thorsten. 2010. “Genes, memes, and the Chinese concept of wen: toward a nature/culture model of genetics.” Philosophy East & West Vol. 60, No. 2. April 2010. University of Hawaii Press, pp. 167–186.

Factors underlying variable DNA methylation in a human community cohort. L.L. Lam et al. PNAS October 16, 2012 vol. 109

The effect of environment on genes can be very profound. Our surroundings may not directly change our DNA sequence but it can surely dictate how our genes are transcribed. Epigenetics studies heritable changes in gene expression caused by non-genetic mechanisms, i.e. mechanisms other than the changes in the DNA sequence itself. DNA methylation is one of the major epigenetic modifications to regulate the gene expression. The addition of methyl groups on DNA sequence acts like a dimmer on a light bulb switch, which will turn certain genes on or off. A recent study showed that a person’s early life experiences shape their DNA methylation patterns. The research team discovered that childhood poverty (not socioeconomic status as an adult) is highly correlated to distinct methylation marks left on genes. Although children in rich and poor households have identical sets of genes, the degree of adversity or stress at home determines which combinations of those genes are activated or silenced through differential DNA methylation. One can imagine that such epigenetic changes might cause some alterations in the gene expression program of blind people to certain environmental signals or make them even more sensitive. Perhaps such changes could make some people more adaptive to harsher life conditions, hence enhance their survival. These findings suggest that environmental conditions early in life shape our epigenomes permanently thereby influence our life experiences, health and probably many other things that we are not yet aware of.

An alien planet next door

An Earth-mass planet orbiting α Centauri B. X.Dumusque et al. Published online 17 October 2012, Nature

Astronomers have just discovered an earth-size alien planet right next to our solar system. A new earthlike planet, named Alpha Centauri, is just 4.4 light-years away. That’s 40 trillion km away from earth! Although this rocky planet’s mass is similar to Earth’s, it orbits much closer (25 times closer than the Earth) to host star Alpha Centauri B. As a result, a year lasts 3236 days and the surface temperature of the planet reaches around to 1200 °C, which makes the planet incapable of supporting any life form we know. However, solar systems with a rocky world are usually predicted to have multiple planets. One possibility is that that Alpha Centauri A, the bigger sibling of Alpha Centauri B, might host some yet to be discovered unknown planets with more habitable zones. Although this recent discovery has sparked people’s dreams to travel to another star system outside of our planetary system, such an exploration mission unfortunately seems impractical in the near future. Even a cell phone-sized probe that is accelerated to 10% of the speed of light would need to travel non-stop for 40 years to reach the target. So, what is the next best thing to do? Will it be taking photos or dropping probes on the planet’s surface to study a potentially modified atmosphere? It seems like while astronomers work hard on the identification and characterization of this new star system, scientists should focus on developing super-fast propulsion systems, which will perhaps include new concepts like nuclear rockets and antimatter fusion drives.

Bad memories, substitute or suppress

Opposing Mechanisms Support the Voluntary Forgetting of Unwanted Memories
Benolt RG et al., Neuron, Volume 76, Issue 2, 450-460, 18 October 2012

For the nervous system, forgetting a memory is almost as complicated as creating one. A recent study probed the mechanism of how the brain allows us to voluntarily forget unwanted memories. Researchers utilized functional magnetic resonance imaging (fMRI) to examine the brain activity of participants who had learned associations between pairs of words and subsequently attempted to forget these memories by either blocking them out or recalling substitute memories. The fMRI results showed that two separate forgetting strategies looked equally effective yet they seemed to use different neuronal circuits in different parts of the brain. For memory suppression, dorsolateral prefrontal cortex inhibits neural activity in the hippocampus which is a critical region for recalling past memories. On the other hand, memory substitution specifically activates caudal prefrontal cortex and midventrolateral prefrontal cortex that are known to bring specific memories into awareness in the presence of distracting memories. These findings can help us to better understand the mechanisms of memory disorders such as posttraumatic stress disorder, and may ultimately help to develop effective treatments. At a more personal level, this study may direct us to explore how we deal with our unpleasant or unwanted memories. We might be surprised to realize that one approach might be working much better for us than another one. In other words, neuronal wiring in our brain might simply favor one approach over another.

The cell is the structural, functional, and biological unit of all organisms. All information needed for numerous processes in a cell, including repair and division, is contained in DNA (Deoxyribonucleic acid). DNA is a huge single molecule with intriguing features. How can a single molecule have such a dominant role in preserving information essential for the continuation of life? What are the mechanisms and levels of organization during its function? What does DNA mean for a single cell or for a human being? It’s impossible to answer these great questions in a single article; however, understanding the ways DNA exerts its role, DNA’s impact on multiple levels ranging from a single cell to an organism, and coordination between various levels, can potentially open up new frontiers in our mind and in our perception of life.

“Double helix” architecture of DNA DNA has an elegant structure that forms the basis for all of its functions. DNA is a repeating structure of nucleotides. Each nucleotide is formed of a phosphate group, 5-carbon sugar (deoxyribose) and a nitrogen-containing base attached to the sugar from outside to inside (See Figure 1a for a schematic view of DNA). There are four types of nucleotides in DNA, differing only in bases. We can consider bases as the identity of nucleotides. These four nucleotides are shown with letters A (adenine), T (thymine), G (guanine) and C (cytosine). Thousands of nucleotides bound with sugar-phosphate covalent bonds come together to form long strings. The sugar-phosphate backbone can be imagined as the steelwork of a skyscraper. The nice thing about nucleotides is their specific match to each other in double helix. A forms a base pair with only T, and G forms a base pair with only C. These pairs are bound to each other with hydrogen bonds. This feature is the key that makes DNA a double ladder. Two strings of nucleotides form a double helix by selective interactions of As with Ts, and Gs with Cs (See Figure 1b for 3-D structure of DNA). In DNA structure, hydrophobic bases tend to stay inside of double helix and hydrophilic sugar-phosphates stay outside interacting with water in nucleus. This feature helps DNA to form a double ladder. The length of the sugar-phosphate backbone is more than the bases. To compensate for the length difference, the sugar-phosphate backbone wraps around the bases inside, as a road wraps around a mountain to climb to the top. This simple difference is the main reason for DNA to form a helix.

