Genetics and Genomics: Week 1 PDF

History scope and significance of genetics and genomics:​ Genomics is a mix of many sciences including genetics, molecular biology, biochemistry, statistics and computer sciences. The developmental sequence of genetics and genomics occurred in different periods in the last few decades, the science...

History scope and significance of genetics and genomics:​ Genomics is a mix of many sciences including genetics, molecular biology, biochemistry, statistics and computer sciences. The developmental sequence of genetics and genomics occurred in different periods in the last few decades, the science of genetics has pervaded all aspects of biology so that it has assumed a central position of great significance in biology as a whole. While on the one hand genetics is used for a study of the mechanism of heredity and variation, on the other hand it has provided tools for the study of the fundamental biological processes examined and taught in areas like plant physiology, biochemistry, ecology, plant pathology, microbiology etc. Genetics in fact provided the modern paradigm that is a prototype for biology. The science of genetics also had a tremendous impact in applied areas including medicine, agriculture, forestry, fisheries, law and religion. Genetic manipulation is one such topic which is receiving considerable attention of both developed and developing countries. Genetics can be broadly classified in the following three areas for the convenience of a discussion on its scope and significance: one- transmission genetics: involving study of transmission of genetic material from one generation to the other. two- molecular and biochemical genetics: involving study of the structure and function of genes third- population and biometrical genetics: involving study of the behavior and effects of genes in population, often using mathematical models. The above classification is arbitrary and the three areas are interrelated and even under other areas of biology. Significance of genetics also stems from the fact that the genetic material containing information for hereditary traits consist of nucleic acids only across the entire spectrum of life on the earth. Genomics is an interdisciplinary field of science focusing on genomes. A genome is a complete set of DNA within a single cell of an organism and as such genomics is a branch of molecular biology concerned with the structure, function, evolution and mapping of genomes. Genomics aims at the collective characterization and quantification of genes which direct the production of proteins with the assistance of enzymes and messenger molecules. Proteins in turn make up body structures like organs and tissues as well as control chemical reactions and carry signals between cells. If a cell's DNA is mutated, an abnormal protein may be produced which can disrupt the body's usual processes and in some cases lead to diseases such as cancer. In contrast to genetics which refers to the study of genes and the roles in inheritance, genomics is the study of genes, their functions and related techniques such as applications of recombinant DNA, DNA sequencing methods and bioinformatics to sequence assemble and analyze the function and structure of genomes. Advances in genomics have triggered a revolution in discovery based research to understand even the most complex biological systems such as the brain. The field includes efforts to determine the entire DNA sequence of organisms and fine scale genetic mapping the field also includes studies of intra genomic phenomena such as heterosis epistasis pleiotropy and other interactions between loss AI and alleles within the genome research carried out into single genes does not generally fall into the definition of genomics unless the aim of this genetic pathway and functional information analysis is to elucidate its effect on placing and response to the entire genomes Network. The various important branches of genomics are the following: Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects such as genome sequencing projects to describe gene functions and interactions. Structural genomics: it seeks to describe the three-dimensional structure of every protein encoded by a given genome. Epigenomics: is the study of the complete set of epigenetic modifications on the genetic material of a cell known as the epigenome. Metagenomics: is the study of metagenomes; genetic material recovered directly from environmental samples. Applications of genomics: genomics has provided applications in many free including medicine, biotechnology anthropology and other social sciences. genomic medicine: next-generation genomic technologies allow clinicians and biomedical researchers to drastically increase the amount of genomic data collected on large study population when combined with the new informatics approaches that integrate many kinds of data with genomic data in disease research this allows researchers to better understand the genetic basis of drug response and disease. synthetic biology and bioengineering: the growth of genomic knowledge has enabled increasingly sophisticated applications of synthetic biology. Conservation genomics: conservationists can use the information gathered by genomic sequencing in order to better evaluate genetic factors, key to species conservation such as the genetic diversity of a population or whether an individual is heterozygous for a recessive