Contents of This Section

1. What is the relevance of the fields of genomics and gene therapy to brain aneurysms?

As you read the section on Genomics, below, and the section on Gene Therapy elsewhere in this Website ( take me to the Gene Therapy section now), you will learn that understanding the genetic basis for why aneurysms form and rupture is extremely important. Why? Because this knowledge may lead to the identification of a precise molecular target for gene-based aneurysm screening and treatment and, hopefully, will pave the way to preventing the formation and rupture of these lesions altogether.

2. What is all this "genomics" stuff, anyway, and how will it affect me?

To begin with, "Genome" was a term coined almost 100 years ago, and currently refers to the complete genetic (DNA, deoxyribonucleic acid) code of an organism. For humans, the term could be used to describe an individual's DNA "blueprint", or the unique blueprint of a species (e.g., "human genome").

Genomics, then, is the comprehensive study of whole sets of genes, gene products, and their interactions. We currently are living in the "genomic revolution", which is a time in which the impact of genomics on biomedical science and our professional and civilian lives can and will be readily explored and appreciated.

Recall that a gene is a piece of biological code that forms part of our "genome". Our genome is essentially derived from our biological parents following conception and is responsible for our development. Although our development is undoubtedly intertwined with the influences exerted on us by our respective environments, we are essentially the products of our genes. In short, "genes code for proteins".

Our DNA, which comprises "genes", can be thought of as a long twisted (helical) code. The DNA molecules are made up of long segments of four critical building blocks (i.e., four "bases": A for adenine, G for guanine, C for cytosine, and T for thymine), linked to a backbone of sugar (deoxyribose) and phosphate. These nucleotides (each a base+sugar+phosphate) pair with each other across the two backbones (i.e., two DNA strands) via hydrogen bonds, such that the A base pairs only with the T, and the G base pairs only with the C. The two DNA strands are in opposite "directions" (one has a 5' to 3' orientation, the other has a 3' to 5' orientation, so these strands are "antiparallel") and form a uniformly twisted structure called a double-helix. The human genome contains about 3 billion base pairs. Drs. Watson and Crick were awarded Nobel Prizes for working out the double-helix conformation of DNA.

The Building Blocks of Genes:

Figure 1 shows key components of genes (DNA). See text above.

There are 46 chromosomes (23 pairs) in a human cell, where each chromosome represents a unique section of the genomic DNA that is tightly packed (compacted) into supercoiled structures, a process helped by histone proteins. Twenty two pairs of these chromosomes represent "autosomal" DNA, and the one other pair represents "gender/sex" DNA. All this material is found in the nucleus of a cell. The information contained (i.e., encoded) in genes is converted through complex molecular processes known as transcription and translation into proteins. The micromachinery and mechanisms for this are well beyond the scope or aims of this Website, but can be found in basic genetics texts and on the Web using appropriate keyword search terms.

Proteins are large molecules that represent the fundamental building blocks of the tissues that make up our bodies. There is an enormous variety of proteins in our bodies as they have evolved to play unique and essential roles in cell structure and function. For example, some proteins are enzymes involved in an array of metabolic pathways, others participate in structural support, while others act as "receptors" or "channels" or "molecular motors" or "chaperones" in cellular communication, signaling, gating, and transport. Note that proteins may have more than one function. There at least 30,000 genes in the human genome, but there a many many more proteins (i.e., one gene can encode for many proteins, based on the occurrence of "posttranscriptional-posttranslational modifications").

DNA Transcription and Translation Model:

Figure 2 depicts the process of DNA to proteins. DNA in the nucleus (1) is converted into mRNA (3) by complex micromachinery (2) in a process known as transcription. The mRNA is then converted into proteins (4) in the cytoplasm of the cell through a process known as translation. These proteins may be used for nuclear work, cytoplasmic work, cell membrane work, or secreted for work outside of the cell (5).

The significance of all this: As elaborated above and below, studying and understanding cell microstructures and processes, and recognizing the number and types and functions of human genes and proteins is fundamental to facilitating recognition of the molecular basis of human disease processes. Only then can we reliably develop ways in which to effectively treat diseases.

