Page 1 : This content has been downloaded from IOPscience. Please scroll down to see the full text., , Download details:, IP Address: 152.57.167.137, This content was downloaded on 20/11/2021 at 12:01, Please note that terms and conditions apply., , You may also like:, Preliminary Studies of the Development of Local Wisdom-Based Biotechnology Module for Biology, Students, Desti, Fitmawati, Putri Ade Rahma Yulis et al., Biotechnology concept: questioning of analysis with lesson study for learning community (LSLC) for, higher ordered thinking skill on coffee area plantation, Suratno, N Komaria, Hobri et al., Educating Society about Biotechnology and Its Impact to The Environment: an Analysis to Practical, Experience at the Group of Farmer at Sukorambi Vilage, Distric of Sukorambi, Regency of Jember,, East Java, Indonesia, Suratno, N Umamah, F Hasan et al., Assessing Prior Knowledge and Needs Assessment for Virtual Laboratorium Development, N Umamah, W Subchan, R P N Puji et al., International Biotechnology Conference on Estate Crops 2017

Page 2 : IOP Publishing, , Introduction to Pharmaceutical Biotechnology, Volume 1, Basic techniques and concepts, Saurabh Bhatia, , Chapter 1, History, scope and development of, biotechnology, , 1.1 Introduction, The utilization of biological processes, organisms or systems to produce products that, are anticipated to improve human lives is termed biotechnology. Broadly, this can be, defined as the engineering of organisms for the purpose of human usage. It can also be, defined as the skill set required for the utilization of living systems or the influencing of, natural processes so as to produce products, systems or environments to help human, development. Currently biotechnology places more emphasis on the establishment of, hybrid genes followed by their transfer into organisms in which some, or all, of the, gene is not usually present. In prehistoric times, a primitive form of biotechnology was, practised by agriculturalists who established better-quality species of plants and, animals by methods of cross-pollination or cross-breeding. Previous forms of, biotechnology include the training and selective breeding of animals, the cultivation, of crops and the utilization of micro-organisms to produce products such as cheese,, yogurt, bread, beer and wine. Early agriculture concentrated on producing food., The most primitive type of biotechnology is the cultivation of plants and the, training (in particular the domestication) of animals. The domestication of animals, stretches back over 10 000 years, when our ancestors also started maintaining plants, as a reliable source of food. The earliest examples of such domesticated plants are, rice, barley and wheat. Wild animals were also controlled to produce milk or meat., The ancient production of cheese, yogurt and bread from micro-organisms is also, reported. Various alcoholic drinks such as beer and wine were developed during this, period, when the process of fermentation was first discovered., Later, it was discovered that micro-organisms, e.g. bacteria, yeast or molds,, hydrolyze sugars when they lack oxygen and are ultimately responsible for, fermentation. This process results in the formation of products (food and drink)., Consequently, fermentation was perhaps first explored by chance, since in earlier, , doi:10.1088/978-0-7503-1299-8ch1, , 1-1, , ª IOP Publishing Ltd 2018

