Paper No. : 08 Human Population Genetics Module : 25 Milestones in the field of genetics

Development Team

Prof. Anup Kumar Kapoor Principal Investigator Department of Anthropology, University of Delhi

Paper Coordinator Prof. Gautam K. Kshatriya Department of Anthropology, University of Delhi

Content Writer Dr. Mamta Jena Department of Anthropology, University of Delhi

Prof. A.Paparao Content Reviewer Sri Venkateswara University, Tirupati, Andhra Pradesh

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Human Population Genetics Anthropology Milestones in the field of genetics

Description of Module

Subject Name Anthropology

Paper Name 08 Human Population Genetics

Module Name/Title Milestones in the field of genetics

Module Id 25

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Human Population Genetics Anthropology Milestones in the field of genetics

INTRODUCTION When we search the published literatures, we can see an exponential increase of literature on genetics in recent decades, which makes it one of the world’s leading sciences. Most of the popular science in the media seems superficially to be about other subjects, but genetics is the indispensable platform on which almost all life and health is based. Although, it is quite difficult to say which discovery is most important from the beginning of this subject. The actual birth of genetics occurred 60 years back when Watson and Crick published structure of DNA. But few of them stand out in the way that the illumination of the genetic code or the transcriptional mechanics of the lac operon did in the late 1950s and early 1960s whereas, genetic codes are triplet was published in 1961. In 1977, it became clear that eukaryotic genes are interrupted due to presence of exons and introns, it clarify that various portions of DNA do not show transcription and translation. In the same time the DNA can be sequenced. PCR, a technique developed by Kary Mullis in 1983, is now a common and often Indispensable for medical and biological research. DNA cloning for sequencing, DNA-based phylogeny, or functional analysis of genehereditary diseases; the identification of genetic fingerprints which is used in forensic sciences and paternity testing; and the detection and diagnosis of infectious diseases became easy by the development of this technique. In 1993, Mullis awarded the Nobel Prize in Chemistry along with Michael Smith for his work on PCR.

In 1976, Walter Fiers was the first to establish the complete nucleotide sequence of a viral RNA completed the first pairs only. In the mid of life were released. New sequencing technologies, such as massive parallel sequencing technique emerged as very easy over sequencing in the last decade.

In 2001s, genome-wide association studies (GWAS) have documented a strong statistical association between common genetic variation at thousands of loci and more than 250 human traits. The functional effects of most GWAS - implicated variants are not explained till this date. The finding that nearly 90% of these sites occur outside of protein-coding sequences suggests that many associated variants may instead have a role in gene regulation. To elucidate the genetic component underlying altered gene expression, expression quantitative trait locus (eQTL) mapping offers a powerful approach in present days. The finding that nearly 90% of these sites occur outside of protein-coding associated variants may instead have a role in gene regulation. To elucidate the genetic component underlying altered gene expression, expression quantitative trait locus (eQTL) mapping offers a powerful approach in present days. eQTLs are common in humans by studies in blood, skin, liver, adipose and brain. Genetic variation can also influence gene expression through alterations in splicing, non-coding RNA expression and RNA stability. Analyzing multiple tissues will be important because evaluation of the functional consequences of a disease-associated SNP is ideally performed in a disease-relevant cell context.

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Human Population Genetics Anthropology Milestones in the field of genetics

However, for most tissue types, human bio-specimens are very difficult to obtain from living donors (for example, brain, heart and pancreas), and most eQTL studies so far have been performed with RNA isolated from immortalized lymphoblasts or lymphocytes and a few additional readily sampled tissues. We can see the gradual increase of the biotech industry all over world, driven largely by the discoveries from molecular biology. However, the expectations for betterment of peoples need have not been fulfilled. Although, a few diseases have been diagnosed and cured using molecular means. Economy of any country in the world has not driven drastic changes due to recent achievements of discoveries. The under developed and developing countries are facing economic crisis for research and development, on the other hand, developed countries are not utilizing the all potentials of human resources available. Investment in the territories of under development and developing countries by the developed countries can provide easy and effective platform for research for development and high quality research in low cost.