3. What is the history of this field?

An excellent and detailed review is provided by Lorentz et al. (Mayo Clinic Proceedings, 2002; see Key References for this and other important reviews in this field). The following is a brief summary of the history of genetics:

Even as early as 2000 years before Christ, there are records of the ancient cultures of Babylon and Assyria practicing artificial pollination at the time of King Hammurabi. Apparently, even in the few hundred years before Christ, the relationship between heredity and the environment, the origin of birth defects, and the determination of gender were topics contemplated by the Greek philosophers Hippocrates, Aristotle and Plato. Aristotle proposed an "epigenesis" theory (in which an individual's development was deemed to be influenced by interactions with his or her environment), as opposed to a "preformation" theory (in which an individual's future developmental path was deemed largely preprogrammed, i.e., determined before birth) expounded by Empedocles and Democritus. Debate regarding “epigenesis” versus “preformation” came to the forefront again in 1694, following publication of an essay by Hartsoeker supporting preformation. In 1752, the Mathematician-biologist Maupertius wrote the first report of an inherited genetic disorder (in this case, a polydactyly condition in four generations of a single family). In 1814, Joseph Adams wrote a landmark work entitled "A Treatise on the Supposed Hereditary Properties of Diseases" in which he discusses heredity versus environment, dominant versus recessive conditions, and the rationale for avoiding mating with one's own relatives! In 1859, "On the Origin of Species", the famous work written by Charles Darwin, is published, describing a theory of evolution by natural selection. In 1865, Gregor Mendel's classic work "Experiments in Plant Hybridization" establishes modern genetics, and represented a scientific validation of the basic tenets of genetics. Mendel is thought of as the father of modern genetics, and his classic genetic hypotheses are referred to as Mendel’s Laws of Segregation and Independent Assortment.

Hand-in-Hand with the above developments in genetics came progress in the understanding of cell biology. In 1665, Hooke used a primitive light microscope to first describe cells while in the 1760s, cell theory takes a more formal shape after the observations of Wolff. In 1838, Schleiden and Schwann suggest that cells with nuclei are the fundamental units of life and in 1855, Virchow proposes that cells generate by division. Between 1860 and the 1890s, nuclein is described by Miescher, chromatin by Flemming, and chromosomes by Weismann.

Cell Components:

Figure 3. The figure immediately above shows some important components of a cell. Our understanding of genomics has developed hand-in-hand with our knowledge of the structure and function of cellular components (organelles). The description of these organelles is beyond the aims and scope of this Website, but can be readily be found in many basic Cell Biology and Histology texts and on the Web by appropriate keyword searches. [1=Cell membrane lipid bilayer, 2=Cytoplasm, 3=Cilia, 4a=Early endosome, 4b=Late endosome, 5=Cell membrane-associated proteins, 6=Nucleus and its nuclear membrane, 7=Nuclear membrane pore complex, 8=Chromatin, 9=Nucleolus, 10=Rough endoplasmic reticulum (rER) studded with protein-synthesizing ribosomes, 11=Energy producing mitochondria, 12=Smooth endoplasmic reticulum (sER), 13=Scavenging peroxisomes and lysosomes, 14=Microfilaments, 15=Centrioles, 16=Microtubules, 17=Cell transport micromotor attached to microtubules, 18=Golgi apparatus, 19=Vesicles targetted to cell membrane, 20=Intracellular macromolecule complex, e.g., a heat-shock protein supercomplex]

The last century: The term genetics was coined by the British zoologist William Bateson in the first part of the 20^th century, aroung which time "Inborn Errors of Metabolism" is published by Garrod, the father of biochemical genetics. At New York's Columbia University, Morgan describes sex-linked traits in the fruit fly, Drosophila melanogaster. while his students make huge leaps in the field of genetics by determining that genes are located on chromosomes and are arranged linearly. Muller, another student of Morgan, induces mutagenesis in Drosophila and discovers the origin of new genes by mutation. In the second quarter of the 20th Century, Griffith and Avery characterize the role of DNA in inheritance, while Linus Pauling describes the molecular (genetic and structural) basis of sickle cell anemia, a landmark contribution in terms of the manner in which the disease is characterized. Soon after, i.e., in the 1950s, Pauling describes the alpha-helical structure of proteins, Chargaff discovers that the ratio of nucleic acid bases (A:T, and G:C) is 1:1, and Franklin and Wilkins produce X-ray diffraction patterns of DNA. Watson and Crick determine the double helical structure of DNA, reported in a landmark and brief paper in the Journal Nature in 1953, for which they each are awarded a Nobel Prize. Crick later proposed the dogma that DNA makes RNA which makes proteins. Also in the 1950s, Tijo and Levan determine that there are 46 chromosomes in human cells, while Trisomy 21 (Down syndrome), 45X (Turner syndrome) and 47XXY (Klinefelter syndrome) are described, marking the birth of the field of clinical cytogenetics. In the 1960s, population-wide screening for phenylketonuria (PKU) begins, representing the first widespread genetic screening test, based on the work of Folling, Guthrie, and Susi. Tremin, Mizutani and Baltimore discover reverse transcriptase showing that RNA can make DNA! Holley, Khorana, Nirenberg, and Leder crack the genetic code by determining the DNA sequence for the 20 most common amino acids. In the 1970s, restriction enzymes are discovered at Johns Hopkins, while Southern develops the Southern Analysis (Blot) for DNA. Sanger develops a DNA sequencing method, and Kan and Dozy describe restriction fragment length polymorphisms (RFLPs). In the early 1980s, Mullis at Cetus Corporation (CA) invents the polymerase chain reaction (PCR), and genetic disease discovery proliferates. Automated PCR is born, and represents a key technology in the Human Genome Project.