inherited genetic disorder now History: In the period varying from mid to late 19th century the developments regarding evolution, natural selection, particulate inheritance has occurred in the 1858 our understanding of the origin of species and how species variability arose was revolutionized by the research of Darwin and Wallace. They describe how new species arose via evolution and how natural selection uses natural variation to evolve new forms a few years later. Gregor Mendel, an Austrian monk summarized his years of research on peas in his famous publication. In that paper he described the unit of heredity as a particle that does not change. This was in contrast to the then-prevailing “blending theory of inheritance.” Equally important, Mendel formalized the importance of developing pure lines by statistically analyzing the data. His approach of crossing individuals with variable phenotypes and following them in successive generations is still the only approach utilized to understand the genetic inheritance of a trait. Research in the 19th century was often performed in isolation with findings made by one, not known to others. While Mendel was concluding that inheritance was particulate in nature, others were trying to figure out the physical nature of the particle. Haeckel correctly predicted that the hereditary material was located in the nucleus. Miescher showed the material in the nucleus was a nucleic acid others observed the behavior of chromosomes and suggested they had a role in heredity. now coming to the early 20th century the Mendelian principles were extended and the chromosomal theory of inheritance got strengthened. Mendel's important findings went unnoticed and it was not until 1900 that others who had performed similar experiments as that of his arrived at the same conclusions. Their publications cited his work leading to a rediscovery of the Mendelian principles and quickly following the rediscovery of other genetic principles such as linkage, “Lidl” genes and a bit later, the maternal inheritance was described. In each case the principles provided to be simple extensions of the Mendelian laws providing further evidence of their importance at the beginning of the century. The work on chromosomes merged into the chromosomal theory of inheritance. This theory focused on the research on chromosome as the location of genes the field of cytogenetics was based on this discovery the first observations of chromosomal abnormalities such as duplications deletions translocations inversions were reported observations such as position effect demonstrate that there is a direct link between chromosome structure and phenotype all of these discoveries justified research with the intention to discover the physical basis of heredity now coming to the mid 20th century DNA was considered as the base of life also the importance of the Darwinian theory of evolution why a natural selection was confirmed as early as the 1870s the material in the nucleus was determined to be a nucleic acid from the 1920s through the mid-1950s a series of experiments demonstrated that DNA was indeed the genetic material the transformation experience of Griffith demonstrated that a factor found in a lethal strain of bacteria could convert a non lethal strain of the bacteria into a lethal strain it was the careful experiments of every MacLeod and McCarty that determined DNA not protein or RNA was the factor responsible for the conversion this was further confirmed by Hershey and chase although their experiments had flaws which prevented them from being definitive Watson and Crick determined the structure of DNA and others suggested that DNA contained agentic code by the mid-1960s that code was deciphered experiments involving the process of transcription and translation led to the development of the central dogma of molecular biology concept by Cree the experiments of the early 19th century that confirmed that Mendelian principles could be extended to many gene systems became a major component of what was to be called a modern synthesis that is neo-darwinism the experimental demonstration that mutations could be induced was also an important component of the concept that natural selection was a major factor in evolution mutations create variation recombination develops new forms the variation extends through the population and based on environmental constraints the variation is finally acted upon by the forces of natural selection to produce more fit individuals coming to the period of mid late 20th century and the early days of the 21st century is the age of molecular genetics phylogenetic studies gains importance the emergence of information technology and genomic science occurs the discoveries of the mid to late 20th century defined processes that would provide the tools for molecular biology recombinant DNA technology and finally the biotechnology industry the elucidation of the process of DNA replication described the necessary components needed for the widely used to chain termination DNA sequencing procedure understanding replication helped determine those tools necessary for the radio labeling of DNA the development was necessary to support southern hybridizations and the early molecular mapping experiments understanding replication also defined the role of the ligase enzyme that is so critical for DNA cloning restriction enzymes were discovered and used to construct recombinant DNA molecules