Page 3 : Introduction to Pharmaceutical Biotechnology, Volume 1, , times nobody knew how it worked. During the prehistoric era some civilizations, considered fermentation to be a gift from their gods. Scientific evidence for, fermentation was first described by Louis Pasteur in the late 1800s. He demonstrated a theory known as germ theory, presenting the survival of micro-organisms, and their further effects on the process of fermentation. Pasteur’s efforts contributed towards several branches of science. In earlier times several traditional, medicines were used as biotechnology products, such as honey, which could be, used to treat several respiratory ailments and as an ointment for wounds. Since, honey contains several antimicrobial compounds it is considered to be a natural, antibiotic and is effectively used in wound healing. Similarly, in China as far back, as 600 BC, soybean curds were used to treat boils. Ukrainian farmers once used, utilized moldy cheese to treat infected wounds. It was later observed that, antibiotics present in such molds killed bacteria and averted the spread of, infection. In 1928 Alexander Fleming extracted penicillin, the first antibiotic,, from mold [1]. This discovery revolutionized the available treatments, with, antibiotics having more potential and being more effective than earlier medicines., The development of biotechnology in terms of crop rotation (including leguminous, crops), vaccinations and animal-drawn technology, was realized between the late, eighteenth century and the commencement of the nineteenth century [1]. The late, nineteenth century was known to be a milestone in biology. Some of the key, developments during this period are highlighted below:, • Structures for examining fermentation and other microbial developments, were identified by Robert Koch, Pasteur and Joseph Lister., • Gregor Mendel’s work on genetics was carried out., • Micro-organisms were discovered., In the 1920s a start was made on the production of useful chemicals through biological, processes, when Chaim Weizmann used Clostridium acetobutylicum for the conversion, of starch into butanol and acetone (the acetone thus produced was used as an essential, component of explosives during World War I) [2]. At the beginning of the eighteenth, century, developments in biotechnology tended to bring industry and agriculture, together. Later, one some basic processes of biotechnology such as fermentation were, refined to develop paint solvents for the emerging automobile industry and acetone, from starch. These processes were promoted during World War I. In the 1930s the, processes of biotechnology moved more into utilizing surplus agricultural goods to, supply industry as a replacement for imports or petrochemicals., The advent of World War II brought the manufacture of penicillin. The, production of antibiotics from micro-organisms became possible when Fleming, discovered penicillin, which was later produced at a large scale from cultures of, Penicillium notatum (this proved useful for the treatment of wounded soldiers during, World War II) [1]. The focus of biotechnology shifted to pharmaceuticals. The Cold, War years were ruled by work on micro-organisms for the preparation for biological, products along with antibiotics and fermentation processes [3]., Biotechnology is now being used in numerous disciplines including bioremediation, energy production and food processing agriculture. DNA fingerprinting is, 1-2

Page 4 : Introduction to Pharmaceutical Biotechnology, Volume 1, , often practiced in forensics. Insulin production and other biotech-based medicines, (biopharmaceuticals) are produced through cloning of vectors with genes of interest, (GOIs). Immunoassays are frequently utilized in medicine for drug efficiency and, pregnancy testing. In addition, immunoassays are also utilized by farmers to find, hazardous levels of pesticides, herbicides and toxins in crops and animal-based, products. These tests also offer rapid field tests for the determination of industrial, chemicals, in particular, in ground water, sediment and soil. Biotechnology also has, vast scope in agriculture for the production of plants that are resistant to insects,, weeds and plant diseases. This can be achieved by the introduction of GOIs using, genetic engineering., Selective breeding of plants and animals was practiced in the past without, awareness of the basic concepts of biotechnology. In this procedure organisms with, desirable traits were allowed to mate to further enhance these traits in their offspring., Consequently, it was revealed that selective breeding could improve yields as well as, productivity. During this time farmers were not aware that selective breeding, innovators were modifying the genetic make-up of organisms. An outstanding, example is the corn plant, which has been enriched by selective breeding to develop, an improved source of food and has given a platform for plant breeders to develop, more hybrid varieties. Regarding animals, dogs are another example of selective, breeding. Breeding between different dogs was promoted to improve traits e.g. size,, agility, shape and color, resulting in breeds from the tiny Chihuahua to the Great, Dane. Another revolutionary development in biotechnology that initiated the era of, genetics was started in 1865 by a monk, Gregor Mendel, who recognized genes as the, unit of inheritance. It took almost another 90 years of research to determine that genes, are made up of DNA. This breakthrough was the beginning of modern biotechnology., Recent developments in biotechnology have led to an expansion in its sophistication,, scope and applicability. As mentioned above, the simplest way to define biotechnology is to split this word into its two constituent parts (biotechnology = biology +, technology). By considering these two key words we can define biotechnology as a set, of techniques that are employed to manipulate living organisms, or utilize biological, agents or their components, to produce useful products/services. The vast nature of, biotechnology has frequently made a detailed definition of the subject rather difficult., Some definitions of biotechnology are as follows:, • ‘Biotechnology means any scientific application that uses biological systems,, living organisms or derivatives thereof, to produce or alter products or, processes for particular use’ [4]., • ‘The utilization of living organisms, systems or processes constitutes biotechnology’ [5]., • Based on the Collins English Dictionary definition [6], biotechnology is the, employment of living organisms, their parts or processes, to develop active, and useful products and to provide services e.g. waste treatment. The term, signifies a broad range of processes, from the use of earthworms as a source of, protein to the genetic modification of bacteria to offer human gene products,, e.g. growth hormones., , 1-3