The double-stranded nature of DNA with specific base pairing is one of its key features as genetic material. DNA is replicated using one strand as a template. Replication machinery reads one strand of DNA and builds the second strand by putting As against Ts and Gs against Cs. If a mutation occurs in one strand, it can be repaired using the second strand. This system is like photocopying DNA from itself instead of building it from scratch every time. That is why specific base pairing of nucleotides in the double helix makes it possible to replicate DNA through generations, protecting its integrity and information content. The code of DNA, an alphabet with four letters DNA contains the information to produce nano-sized cellular machineries called proteins. We mentioned that there are four types of nucleotides. Nucleotides are like letters in DNA, three of them are code for one amino acid of protein. We can make it more understandable by giving an example: “ATG-GCC-CTG-TGG-ATG” as a nucleotide sequence of DNA corresponds to the first five amino acids of a protein called insulin (a hormone regulating blood glucose level that is important in diabetes) and amino acid sequence is methionine-alanine-leucine-tryptophan-methionine. The code is so sensitive that even a single mistake in the sequence of DNA can cause serious diseases in humans such as sickle-cell disease or cystic fibrosis. With all these nucleotides, DNA can be thought of as a book containing amino acid sequence information for thousands of proteins (about 30,000 in humans). The amount of information contained in DNA is incredible: a typical human cell contains 2 meters of DNA that is tightly packed by proteins in the nucleus. If we tried to write the information from DNA into books, the book would contain over one billion words and 1,500,000 pages. DNA-protein interdependency and the cell as a micro-factory DNA can be thought of as an instruction manual that stores information for proteins and RNAs. Proteins, as molecular machines, perform particular tasks such as energy production and synthesis of DNA and RNA (See Figure 2 for the structure of proteins). Certain proteins read the information on DNA and make a transient copy of certain regions of DNA. These copies are called messenger-RNAs (mRNAs) and mRNAs are transported from nucleus to cytoplasm (See Figure 3 for representation of mRNA production from DNA by proteins). In cytoplasm, the information on mRNAs is read by protein complexes called ribosome. Ribosomes produce new proteins processing the data from mRNAs. This information flow from DNA to proteins is called central dogma in molecular biology (Figure 4). The data that is encoded in DNA can be read, translated, and put into the form of product only by proteins. We can conclude that for a protein to be produced, DNA is essential; for DNA regions to be read into proteins, proteins are essential. So, there is interdependency between proteins and DNA. Proteins without DNA have no future and no ability to regenerate and DNA without proteins is just like an instruction and manufacture manual of a computer without the user and computer itself. We can imagine the cell as a sophisticated factory, and proteins as the machines of the factory. DNA includes the instructions for the factory to be rebuilt and for itself to be rewritten for every new factory. It has instructions on how to build every machine in the factory. It has also codes for when and how much of these machines should be produced (we will discuss more about these codes on DNA in the next section). On the other hand, the timing and control of all these productions also depend on machines in the factory. Some of these machineries read and decode the instruction manual, some of them produce new machines by reading the decoded copies of the instruction manual, some of them act as sensors for the signals, some of them transmit signals to other machines, some of them produce signals by measuring the levels of materials in the factory, some of them function in communication with other factories, and so on. As we can see, DNA and proteins are meaningful for life only when they are together in the excellent cell context. This is a perfect example of the principle that the whole is bigger than the sum of its parts, because each element of the cell system has limited potential, until it comes together with the others to blossom into life.

The famous term “Gene” We can think of genes as functional units of DNA. A gene has the information content for at least one protein. Humans have about 20,500 genes that are read by protein machineries to produce proteins. Special proteins read the information on genes and make a transient copy of these certain regions of DNA. The process of making a copy of a gene as an mRNA is called transcription.

Genes don’t only store information; they have an intrinsic architecture of design to coordinate transcription utilizing three main components: promoter, coding region, and terminator. The promoter is the gene region that signals for the start of transcription. Protein machineries bind to the promoter and activate transcription. The coding region has the information for the amino acid sequence of the protein. The terminator region gives the stop signal for transcription. There are different functional regions on DNA located between separate genes such as enhancer regions that are platforms for binding regulatory proteins to tune the transcription.

The coding region of genes has multiple reading blocks for amino acid sequences and these reading blocks are called as exons. For some genes, different combinations of exons can be put together to give rise to different proteins. This mechanism allows one gene to be able to produce multiple proteins, increasing the efficiency of genetic material. A similar mechanism is used to produce antibodies (proteins recognizing foreign antigens) by the immune system. Different regional genes come together by a mechanism of DNA rearrangement (V(D)J recombination) and their differential combinations form many different antibodies. For example, a part of the antibody that is called a heavy chain is produced by a DNA region containing 65 variable (V) genes plus 27 diversity (D) genes and 6 joining (J) genes (5, 6). This produces a combination of 65 V genes x 27 D genes x 6 J genes = 10,530 heavy chains. There is a similar mechanism of rearrangement for light chain and variable region of antibodies, which result in millions of different antibodies for host antigens. A single example in the immune system shows us that DNA not only has a decent design for the coding system, but it also has ingenious and creative mechanisms to maximize its potential.

Gene expression is orchestrated during development and formation of organs The human body which consists of more than 1013 (ten trillion) cells is generated from a single cell called the zygote (see Figure 5). This tells us that, in a single cell, all the information and instructions to build and coordinate the systems of human body is encoded. Different tissues and organs including muscles, nerve cells, connective tissue, and eyes are fruits of one single cell. They all contain the same genetic information. Then what makes them different?

Promoters, enhancers, and repressors located in and nearby genes are important in spatial and temporal control of gene expression in different cell types of the body. Each cell type in our organs expresses a different subset of genes; this is what gives a cell its identity. For example, in muscles, myosin is expressed and in the eye’s retina, rhodopsin is expressed. Myosin functions in contraction and rhodopsin functions in vision. What determines the expression of rhodopsin in the eye but not in a muscle? The determination process occurs during development by programmed interactions of specific proteins called transcription factors, and restricted regions of DNA including promoters and enhancers. During development, certain regulatory proteins in a specific cell type, bind to DNA regions of only some genes (for example, in future retinal cells of the eye, rhodopsin gene would be activated but not myosin) and this predetermination orchestrates differential expression of genes to give rise to hundreds of different types of cells.

Different layers of complexity and organization related to DNA

There are different layers of function for DNA—each subtitle of this article tries to focus on a certain layer of function. DNA as a molecule has a double helix structure and is replicated through generations to preserve genetic information. It stores genetic information and has a four-letter alphabet for the expression of proteins. In the second layer, DNA has an informational unit called gene and thousands of genes are encoded in DNA to contain information for proteins. Each gene is controlled individually by making use of promoters and enhancers. In the third layer, all processes in the cell micro-factory as an entity are performed through interactions of DNA and proteins with each other and among themselves. Proteins read DNA code and work as cellular nano-machineries. In another layer, temporal and spatial expression of genes on DNA are orchestrated and different subsets of genes give rise to different cell types and organs. Organs communicate with each other to function properly and keep the balance and homeostasis of the body. The information stored in DNA not only coordinates highly sophisticated processes of a single cell, it simultaneously projects the whole body system of a human being, which is billions times bigger than a single cell.

DNA functions in all these different layers and keeps a great harmony in coordination between various layers of function. After grasping this complexity, organization and communication from a single molecule, to proteins, to a single cell, to tissues and organs, and to a human being by utilization of DNA, should not we ask ourselves, “can these elements come into existence by random forces and collisions?

References

1. Calladine, C. R. et al. 2004. Understanding DNA: The Molecule and How It Works, Academic Press

2. http://www.genome.gov

3. Li A, Rue M, Zhou J, et al. 2004. “Utilization of Ig heavy chain variable, diversity, and joining gene segments in children with B-lineage acute lymphoblastic leukemia: implications for the mechanisms of VDJ recombination and for pathogenesis.” Blood 103 June (12): 4602–9.

Spending so much time in the library for a particular book further amazed me about the answer I was searching for in my research. I am trying to understand how our genome is organized and how it functions. In order to make myself clear, let me first try to explain what the genome is. I bet you will be amazed by the impressive genome organization and its flawless function, too.