4. What is the Human Genome Project?

In 1985, a scientific meeting convened by Robert Sinsheimer, chancellor of UC Santa Cruz, proposes the concept of human genome sequencing. Separately, Charles DeLisi, Director of Health and Environmental Research at the Department of Energy (DOE, USA), is asked to assess the utility of DNA sequencing in detecting induced mutations in atomic bomb survivors. In 1987, DeLisi starts the Human Genome Initiative (HGI), the first U.S. Government program on genome research, which is funded by Congress in 1988 ($17.3m to NIH, $11.8m to DOE). In 1988, the National Institutes of Health (NIH) establishes the Office of Human Genome Research, renamed as the National Center for Human Genome Research (NCHGR), directed by James Watson. In 1990, The International Human Genome Sequencing Consortium (IHGSC) is (officially) born, comprised of more than 2000 scientists from 20 institutions in 6 countries. Their combined goal is referred to as The Human Genome Project (HGP), originally a 15-year plan to map and sequence the entire human genome. Francis Collins takes over NCHGR from Watson in 1992. Craig Venter pioneers rapid genetic ("shotgun") sequencing methods and establishes a nonprofit organization, the “Institute for Genomic Research” (IGR). The bioinformatics arm of IGR becomes so robust that the entire (1.8 megabase) genome of the microorganism (bacterium) H. Influenzae is sequenced in less than 1 year. This feat represents the first complete genome determination of a free living organism. Celera Corporation is formed by Venter in 1998, at which time Celera projects that three years is left till the sequence of the human genome is determined. A “Private” (Venter, Celera) versus “Public” (Collins, NIH, IHGSC) sector race to sequence the human genome begins. The first entire human chromosome to be completely sequenced was Chromosome 22 (a collaboration between the Sanger Institute in England, the University of Oklahoma, Washington University in St. Louis, and Keio University in Japan). The sequence was published in Nature, in December 1999. In January 2001, the Genome issues of Science and Nature are published: they detail the first draft sequence of entire human genome.

Key statistics from the Genome issues:

The field blossoms into a bunch of subfields:

5. What is proteomics?

First note that the proteome (a fusion of the words protein and genome, and a term coined in 1994) refers to the total complement of proteins encoded by the genome of a species. The proteome represents the functional endproduct of the genome; unlike the genome, the proteome is in constant flux.

Proteomics, then, is the study of all proteins, including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules in a given environment.

The subfields of proteomics inlcude: expression proteomics pertaining to the relative abundance of proteins; cellular proteomics pertaining to protein-protein interactions; and structural proteomics pertaining to protein shape/conformation/structure. Core techniques used in proteomics include Western blot, 2-D PAGE, mass spectrometry, liquid chromatography, immunoprecipitation, protein microarray technology, immunohistochemistry and immunoelectron microscopy, x-ray diffraction, cellular recombinant protein expression systems, enzyme assays, etc.

Finally, it should be noted that diversity of proteins goes against the central tenet: one gene, one protein. Proteomic diversity (which distinguishes species) arises from events such as alternative splicing of mRNA and posttranslational modification of proteins. This accounts for the structural and functional differences between, e.g., a human being and a fruit fly or a worm, despite the differences in the number of genes being relatively small (approx. 2:1).