MOLECULAR & CELLULAR NEUROBIOLOGY 
Master Course Cognitive Neuroscience - Radboud University, Nijmegen

 

INDEX

INTRODUCTION CELLS AND WITHIN CELLS IN A NUTSHELL GENOMICS MOLECULAR BIOLOGICAL RESEARCH METHODOLOGY NEURODEVELOPMENT  

 

Chapter 4: Genomics

  The genome Functional Genomics Genome-wide association studies (GWAS)
  Genomics research Pharmacogenomics Molecular networks
  The Human Genome and HapMap Projects Genetic variations: SNPs and CNVs  

 

 

Genomics research   

Research in genomics may have a number of different focuses. It may concentrate on sequencing an entire genome or one chromosome or a specific gene. Or it may be interested in the function of a gene or the interaction of several genes. Genomics research will let us, for the first time, grasp the language of life and understand, for example, the tiny genetic differences that determine the colour of an eye, or the shape of a mouth. Some of what is learned from this research might help doctors prevent and treat diseases better. There may be applications and possibilities that we have not even thought of yet.

 

1) Photo: Helicobacter pylori, Bacteria.

Helicobacter pylori, Bacteria

2) Photo: Hybridoma.

Hybridoma

3) Photo: Proteus mirabilis.

Proteus mirabilis, Bacterium

For instance, genomics research could also lead to new energy sources like biofuels (environment), as well as to disease-, insect- and drought-resistant crops (agriculture), more nutritious products and healthier, more productive farm animals and livestock (agriculture, fisheries). This knowledge could also be applied to solve forensic mysteries and to save species facing extinction.

Commonality with other organisms   

Although we each have our own individual genetic code, we share a portion of this code with other species. Humans have in the genome traces of ancient genes stemming from the beginning of time that they share with every living organism. So, if humans have so much in common with other species, what is it that defines them as being human? What is it that turns human into the complex being capable of learning, speaking, thinking and feeling? What is it that makes an individual different from other human beings? What do humans have in common with a mouse or a worm? Humans share a surprising number of genes with other species. Although these genes don't all have the letters in the same order, their function is similar enough for them to be considered comparable. These genes likely stem from a common ancestor, one that lived 3.5 billion years ago. Scientists theorize that through evolution this ancestor's genome became the basis for every species that we know today.

 

% Common with Humans

Chimpanzee, Pan troglodytes
21 000 genes; Just like humans, chimpanzees have around 21 000 genes. But then why can't they speak? The difference could be in a single gene, FOXP2, which in the chimpanzee is missing certain sections.

98%

Mouse, Mus musculus
21 000 genes; Thanks to mice, researchers have been able to identify genes linked to skeletal development, obesity and Parkinson's disease, to name but a few.

90%

Zebrafish, Danio rerio
25 000 genes; 75% of the genes in these little fish are the same as in humans. Researchers use them to study the role of genes linked to blood disease, such as anemia falciforme and heart disease.

75%

Fruit Fly, Drosophila melanogaster
13 600 genes; For the past 100 years, the fruit fly has been used to study the transmission of hereditary characteristics, the development of organisms, and, more recently, the study of changes in behaviour induced by the consumption of alcohol.

36%

Thale cress, Arabidopsis thaliana
25 000 genes; This little plant, from the mustard family, is used as a model for the study of all flowering plants. Scientists use its genes to study hepatolenticular degeneration, a disease that causes copper to accumulate in the human liver.

26%

Yeast, Saccharomyces cerevisiae
6 275 genes; Humans have certain genes in common with this organism that is used to make bread, beer and wine. Scientists use yeast to study the metabolism of sugars, the cell division process, and other diseases such as cancer.

23%

Roundworm, Caenorhabditis elegans
19 000 genes; Just like humans, this worm possesses muscles, a nervous system, intestines and sexual organs. That is why the roundworm is used to study genes linked to aging, to neurological diseases such as Alzheimer's, to cancer and to kidney disease.

21%

Bacterium, Escherichia coli
4 800 genes; The E. coli bacterium inhabits the intestines. Researchers study it to learn about basic cell functions, such as transcription and translation.

