Arxiu de la categoria: GENETICS

The extended phenotype: genetics beyond the body

Genes determine our eye color, height, development throughout life and even our behavior. All living beings have a set of genes that, when expressed, manifest themselves in a more or less explicit way in their body, modeling it and giving it a wide diversity of traits and functions. However, is it possible that the expression of some genes has effects beyond the body itself?

Discover some basic ideas about the extended phenotype theory.

The extended phenotype: genetics beyond the body

First of all, let’s talk about two basic, but not less important, concepts that will help you to understand the extended phenotype theory: genotype and phenotype.

Genotype

Genotype is the collection of genes or the genetic information that a particular organism possesses in the form of DNA. It can also refer to the two alleles of a gene (or alternative forms of a gene) inherited by an organism from its parents, one per parent.

The genetic information that a particular organism possesses in the form of DNA constitutes its genotype. Public domain image.

It should not be confused with the genome: the genome is the set of genes conforming the DNA that a species has without considering its diversity (polymorphisms) among individuals, whereas the genotype does contemplate these variations. For example: the human genome (of the whole species Homo sapiens sapiens) and the genotype of a single person (the collection or set of genes and their variations in an individual).

Phenotype

The genotype, or at least a part of it, expresses inside an organism thus contributing to its observable traits. This expression takes place when the information encoded in the DNA traduces to synthetize proteins or RNA molecules, the precursor to proteins. The set of observable traits expressed in an organism through the expression of its genotype is called phenotype.

Eye color (phenotype) is determined by the expression of a set of genes within an organism (genotype). Picture by cocoparisienne on Pixabay (public domain).

However, genes are not always everything when defining the characteristics of an organism: the environment can also influence its expression. Thus, a more complete definition of phenotype would be the set of attributes that are manifested in an organism as the sum of its genes and the environmental pressures. Some genes only express a specific phenotype given certain environmental conditions.

The extended phenotype theory

The concept of extended phenotype was coined by Richard Dawkins in his book “The Extended Phenotype” (1982). Dawkins became famous after the publication of what would be his most controversial work, “The Selfish Gene” (1976), which was a precursor to his theory of the extended phenotype.

In the words of Dawkins himself, an extended phenotype is one that is not limited to the individual body in which a gene is housed; that is, it includes “all the effects that a gene causes on the world.” Thus, a gene can influence the environment in which an organism lives through the behavior of that organism.

Dawkins also considers that a phenotype that goes beyond the organism itself could influence the behavior of other organisms around it, thus benefiting all of them or only one… and not necessarily the organism that expresses the phenotype. This would lead to strange a priori scenarios such as, for example, that the phenotype of an organism was advantageous for a parasite which afflicts it rather than for itself. This idea is summed up in what Dawkins calls the ‘Central Theorem of the Extended Phenotype’: ‘An animal’s behaviour tends to maximize the survival of the genes ‘for’ that behaviour, whether or not those genes happen to be in the body of the particular animal performing it’.

A complex idea, isn’t it? However, it makes sense if we take into account the basic premise from which Dawkins starts, which addresses in his work ‘The selfish gene’: the basic units of evolution and the only elements on which natural selection acts, beyond individuals and populations, are genes. So, organisms’ bodies are mere ‘survival machines’ improved to ensure the perpetuation of genes.

Examples of extended phenotype

Perhaps all these concepts seem very complicated, but you will understand them better with some examples. According to Dawkins, there exist three main types of extended phenotype.

1) Animal architecture

Beavers build dams and modify their surroundings, in the same way that a termite colony builds a termite mound and alters the land as part of their way of life.

Dam built by beavers. Picture by Hugo.arg (CC 4.0)
Termite mounds in Autralia. Public domain image.

On the other hand, protective cases that caddisflies build around them from material available in the environment improve their survival.

Caddisfly larva inside its protective case made up of vegetal material. Picture by Matt Reinbold (CC 2.0)

These are all examples of the simplest type of extended phenotype: the animal architecture. The phenotype is, in this case, a physical or material expression of the animal’s behavior that improves the survival of the genes that express this behavior.

2) Parasite manipulation of host behavior

In this type of extended phenotype, the parasite expresses genes that control the behavior of its host. In other words, the parasite genotype manipulates the phenotype (in this case, the behavior) of the host.