MAJOR MILESTONES IN GENETICS:

1. Genomics is complete reading of DNA sequences.

2. Silencing genes is the new genetics.

3. Biomes are the discovery of extreme habitats.

4. Synthetic Biology includes biobricks.

5. Building novel biological systems from interchangeable and standardized parts. 6. Registry of standardized DNA BioBricks .BioBricks can be assembled to form devices and systems to operate in living cells.

BIOBRICKS

A BioBrick must have a genetic structure that enables it to send and receive standard biochemical signals and to be cut and pasted into a linear sequence of other BioBricks, in a manner analogous to the pieces in a Lego set. Emulating the approach employed by opensource software developers, the M.I.T. group has placed the registry on a public website (http://parts.mit.edu/

Examples of Assembled biobricks

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Human Population Genetics Anthropology Milestones in the field of genetics

Biobrickcombined to obtain a film of bacteria sensitive to light, so that it can capture an image like a photographic negative, yielding gigapixel screens. BioBricks have been combined into devices that function as logic gates and perform simple Boolean operations, such as AND, OR, NOT, NAND, and NOR.For example, an AND operator generates an output signal when it gets a biochemical signal from both of its inputs; an OR operator generates a signal if it gets a signal from either input

BIOFREEWARE

• Computers: from giant mainframe to personal laptops

• Biotechnology: from giant conglomerates to small labs or bio farms with free access to “biobricks”

Discovery

Charles Darwin wrote “On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life.” Natural Selection discovered in 1859.Heredity Transmitted in Units Discovered in1865.Gregor Mendel’s experiments on peas demonstrate that heredity is transmitted in discrete units. The understanding that genes remain distinct entities even if the characteristics of parents appear to blend in their children explains how natural selection could work and provides support for Darwin’s proposal. In1869 Frederick Miescher isolates DNA from cells for the first time and calls it “nuclein”. Walter Flemming describes chromosome behavior during animal cell division in 1879. He stains chromosomes to observe them clearly and describes the whole process of mitosis in 1882. In 1860s Mendel proposed that discrete inherited factors segregate and assort independently during gamete formation. In 1875 cytologists worked out process of mitosis and in1890 cytologists worked out process of meiosis. Mendel’s work rediscovered in1900.

Genetic Databases and Maps:

Genetic maps have been constructed since 1902. They show the sites of genes (loci) on chromosomes, and genetic distances between them calculated from recombination in experimental crosses. Genetic maps can show whether genes with related functions are on the same chromosome, and are useful in cloning and genome sequencing. In 1902 Botanists DeVries, Correns, and von Tschermak independently rediscover Mendel’s work while doing their own work on the laws of inheritance. The 5

Human Population Genetics Anthropology Milestones in the field of genetics

increased understanding of cells and chromosomes at this time allowed the placement of Mendel’s abstract ideas into a physical context. In 1902 orderly Inheritance of disease discovered. A British physician, Archibald Garrod, observes that the disease alkaptonuria is inherited according to Mendelian rules. This disease involves a recessive mutation, and was among the first conditions ascribed to a genetic cause.

Transmission of Genetic Information

Mendel died in 1884, the material basis of gene segregation was shown until 1902.In 1902, Walter Sutton and Boveri proposed that genes are on chromosomes and their movement explainable by the segregation of chromosomes during meiosis. Chromosome Theory of Inheritance discovered in1902 by Sutton who observes that the segregation of chromosomes during meiosis matched the segregation pattern of Mendel’s.

Figure: 1 Foundational Milestones in Genetics & Genomics.

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Human Population Genetics Anthropology Milestones in the field of genetics

The Word Gene is coined in 1909.Wilhelm Johannsen coins the word “gene” to describe the Mendelian unit of heredity. He also uses the terms genotype and phenotype to differentiate between the genetic traits of an individual and its outward appearance. Chromosomes Carry Genes Discovered in 1911.Thomas Hunt Morgan and his students study fruit fly chromosomes. They show that chromosomes carry genes, and also discover genetic linkage.