The genome can be thought of as a library. Each book in the “genome library” is what we call a “gene”. Every gene is different in size and the information they contain, just like the books in the library. Like the different sections in the library, our genes are also compartmentalized into different chromosomes. We have 23 pairs of chromosomes. One pair contains the information from our father and the other one from our mother. Therefore, unlike libraries, where you may find more than one copy of a book, our genome has two copies of each gene (except the genes on the X and Y chromosomes which carry only one set of genes).

Every cell in our body carries its own library: the genome. Our genome is the smallest library in terms of physical volume, yet contains relatively the largest amount of information. In our body, which contains roughly 100 trillion cells, we carry 100 trillion of these libraries. Here comes the amazing part; each of these libraries contains 3 billion letters of information. If this information were to be printed, it would take 1000 books of 200 pages each. The information in our genome is coded by a 4 letter alphabet; Adenine (A), Guanine (G), Cytosine (C) and Tymine (T). These four letters (A,G,C,T), called deoxyribonucleic acids, are the building blocks of every DNA strand on earth. The collective amount of these letters in any organism constitutes of its genome. We, as humans, have about 3 billion of these letters in our genome, which is encapsulated in the nucleus of every cell in our body. The total length of our genome is 2 meters long. This 2 meter long stretch of DNA (3 billion letters of information) is highly compacted and packaged in the nucleus, which is only 2 micrometer in diameter, an amazing 1,000,000 fold compaction!

How is our genome, which is 2 meters long, compacted so much that it fits in a nucleus only 2 micrometer in size? In the nucleus, DNA is wrapped around a group of 8 proteins called histones. This combination of DNA and histone proteins forms a special structure called “beads on the string”. Each bead is called “nucleosome” (Figure 1).

Multiple nucleosomes are then coiled together and stacked on top of each other. This organisation further packs the DNA up into a thicker fiber called “chromatin”. This chromatin fiber further condenses by forming tight loops. The structure which we call a “chromosome” is actually the most compact form of the chromatin fiber, which is only visible under the microscope during cell division. This remarkable chromatin organization allows a 2 meter long DNA to fit into the nucleus of each cell, an object so small that 10,000 of these nuclei can fit on the tip of a needle!

This remarkable genome organization further impresses us when we think about the utilization of this genetic information by over one hundred trillions of cells in our body. These many cells in our body are not all similar to one another. Most of the cells in our body are specialized to carry out specific functions. We have more than 200 different cell types specialized for unique functions. Some cells, like B and T cells in our immune system, are dedicated to fighting against infectious agents, whereas other cells, like neurons, function by transmitting signals between our brain and muscles. Since these cells have different structures and carry out different functions, they require different sets of instructions coded by genes in the genome. There are roughly 20.000 genes in our genome. Importantly, each specialized cell in our body utilizes only a subset of these genes, not all of them, at any given time. In other words, from the library analogy, roughly two third of the books (i.e., genes) are needed for each cell to function. The remaining one third of the genes is not necessary for that particular cell type. For example, the MYOD1 gene encodes a protein required for muscle cell differentiation. Therefore, this gene is absolutely required for muscle cells. However, the same gene is not required for the B or T cells that function in our immune system. While the MYOD1 gene has to be stored in an easy access location (open chromatin) for muscle cells, immune cells do not need this gene, and therefore it is stored in the depository section of the “genome library” (closed chromatin), which is not used very often.

In line with this, each cell has to organize its genome in a special way so that the genes needed for its function should be easily accessible. This remarkable genome packaging and organization allows each cell to easily and very quickly access the required genes for transcription into the proteins. On the other hand, those genes that are not going to be used are stored in relatively inaccessible regions in the genome library. Therefore, the genome is not packaged similarly all along. Certain regions of the genome are “open” and therefore easily accessible (called euchromatin) for transcription, while other regions are kept “closed” by condensed and packed structure (called heterochromatin). Since each cell type requires different set of genes, the genome is also differentially organized between cell types. Genome organization in a muscle cell is remarkably different than genome organization in, let’s say, a skin cell.

After all these explanations, I hear you asking, “How does each cell in our body know how to organize their genome? How does, lets say, a muscle cell decides to become muscle but not a blood cell?” These are exactly the same questions that many scientists are asking nowadays. Since the completion of the Human Genome Project (HGP)1,2, which determined the entire sequence of information of our DNA, scientists have been trying to understand how this amazing alphabet is being used in each and every cell in our body. Francis Collins, one of the great scientists of our time and the current director of National Institute of Health (NIH-USA), is especially noted for his landmark discoveries of diseases associated genes, as well as his leadership in the Human Genome Project. He calls the information coded in our DNA the “Language of God” in his recent book.3 Recent technological advancements allow scientists to better study the structure and function of this language and get better clues about the organization of this genomic library.

Whether we believe that this genomic information is “the language of God” or not, we are closer than ever to understanding the codes of this amazing language. New technological advancements allow us to get better insights about the organization and utilization of this information. The more we learn about it, the more we are amazed about not only its flawless packaging but also its differential utilization in each cell. At any time and in any tissue, trillions of cells are using different sections of the genome library to get the necessary instructions decoded from “the Language of God” and continue their journey in our bodies without any conscious decision making on our part.

Ahmet Mir Fazil holds Ph.D. degree in molecular Biology. He is a research scientist in Boston.

References

1. International Human Genome Sequencing Consortium (2001). “Initial sequencing

and analysis of the human genome.” Nature 409 (6822): 860–921.

2. Venter, JC, et al. (2001). “The sequence of the human genome.” Science 291

(5507): 1304–1351.

3. Francis S. Collins. 2006. The Language of God: A Scientist Presents Evidence for Belief. Free Press.

A particularly interesting class of all these non-coding RNAs comprises riboswitches. Riboswitches are structured mRNA elements that regulate gene expression upon binding of a specific small metabolite. These biosensors were first discovered in 2002 in bacteria. Later, it was shown that plants, green algae and fungi also posses riboswitches. Although, only one type of riboswitch is found in plants and none has beeen detected in mammals yet, metabolite-sensing riboswitches are commonly used for the regulation of fundamental biochemical pathways in bacteria. Riboswitches help cells monitor the environmental conditions and determine if a compound is present at sufficient levels or not. Based on this decision, production, degradation or transport of the related metabolite is either turned on or off.

Architecture of a Riboswitch

A standard riboswitch is divided into two parts: a ligand-binding domain and a gene expression domain (Figure 1). Small molecular metabolites bind to the ligand-binding domain, which is called aptamer, of riboswitches with astonishing specificity. For instance, purine riboswitches differentiate guanine from adenine by at least 10,000-fold based on the identity of a single pyrimidine (thymine or cytosine) that binds to the ligand (1). When a ligand binds to aptamer, conformational changes of the RNA’s structure occur at the gene expression domain. Eventually, this leads to the modulation of gene expression. Some of the riboswitch mechanisms to regulate the expression of genes include formation of stem-loops, lollipop-like RNA structures, which lead to the blocking of transcription or translation, which are the processes where proteins are synthesized using the mature mRNA, self cleavage or mRNA destabilization (Figure 2).