A classic example is that of crickets being controlled by nematomorphs or gordiaceae, a group of parasitoid ‘worms’ commonly known as hair worms, as explained in this video:

To sum up: larvae of hair worms develop inside aquatic hosts, such as larvae of mayflies. Once mayflies undergoe metamorphosis and reach adulthood, they fly to dry land, where they die; and it is at this point that crickets enter the scene: an adult cricket feeds on the remains of mayflies and acquires the hair worm larvae, which develop inside the cricket by feeding on its body fat. Adult worms must return to the aquatic environment to complete their life cycle, so they will control the cricket’s brain to ‘force’ it to find a water source and drop in. Once in the water, the worms leave the body of the cricket behind, which drowns.

Other examples: female mosquitoes carrying the protozoan that causes malaria (Plasmodium), which makes female mosquitoes (Anopheles) to feel more attracted to human breath than uninfected ones, and gall induced by several insects on different host plants, such as cynipids (microwasps).

3) Action at a distance

A recurring example of this type of extended phenotype is the manipulation of the host’s behavior by cuckoo chicks (group of birds of the Cuculidae family). Many species of cuckoo, such as the common cuckoo (Cuculus canorus), lay their eggs in the nests of other birds for them to raise in their place; also, cuckoo chicks beat off the competition by getting rid of the eggs of the other species.

Look how the cuckoo chick gets rid of the eggs of reed warbler (Acrocephalus scirpaceus)!

In this case of parasitism, the chick is not physically associated with the host but, nevertheless, influences the expression of its behavioral phenotype.

Reed warbler feeding a common cuckoo chick. Picture by Per Harald Olsen (CC 3.0).

.            .            .

There are more examples and studies about this concept. If you are very interested in the subject, I strongly recommend you to read ‘The selfish gene’ (always critical and from an open minded perspective). Furthermore, if you have good notions of biology, I encourage you to read ‘The extended phenotype’.

Main picture: Alandmanson/Wikimedia Commons (CC BY-SA 4.0)

Transponable elements: the jumping genes of our genome

In the same way that grasshoppers are jumping and moving through the field, there is a type of genes that jump through our genome and change its position. Our genome is not static, so read on to know everything about these kinds of genes.

THE DISCOVERY OF TRANSPONABLE ELEMENTS

Barbara McClintock discovered transposable elements, or also called mobile genetic elements because of their ability to move around the genome. The “jumping genes,” as this American geneticist christened them, changed the knowledge about genetics so far, since at first the scientific community did not believe in the idea that a DNA sequence could move on its own.

She had a special relationship with corn, a plant domesticated by man for 10,000 years and has become one of the three most cultivated cereals in the world. In addition, it is one of the most important staple foods since from it many derived products are made, such as flours and oils. Its great industrial value has made it have been studied in depth and its genome has been sequenced.

McClintock began studying the DNA of corn and observed that there were a number of genetic sequences that, without knowing how, changed position within the genome. Somehow, these sequences turned on or off the expression of other corn genes and this was observed with the naked eye; the grains of a corn cob could be of different colours (Figure 1), even within the same grain there were areas of various colours. Then McClintock sought the answer of how this was possible if the genes responsible for colour were inherited from the parents. The result was the discovery of the transposable elements, which led her to win the Nobel Prize in Medicine in 1983.

elemento transponible maiz
Figure 1. (A) P gene gives a purple grain. (B) A transponable element is inserted in the middle of the P gen and the grain has no pigmentation. (C) Corn cob wit some grains with P gene intact and others with P gene interrupted by a mobile genetic element. (Source: Porque biotecnología, adaptation)

EFFECTS OF THE CHANGE OF POSITION

When the transposable elements jump and change position they produce a loss of bases when leaving the place where they rested. This loss of some bases does not have “much” importance. But if the transposable element is inserted into a gene, there is an addition of a large number of bases that will cause the loose of gene’s function. For this reason, mobile genetic elements produce mutations because by jumping and changing their location, they alter the DNA sequence and prevent genes from encoding proteins through the genetic code. However, when they jump again, the gene regains its functionality and expresses itself as if nothing had happened.

Often, these jumping genes are considered parasites, because the cell cannot get rid of them. Although they can also bring benefits to the cell, such as transporting advantageous genes. The best known example is not found in humans, but in bacteria and their resistance to antibiotics such as penicillin, discovered by Alexander Fleming. The spread of antibiotic resistance is due to genes that encode enzymes that inactivate them, and that are located in mobile genetic elements. It is usually related to the horizontal transfer of genes, in which they can move from one cell to another as if they were bees that go from flower to flower. When this happens, the transposable element is introduced into a new cell and inserted into the genome of this new cell. That is when it will be faithfully transmitted to its progeny through the normal process of DNA replication and cell division.