that contained foreign DNA that could be grown in abundance in bacterial cells the discovery of reverse transcriptase also enabled cDNA cloning cloning is essential for the discovery of gene structure and function it is also an essential step for all of the genome sequencing the advent of protein and DNA sequencing launched a new era of phylogenetics species could now be compared at the molecular level new procedures for the development of phylogenies are developed the neutral theory of molecular evolution is proposed this was a direct blow to the preeminence of selection as the driving force of evolution the theory suggests that most mutations are neutral and are fixed by genetic drift and not selection it is debated whether the evolution of species is driven more by neutral effects or selection some field the two theories are compatible and exert their effects on different genes the information age is essential to genomics the electronic analysis distribution and storage of genomic data is a hallmark of the science critical to this was the development of computers both large and small which put computing power in the hands of all scientists the free distribution of analytical software provided scientists with the tools to study the details of their experiments the internet spawned the distribution of information from central databases email connected scientists and foster the rapid exchange of ideas the advent of the www provided a new medium for the presentation of information whole genome were sequence for the first time for other species the gene content was described using est s microarray analysis provided the first glimpse of global expression patterns proteomics begins to describe the protein component of the genome in the spirit metabolomics was established massively parallel sequencing technology was introduced this new technology greatly increases the amount of DNA sequence that can be collected in a short period it will also dramatically decrease the cost of sequencing importantly it launches the age of individual genome sequencing which will support an era of individualized medicine now let us see the historical progress of genetics and genomics in detail in 1865 Gregor Mendel introduced the concept of particulate that is gene inheritance and also demonstrated the laws of segregation and independent assortment he outlined the famous P experiments and published article and titled experiments in plant hybridization in 1866 Ernst Haeckel proposed the idea that the hereditary material resides in the nucleus Friedrich Miescher in the Year 1871 coined the term new clean for this Hedda tree material and in 1874 he discovered that new clean consists of nucleic acid and protein first accurate counting of chromosomes was done by Walter Fleming in 1879 in 1892 Edward Strassburger and Edward van beneden observed solution and they coined terms such as chromatin mitosis cytoplasm nucleoplasm prophase and metaphase August wasteman in 1887 proposed universal theory of chromosome behavior which predicted that meiosis occurs in sex cells in 1888 Hendrik William got pride while they are applied the term chromosome to the condensed version of material found within the nucleus in 1899 William Bateson described a hybridization between two individuals as a tool of the scientific analysis of heredity Mendel's work was rediscovered by Carl Correns Hugo DeVries and Erik Juan shemagh independently in 1900 in 1900 who God ever is coined the term mutation for the spontaneous appearance of new traits in evening primrose in nineteen not to see McClung proposed that specific chromosomes were responsible for sex determination in animals Walter Sutton and Theodore Bowery in 1902 showed that chromosomes occur in pairs one parent contributes each member of the pair and the pairs separate during meiosis Sutton suggested that unit of heredity resided on chromosomes and it is known as the chromosomal theory of inheritance Archibald Garrod in the year nineteen ought to describe the first human disease that exhibits Mendelian inheritance and it was all kept non urea the terms gen tics homozygote heterozygote epistasis f1 f2 and Ali Lomov which was later shortened as allele were introduced by William Bateson in the year nineteen not two in 1903 wilhelm johansson explained the important concepts of phenotype genotype and selection William Bateson and RC Pinet in the year nineteen odd five performed experiments on sweet pea and demonstrated the concept of linkage in the same year little genes were discovered in the classic experiment involving a cross between two yellow mice in 19.7 Frederick Leigh batch suggested Arab topsis as a model organism G H Hardy and W Wayne Berg formulated the hardy-weinberg principle of genetic equilibrium in 1908 gh rule in 19.9 produced commercial seed from self-fertilize gone and it was the direct application of the Mendelian theory the terms gene phenotype and genotype were introduced by William Johansson in 1909 in the same year H Nilsson halay explained the role of multiple gene interactions in seed coat color of wheat and earth this was the beginning of quantitative genetics in 1910 Thomas Hunt Morgan demonstrated sex linkage in Drosophila and suggested that genes reside on chromosomes also the year of fruit fly as a model organism begins the first genetic map was developed by Alfred strootman in 1913 in Drosophila Calvin bridges in 1914 observed nondisjunction in