Classes of Riboswitches

The numerous distinct classes of riboswitches discovered so far are differentiated by their ligands and remarkably, the same class of riboswitches can control gene expression through different mechanisms in various organisms. For example, a riboswitch that recognizes and binds thiamin pyrophosphate (TPP), a derivative of vitamin B1, is called as TPP riboswitch (2). In plant cells, when TPP levels are high, excess TPP binds to a TPP riboswitch located in one of the TPP biosynthesis genes. As a result of TPP binding, conformation of that RNA segment changes, which leads to the formation of an unstable mRNA product which degrades quickly. Although, a very little amount of stable mRNA is also produced, it is not enough for the protein synthesis of an important component of TPP biosynthesis. Therefore, TPP biosynthesis can not be completed and consequently TPP levels drop in the cell. On the other hand, when TPP levels are low in plants, more stable mRNA is formed because there is not enough TPP that can bind to the riboswitch and cause structural changes which will result in the formation of unstable mRNA. The stable mRNA produced in the absence of excess TPP is used for the protein biosynthesis of TPP metabolism successfully and thus TPP levels increase in the cell. Unlike plants in bacteria, when TPP concentration is high, riboswitches down-regulate expression of thiamin biosynthesis genes by either blocking the formation of any type of mRNA (both stable and unstable) or preventing the mRNA process rather than destabilizing the mRNA. Some of the other riboswitches that bind vitamin derived compounds are adenosylcobalamin, the coenzyme form of vitamin B12, and flavin mononucleotide, a biomolecule produced from vitamin B2, riboswitches. There are also riboswitches that can bind to amino acids such as lysine riboswitch. The cyclic diguanylate (c-di-GMP) riboswitch is the first known example of an RNA that binds a second messenger, which carries signals from receptors on the cell surface to target molecules inside the cell (3). Purine riboswitches selectively recognize guanine or adenine and regulate purine biosynthesis and transport, which is important for DNA/RNA synthesis. Another interesting type of riboswitch is the glmS riboswitch. It modulates gene expression by undergoing self-cleavage when there is a sufficient concentration of glucosamine-6-phosphate, an important amino sugar. The spectrum of ligands that can be recognized by riboswitches also includes a metal ion, as well. Mg(2+) riboswitches control Mg(2+) transportation when cells are grown in high Mg(2+) environments. In brief, the growing list of studies on riboswitches shows how novel mechanisms are which they use to regulate the gene expression of many fundamental metabolic pathways.

Applications for Riboswitches as drug targets and chemosensors

Riboswitches are powerful and essential components in all three domains of life which are bacteria, archaea (a group of single-celled microorganisms) and eukaryotes ( organisms whose cells contain complex structures inside membranes such as plants and fungi) functioning as intracellular biosensors and regulators. They regulate gene expression in a highly efficient, precise and fast way. Therefore, they can be engineered for various applications.

First of all, riboswitches are excellent candidates as drug targets since they control many important bacterial and fungal genes. Chemical analogs that mimic the actual ligands of the riboswitches can be designed to silence or regulate the expression of defective genes responsible for disease development or even kill certain bacterial pathogens by turning off the genes that are involved in fundamental metabolic pathways. A great example of this strategy is presented by the Breaker laboratory at Yale University. The Breaker group chose guanine-binding riboswitches as targets for the development of novel antibacterial compounds. They have designed several guanine analogues and tested their ability to be bound by the riboswitch and repress bacterial growth (4). They have been able to inhibit the bacterial growth by inducing guanine riboswitch action. Their approach could be used to discover new antibacterial compounds that specifically target other riboswitch classes.

In addition to being drug targets, riboswitches can open new frontiers in bioremediation, bionanotechnology, and synthetic biology. In 2007 Shana Topp and Justin P. Gallivan from Emory University demonstrated that Escherichia coli can be reprogrammed to detect, follow, and precisely localize to a completely new chemical signal by using a synthetic riboswitch (5). They suggest that the bacteria with synthetic or mutated riboswitches could be used to follow and degrade pollutants in soil or target small-molecule signals of disease. Overall, their work to equip the bacteria which can autonomously follow chemical signals, degrade, synthesize or release compounds can help scientists invent new technologies in bioremediation, drug transport, and synthetic biology.

Furthermore, riboswitches are ideal candidates for use in analytical devices and techniques. Their binding features make them suitable in all specific analytical applications in which selective recognition is required. Therefore, these powerful molecular tools can be utilized in analytical chemistry, molecular biology and biosensor technology (6).

As a result, living systems utilize riboswitches to detect the concentrations of small-molecule metabolites and to modulate the expression of related genes via numerous elegant mechanisms. The use of genetic engineering of riboswitches holds enormous potential for inventing new applications to sense and destroy pathogens, deliver drugs, perform bioremediation, detect chemicals and many others that might have significant impacts on our lives. It is also remarkable that only a couple of decades ago most of the non-coding RNAs were assumed to be useless, and are called junks since they do not provide any information for protein synthesis. Yet riboswitches by themselves are enough to prove that God has created everything with a purpose. He is All-Wise and he does nothing in vain. Riboswitches are not useless at all. They are such complex, and perfectly working systems that they can serve humanity as well-designed on/off switches in numerous applications.

Safiye Arslan is a research fellow in the area of biological chemistry and lives in Nevada.

References

1. Gilbert SD, Reyes FE, Edwards AL, Batey RT. 2009. Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure 17, 857-868

2. Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. 2007. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19, 3437-3450.

3. Kulshina N, Baird NJ, Ferré-D’Amaré AR. 2009. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nature Structural & Molecular Biology 16, 1212-1217.

4. Kim JN, Blount KF, Puskarz I, Lim J, Link KH, Breaker RR. 2009. Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chemical Biology 4, 915-927.

5. Topp S, Gallivan JP. 2007. Guiding bacteria with small molecules and RNA. Journal of the American Chemical Society 129, 6807-6811.

6. Mairal T, Ozalp VC, Lozano Sanchez P, Mir M, Katakis I, O’Sullivan CK. 2008. Aptamers: molecular tools for analytical applications. Analytical and Bioanalytical Chemistry 390, 989-1007.

Almost all of us are familiar with the fact that our bodily organs are composed of tissues, which are made of cells. The perfect machinery of the cells is controlled by our genes; i.e. DNA and RNA. Therefore, a minor defect or mutation in the genetic code may affect either partial or entire systems within the body. Some of these genetic diseases are inherited from our parents or relatives. Others may be introduced into our body through environmental mutagens, such as ionizing radiation, ultraviolet rays, or different chemicals within our food and drink; these can result in cancer or cardiovascular diseases. We can protect ourselves from the latter by using appropriate outfits, taking care with our diet, etc. However, inherited genetic disorders are usually unavoidable and sometimes have fatal consequences. Modern medicine is striving to find a way to treat these diseases. Although there are some medical procedures that may lessen the pain of patients or extend their life expectancy, there is no available comprehensive curative therapy for genetic disorders.

Gene therapy has become one of the rising stars in the field of molecular medicine during the last decade, with more than 1500 proposed or ongoing clinical trials worldwide. Gene therapy promises to provide curative therapies for a large number of inherited or acquired diseases, such as monogenic disorders, cancer, or cardiovascular disease. Gene therapy is universally defined as the replacement of an abnormal/dysfunctional gene in the cells of an individual with its correct and functional version. Mechanics use a number of tools to fix our cars for us when they give us trouble; in the same way, gene therapy can be used by doctors to alleviate or completely eradicate some diseases from our bodies.