TYPES OF TRANSPONABLE ELEMENTS

It is estimated that in the human genome there are 44% transposable elements, which can amount to 66% taking into account repeated fragments and short sequences derived from them. The consequence is that we have more than 1000 genes regulated, directly or indirectly, by sequences from transposable elements.

So far, two types of transposable elements are known: class I transposable elements or retrotransposons and class II transposable elements or DNA transposons. They are classified according to whether they require reverse transcription to jump and transpose or not.

Reverse transcription is similar to the transcription process, but with the difference that it occurs in reverse. That is, if in the classical transcription process a single strand of RNA is obtained from a double strand of DNA, in reverse transcription of an RNA molecule a DNA molecule is obtained. This is common in viruses such as HIV virus (AIDS) or hepatitis virus, but also in some class I transposable elements. These are very abundant and represent 90% of the transposable elements of our genome.

Instead, the others are class II transposable elements or DNA transposons. These are the elements that McClintock discovered in corn, with a 10% representation in our genome and responsible for the spread of antibiotic resistance in bacterial strains.

It should be noted that DNA transposons never use intermediaries, but are autonomous. They jump from one place of the genome to another by themselves, without any help. The mechanism they use is called “cut and paste” and is similar to the cut and paste we use on the computer. The DNA transposon cuts the DNA sequence that has end and look for another place to settle. Then there it also cuts the DNA sequence and is “hooked” (Figure 2).

transposon
Figure 2. Mechanism of cutting and pasting (Source: SITN: science in the news)

It is currently known that the activity of transposable elements is a source of evolutionary innovation due to the generation of mutations, which could have been key both in the development of organisms and in different evolutionary phenomena such as speciation; the process by which a population of a given species gives rise to another or other species.

The vast majority of these mutations are deleterious to organisms, but some of them will lead to adaptive improvement and tend to spread throughout the population. We could put our hand in the fire and we probably wouldn’t burn to ensure that much of the variability that life shows around us originally comes from the displacement of mobile genetic elements or transposable elements.

(Main picture: ABC Canada)

Model organisms in genetics

For scientists it is basic to work with models to discover what happens in a complete organism, which is more complex than the sum of its parts. It is for this reason that there are certain organisms, that by their characteristics, it is easy to use them as model in science. Below I present the 7 most commonly used species as model organisms in genetics.

WHAT IS A MODEL ORGANISM?

Model organisms are easily studied organisms, which thanks to them we can study important phenomena and extrapolate them to the organism that interests us. As Jacques Monod, Nobel Prize in Medicine in 1965, said, “What is true for bacteria is for elephants“.

These are characterized by:

  • Easy maintenance: it is not a big cost to have them in the laboratory.
  • Rapid biological cycle: in a few hours or days your biological cycle is completed.
  • High number of descendants: they have a high number of children in a short time.
  • Simple genome: they have few genes.

Model organisms are used to obtain information about other species that are more difficult to study directly. These are widely studied because they are easy to maintain and reproduce in a laboratory environment and have particular experimental advantages (Video 1).

Video 1. What is model organism? What does model organism mean? Model organism meaning & explanation (Source: YouTube)

The most commonly used are: Drosophila melanogaster (fruit fly), Mus musculus (mouse), Escherichia coli (colon bacteria), Arabidopsis thaliana (meadowsweet), Caenorhabditis elegans (worm), Sacharomyces cerevisiae (yeast) i Danio rerio (fish).

DROSOPHILA MELANOGASTER

Drosophila melanogaster (Figure 1) is better known as the fruit fly or vinegar. Surely you have seen in your kitchens, flying over ripe fruit or initial decomposition, and sweetened or alcoholic liquids.

It is one of the best-known animals, each of its body parts and the different stages of its life cycle is known up to the formation of an adult animal. It can live 30 days and the process from egg to adult lasts 7 days. In addition, its genome was sequenced in 2000.

In research it has a prominent role in biomedicine because it is used to study aspects related to cancer, neurodegenerative diseases or drug addiction.

drosophila melanogaster
Figure 1. Drosophila melanogaster (Source: YourGenome)

MUS MUSCULUS

Mus musculus (Figure 2) is the scientific name of the common mouse, the most commonly used mammal in the laboratory. The adult mice gets to measure (from the nose to the tail) between 7.5 and 10 cm long and weighs between 10 and 25 grams. Its gestation period is 19-21 days and it has between 3 and 14 offspring.

Its genome was completely sequenced in 2002. This phenomenon generated a great expectation for being a mammal that has a great scientific relevance for the human species.

Laboratory mice are not within the general laws of animal protection, but bioethical protocols and standards are followed.