7%

 

Heredity   

Similarities among family members have been recognized for thousands of years, but only in the last couple of centuries have we really started to understand how family traits get passed on. Genetics is the study of heredity and variation of organisms. Heredity is the passing on of traits from ancestors to their descendants through the genes. Because of heredity, offspring usually resemble their parents, so that cats have kittens and pumpkin seeds produce pumpkin plants. Genetic variation is when differences occur among individuals within the same population or species. Variation may result from mutation, or simply from the different combinations of the parents' genes. While humans are 99.9 per cent genetically similar, we are even more like members of our own family. We pass on a copy of our genome to our descendants and, as a result, all humans inherit half of their mother's and half of their father's genome. There is only one race - the human race. With the sequencing of the human genome, scientists have confirmed what they have known for a long time: there is no biological basis for race. Cultural and social differences are what distinguish one group from another. Indeed, genetic variations found within one racial group are often greater than those found between two different groups.

A neighbor-joining network of population similarities. The network was based on the frequencies of 100 Alu insertion polymorphisms (i.e. differences in the occurrence of so-called Alu DNA repeat sequences).

 

 

Sex and reproduction    

Sexual reproduction involves the merging of genetic material from different parents. It depends on reproductive cells (egg and sperm cells), each containing one half of the parent's genome. Such reproduction underlies evolution and genetic variation. Sexual reproduction is needed for some species like humans to survive, and so not surprisingly, it is one of the most powerful of all drives. For humans, each reproductive cell has 23 chromosomes (half the full set). Because these chromosomes come in pairs, when the cells combine genetic material, each chromosome from one parent must match up with the same chromosome from the other. But before this combination takes place, the male and female's genes each line-up on their respective sides in a process called meiosis. This process guarantees variation in the reproductive cells. The chromosomes unite to scramble the genetic information before dividing in two again. They then form four sex cells, each with different genetic compositions. This is the process that makes you different from your sister or brother.

Human sperm and egg

 

Variations   

Every living thing is the product of the interaction that takes place between genes and the environment. So the genetic input from parents is partly responsible, but also the environment plays a role.  What are the proportions? Genomics may help us figure this out. For organisms that produce children through sexual reproduction (where different genes from each parent are combined), an offspring is never an exact copy of its parents. And in almost every case, no two children of the same parents are genetically identical to each other. The exception is identical multiples like monozygotic twins, who share the same genome. Thanks to genetic variations received from their parents, certain organisms are better adapted to their environment than others. For example, good camouflage means better chances of escaping from predators, finding food, and having many descendants. This can be seen in these different species.

Click here for an animation on Accumulating mutations

Click here for a movie on Radiation can cause DNA mutations

See also under Genetic variations: SNPs and CNVs.

 

 

 

Coquina Donax, Donax variabilis

Manus Island Tree Snails, Papustyla pulcherrima

Noble Scallops, Chlamys senatoria

 

 

 

 

 

 

 

Non-genetic variations   

  Bonsai tree

  Scotch pine, Pinus sylvestris

Certain variations do not have a genetic origin. When plants do not have enough water and food, they will not grow as well as those that do. This variation is not passed on to the next generation. For example, this bonsai tree is a Scotch pine that has been transformed by humans through control of its environment. If its seeds were planted outdoors, its descendants could grow to a height of more than 20 meters.

 

Using Genomics   

The sequencing of the human genome has opened the door to new diagnoses and new therapies. However, these very advances in technology are forcing us to make some difficult decisions, both individually and as a society. New technology - such as cloning and stem cell therapy - may offer great hope, but at what price? Genetically modified organisms are a reality. What impact are they having on humans, on the environment and on biodiversity?

Genetic diseases   

Some genetic diseases can be traced back to a single gene. Others are caused by abnormalities in the interaction of two or more genes, compounded by environmental factors. Certain genetic diseases can be diagnosed and treated with medication or with gene therapy. Genetic diseases can have a profound impact on the lives of those who have them, and on their loved ones. Genomics offers new optimism for solutions. Many people live life with a genetic disease such as Alzheimer's disease or muscular dystrophy. Thanks to genomics it is now possible to move quickly to identify the defective genes that cause these diseases. Scientists may then be able to slow down the progress of the disease or even create made-to-measure drugs to match the patient's genetic profile.

Click here for an animation on the Cause of Alzheimer.