Gene therapy is classified into two categories based on the target cells that are to be treated. The transduction of the differentiated cells of an individual, i.e. the somatic cells, is known as somatic gene therapy; the transduction of reproductive cells, i.e. gametes (sperm or ova), is known as germ-line gene therapy. Currently, there are many regulations in place that limit the likelihood of the modification of the germline in any gene therapy approach. This is because fear exists that the ability to alter the germline will result in the widespread application of gene therapy to achieve eugenic genetic enhancements, such as improvement of intelligence or physical characteristics. On the other hand, transgenic animals, which are used to detect the function of the genes within an organism, can be generated by modifying the germ-line. Furthermore, gene therapy is also classified into two groups: adult and fetal (in utero) gene therapy, according to the individual to be treated. There are several advantages and disadvantages to these methods, such as immune response, the pooling of mitotic cells, the amount of vector that is required, etc.; however, these are matters for a different article.

Gene therapy is achieved by using special exogenous genetic material transfer agents which are called vectors; these can be compared to the special tools used by auto mechanics. Over the years, a number of gene transfer vehicles, i.e. vectors, have been developed and these can be divided into two principal categories: non-viral (synthetic) and viral (virus-based) gene delivery systems.

Non-viral gene transfer can be achieved by using both physical and chemical methods. The physical methods include: i) Electroporation, in which areas of the cell membrane break down as result of an applied electric pulse, thus allowing DNA to enter the cell, ii) Ballistic gene transfer (the Gene Gun), which bombards particles coated with DNA into the cells, and iii) Microinjection, in which DNA is transferred through microcapillaries into the cells [1]. In terms of chemical gene transfer, lipofection is the most promising method; in this method negatively-charged DNA molecules bind to cationic lipid particles through electrostatic interaction and the DNA–lipid complex enters the cell through endocytosis/pinocytosis. Although these non-viral delivery systems exhibit low toxicity and can be easily produced in high concentrations on a commercial scale, in general, gene transfer using these agents is inefficient and often transient. Therefore, as a result of the viral vectors’ ability to efficiently deliver and integrate genes into the host genome, they are being engineered extensively to achieve a sustained and high-level expression of the gene of interest (transgene).

Viral vectors

Have you ever thought that one of the major pathological agents that cause catastrophic and even fatal diseases could be used to treat the same or a similar disease?

Viruses are equipped with specialized molecular mechanisms that allow them to efficiently transport the genomes into the cells they infect and use the cell’s machinery for their own reproduction. Molecular biologists first harnessed this machinery of transduction in the 1970s. Paul Berg used a modified SV40 virus containing DNA from the bacteriophage lambda to infect monkey kidney cells that were being maintained in culture. Viral delivery systems are based on replicating viruses that have the ability to deliver genetic information into the host cell, a process known as transduction [2]. Due to the fact that there are several advantages to viral vectors, these are the vehicles being employed in approximately 75% of all ongoing clinical trials worldwide. Numerous viruses are being used as the basis for the vectors, including, but not limited to, adenovirus (24%, n=377), retrovirus (20.9%, n=329), adeno-associated virus (4.3%, n=67), herpes simplex virus (3.2%, n=51), vaccinia virus (7.9%, n=124), poxvirus (5.8%, n=91), and baculovirus (more detailed information is available at www.wiley.co.uk/genmed/clinical). The first step to construct a viral vector for transferring the gene of interest involves the identification of the viral sequences that are necessary for replication and pathogenesis. Then some of the genes are removed to make room for the transgene and to render the viral vector replication-incompetent. Consequently, the vector is unable to replicate within the host, and therefore is safe for delivering genes to human cells or tissues (Figure 1).

There are advantages and disadvantages to all of the currently available vectors; the suitability of the vector, therefore, actually depends on the disease or condition that is being treated. For instance, if the goal of the gene therapy is to increase bone marrow engraftment with the transient expression of a growth factor, the use of chemical transfection or naked DNA transfer methods would suffice. However, if the objective is to provide long-term treatment for an inherited disease, then the use of an integrating viral vector is more desirable. Thus, a vector that might be ideal for treating one defect may not be ideal for another. Driven by the desire to develop the “perfect” vector, scientists are continually striving for novel forms of gene delivery that might become the “magic bullet.” Somia and Verma [3] have proposed that the ideal gene therapy vector should include all of the following properties: 1) easy production at a high titer on a commercial scale with a reasonable shelf-life for transport and distribution 2) sustained or regulated expression of the transgene product that is adjustable to the nature of the disease, 3) absence of immune response against the vector and the transgene product, 4) ability to target specific tissues and/or cell types while avoiding professional antigen-presenting cells, 5) absence of size limitations for the genetic material to be delivered by the vector, 6) site-specific integration of the transgene into the chromosome of the target cell to avoid insertional mutagenesis, or faithful division and segregation if it is to reside in the nucleus as an episome independent of local chromatin environments, and 7) an ability to infect dividing and post-mitotic cells. Unfortunately, none of the currently available gene delivery vectors carry all of these features; however, many vectors have enough of the attributes to make them promising for clinical use.

Candidate diseases

During the last 4 decades, gene therapy for many diseases has progressed from preclinical to clinical studies; these range from monogenic recessive disorders such as hemophilia and cystic fibrosis to more complex diseases such as cancer, cardiovascular disorders, human immunodeficiency virus (HIV), neurological and ocular pathologies. The prevalence of diseases that fall under the scope of gene therapy is enormous and most of them have catastrophic or fatal outcomes. Therefore, gene therapy approach for almost any of the diseases mentioned above has an obvious appeal and rationale. To date, more than 1,540 gene therapy clinical trials have been initiated, and these are continuing or have been completed in 28 countries, using more than 100 genes, including antigens, cytokines, tumor suppressors, growth factors, and deficiency genes [4].

Candidate monogenic disorders that are considered to be good candidates for treatment by gene therapy include the hemoglobinopathies, X-linked genetic disorders, amino acid metabolism disorders, and lysosomal and other storage diseases. Currently, there are more than 4000 monogenic diseases registered in the OMIM database. The ultimate aim in treating monogenic diseases with gene therapy is the correction of the disorder by the stable transfer of the functioning gene into dividing cells (stem/progenitor cells), which will ensure the permanence of the correction [5]. The first recognized successful clinical gene therapy trial involved the treatment of 11 children who suffered from SCID-X1 (Severe Combined Immunodeficiency), an X-linked inherited monogenic disorder caused due to a mutation in the common cytokine receptor gamma chain (γc). In these patients, immunity was not fully developed due to the blocking of T-cell and natural killer cell development as a result of mutation. Unfortunately, the trial in SCID-X1 also exemplified one of the potentially serious side effects of gene therapy. Three of the children developed uncontrolled clonal T-cell proliferation, that is, leukemia, almost 3 years after treatment. This case was associated with the integration of the retroviral vector close to the promoter of the LMO-2 proto-oncogene. As a result, LMO-2 protein expression was up-regulated in an abnormal way and resulted in leukemia [7]. Another candidate monogenic disorder for gene therapy is cystic fibrosis (CF), in which abnormally thick mucus is produced in the lungs of the patients, causing difficulty in breathing and increasing the frequency of serious lung infections. CF is known as the most common inherited genetic disease in Europe and USA, especially within the Ashkenazi Jewish population. The average life expectancy of patients with CF is less than 40 years; hence the treatment of this disease has become one of the prime targets of gene therapy research.