It is used as a model in many fields, such as in the investigation of cardiovascular diseases, diabetes, neurological disorders, cancer … and in genetic engineering.

mus musculus
Figure 2. Mus muculus (Source: eLife)

ESCHERICHIA COLI

Escherichia coli (Figure 3) is the best known organism in the scientific field. It is a bacterium that lives in the lower part of the intestines of warm-blooded animals, including birds and mammals, and is necessary for the proper digestion of food. Its genome was sequenced in 1997 and it could be observed that the number of genes that comprise it is one seventh of the number of genes in humans.

In recent decades, this bacterium has become an instrument in the laboratory, especially in the field of molecular biology. Thanks to this, it has reached the knowledge of the foundations of modern biology and has earned the recognition of different Nobel prizes, such as the processes of genetic recombination of bacteria, RNA transcription, DNA replication and gene regulation.

ecoli
Figure 3. Escherichia coli (Source: Public Health England)

ARABIDOPSIS THALIANA

It is an annual plant (Figure 4) that was introduced into laboratories about 40 years ago. You can complete your entire life cycle in six weeks. The central floriferous stem grows in about three weeks from germination and the flowers naturally self-pollinate. In the laboratory, it can grow inside plates or sherds under fluorescent light or in greenhouses.

Like Drosophila melanogaster, its genome was sequenced in 2000 and it was the first sequenced genome.

Currently, researchers try to discover the secrets behind their development, growth or flowering.

arabidopsis
Figure 4. Arabidopsis thaliana (Source: Biology pages)

CAENORHABDITIS ELEGANS

It is a 1 mm long earthworm (Figure 5) that lives in temperate environments. Although more than 40 years ago we can find it in the laboratory, in the last decades it has achieved the prestige of more traditional organisms, such as Drosophila melanogaster or Mus musculus. The sequence of its genome as the first multicellular organism was published in 1998 and is considered complete today.

In research it has helped in the knowledge of the causes of aging, cell death and the structure of the genome.

C.-elegans
Figure 5. Caenorhabditis elegans (Source: Society for mucosal immunology)

SACHAROMYCES CEREVISIAE

Sacharomyces cerevisiae is a yeast (Figure 6), the yeast of bread, wine and beer. Its sequencing, specifically of strain S288C, was completed in 1996, after four years of a project led by the European Union and the participation of more than 100 laboratories from around the world. It was the first eukaryotic organism to be sequenced and it is currently the most known eukaryotic genome. This has made it gain weight and has become a powerful biological model of eukaryotic organisms.

It is used above all in biotechnological research, improving and innovating the processes of baking and production of alcoholic beverages.

yeast
Figure 6. Sacharomyces cerevisiae (Source: Fratelli Pasini)

DANIO RERIO

It is a zebrafish (Figure 7), a tropical freshwater fish that is surely known to lovers of aquariums. Genetically speaking, it is more similar to the human species than the Drosophila melanogaster or Caenorhabditis elegans and it is easier to manipulate, maintain and breed than Mus musculus. It is capable of producing between 300 and 500 eggs per laying and it can live up to 5 years. The draft of the sequencing of its genome was published in 2002.

A little more than 30 years ago, it was introduced as a model species for research in the field of development biology and genetics. It is widely used for the study of human biology.

danio-rerio
Figure 7. Danio rerio (Source: NCBI)

(Main picture: eLife)

 

From lab to big screen (II)

As I told you in the previous article on genetics and cinema, there is a wide variety of films that talk about genetics. In the next article we will talk about science fiction, with two well-known films. Beware: spoilers!

GATTACA (1997)

Director: Andrew Niccol

Cast: Ethan Hawke, Uma Thurman, Jude Law

Genre: Science fiction

Story line: Vincent is one of the last “natural” babies born into a sterile, genetically-enhanced world, where life expectancy and disease likelihood are ascertained at birth. Myopic and due to die at 30, he has no chance of a career in a society that now discriminates against your genes, instead of your gender, race or religion. Going underground, he assumes the identity of Jerome, crippled in an accident, and achieves prominence in the Gattaca Corporation, where he is selected for his lifelong desire: a manned mission to Saturn’s 14th moon (titan). Constantly passing gene tests by diligently using samples of Jerome’s hair, skin, blood and urine, his now-perfect world is thrown into increasing desperation, his dream within reach, when the mission director is killed – and he carelessly loses an eyelash at the scene! Certain that they know the murderer’s ID, but unable to track down the former Vincent, the police start to close in, with extra searches, and new gene tests. With the once-in-a-lifetime launch only days away, Vincent must avoid arousing suspicion, while passing the tests, evading the police, and not knowing whom he can trust.

