Genetics: the early days
What is genetics?
Genetics can be defined as the study of genes at all levels. This means you can look at them at the level of molecules, genome as well as the level of populations. Over the years several experiments and theories have given new insights in the knowledge of genetics. This is a short overview of the most important happenings in the world of molecular biology and genetics, from where on the field of bioinformatics has appeared.
1859 Charles Darwin introduces"On the Origin of Species"
Charles Darwin publishes in 1859 "On the Origin of Species by Means of Natural Selection or The Preservation of Favored Races in the Struggle for Life". Darwin’s landmark theory did not specify the means by which characteristics are inherited. The mechanism of heredity had not been determined at that time. His key premise was that evolution occurs through the selection of inherent and transmissible rather than acquired, characteristics between individual members of a species.
1865 Gregor Mendel demonstrates traits passed from parents to offspring
The Augustinian monk Gregor Mendel, through his work on the garden pea Pisum sativum,
discovered the fundamental laws of inheritance. He deduced that genes come
in pairs and are inherited as distinct units, one from each parent. Mendel
tracked the segregation of parental genes and their appearance in the offspring
as dominant or recessive traits. He recognized the mathematical patterns of
inheritance from one generation to the next. Mendel's Laws of Heredity are
usually stated as:
- The Law of Segregation: a gene pair defines each inherited trait. Parental genes are randomly separated to the sex cells so that sex cells contain only one gene of the pair. Offspring therefore inherit one genetic allele from each parent.
- The Law of Independent Assortment: Genes for different traits are sorted from one another in such a way that the inheritance of one trait is not dependent on the inheritance of another.
- The Law of Dominance: An organism with alternate forms of a gene will express the form that is dominant.
The genetic experiments Mendel did with pea plants took him eight years (1856-1863) and he published his results in 1865. During this time, Mendel grew over 10,000 pea plants, keeping track of progeny number and type. Mendel's work and his Laws of Inheritance were not appreciated in his time. In 1900, Mendel's work was independently rediscovered by DeVries, Correns, and Tschermak. Each of them announced Mendel’s discoveries and his own work as a confirmation of them.
1910 Thomas Hunt Morgan places genes on chromosomes and the phenomenon of crossing-over
In 1910, after the rediscovery of the work of Mendel, Thomas Hunt Morgan did crossing experiments with the fruit fly (Drosophila Melanogaster) at the Columbia University. He proved that the genes responsible for the appearance of a specific phenotype were located on chromosomes. He also found that genes on the same chromosome do not always assort independently. Morgan suggested that the strength of linkage between genes depended on the distance between them on the chromosome. The nearer two genes lie on a chromosome, the greater the chance of being inherited together. Likewise the farther away they are from each other, the more chance of being separated by the process of crossing-over. The genes are separated when a crossover takes place in the distance in between the two genes during cell division. Morgan’s experiments also lead to Drosophila‘s unusual position as one of the best-studied organisms and most useful tools in genetic research to this day.
In 1911, Alfred Sturtevant, then an undergraduate researcher in the laboratory of Thomas Hunt Morgan mapped the locations of the fruit fly genes whose mutations the Morgan laboratory was tracking over generations. This was the first genetic map ever made.
1944 Barbara McClintock discoveres transposable genetic elements
In 1944 Barbara McClintock discovers that genes can move on a chromosome and jump from one chromosome to another. McClintock’s discovery of transposable or movable, genetic elements was greeted with initial skepticism. She studied at that time the inheritance of color and pigment distribution in corn kernels at the Carnegie Institution Department of Genetics in Cold Spring Harbor, New York. At age 81 she was awarded a 1983 Nobel Prize. Scientists now think transposons may be linked to some genetic disorders such as hemophilia, leukemia, and breast cancer. They also think that transposons have played a crucial role in evolution.