In addition to its use in the treatment of monogenic diseases, gene therapy is also becoming a therapeutic alternative for the treatment of various forms of cancer. Indeed, almost 65% of ongoing clinical trials are related to cancer (more detailed information is available at www.wiley.co.uk/genmed/clinical), an area in which much more promise can be seen; this is also a reflection of the urgent need for new therapies to tackle the escalating incidence of this disease. Several different principles are used to treat cancer, including gene therapy that is targeted at tumor suppressor genes, such as p53, or central signaling molecules, as well as “suicide gene” therapy, in which the transgene is capable of converting pro-drugs (selectively less active drugs) into drugs that are toxic for tumor cells. Furthermore, various gene therapy protocols have been developed to strengthen the host’s anti-tumor immune responses by immunotherapy. Most of these studies have been early clinical trials designed primarily as studies of the safety, applicability, and toxicity of gene therapy. Several of these phase I and II studies have, however, shown partial remission of tumors and, in rare cases, complete remission. However, complete cure of the tumor has not yet been achieved. In some trials, including TP53 gene therapy trials, regression in tumor size has been observed in up to 50% of patients. China has become the first country to license gene therapy as a regular treatment for neck and head cancer; here Gendicine, a replication-defective Ad5 vector expressing p53 from a Rous sarcoma virus (RSV) promoter, is used for therapy [6].

In addition to its applications for cancer and monogenic diseases, gene therapy has become one of the favorite methods in cardiovascular research field. This is in step with the rise in clinical trials for cardiovascular gene therapy from 8.3% to 9.1% during the last few years, becoming the second most popular application for gene therapy. In accordance with the variety and occurrence of cardiovascular diseases, different gene therapy strategies have been developed to tackle each disease on its own terms. The expectation is that gene therapy will provide a new avenue for therapeutic applications in the growth of blood vessels, as well as the protection, regeneration, and repair of heart tissue, the prevention of the reoccurrence of constricted or narrowed arteries following cardiovascular intervention, the prevention of the rejection of a bypass, and risk-factor management [4]. Long-term therapeutic gene expression is required in some diseases, such as hypertension research, where reversal and prevention are the key targets. On the other hand, for some other types of cardiovascular diseases, such as ischemia, atherosclerosis, and restenosis, shorter-term gene control will be sufficient to prevent further progress of the symptoms. Therefore, different gene-therapy vectors have to be considered for the treatment of each specific cardiovascular disorder.

Consequently, gene therapy offers new avenues of treatment for diseases including monogenic disorders, cancer, cardiovascular diseases, infectious pathologies and many more. As we follow the tradition, “God did not send down any illness for which He did not also send a cure (Bukhari)”, gene therapy using either viral, non-viral, or any other novel methods may pave the way for the cure of many diseases that are highly prevalent in the world and which for decades have been perceived as untreatable.

Dr. Ferhat Ozturk is a postdoctoral research associate at University of Nebraska Medical Center.

References

1. Wells DJ. “Gene therapy progress and prospects: electroporation and other physical methods.” Gene Ther. 2004 Sep;11(18):1363-9.
2. Kootstra, N.A. and I.M. Verma, “Gene therapy with viral vectors.” Annu Rev Pharmacol Toxicol, 2003. 43: p. 413-39.
3. Somia, N. and I.M. Verma, “Gene therapy: trials and tribulations.” Nat Rev Genet, 2000. 1(2): p. 91-9.
4. Edelstein, M.L., M.R. Abedi, and J. Wixon, “Gene therapy clinical trials worldwide to 2007–an update. J Gene Med, 2007. 9(10): p. 833-42.
5. http://www.biomedisch.nl/en/gene_therapy_targeted_diseases.php
6. Peng, Z., “Current status of gendicine in China: recombinant human Ad-p53 agent for treatment of cancers.” Hum Gene Ther, 2005. 16(9): p. 1016-27.
7. Cavazzana-Calvo M, Fischer A, Gene therapy for severe combined immunodeficiency: are we there yet? J Clin Invest. 2007 June. 117(6):1456-65

We inherit our hereditary characteristics from our parents. The basic unit responsible for inheritance in our body is the gene. More technically, a gene is a hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism. Genes are like words on the long string of DNA. The description of the fundamental process of synthesizing proteins from the information on genes is called the “Central Dogma.” According to this dogma, DNA is used to synthesize RNA, and in turn, RNA is used to synthesize proteins. Hence, this dogma dictates the link between genes and proteins. Proteins are actually a translated and three-dimensional version of the linear information stored in genes.

The Structure of DNA

DNA (Deoxyribonucleic acid) is our repository of genetic information. Although there are organisms such as RNA viruses that possess RNA (ribonucleic acid) as their genetic material, virtually all other living organisms inherit their genes through DNA. Hence, DNA is vital for the existence and perpetuation of life on Earth.

In a simple comparison, DNA can be likened to a sequence of letters where each letter is a single nucleotide, and the alphabet has only four letters: A, T, C and G. Although this alphabet is extremely small compared to those used in human communication today, we are still capable of capturing the vast size of human DNA with this analogy: Our DNA is composed of a sequence of nearly 3 billion (3,000,000,000) of these letters. What this means is that, if you were to type out your genetic code, you would have a 5,000-volume encyclopedia, with each volume containing 400 pages, and each page having 1,500 letters! But then, how do we even fit this formidable size of information in every single cell of our body? The answer lies in the astonishing folding, packaging and wrapping steps DNA goes through upon synthesis. Positioning nucleotides side by side, each DNA molecule would take up about 6 feet (~2 meters) of space. However, after all the packaging steps, DNA becomes compact enough to fit in not only a cell, but also in the microscopic nucleus of each cell.

Genes and the Human Genome Project

Unfortunate for our alphabet analogy above, the 3 billion nucleotides in DNA do not contain any spaces to let us know where each word begins and ends. The Human Genome Project accomplished the task of unraveling what these 3 billion letters are (each one is one of A,T,C and G) and this was a major achievement of humanity. However, it was not until then that we realized the real challenge DNA posed us: Where were the genes in DNA? In other words, how would we understand the words and sentences in this 3-billion string of letters? Apart from efforts to discover the DNA sequences of other organisms, it is not unfair to say that the interest and workforce once focused on the Human Genome Project has now almost completely shifted to this latter “real” challenge of discovering the genes in DNA.

How we wish life could be that easy! Just as completing the human DNA sequence made us realize that we did not know where the genes are, discovering some genes allowed us to understand that we would still be missing a major part of the picture even if we knew exactly where each gene was. Do we not frequently encounter instances in everyday life where one word means different things depending on context? So, is there any good reason to think that genes on our chromosomes will be any less complex? Unfortunately not. Quite to the contrary, the sense is growing that genes are actually far more complex and intricate than we originally thought. For one thing, a single gene may not cause an immediate effect, but may interact with a network of other genes to produce the final effect. Diseases that are caused by individual genes are actually very few, a famous example being cystic fibrosis. But diseases that are affected by the interaction of many genes are far more numerous and prevalent, for example, breast cancer, Alzheimer’s disease, Type 1 diabetes mellitus, multiple sclerosis and obesity.