Relation with genetics: GATTACA is the “genetic” film par excellence. Starting with the title, this is formed by the initials of the four nitrogenous bases that make up DNA (guanine, adenine, thymine and cytosine). In addition, the helical shape of the DNA is repeated in several moments of the film, as in the stairs of Vincent’s house.

The main issue is about genetic selection, all children born have been genetically selected, closely linked to bioethics. The idea of ​​this selection is to reach eugenics, that is, to improve the population by selecting the “best” humans. This concept can be related to the Hitler’s Germany, who believed that Germans belonged to a superior group of races called “Aryan”. Hitler said that German Aryan race had been better endowed than the others and that this biological superiority destined Germans to oversee an empire in Eastern Europe.

Although nowadays genetic selection is valid and is used to avoid diseases, it is not applied with the same purposes as those of the film. At present, it is decided to carry out genetic selection after having studied the family and carried out the appropriate genetic counselling. It aims to help patients and their families avoid the pain and suffering caused by a genetic disease and should not be confused with the eugenic objective of reducing the incidence of genetic diseases or the frequency of alleles considered to be deleterious in the population.

This is very related to the genetic discrimination, case also exposed in the film. Gattaca is situated in a possible future in which genetics, trying to improve the quality of life of society, causes a movement of discrimination.

When we talk about discrimination, we tend to think about racial discrimination. This is defined as the different or exclusive treatment of a person for reasons of racial or ethnic origin, which constitutes a violation of the fundamental rights of individuals, as well as an attack on their dignity. Racism has been present throughout the history of mankind, especially in the twentieth century with racial discrimination in the United States and apartheid in South Africa.

For some time now, genetic discrimination has been gaining weight. It happens when people are treated differently by their company or insurance company because they have a genetic mutation that causes or increases the risk of a hereditary disorder. Fear of discrimination is a common concern among people who undergo genetic testing, and is a current problem that concerns the population because your own genome does not have to be a curriculum vitae that opens or closes doors as happens in the film. Vincent goes to work in Gattaca after performing a urine test and a blood test, since in Gattaca they do not choose workers for their ability or ability but for their DNA.

However, the film ends with the sentence “There is no gene for the human spirit”. This means that, although the society in which Gattaca is located is based on genetic modification, it does not affect the morality and final character of people because there is no way to genetically relate to the spirit, only the body has the genetic information.

Video 1. Trailer Gattaca (Source: YouTube)

JURASSIC PARK (1993)

Director: Steven Spielberg

Cast: Sam Neill, Laura Dern, Jeff Goldblum

Genre: Science fiction

Story line: Huge advancements in scientific technology have enabled a mogul to create an island full of living dinosaurs. John Hammond has invited four individuals, along with his two grandchildren, to join him at Jurassic Park. But will everything go according to plan? A park employee attempts to steal dinosaur embryos, critical security systems are shut down and it now becomes a race for survival with dinosaurs roaming freely over the island.

Relation with genetics: In the first film of this saga, from dinosaur’s fossils scientists extract DNA to be able to clone dinosaurs. The cloned dinosaurs will be part of the Jurassic park on which the film is based.

It is true that DNA can be extracted from bones, widely used in forensic genetics. Same as the issue of cloning, which was known by the Dolly sheep, the first large animal cloned from an adult cell in July 1996. But the film goes further and raises the possibility of reintroducing, in today’s world, extinct species and challenge natural selection.

Video 2. Trailer Jurassic Park (Source: YouTube)

REFERENCES

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Pharmacogenetics: a drug for each person

Sometimes, some people say that the medications prescribed by doctors are not good. Can this be true? Not all drugs work for the same population. Keep reading and discover the secrets of pharmacogenetics.

INTRODUCTION

The same that happens with nutrients, happens with drugs. Another objective of personalized medicine is to make us see that not all medicines are for everyone. However, it does not come again because around 1900, the Canadian physician William Osler recognized that there was an intrinsic and specific variability of everyone, so that each one reacts differently to a drug. This is how, years later, we would define pharmacogenetics.

It is important to point out that it is not the same as pharmacogenomics, which studies the molecular and genetic bases of diseases to develop new treatment routes.

First, we need to start at the beginning: what is a drug? Well, a drug is any physicochemical substance that interacts with the body and modifies it, to try to cure, prevent or diagnose a disease. It is important to know that drugs regulate functions that our cells do, but they are not capable of creating new functions.

Apart from knowing if a drug is good or not for a person, you also have to take into account the amount that should be administered. And we still do not know the origin of all diseases, that is, we do not know most of the real molecular and genetic causes of diseases.