More about transposable elements
1953 James Watson and Francis Crick propose a double helix model for DNA
DNA
is made of three
basic components, a sugar, an acid and an organic "base". The base always was
one of the four: adenine, thymine, guanine or cytosine. These four different
bases are categorized in two groups: purines (adenine and guanine) and pyrimidines
(thymine and cytosine).
In 1950 Erwin Chargaff found that in DNA the amounts of adenine and thymine are about the same, as are the amounts of guanine and cytosine. These relationships became known later as "Chargaff's Rules" and led to much speculation about the three dimensional structure DNA would have. Rosalind Franklin, a British chemist, used the X-ray diffraction technique to capture the first high-quality images of the DNA molecule. Franklin’s colleague Maurice Wilkins showed the pictures to James Watson, an American zoologist, who had been working with Francis Crick, a British biophysicist, on the structure of the DNA molecule. These pictures gave Watson and Crick enough information to propose the double-stranded, helical, complementary, anti-parallel model for DNA in 1953. Crick, Watson, and Wilkins shared the Nobel Prize in medicine and physiology for the discovery that the DNA molecule has a double-helical structure in 1962. Rosalind Franklin, whose images of DNA helped lead to the discovery, died of cancer in 1958 and, under Nobel rules, was not eligible for the prize.
In 1957 Francis Crick and George Gamov worked out the "Central Dogma", explaining how DNA functions to make protein. Their "sequence hypothesis" posited that the DNA sequence specifies the amino acid sequence in a protein. They also suggested that genetic information flows only in one direction, from DNA to messenger RNA to protein, the central concept of the central dogma.
1966 Marshall Nirenberg, Heinrich Mathaei and Severo Ochoa crack "the Genetic Code"
In
1966 the genetic code
was finally "cracked". Marshall Nirenberg, Heinrich Mathaei and Severo
Ochoa demonstrated that a sequence of three nucleotide bases, a codon, determines
each of the 20 amino acids. This means that there are 64 combinations possible
for 20 amino acids. The formed synthetic mRNA by mixing
the nucleotides of RNA with a special enzyme called polynucleotide phosphorylase.
This resulted in the formation of a single-stranded RNA in this reaction. The
question was how this genetic code, built up out of four different nucleotides,
could code for the twenty different amino acids, which were found in nature.
Nirenberg and Matthaei synthesized poly(U) by reacting only uracil nucleotides
with the RNA synthesizing enzyme, producing -UUUU-. They mixed this poly(U) with
the protein synthesizing machinery of E.
Coli in vitro and observed the formation of a protein. This protein turned
out to be a polypeptide of phenylalanine. So, they showed a triplet of uracil
must code
for phenylalanine. A few more codons were identified over the next few years.
Philip Leder and Nirenberg found an even better experimental protocol, and by 1965 the genetic code was almost completely solved. They found that the "extra" codons are merely are redundant: Some amino acids have one or two codons, some have four, and some have six. Three codons serve as stop signs for RNA synthesizing proteins.
1972 Paul Berg creates the first recombinant DNA molecule
In 1972, Paul Berg of Stanford University (USA) created the first recombinant DNA molecules by combining the DNA of two different organisms. Berg used a restriction enzyme to isolate a gene from a human-cancer-causing monkey virus. Then, he used ligase to join the section of virus DNA with a molecule of DNA from the bacterial virus lambda, creating the first recombinant DNA molecule. Berg realised the risks of his experiment and temporarily terminated it before the recombinant DNA molecule was added to E. coli, where it would have been quickly reproduced. He proposed a one-year moratorium on recombinant DNA studies while safety issues were addressed. Berg later resumed his studies into recombinant DNA techniques, and was awarded the 1980 Nobel Prize in chemistry. His experiments founded the field of genetic engineering and the modern biotechnology industry based on it.