This latter group of diseases is appropriately called “complex diseases.” Efforts are under way to decipher the intricate genetic and protein networks responsible for such diseases; however, there are so many (known and also unknown) variables that biologists have already called for help. Research problems such as complex diseases that require the interaction of biologists, mathematicians, computer scientists and statisticians alike have led to the advent of the currently very popular field of “Systems Biology.” Viewing the cell as a large factory, this field aims to understand all molecular networks and interactions that make up the very sophisticated machinery in living systems. After deciphering how cells operate flawlessly as a complex system, humans will be better able to discover causes of diseases, and will also be in a much better position to manipulate cells to cure diseases.

The idea of manipulating cells and cell components such as genes and proteins has actually led to “Synthetic Biology,” which is, in essence, the engineering approach to Systems Biology. Synthetic biologists try to engineer gene and protein networks in the cellular machinery to program cells for synthesizing custom-tailored molecules. This can be in the form of redesigning or producing mass amounts of existing molecules, or synthesizing nonexistent molecules that have medical or other potential uses. The overall significance of the field can be well understood by the following quote from one of the pioneers of the field, UC Berkeley professor Jay Keasling: “(Synthetic biology is) doing for biology what electrical engineering did for physics and what chemical engineering has done for chemistry.”

One example of synthetic biology comes from Jay Keasling’s lab. In collaboration with the Gates Foundation and OneWorld Health, the first nonprofit pharmaceutical in the US, Dr. Keasling’s lab is engineering a new metabolic pathway in E.coli to produce the precursor to artemisinin, currently the most effective treatment for malaria. The prospects include a drastic drop in cost, from dollars to dimes. Moreover, success in redesigning a metabolic pathway in bacteria holds great promise for reproducibility for other similar pathways important for the pharmaceutical, cosmetics and food industries.

Genomics vs. proteomics

Molecular biologists, today, are inundated with neologies ending with the suffix “-ome” and “-omics.” The consequence is that the expression “–omics” craze has found its place in the everyday language of these scientists. Basically, the suffix “-om-” refers to a totality of some sort. All the genes considered as a whole in an organism’s cell are called the “genome, and similarly all the proteins this genome can synthesize are referred to as the “proteome.” “Genomics” and “proteomics” refer to the study of the relevant “-ome,” as opposed to studying genes and proteins one by one.

Even though there exist so many –omics words in the literature these days, genomics and proteomics remain the most popular and useful ones. Proteomics can be thought of as the natural successor to genomics because it is fundamentally the next level of complexity after genomics. While scientists explore gene networks and their interactions in genomics, proteomics involves the study of all the proteins and their interactions in the cellular machinery of an organism. Unfortunately, the next level of complexity does not mean “linearly more complex” in this case; studying networks of three-dimensional molecules is an immensely more daunting task than studying those of one-dimensional DNA sequences. However, luckily for us, scientists are up to this challenge. Yet again, we observe a shift in focus in the scientific community from genomics to proteomics.

The main motivation for this shift can be roughly understood with an analogy from marketing or another one from military warfare. In the former, if you want a better marketing strategy for your product, you should target end-users first and foremost. Understanding behavioral patterns and preferences of end-users is much more important than understanding likes of your vendors, because eventually it is the end-user who will determine the demand for your product. In the latter analogy, we think of an army of soldiers who receive orders from a general commander; however, these orders can later be modified or completely annulled by orders from other commanders still in the hierarchical order. If you think about how reliable and informative knowing the orders that each soldier has received from the general commander is going to be, you will understand how useful it will be to have information on genes without supplementary information on proteins. Gene products, either RNAs or proteins, may undergo some steps called “post-translational modification” that are not completely understood, and worse yet may not be completely deterministic (implying random factors).

So, with the help of the analogies mentioned above, we can reason that the shift in focus of the scientific community from genomics to proteomics is mainly due to the fact that biological functions are carried out, not by DNA or genes, but by proteins and (although much less frequently than by proteins) by RNA molecules. For medical and other practical purposes, it is more important to acquire information on the proteome rather than the genome. This, of course, is not to suggest underestimating the importance of the genome. The genome preserves its significance as the origin and source of genetic information. It is just not as beneficial to think about the genome without looking at the final product, that is the proteome.

Conclusion

The completion of the rough draft of the Human Genome Project in 2000 marked the end of the Genetic Era and paved the way to the Genomic Era. The breakthroughs that have taken place since this cornerstone event have been breathtaking, awe-inspiring and maybe even hard to catch up with. The Genomic Era had given birth to different fields in a span of few years, and the biological scientific community has had to shift its focus from genomics to proteomics even without having sorted out the puzzles of the genome. The advent of the “-omics craze” was probably a by-product of this shift because suddenly each sub-field of molecular biology had to adapt a holistic approach in its explorations. Investigating a single entity, whether it be a gene or a protein or another molecule, quickly became stigmatized as “obsolete.”

This transition to a holistic approach has resulted in the interaction of biologists with scientists from quantitative fields such as mathematics, statistics and computer science. These interactions gave rise to truly interdisciplinary research fields such as systems biology, synthetic biology and computational biology. More and more scientists today believe that competence in the future will rely on incorporating expertise from these different fields. With each new discovery, realizing the level of complexity and the intricacy in the design of our body leaves us in true awe. Moreover, these discoveries only make it easier for us to grasp how little we know about the miraculous design of biological systems. On the other hand, this awareness makes us even more motivated to delve into scientific efforts because understanding the science behind creation takes us directly to the understanding of our Creator.

Jason Newfoundland is a PhD candidate in Bioinformatics at University of Michigan.

Notes

1. http://www.answers.com/topic/gene?cat=technology
2. This amazing process is demonstrated in this link: http://www.dnai.org/text/mediashowcase/index2.html?id=556
3. Synthetic Biology: Change on the Horizon, Karsten Temme, http://no.oneslistening.com/277
4. A glossary for –omics words exists at http://www.genomicglossaries.com/content/omes.asp

The complex nature of genetics and its wide implications for all living organisms from viruses to humans provide raw materials for creative imaginations. In the present scenario, many consider it vital to comprehend all the genetic information necessary to support life on this universe. One of the common constraints on the understanding of genetics is the assumption that genes are the sole causes of all activities of living organisms and can explain all aspects of biological life on earth. For example, some believe the behavior and development of an organism can be predicted, if its genetic information is known-this belief is called “genetic determinism.” However, it is true that neither all aspects of inheritance are in all cases well explained, nor that the mere effect of genes on complex traits is well interpreted. The boundaries of the effects of genes on physical existence, development, survival, and the behavior of organisms are not always simple and straightforward. The capacity of humans for genetic manipulation-at least as it is commonly assumed or claimed-is limited in several ways and some of the basic causes of such barriers have yet to be explained. The focus of this article is to point out the limitations on attempts to appoint genes as the driving force of life.

The Central Dogma

Genes are small fragments of genomic DNA, encoding mRNAs which are later translated into proteins that participate in different biological metabolisms, hence conferring different traits on an organism. The biological functions and transmission patterns of genes over generations were being investigated well before the discovery of DNA as hereditary material and date back to the recognition of Mendel’s laws in the early twentieth century. Genetic information is coded in the form of a short string of DNA called a gene, which is employed in the expression of a trait(s) or mechanism(s) through synthesizing a chain of amino acids called proteins. These proteins either can be stored in different body parts or serve as enzymes in various biochemical reactions such as fighting infections. This flow of genetic information from gene–mRNA–protein synthesis is called the “Central Dogma” in biological sciences. In this biological doctrine, a very solid and predictable mechanism is assumed. Prior to the release of the human genome sequence information, the number of genes in the human genome was estimated as ~100,000. However, this estimate was far more than the actual number of genes (~35,000), which led us to question the validity of the “Central Dogma” as an explanation of the complexity of human beings. Out of these ~35,000, only 300 genes are unique to the human species.¹ This is another blow to the authenticity of the original central dogma theory. Are those 300 genes the foundation of all humankind and do they distinguish us from the rest of the mammals? Reducing humankind to its biology and explaining it based on genes has been questioned extensively and could be the subject of another discussion. But even considering such a view valid for purely practical purposes, the big gap between humans and other mammals cannot be due to the existence of this small number of genes.