Basic Concepts of Genetics:

Genetic material of both eukaryotes and prokaryotes is DNA (deoxyribonucleic acid). Many viruses also have DNA, but some have RNA genomes instead. DNA has two chains, each made of nucleotides composed of a deoxyribose sugar, a phosphate group and a base. The chains form a double helix (Figure 2). DNA Has a Regular Periodic Structure discovered in 1943. William Astbury, a British scientist, obtains the first X-ray diffraction pattern of DNA, which reveals that DNA must have a regular periodic structure. He suggests that nucleotide bases are stacked on top of each other.In 1944 DNA Transforms Cells Discovered. Oswald Avery, Colin MacLeod, and Maclyn McCarty show that DNA (not proteins) can transform the properties of cells --thus clarifying the chemical nature of genes.

Research is unpredictable, which helps motivate scientists by making the work exciting. An example of unpredictability is McClintock’s work with corn kernel color, which led to the discovery of transposons. In1944 Jumping Genes Barbara McClintock, using corn as the model organism, discovers that genes can move around on chromosomes. This shows that the genome is more dynamic than previously thought. These mobile gene units are called transposons and are found in many species.

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Human Population Genetics Anthropology Milestones in the field of genetics

(Figure 2). Double helical structure of DNA.

In1952 genes are made of DNA discovered. Alfred Hershey & Martha Chase show that only the DNA of a virus needs to enter a bacterium to infect it, providing strong support for the idea that genes are made of DNA. DNA Double Helix structure discovered in 1953. Francis H. Crick and James D.Watson described the double helix structure of DNA. They receive the Nobel Prize for their work in 1962.

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Human Population Genetics Anthropology Milestones in the field of genetics

In1955 46 Human Chromosomes discovered. Joe Hin Tjio defines 46 as the exact number of chromosomes in human cells. DNA copying enzyme discovered in 1955. Arthur Kornberg and colleagues isolated DNA polymerase, an enzyme that would later be used for DNA sequencing. Cause of Disease Traced to Alteration discovered in 1956.Vernon Ingram discovers that a specific chemical alteration in a hemoglobin protein is the cause of sickle cell disease. Semiconservative replication of DNA discovered in 1958.Matthew Meselson and FranklinStahl demonstrate that DNA replicates semiconservatively and each strand from the parent DNA molecule ends up paired with a new strand from the daughter generation. Chromosome abnormalities identified in1959.Jerome Lejeune and his colleagues discover that Down syndrome is caused by trisomy 21. There are three copies, rather than two, ofchromosome21, and this extra chromosomal material interferes with normal development.

Expression of Genetic Information:

Gene expression is the process by which a gene produces its product and the product carries out its function. George Beadle and Edward Tatum (1941) showed in the fungus Neurospora crassa (red bread mold) that there is a relationship between a gene and each enzyme needed in a biochemical pathway, resulting in the one gene-one enzyme hypothesis (now modified to one gene-one polypeptide, since not all proteins are enzymes and some require more than one polypeptide).Only some of the genes in a cell are active at any given time, and activity also varies by tissue type and developmental stage. Regulation of gene expression is not completely understood, but it has been shown to involve an array of controlling signals.

Jacob and Monod (1961) proposed the operon model to explain prokaryotic gene regulation, showing that a genetic switch is used to control production of the enzymes needed to metabolize lactose. Similar systems control many genes in bacteria and their viruses. Genetic switches used in eukaryotes are different and more complex, with much remaining to be learned about their function. In 1961first Screen for Metabolic Defect in Newborns discovered. Robert Guthrie develops a method to test newborns for the metabolic defect, phenylketonuria (PKU). Sydney Brenner, François Jacob and Matthew Meselson discover that mRNA takes information from DNA in the nucleus to the protein- making machinery in the cytoplasm in1961.In 1966 Marshall Nirenberg and others figure out the

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Human Population Genetics Anthropology Milestones in the field of genetics

genetic code that allows nucleic acids with their 4 letter alphabet to determine the order of 20 kinds of amino acids in proteins. First restriction enzyme described in1968. Important milestones in genetics:

In 1972 first recombinant DNA discovered. Scientists describe restriction nucleases, enzymes that recognize and cut specific short sequences of DNA. The resulting fragments can be used to analyze DNA, and these enzymes later became an important tool for mapping genomes. Scientists produce recombinant DNA molecules by joining DNA from different species and subsequently inserting the hybrid DNA into a host cell, often a bacterium. In1972 Berg’s constructed the first recombinant DNA molecule in vitro. Boyer and Cohen’s first cloning (1973) of a recombinant DNA molecule. 1973 Discovery: First animal gene cloned Researchers fuse a segment of DNA containing a gene from the African clawed frog Xenopus with DNA from the bacterium E. coli and placed the resulting DNA back into an E. coli cell. There, the frog DNA was copied and the gene it contained directed the production of a specific frog protein.