The classification of diseases is based mainly on symptoms and signs and not on molecular causes. Sometimes, the same group of pathologies is grouped, but among them there is a very different molecular basis. This means that the therapeutic efficacy is limited and low. Faced with drugs, we can manifest a response, a partial response, that produces no effect or that the effect is toxic (Figure 1).

efectivitat i toxicitat
Figure 1. Drug toxicity. Different colours show possible responses (green: drug not toxic and beneficial; blue: drug not toxic and not beneficial; red: drug toxic but not beneficial; yellow: drug toxic but beneficial) (Source: Mireia Ramos, All You Need is Biology)

DRUGS IN OUR BODY

Drugs usually make the same journey through our body. When we take a drug, usually through the digestive tract, it is absorbed by our body and goes to the bloodstream. The blood distributes it to the target tissues where it must take effect. In this case we talk about active drug (Figure 2). But this is not always the case, but sometimes it needs to be activated. That’s when we talk about a prodrug, which needs to stop in the liver before it reaches the bloodstream.

Most of the time, the drug we ingest is active and does not need to visit the liver.

active and prodrug
Figure 2. Difference between prodrug and active drug (Source: Agent of Chemistry – Roger Tam)

Once the drug has already gone to the target tissue and has interacted with target cells, drug waste is produced. These wastes continue to circulate in the blood to the liver, which metabolizes them to be expelled through one of the two routes of expulsion: (i) bile and excretion together with the excrement or (ii) purification of the blood by the kidneys and the urine.

THE IMPORTANCE OF PHARMACOGENETICS

A clear example of how according to the polymorphisms of the population there will be different response variability we find in the transporter genes. P glycoprotein is a protein located in the cell membrane, which acts as a pump for the expulsion of xenobiotics to the outside of the cell, that is, all chemical compounds that are not part of the composition of living organisms.

Humans present a polymorphism that has been very studied. Depending on the polymorphism that everyone possesses, the transporter protein will have normal, intermediate or low activity.

In a normal situation, the transporter protein produces a high excretion of the drug. In this case, the person is a carrier of the CC allele (two cytokines). But if you only have one cytosine, combined with one thymine (both are pyrimidine bases), the expression of the gene is not as good, and the expulsion activity is lower, giving an intermediate situation. In contrast, if a person has two thymines (TT), the expression of the P glycoprotein in the cell membrane will be low. This will suppose a smaller activity of the responsible gene and, consequently, greater absorption in blood since the drug is not excreted. This polymorphism, the TT polymorphism, is dangerous for the patient, since it passes a lot of drug to the blood, being toxic for the patient. Therefore, if the patient is TT the dose will have to be lower.

This example shows us that knowing the genome of each individual and how their genetic code acts based on it, we can know if the administration of a drug to an individual will be appropriate or not. And based on this, we can prescribe another medication that is better suited to this person’s genetics.

 APPLICATIONS OF THE PHARMACOGENETICS

The applications of these disciplines of precision medicine are many. Among them are optimizing the dose, choosing the right drug, giving a prognosis of the patient, diagnosing them, applying gene therapy, monitoring the progress of a person, developing new drugs and predicting possible adverse responses.

The advances that have taken place in genomics, the design of drugs, therapies and diagnostics for different pathologies, have advanced markedly in recent years, and have given way to the birth of a medicine more adapted to the characteristics of each patient. We are, therefore, on the threshold of a new way of understanding diseases and medicine.

And this occurs at a time when you want to leave behind the world of patients who, in the face of illness or discomfort, are treated and diagnosed in the same way. By routine, they are prescribed the same medications and doses. For this reason, the need has arisen for a scientific alternative that, based on the genetic code, offers to treat the patient individually.

REFERENCES

  • Goldstein, DB et al. (2003) Pharmacogenetics goes genomic. Nature Review Genetics 4:937-947
  • Roden, DM et al. (2002) The genetic basis of variability in drug responses. Nature Reviews Drug Discovery 1:37-44
  • Wang, L (2010) Pharmacogenomics: a system approach. Syst Biol Med 2:3-22
  • Ramos, M. et al. (2017) El código genético, el secreto de la vida. RBA Libros
  • Main picture: Duke Center for Applied Genomics & Precision Medicine

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Insulin: a point in favour for transgenics

Despite the arguments and positions against transgenics, it is undeniable that insulin is a great transgenic success. It is essential in some types of diabetes; and since it was discovered, the life expectancy of diabetics has increased more than 45 years. Therefore, let’s know in detail.