Recent scientific discoveries have revealed a key point about the structure of genes-that each gene has a set of sub-segments called exons. Each exon can make a new protein. Hence, the gene can be the template for more than one protein. In the presence of other genes and proteins, the code of a particular gene can yield different kinds of proteins under variable circumstances. The flow of information can be both ways, and hence there are no predetermined factors controlling the flow of information. That means, we might know the information on what genes are present, and we can even decode it to know what is in there, but we cannot be sure what result (proteins in this context) will come out at the end when it is in the context of real life.

From physical characteristics to their genetics

Working back from a particular trait and trying to infer the genes that are involved in expression of such trait is a different approach to reveal the role of genes but surely it is not an easy task. Traits that are expressed by a single gene or a small number of genes are known as Mendelian/qualitative traits and their pattern of inheritance is simple and detection of the gene(s) is straightforward. Some of the disease resistance in plants and blood groups in humans are classic examples of Mendelian traits. The main distinction between such traits and the quantitative ones is their discreteness. For example a human being can have only one of four blood types: A, B, AB or O, and each of these groups is solid and no other blood types exist in between. In this type of trait, the role of a particular gene(s) is usually predictable and the pattern of transmissions over generations both for the future and the past can be inferred.

However, only a small percentage of traits is qualitative and expresses Mendelian inheritance. Most traits, such as intelligence, skin color in humans, height of an organism, seed yield of a grain, and diseases that have genetic causes like cancer, are quantitative traits and complex in nature. The ultimate phenotype (what we can see or measure from a trait) emerges from the joint effect of many genes as well as interaction with the particular environment in which the individual develops. The number of genes that is involved in the expression of a particular trait can be hundreds or even more. An objective assessment of each trait and quantification (called the phenotype) is impractical in most cases and could lead to another discussion. But assuming that we can measure a trait feasibly, the inference of genetic bases could still be controversial. Considerable efforts have been devoted to unveiling the effect of genes in the expression of complex traits whose inheritance pattern deviates from Mendelian inheritance. A special genetic technique, known as genetic mapping, is used to identify multiple genes that underlie a complex trait and this has practical applications for crop improvement. In humans, efforts are directed toward the detection of genes which predispose to complex inherited diseases. In this type of situation, the effects of genes on a trait are additive and can only explain a certain amount of change in the trait that we are interested in. Detection of all genes involved in the expression of a quantitative trait is practically impossible. The environment is an important factor with a pivotal role in the expression of such traits. The term “environment” is not restricted to what is present within the cell or surrounding the cell or individual. It rather refers to larger scale effects in the process of biological life that cannot be explained by genetics and the term can be used interchangeably with non-genetic effects.

One of the most striking examples of the role of genes on the expression of the phenotype is the presence of differences between identical twins. Despite the fact that they have completely identical sets of genes, studies have shown that twins can indicate different degrees of psychiatric diseases such as bipolar disorder.² Similar phenomena may be observed in crop species. In crop breeding programs different varieties are usually tested in different environments. In most cases varieties rank differently based on their performance in different environments.³

Genetic background

Genes that do not code any information for the trait of interest can also be a part of the process of expression of the trait. In other words, certain genes can be employed to stop or alter the function of a particular gene. Modifying the utility of a gene can also be done by a series of complicated reactions within each organism through mechanisms known as epigenetics. This type of alteration in gene function is also observed empirically during the process of transferring genes between different organisms through genetic engineering.⁴ Most transferred genes are silenced (turned off) by different mechanisms in a new organism regardless of patterns of inheritance. This is particularly interesting because it clearly indicates that the existence of a particular gene in the body does not necessarily guarantee that it will be functional. Even if it is functional in one individual, it might be silent in others. Even if a gene is functioning in all the individuals carrying it, the degree of expression may be variable.

The end of genetic determinism

With the discovery of the code of genes, we now know more about the biology of living organisms than ever before, as new genetic tools have enabled us to better understand what kind of information is stored in each gene.

Most of the traits of living organisms are affected by the existence of many genes as well as non-genetic effects (denoted as environment in genetics). Although Mendelian traits can be predictable to some degree, yet we can not completely infer all the genes that are employed in the expression of a complex trait, nor the amount of contribution from each single gene and portion attributed by non-genetic factors. So we cannot determine the presence of genes by simply observing the phenotype or expression of a trait.

Considering each individual gene separately will allow us to understand its possible functions more clearly and accurately. Nevertheless, the knowledge of possible functions and structure is not enough to predetermine if the information coded in the gene will be used by the organism, and, even if it will be used, how much of that information will be processed is uncertain. Whether the information that is processed will be observed or not is another ambiguity.

Assuming that we can and will know all components of life by having the knowledge of genes is known as genetic determinism. In some cases, genes are described as independent entities that drive living organisms and manage life because of the assumption that their presence will be enough to predetermine all the biology and the behavior of an organism.

Simply, in order for a gene to be an independent agent by itself, it needs to have the knowledge of all other genes as well as all the non-genetic factors for expression of a simple trait. In reality, genes contain a very limited amount of knowledge which makes them no more than tools or parts of living organisms that are employed in the existence of life on earth. Biological life itself is incredibly complex and its sustainability requires a more comprehensive knowledge that is beyond our current understanding based on the genetic code.

Seyyidhan Mirza is a PhD candidate of Plant Breeding, Genetics, and Genomics. He can be contacted at seyyidmirza@gmail.com.

Notes

1. Siepel A., M. Diekhans, B. Brejová, L. Langton, M. Stevens, C. L.G. Comstock, C. Davis, B. Ewing, S. Oommen, C. Lau, H. Yu, J. Li, B. A. Roe, P. Green, D. S. Gerhard, G. Temple, D. Haussler, and M. R. Brent. 2007. “Targeted discovery of novel human exons by comparative genomics.” Genome Research. Cold Spring Harbor Laboratory Press; ISSN 1088-9051/07; www.genome.org
2. Cardno, A. G., Rijsdijk, F. V., Sham, P. C., Murray, R. M. & McGuffin, P. “A Twin Study of Genetic Relationships Between Psychotic Symptoms.” 2002. Am. J. Psychiatry 159, 539-545
3. Epinat-Le Signor, C., S. Dousse, J. Lorgeou, J.B. Denis, R. Bonhomme, P. Carolo, and A. Charcosset. 2001. “Interpretation of genotype x environment interactions for early maize hybrids over 12 years.” Crop Sci. 41:663–669
4. Kooter, J.M., Matzke, M.A., and Meyer, P. 1999. “Listening to the silent genes: Transgene silencing, gene regulation and pathogen control.” Trends Plant Sci. 4: 340–347