1974 Frederick Sanger develops a DNA sequencing technique
In early 1974, Frederick Sanger (U.K. Medical Research Council) was first accredited with the invention of DNA sequencing techniques. During experiments to uncover the amino acids in bovin insulin, he developed the basics of modern sequencing methods. Sanger's approach involved copying DNA strands which would show the location of the nucleotides in the strands. Scientists had to analyse the composite collections of DNA pieces detected from four test tubes, one for each of the nucleotides found in DNA (Adenosine, Cytosine, Thimidine, Guanine). Then they needed to be arranged in the correct order.This technique is very slow and tedious, usually taking many years to sequence only a few million letters in a string of DNA that often contain hundreds of millions or even billions of letters. Almost simultaneously, the American scientists Alan Maxam and Walter Gilbert were creating a somewhat different method called the cleavage method. The base for virtually all DNA sequencing was the dideoxy-chain terminating reaction, developed by Sanger and for which he received his second Nobel Price. He already had one for his research on bovine insulin.
In 1986, scientists presented a means of detecting the ddNTPs with fluorescent tags, which required only a single test tube instead of four. As a result of this discovery, the time required to process a given batch of DNA was reduced by one fourth. The amount of sequenced base pairs increased from there on rapidly. In 1991, working with Nobel laureate Hamilton Smith, Venter's genomic research project (TIGR) created a bold new sequencing process coined shotgunning. This new method not only uses super fast automated machines, but also the fluorescent detection process and the PCR DNA copying procedure. This method is very fast and accurate compared to older techniques.
More information about sequencing
1978 David Botstein develops restriction fragment length polymorphisms
Indiviual humans differ one basepair in every 500 nucleotides or so. The most interesting variations for geneticists are those that are recognised by certain enzymes, called restriction enzymes. These enzymes, each of which cut DNA only when they see a specific sequence, for instance GAATTC in case of the restriction enzyme EcoR1. This sequence is called a restriction site. The enzyme will bypass the region if it has mutated to GACTTC. Thus, when a specific restriction enzyme cuts the DNA of different people, it may produce fragments of different lengths.
These DNA fragments can be separated according to size by making them move through a porous gel in an electric field. Since the smaller fragments move more rapidly than the larger ones, their sizes can be determined by examining their positions in the gel. Variations in their lengths are called restriction-fragment-length polymorphisms, or RFLPs.
1980 Kary Mullis at Cetus Corporation invented polymerase chain reaction (PCR)
PCR is a method for multiplying DNA sequences in vitro. The idea was not the product of a painstaking laboratory discipline, but was conceived by while Kary Mullis was cruising in his car on Highway 128 from San Francisco to Mendocino.
The purpose of the Polymerase Chain Reaction is to make a huge number of copies of a specific DNA fragment, a gene for instance. The use of thermostable polymerase allows the dissociation of newly formed comlimentary DNA and subsequent annealling or hybritization of the primers to the target sequence with minimal loss of enzymatic activity. PCR can be necessary to receive enough starting template for for instance sequencing.
1987 First "Yeast artificial chromosomes" used
A technique using modified yeast chromosomes, known as "Yeast Artificial Chromosomes," or YACs, enables scientists to borrow the DNA duplication machinery of cells.
Before YACs were developed, scientists relied on the duplication machinery of the bacterial Escherichia coli to make millions of copies, or "clones", of a piece of DNA they were interested in studying. But the size of a DNA piece that can be reproduced in YACs is 10 times greater than that which can be reproduced in bacteria. Because of this capacity, YACs enable scientists to isolate and study large portions of the genetic endowment of organisms whose chromosomes are big and complex, such as those of humans.
But to use yeast cells for reproducing DNA, scientists first had to know which parts of the yeast chromosome were necessary to direct the duplication process. Only 1 percent of a yeast cell's total DNA is necessary for replication, including the center of the chromosome (the centromere), the ends of the chromosome (telomeres), and another short stretch of DNA called the autonomous replication sequences (ars). As long as these genetic parts are attached to DNA from humans or other organisms, the yeast cell is tricked into making copies of that DNA during its own cell division.