REMINDER OF GENETIC ENGINEERING

Genetic engineering allows to clone, that is, to multiply DNA fragments and produce the proteins for which these genes encode in organisms different from the one of origin. That is, if in an organism there is an alteration or mutation of a gene that prevents the genetic code from translating it into proteins, with the techniques of recombinant DNA a gene is obtained without the mutation in another organism. Thus, it is possible to obtain proteins of interest in organisms different from the original from which the gene was extracted, improve crops and animals, produce drugs and obtain proteins that use different industries in their manufacturing processes. In other words, through genetic engineering, the famous transgenics are obtained.

They offer many possibilities in the industrial use of microorganisms with applications ranging from the recombinant production of therapeutic drugs and vaccines to food and agricultural products. But, in addition, they have a promising role in medicine and in the cure of diseases.

And is that the result of obtaining a recombinant DNA, from it, will be made a new protein, called recombinant protein. An example of this is the case of insulin.

WHAT IS INSULIN?

Insulin is a hormone produced in the pancreas and with an important role in the metabolic process. Insulin comes from the Latin insulae, which means island. Its name is due to the fact that inside the pancreas, insulin is produced in the islets of Langerhans. The pancreas is related to the general functioning of the organism. It is located in the abdomen and is surrounded by organs such as the liver, spleen, stomach, small intestine and gallbladder.

Thanks to it we use the energy of the food that enters our body. And this happens because it allows glucose to enter our body. This is how it provides us with the necessary energy for the activities we must perform, from breathing to running (Video 1).

Video 1. Insulin, Glucose and You (Source: YouTube)

HOW DOES INSULIN WORK?

Insulin helps glucose enter the cells, like a key that opens the lock on the cell doors so that glucose, which is blood sugar, enters and is used as energy (Figure 1). If glucose cannot enter because there is no key to open the door, as with people with diabetes, blood glucose builds up. An accumulation of sugar in the blood can cause long-term complications. That’s why it’s important for diabetics to inject insulin.

7-768x768
Figure 1. Picture of the funcioning of insulin in cells (Source: Encuentra tu balance)

WHY DO WE USE TRANSGENIC INSULIN?

First, the insulin obtained from animals such as dogs, pigs or cows was used. But although, above all, pork insulin was very similar to human insulin, it was not identical and contained some impurities. This fact caused rejection and, in some cases, allergies. In addition, to be obtained from the pancreas of pigs, for each pancreas only insulin was obtained for the treatment of 3 days (at more than the cost of care of the animal). The result was low performance and high costs.

But with recombinant DNA insulins, more is obtained at a lower cost. For this reason, currently, the original insulin is obtained from a human of genetic engineering, despite the fact that animal insulins are still a perfectly acceptable alternative.

Through genetic engineering, insulin has been produced from the E. coli bacterium. It was in 1978 when the sequence of the insulin was obtained and introduced inside the bacteria so that it produced insulin. This is how E. coli has gone from being a common bacterium to a factory producing insulin. Insulin is extracted from the bacteria, purified and marketed as a medicine.

The advantages of “human” insulin, obtained by genetic engineering, are the easy maintenance of bacteria, a greater quantity of production and with lower costs. More or more, the compatibility of this insulin is 100%, however there may be reactions due to other components.

On an industrial scale, the production of recombinant proteins encompasses different stages. These stages are fermentation, in which the bacteria are cultivated in nutritious culture media; the extraction to recover all the proteins inside, the purification, which separates the recombinant protein from the other bacterial proteins; and finally the formulation, where the recombinant protein is modified to achieve a stable and sterile form that can be administered therapeutically.

Each of the previous phases implies a very careful handling of the materials and a strict quality control to optimize the extraction, purity, activity and stability of the drug. This process can be simple or more complex depending on the product and the type of cell used. Although the complexity of the process would increase the final cost of the product, the value will not exceed the expense of isolating the compound from its original source to reach medicinal quantities, which is what we have shown with insulin. That is, producing human insulin has a lower cost than obtaining insulin from pigs.

Genetic engineering allows numerous potentially therapeutic proteins to be made in large quantities. Currently, there are more than 30 proteins approved for clinical use, in addition to hundreds of therapeutic protein genes that have been expressed at the laboratory level and that studies continue to demonstrate their clinical adequacy.

REFERENCES

  • Ramos, M. et al. El código genético, el secreto de la vida (2017) RBA Libros
  • Alberts, B. et al. Biología molecular de la célula (2010). Editorial Omega, 5a edición
  • Cooper, G.M., Hausman R.E. La Célula (2009). Editorial Marbán, 5a edición
  • Naukas
  • Vix
  • Main picture: UniversList

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The reality of mutations

Do you remember the ninja turtles? Leonardo, Raphael, Michelangelo and Donatello were four turtles that suffered a mutation when they were bathed with a radioactive liquid. Fortunately or unfortunately, a mutation cannot turn us into ninja turtles, but it can have other effects. Next, I tell you what mutations are.