sex chromosomes which proves the chromosome theory of inheritance and also chromosome deficiencies duplications and translocations were observed first time in row sofala in 1919 Thomas Hunt Morgan proved that the number of chromosomes equals the number of linkage groups a boycott and sea diver in 1923 explained maternal inheritance based on shell coiling direction in snail in 1925 Alfred strootman demonstrated position effect based on Drosophila Barra effect he observed inversion in Drosophila in the year 1926 JBS Haldane in 1927 observed cod color in rodents and carnivores and proposed the concept of homologs in 1928 LJ Statler demonstrated the relationship between the number of mutations and the x-ray dosage effect in corn transformation experiment in pneumococci was done by F Griffith in 1928 it leads to the discovery that DN is the genetic material which transform information from one generation to the next in 1931 Harriet Craig turn and Barbara McClintock reported that crossing over between two homologous chromosomes involves the physical exchange of genetic material between the two chromosomes RA Fisher and Theodore Davos in skåne formulated modern synthesis this couples the laws of Mendelian inheritance and knowledge of mutation with the Darwinian theory of evolution via natural selection in 1941 George Biddle and DL Tatem proposed one gene one enzyme hypothesis based on biochemical studies of neuro spora K made in 1941 coined the term poly genes SC Luria and max delbruck in the Year 1943 demonstrated that bacteria capable of undergoing spontaneous mutations this led to the onset of the field bacterial genetics in 1944 oswald t every call in M McCloud and MacLean McCarty extended the experiments of the Griffith in 1929 and showed that DN is the Genting material bacterial genetic recombination was demonstrated by J letter Berg and he Eltham in 1946 it involves the movement of DNA from one bacterium to another in 1948 Barbara McClintock proposed the concept of transpose of alignments JB Neil in 1949 observed that sickle-cell anemia was inherited as single recessive gene Mendelian trait in 1953 James Watson and Francis Crick presented double strand structure of DNA held together by hydrogen bond George Gamow in 1954 suggested that DNA contains a code which is responsible for the production of proteins in 1955 severo ochoa discovered RNA polymerase which has an important role in the mechanism of transcription LOD score method of determining linkage distance in humans was developed by Newton Morton in the year 1955 coming to the year 1956 Arthur Kornberg purified DNA polymerase 1 from a coli which is a major component of DNA replication jacob and he L wool man in the year 1956 showed that bacterial conjugation involves the physical exchange of DNA between two bacterial strains in the year 1957 Francis Crick proposed the central dogma of molecular biology in the next year he predicted the role of tRNA in translation process coming to the year 1958 Mathieu meselson and FW star proved semiconservative mode of DNA replication using the technique density equilibrium centrifugation F Jacob and J Minard in 1961 published gentle regulatory mechanisms in the synthesis of proteins which explains the lac operon controlling Network in e.coli in the same year Marshall nirenberg proposed the concept that each amino acid corresponds to a triplet code the first identified amino acid which was the phenylalanine which is coded by Triple A also Sydney Brenner franchise Jacob and Mathieu meselson described ribosomes as the site of protein synthesis it was also proven that mRNA exists and binds to ribosome in 1965 Margaret Dayhoff published Atlas of protein sequence and structure it contains the sequence of 65 proteins and was considered as the first publication in bioinformatics he my saccharine and Lina's falling introduced molecular clock concept according to this theory the rate of amino acid substitutions are linear over the time Marshall nirenberg and at Gobin Khorana in 1966 completed the Ghent Accord that correlates the triplet code for each amino acids in 1967 were close Cebulski and w summers showed that only one DNA strand act as template during the process transcription WM Fitch and E Margolis developed the phylogenetic tree in the same year it involves the comparison of the amino acid sequence of cytochrome C from turn D species that ranged from fungi to mammals Werner Arber and Hamilton Smith in 1970 isolated first restriction enzyme Hin to David Baltimore and Howard Temin explained the importance of reverse transcriptase in the same year in 1975 Irwin Southern introduced the technique southern hybridization which play main role in the gene mapping using RFLP s-- Frederick Sanger and Walter Gilbert in the year nineteen hundred and seventy-seven developed the chain termination and chemical methods of DNA sequencing philip sharp and rich Roberts showed that mammalian viral gene was interrupted by DNA sequences which are not found in the mature mRNA Gilbert in 1978 named this sequence as introns and it was a common feature of eukaryotic genes Sanger group in 1980 published the first complete genome sequence of bacteriophage X 174 GenBank was established in 1982 which is the database of all DNA sequences in nineteen hundred and eighty-three Kary Mullis explained the procedure to amplify a large amounts of DNA using PCR ecology the procedure was later improved by the use of a DNA