 

Defective genes

Missing or abnormal genes are responsible for genetic diseases. Sometimes only these defective genes result in disease, but they are usually compounded by environmental factors. Some of these illnesses can be attributed to a defect in one gene. They are called monogenic. This is the case with cystic fibrosis. A disease such as cancer, or a condition like dyslexia, is the result of several genes interacting with environmental factors, such as food and lifestyle. These genes are called susceptibility genes. We all probably carry several of such genes.

Karyotype of a man showing the 23 pairs of chromosomes. A karyotype is a display of the chromosomes within a single cell. The chromosomes are stained with dyes to accentuate differences between them.

 

 

Click here for an animation on the Cause of Phenyl Ketonuria (PKU)

Click here for an animation on What is Fragile X

Click here for an animation on Huntingtons disease

 

Genetic testing and new treatments

There are many tests that can be used to detect defective genes. For instance, with pre-natal diagnostics one can find out whether a baby has a genetic disease to get parents psychologically prepared or consider terminating the pregnancy. If a family member contracts cancer, a predictive gene test can indicate whether another member is likely to develop the same type of cancer allowing to take preventive measures. Whatever type of diagnostic testing used, it mostly implies difficult choices. For parents with a serious genetic disease, preimplantation diagnostics and in-vitro conception allow doctors to select and implant a healthy embryo in the mother's uterus. Genomics offers the hope of new treatments that may adjust and even correct defective genes (gene therapy) and treatments based on Pharmacogenomics (personalized medication).

DNA detectives

The variations in the genetic composition of living things help people resolve all kinds of mysteries. Detectives use DNA to identify criminals; anthropologists use it to understand human migration across the centuries; biologists use it to learn more about the origin and behaviour of various plants and animals; and conservationists use it to try to preserve endangered species. A human genetic makeup has 3.2 billion letters in an arrangement that is unique. Detectives, customs agents and game wardens use DNA fingerprinting to identify criminals, traffickers and poachers. This fingerprint, which can be obtained from a single hair, allows precise identification of the owner. Often, in the case of a fatal accident, victims can often be identified from their DNA fingerprint.

DNA autoradiogram

Genetically modified organisms (GMOs)

A genetically modified organism (GMO) is a plant, animal or microorganism whose genetic code has been altered, subtracted, or added (either from the same species or a different species) in order to give it characteristics that it does not have naturally. Genes can be transferred between species that otherwise would be incapable of mating, for example, a goat and a spider. This is called transgenesis. GMOs are found extensively in many food products. The soybean is by far the world's most cultivated transgenic plant, followed by corn, cotton, and canola. The United States, Argentina, Canada and China, in that order, are the biggest producers. Different countries have adopted different approaches to the touchy topic of labelling GMOs. In Europe, the labelling of GMOs is obligatory, and caution prevails. Products are labelled, and it is left to the consumer to make their choice. In Canada and the United States, the labelling of GMOs is optional. There are several methods to generate a GMO, from recombinant DNA technologies (production of new strains of organisms by combining DNA strands) to micro-injections.

Click here for a movie on Foodmap GMO (i.e. in which countries GMOs are applied)

 

 

Applications of transgenesis are:

Agriculture - Agricultural products with a higher yield; insect and herbicide resistant. Fruits and vegetables that grow in dry environments and are cold resistant. But what if insects develop immunity to pesticides.

Food Production - Tomatoes that do not rot. Salmon that fatten up quickly. Pigs with less fat and better nutritional value.

Forestry - Fast-growing trees whose ligneous fibre is of higher quality, less difficult to process, and resistant to harmful insects, illnesses and environmental stresses.
 

Health - Rice enriched with vitamin A. Bananas as vaccines. Sheep whose milk contains insulin. Alfalfa that produces hemoglobin. But what if these medications have unsuspected side effects.

Environment - Fish that detect pollutants in the water. Plants that create biodegradable plastics. PCB-decomposing bacteria. Sugar beets that produce gas.
 

Basic Research - Mice with human diseases to test vaccines and medications. Fruit flies to study the structure and function of genes. Fluorescent fish to understand human development. But what if you could modify the human being?

 


Next page: The Human Genome and HapMap Projects Go back to:  The genome