Invention by Mullis (1986) of the polymerase chain reaction (PCR) to amplify specific DNA sequences. Completion of genomic sequencing for an increasing number of organisms has spawned the new field of genomics. Knowledge of individual genes and their regulation will be important to basic biological research, as well as to specific applications such as medical genetics. Powerful new techniques in genetics raise important ethical, legal and social issues that will need thoughtful solutions. In 1975 DNA Sequencing discovered. Two groups, Frederick Sanger and colleagues, and Alan Maxamand Walter Gilbert, both develop rapid DNA sequencing methods. The Sanger method is most commonly employed in the lab today, with colored dyes used to identify each of the four nucleic acids that make up DNA.

First Genetic Engineering Company discovered in1976.Herbert Boyer founds Genentech. The company produces the first human protein in a bacterium, and by1982 markets the first recombinant DNA drug, human insulin. In1977 Introns discovered. Richard Roberts’ and Phil Sharp’slabs show that eukaryotic genes contain many interruptions called introns. These noncoding regions do not directly specify the amino acids that make protein products. First Transgenic Mice and Fruit Flies discovered

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Human Population Genetics Anthropology Milestones in the field of genetics

in1981. Scientists successfully add stably inherited genes to laboratory animals. The resulting transgenic animals provide a new way to test the functions of genes. GenBank Database Formed in 1982. Scientists begin submitting DNA sequence data to a National Institutes of Health (NIH) database that is open to the public. First Disease Gene Mapped in 1983. A genetic marker for Huntington’s disease is found on chromosome 4. PCR Invented in 1983. The polymerase chain reaction, or PCR, is used to amplify DNA. This method allows researchers to quickly make billions of copies of a specific segment of DNA, enabling them to study it more easily. First Time a disease gene is positionally cloned in 1986. A method for finding a gene without the knowledge of the protein it encodes is developed. So called, positional cloning can help in understanding inherited disease, such as muscular dystrophy. First Human Genetic Map discovered in 1987. The first comprehensive genetic map is based on variations in DNA sequence that can be observed by digesting DNA with restriction enzymes. Such a map can be used to help locate genes responsible for diseases. Yeast Artificial Chromosomes discovered in 1987. Scientists discover that artificial chromosomes made from yeast can reliably carry large fragments of human DNA containing millions of base-pair pieces. Earlier methods used plasmids and viruses, which can carry only a few thousand base-pair pieces. The ability to deal with much larger pieces of DNA makes mapping the human genome easier. Microsatellites Are New Genetic markers discovered in 1989. Repetitive DNA sequences called microsatellites are used as genetic landmarks to distinguish between people. Another type of marker, sequence tagged sites, are unique stretches of DNA that can be used to make physical maps of human chromosomes. Launch of the Human Genome Project is in 1990. The Department of Energy and the National Institutes of Health announce a plan for a 15-year project to sequence the human genome. This will eventually result in sequencing all 3.2 billion letters of the human genome. ESTs, Fragments of Genes discovered in1991. An expressed sequence tag (EST) an identified piece of a gene is made by copying a portion of a messenger RNA (mRNA) molecule. As such, ESTs provide a way to focus on the“expressed” portion of the genome, which is less than one-tenth. In 1992 Second-Generation Genetic Map of Human Genome discovered. A French team builds a low-resolution, microsatellite genetic map of the entire human genome. Each generation of the map helps geneticists more quickly

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Human Population Genetics Anthropology Milestones in the field of genetics

locate disease genes on chromosomes. FLAVR SAVR Tomato discovered in 1994.The Food and Drug Administration approves the sale of the first genetically modified food. In 1995 there is Ban on Genetic Discrimination in the Workplace. Protection under the American with Disabilities Act is extended to cover discrimination based on genetic information. Mouse Genetic Map Completed in 1996. E. coli Genome Sequenced in 1997. The lab mouse is valuable for genetics research because humans and mice share almost all of their genes, and the genes on average are 85% identical. The mouse genetic increases the utility of mice as animal models for genetic disease in humans. Map The complete sequence of the E. coli genome will help scientists learn even more about this extensively studied bacterium.