polymerase from the thermos aquaticus bacteria the first automated DNA sequencer was released by Leroy hood Lloyd Smith Michael hyung Coppola and Tim hyung a pillar in 1986 this development was based on fluorescent labeling of nucleotides and the Sanger sequencing technique in 1987 Eric Lander and group introduced a mapmaker a computer program for the development of genetic linkage maps from molecular marker HD he gains and p.m. sharp published the clustered multiple sequence alignment approach in 1988 the sinner abilities elegans database was developed by Jean Pierre meek and the chard Durbin in 1989 it was the first database developed for genomic information in 1990 US government launched a 15 year human genome program the goal was to find all the genes on every chromosome in the body and to determine their biochemical nature in 1990 Alta Shirl and co-workers introduced to blast a computational approach for aligning two DNA sequences the first est that is expressed sequence tags sequence was published by craig Venter in 1991 gen Thorne in the year 1993 to 1994 published the first high density linkage map of the human genome the Ender Haemophilus influenzae genome sequence consisting of 1.8 mega base pair was analyzed by shotgun genome sequencing approach by Solera corp and craig Venter in 1995 in the same year Pat Brown and Ron Davis described microarray system and in 1997 Dec and the group used this technology to study the regulatory pathways the entire Saccharomyces cerevisiae that is the East genome sequence consisting of 12.1 mega base pair was published in 1996 by East genome consortium he coli genome project was launched in 1997 for sequencing its genome cluster analysis approaches were described by Hazen and group in 1998 the oligo nucleotide microarray system was developed in the same year IRA Bob systole and a genome consisting of 125 mega base pair and drosophila genome consisting of 123 mega base pair was sequenced in the year 2000 and Stephen tens clay did the first cloning in the same period Human Genome Project was considered as the turning point in molecular biology and human welfare the huge data produced by international human genome sequencing consortium led to the invention of n sample genome browser in 2001 most genome sequencing consisting of two thousand five hundred mega base pair and rice genome sequencing consisting of four hundred and seventy mega base pair were completed in the year 2002 pufferfish genome consisting of 365 mega base pair malaria parasite carrying mosquito genome Plasmodium falciparum genome and the SARS Associated coronavirus genome sequencing completed in following years next-generation sequencing was introduced by celexa in the year 2004 pyrosequencing technology was automated by Roche in next year applied Biosystems a leading group in molecular data analysis developed oligo nucleotide allegation and detection in 2005 Pacific Biosciences released a single molecule DNA sequencer in 2010-2011 onwards sequencing of many organisms are in progress microbial world have an outbreak in the sequencing and the sequencing of almost two thousand six hundred and eighty-eight viruses were completed thousand seven hundred and ten microbial genomic data sequencing were completed and almost 6085 microbial genome he is in screening 280 fungal genomic DNA was sequenced and 205 fungal genomic DNA sequencing is in process kingdom plants and animals have complex genomes so competitively less number of organisms in these groups are completely sequenced 182 members of animals and 47 members of plans got sequenced and sequencing is proceeding for 256 and 107 members of animals and plants respectively now I will give you certain assignments based on the portion which we have covered one what are the various important branches of genomics - what are the different applications of genomics three elaborate on the historical developments of genetics in the period mid to late nineteenth century for elaborate on the historical developments of genetics in the period of early 20th century fie elaborate on the historical developments of genetics in the period of mid 20th century and six elaborate on the historical developments of genetics and genomics in the period of mid late 20th century and the early days of the 21st century I will give you certain references for further reading on this particular topic one an article entitled the evolution of genetics to genomics published in Journal of human growth and development and ordered by Allen T Bronco in the year 2016 volume 26 number one - a history of genetics third edition ordered by strootman a H 2001 published by Cold Spring Laboratory press Cold Spring Harbor New York third reference the and in debate history ordered by Mukherjee s in the year 2016 published by penguin UK fourth reference a book entitled Jen takes and the unsettled the past the coalition of DNA race and history ordered by velu Kay Nelson a lessee in the year 2012 published by Rogers University Press a fifth reference is with the title from molecular genetics to genomics the mapping cultures of 20th century genetics ordered by good Leary J rain Berger H in the year 2004 published by Routledge New York sixth reference Jen takes and the Origin of Species ordered by doe bosanski T G in the year 1951 published by Columbia University Press so we have come to the end of this session we will meet in another session with a new topic until then bye