Mel Simon and coworkers announce the use of BACs for cloning in 1992. BACs are based on a vector of E. coli which can carry fragments of foreign DNA op to 300 kb, athough the avarage is often around 100 kb. BACs can not contain inserts as large as YACs, but have several advantages over YACs. First, they can be isolated and manipulated simply with basic bacterial plasmid technology, and second they form less hybrid inserts than YACs do.
1988 National Center for Biotechnology Information (NCBI) founded
Established in 1988 as a national resource for molecular biology information, NCBI carry out diverse responsibilities. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. NCBI conducts research on fundamental biomedical problems at the molecular level using mathematical and computational methods.
The European equivalent of the NCBI is Hinxton.
In Europe a different information centre was founded: the European Molecular Biology Laboratory (EMBL) was established in 1974 and is supported by sixteen countries including nearly all of Western Europe and Israel. EMBL consists of five facilities: the main Laboratory in Heidelberg (Germany), Outstations in Hamburg (Germany), Grenoble (France) and Hinxton (U. K.), and an external Research Programme in Monterotondo (Italy).
EMBL was founded with a four-fold mission: to conduct basic research in molecular biology, to provide essential services to scientists in its Member States, to provide high-level training to its staff, students, and visitors, and to develop new instrumentation for biological research. Over its 25-year history, the Laboratory has had a deep impact on European science in all of these areas. EMBL has achieved much because it is a truly international, European institution, because it has achieved a critical mass of services and facilities which are driven by cutting-edge biological research, and because it regards education.
The European Bioinformatics Institute (EBI) is a non-profit academic organisation that forms part of the European Molecular Biology Laboratory (EMBL). The roots of the EBI lie in the EMBL Nucleotide Sequence Data Library, which was established in 1980 at the EMBL laboratories in Heidelberg, Germany and was the world's first nucleotide sequence database. The original goal was to establish a central computer database of DNA sequences, rather than have scientists submit sequences to journals. What began as a modest task of abstracting information from literature, soon became a major database activity with direct electronic submissions of data and the need for highly skilled informatics staff. The task grew in scale with the start of the genome projects, and grew in visibility as the data became relevant to research in the commercial sector. It became apparent that the EMBL Nucleotide Sequence Data Library needed better financial security to ensure its long-term viability and to cope with the sheer scale of the task.
1990 Human Genome Project launched
The U.S. Human Genome Project started as a 15-year effort co-ordinated by the U.S. Department of Energy and the National Institutes of Health. The estimated costs were $13 billion. The project originally was planned to last 15 years, but rapid technological advances have accelerated the expected completion date to 2003. Project goals were to:
1) identify all the genes in human DNA,
2) determine the sequences of the 3 billion chemical base pairs that make up human DNA, store this information in databases,
3) improve tools for data analysis,
4) transfer related technologies to the private sector, and
5) address the ethical, legal, and social issues (ELSI) that may arise from the project.
To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, the nematode Caenerhabditis elegans, the rat and the mouse. A unique aspect of the U.S. Human Genome Project is that it is the scientific undertaking to address the ELSI implications that may arise from the project.
1996 The cloned sheep"Dolly" is presented
On
July 5 1996 a sheep was born as a clone of the cell of another sheep. This
sheep,
called Dolly, was the first mammal to be cloned from an adult cell.
Her birth sparked off a heated debate about
the
ethics
of animal cloning: a dispute that
has
continued
with the claims of human cloning later on.
In January 2002, Dolly was diagnosed as having arthritis, a condition usually expected in older animals. A year later Dolly was euthanised after being diagnosed with progressive lung disease. It is still unclear if Dolly's early death had to do with the cloning.