M. tuberculosis Bacterium sequenced in 1998. Mycobacterium tuberculosis causes the chronic infectious disease tuberculosis. The sequencing of this bacterium is expected to help scientists develop new therapies to treat the disease. In 1998 Roundworm C. elegans Sequenced. The first genome sequence of a multicellular organism, the round worm, Caenorhabditis elegans, is completed. Chromosome 22 Sequenced in 1999. The first finished, full-length sequence of a human chromosome is produced. Chromosome 22 was chosen to be first because it is relatively small and had a highly detailed map already available. Such a map is necessary for the clone by clone sequencing approach.

Classical and Modern Genetics:

Humans have long understood that offspring tend to resemble parents, and have selectively bred animals and plants for many centuries. The principles of heredity were first explained by Mendel in the mid nineteenth century, using defined crosses of pea plants. In the last century, genetics has become an important biological tool, using mutants to gain an understanding of specific processes. This work has included: Analyzing heredity in populations, analyzing evolutionary processes, Identifying genes that control steps in processes, Mapping genes, Determining products of genes, analyzing molecular features of genes and regulation of gene expression. Human Genome Working Draft Completed By the end of spring 2000, HGP researchers sequence 90 percent of the human genome with 4-fold redundancy. This working draft sequence is estimated to be 99.9% accurate. Mouse Genome Working Draft Assembled and Analyzed in2002. The Mouse Genome Sequencing Consortium publishes an

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Human Population Genetics Anthropology Milestones in the field of genetics

assembled draft and comparative analysis of the mouse genome. This milestone was originally planned for 2003. Rat Genome Working Draft Completed - By Fall 2002, researchers sequence over 90% of the rat genome with over 5-fold redundancy. Completion of the Human Genome Sequencing in 2003. The finished human genome sequence will be at least 99.99% accurate.

Human Genome Project

Human Genome is arranged on multiple chromosomes which consist of twenty three pairs of chromosomes in which twenty two pairs (autosomes) and one pair (sex chromosome) (xx) (female) or (xy) (male). Humans have 23 pairs of chromosome in every cell (except mature red blood cells). Gametes or sex cells (sperm and eggs) have half the normal complement of chromosomes.

HGP is an international project aiming for: Sequencing and localization of the base sequence that makes up human DNA. Store this information in databases. Mapping of human genome requires a set of landmarks; some of these land markers are genes but many more are nameless stretches of DNA such as RFLPs, VNTRs, and STSs. In 1990, American geneticists started an ambitious quest to map and sequence the entire human genome. 1999, the final draft of human chromosome 22. 2000, the final draft of human chromosome 21. 2001, working draft of the whole human genome. In 2004, the finished sequence of the euchromatic part of human genome.

SUMMARY

Once a new generation of children has grown up, as familiar with biotech “games” as our grandchildren are now with computer games, biotechnology will no longer seem weird and alien. It will take decades of research for scientists to understand all of the information that is contained within the human genome. In time, more human diseases will be understood at the level of the molecules that are involved, which could dramatically change the practice of medicine by leading to the development of new drugs, as well as to genetic testing to improve and individualize treatments.Some diseases can now be cured or controlled effectively with biologics, and become part of the standard of care. Biologics are important tools of targeted therapy and help to fulfil the principles of personalized medicine. Intensive research is ongoing for new biotech therapies. Hungary is strong in the research

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Human Population Genetics Anthropology Milestones in the field of genetics

and production of biotechnological treatments. Further innovative products are expected in the future especially in the field of the regenerative medicine. It is likely that genetic engineering will remain unpopular and controversial so long as it remains a centralized activity in the hands of large corporations. The domestication of biotechnology will dominate our lives during the next fifty Years. Genetically modified tropical fish with new and brilliant colors appeared in pet stores. Similar to the world of natural breeders the next step is to become user- friendly. In the era of Open Source biology, the magic of genes will be available to anyone with the skill and imagination to use it.

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Human Population Genetics Anthropology Milestones in the field of genetics