WHAT ARE MUTATIONS?

Our body is like a great factory in which our cells are the workers. These, thanks to their internal machinery, make the factory stay afloat with the least possible problems. The constant operation of our cells (24/7), sometimes causes errors in their machinery. This generates imperfections in the genetic code, which generally go unnoticed. It is true that cells do everything possible to fix the failures produced, but sometimes they are inevitable and lead to the generation of diseases or even to the death of the cell.

Mutations are these small errors, it means, mutations are stable and inheritable changes that alter the DNA sequence. This fact introduces new genetic variants in the population, generating genetic diversity.

Generally, mutations tend to be eliminated, but occasionally some can succeed and escape the DNA repair mechanisms of our cells. However, they only remain stable and inheritable in the DNA if they affect a cell type, the germ cells.

The organisms that reproduce sexually have two types of cells: germinal and somatic. While the former transmit genetic information from parents to children, somatic cells form the body of the organism. Because the information of germ cells, which are what will give rise to gametes (sperm and oocytes) passed from generation to generation, they must be protected against different genetic changes to safeguard each individual.

Most mutations are harmful, species cannot allow the accumulation of large number of mutations in their germ cells. For this reason not all mutations are fixed in the population, and many of these variants are usually eliminated. Occasionally some may be incorporated into all individuals of the species.

The mutation rate is the frequency at which new mutations occur in a gene. Each specie has a mutation rate of its own, modulated by natural selection. This implies that each species can be confronted differently from the changes produced by the environment.

Spontaneous mutation rates are very low, in the order of 10-5-10-6 per gene and generation. In this way, mutations do not produce rapid changes in the population.

THE ROLE OF NATURAL SELECTION

Changes of nucleotides in somatic cells can give rise to variant or mutant cells, some of which, through natural selection, get more advantageous with respect to their partners and proliferate very fast, giving us as a result, in the extreme case, cancer, that is, uncontrolled cell proliferation. Some of the cells in the body begin to divide without stopping and spread to surrounding tissues, a process known as metastasis

But the best way to understand the role of natural selection of which the naturist Charles Darwin spoke is with the example of spotted moths (Biston betularia). In England there are two types of moths, those of white colour and those of black colour (Figure 1). The former used to be the most common, but between 1848 and 1898 black moths were imposed.

biston
Figure 1. Biston betularia, white and black moths (Source: TorruBlog)

This change occurred at the same time that cities became more industrial, in which coal became the main fuel for power plants. The soot of this rock dyed the sky, the soil and the buildings of the cities black. Tree trunks were also affected, where the moths were camouflaged.

The consequence of this fact was that white moths could not hide from their predators, whereas those that were black found a successful exit camouflaging well on the tinted trunks. With the change of colour of their hiding place they had more opportunities to survive and reproduce (Video 1).

Video 1. Industrial melanism, white and black moth (Source: YouTube)

This is a clear example of how changes in the environment influence the variability of gene frequencies, which vary in response to new factors in the environment.

TYPES OF MUTATIONS

There is no single type of mutation, but there are several types of mutation that can affect the DNA sequence and, rebound, the genetic code. However, not all mutations have the same effect.

There are many and different types of mutations, which are classified by mutational levels. These levels are based on the amount of hereditary material affected by the mutation and go up in rank according to the number of genes involved. If the mutation affects only one gene we speak of gene mutation, whereas if it affects a chromosomal segment that includes several genes we refer to chromosomal mutation. When the mutation affects the genome, affecting whole chromosomes by excess or by defect, we speak of genomic mutation.

An example of a point mutation is found in cystic fibrosis, a hereditary genetic disease that produces an alteration in the secretion of mucus, affecting the respiratory and digestive systems. A point mutation affects the gene that codes for the CFTR protein. The affected people receive from both parents the defective gene, which, having no copy of the good gene, the protein will not be functional. The result is that the secretions produced by the human body are thicker than usual, producing an accumulation in the respiratory tract.

REFERENCES

  • Ramos, M. et al. El código genético, el secreto de la vida (2017) RBA Libros
  • Alberts, B. et al. Biología molecular de la célula (2010). Editorial Omega, 5a edición
  • Cooper, G.M., Hausman R.E. La Célula (2009). Editorial Marbán, 5a edición
  • Bioinformática UAB
  • Webs UCM
  • Main picture: Cine Premiere

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