Cloning has several promising applications. Two of them involves stem cells. Stem cells are unprogrammed cells", and they have the ability to generate a variety of cell types. This can makes them very useful for the treatment of several diseases. replacement of A promising example is cancerous stem cells in bone marrow with healthy stem cells from a donor are used to treat leukemia. In many cases, though, the patient's immune system rejects the donated cells. Cloning solves this problem. If the person's own cells can be used to generate stem cells, there would be no risk of rejection. Similarly, cloned stem cells could generate organs for transplantation. This would not only solve the same problem of immune system rejection, but the overall shortage of donated organs as well.
In January 2002, the first cloned pigs genetically modified specifically for the purposes of replacement human organ transplantation were born at the Roslin Institute. The born of cloned piglets might be a step further toward xenotransplantation, the transplantation of nonhuman organs into humans.
(Picture taken from: http://www.islamset.com/healnews/cloning/msnbc_quest.html)
2000 Completion of the Arabidopsis thaliana sequence
The Arabidopsis
Genome Initiative (AGI) was an international collaboration to sequence
the genome of the model plant Arabidopsis thaliana. Begun in 1996 with
the goal of completing the genome sequence by 2004, the genome was
completed at the end of 2000.
Hundreds of researchers in five nations contributed to the plant gene-mapping project, which was funded by government agencies in the United States and the European Union. The results of the five-year effort were published in the journal Nature.
Arabidopsis is a close relative to many field crops, an is used a model plant for them. Many genes are equivalent to those in for instance broccoli. The complete sequence of Arabidopsis is also directly relevant to human biological functions, because many fundamental life processes at the molecular and cellular levels are common to all higher organisms. Some of those processes are easier to study in Arabidopsis than in human or animal models. Arabidopsis contains numerous genes equivalent to those that prompt disease in humans -- ranging from cancer and premature aging, to ailments such as Wilson's disease, in which the human body's inability to excrete copper can be fatal.
Several fields can benefit from the research on Arabidopsis thaliana: In industrial nations, scientists hope to turn cornfields into renewable sources of industrial oils and chemicals, replacing fossil fuels. Even medicine could benefit by learning how the plant's DNA repairs itself after infection or injury. In the project's second phase, researchers hoped by 2010 to determine the biological function controlled by each of the plant's 25,500 genes.
2001 Publishing of the draft version of the Human Genome
In 1991, working with Nobel laureate Hamilton Smith, Venter's genomic research project (TIGR) created the 'shotgunning' method. A method at first controversy among Venter's colleagues who called it crude and inaccurate. However, "Venter cross-checked his results by sequencing the genes in both directions, achieving a level of accuracy that greatly impressed his initial sceptical rivals. Within a year, TIGR published the entire genome of Haemophilus influenzae, a bacterium with nearly 2 million nucleotides.
In 1998, after some dispute over patenting and publications, Venter left TIGR and joined PE Corporation to form his own company Celera (Latin for "quick"). His announcement to sequence the human genome within three years with Celera accelerates the work of the publicly funded Human Genome Project. Celera uses Applied Biosystem's ABI Prism 3700 (a DNA sequencer five times faster and more automated than rival machines) to sequence DNA. This new method not only uses super fast automated machines, but also the fluorescent detection processery fast and accurate compared to older techniques. While much of the scientific community still shuns Venter's 'shotgunning' technique, it is without a doubt the fastest and most accurate method currently utilised by the biotech community. Celera built their genome sequence on their own as well as on the publicly available sequences.
The biotech community stood still as Venter's 'shotgunning' technique churned out nucleotides faster than even he expected and the NIH redoubled its efforts, mechanically pumping out chunks of the human genome. During the winter of '99 both institutes projected a finished project by spring of 2000, however, the NIH's genome was still way behind that of Celera's. Then on April 7, President Clinton announced that all sequenced DNA was to become public knowledge and thereafter the two institutes began working together. Thus, the project ended early summer (July, 2000) as the two institutes worked simultaneous cracking the entire genome. The draft human genome sequence was published on February 15th 2001, in the journals Nature (publicy funded Human Genome Project) and Science (Craig Venter's firm Celera).