Page 5 : Introduction to Pharmaceutical Biotechnology, Volume 1, , • According to the Golden Treasury of Science and Technology [7], biotechnology is a discipline based on the harnessing of life processes which are, controlled for the bulk production of valuable substances., It is obvious from the above definitions that biotechnology includes different, technologies that rely on information gained by modern discoveries in biochemistry,, cell biology and molecular biology. These technologies are already having a huge, impact on diverse areas of life, including agriculture, food processing, medical, technology and waste treatment., • Biotechnology consists of ‘the controlled employment of biological agents,, e.g. micro-organisms or cellular components, for favorable use’ [8]., • Biotechnology has been defined as ‘Janus-faced’ [9]. This means that there are, two sides to it. On one side, we know that the technology allows DNA to be, modified so that genes can be moved from one organism to another. On the, other, it also entails comparatively new techniques whose results are untested, and should be met with care., • Biotechnology is ‘the integrated use of microbiology, biochemistry and, engineering sciences in production or as service operation’ [10]., • Biotechnology is the commercial employment of micro-organisms and living, plant and animal cells to create substances or effects beneficial to people. It, includes the production of antibiotics, vitamins, vaccines, plastics, etc [11]., • ‘Bio’ refers to life and ‘technology’ refers to the application of information for, practical use, i.e. the application of living organisms to create or improve a, product [11]., • It involves the industrial application of living organisms or their products,, which entails the intentional manipulation of their DNA molecules. It may, mean making a living cell execute a particular task in a predictable and, controllable way [11]., • The term biotechnology is occasionally also applied to processes in which, micro-organisms such as yeasts and bacteria are cultured under strictly, controlled environmental conditions. For this reason, fermentation is occasionally called the oldest form of biotechnology. Genetic engineering techniques are frequently, but not always, used in biotechnology [11]., • The Universities Press Dictionary of Biology defines biotechnology as ‘the, application of technology to biological processes for industrial, agricultural, and medical purposes’ [12]., • The Oxford Dictionary of Biology [13] defines biotechnology as ‘the development of techniques for the application of biological processes to the, production of materials of use in medicine and industry.’, • The employment of cells and biological molecules to explain problems or, make valuable products. These biological molecules include DNA, RNA and, proteins., , 1-4

Page 6 : Introduction to Pharmaceutical Biotechnology, Volume 1, , • Biotechnology may be defined as ‘the utilization of living organisms in, systems or processes for the production of valuable products; it may involve, algae, bacteria, fungi, yeast, cells of higher plants and animals or subsystems, of any of these or isolated components from living matter’ [14]., It may be seen that the diverse definitions of biotechnology above differ in their, approach, content and emphasis. But there are two main characteristics common to, them all are. First, biotechnology involves the exploitation of biological entities (i.e., micro-organisms, cells of higher organisms—either living or dead), their components or constituents (e.g. enzymes), in such a way that some functional product or, service is generated. Second, this product or service should aim to improve human, welfare., In summary, biotechnology is the ‘[a]pplication of the theory of engineering and, biological science to generate new products from raw materials of biological origin,, e.g. vaccines or food’, or, in other words, it can also be defined as ‘the exploitation of, living organism/s or their product/s to change or improve human health and human, surroundings’ [15]., Hungarian engineer Karl Ereky first coined the term ‘biotechnology’ in 1919,, meaning the production of products from raw materials with the aid of living, organisms [16, 17]. As mentioned above, biotechnology is not new, since human, civilization has been exploiting living organisms to solve problems and improve our, way of life for millennia. The production technologies and processes involved in, animal husbandry, agriculture, horticulture, etc, utilize plants and animals to produce, useful products. However, such technologies are not regarded as biotechnology since, they are long recognized and well-established disciplines in their own right. Today, the, exploitation of animal and plant cells cultured in vitro as well as their constituents for, generating products/services is an integral part of biotechnology., , 1.2 Branches of biotechnology, The definition of biotechnology can be further divided into different areas known as, red, green blue and white., • Red biotechnology: This area includes medical procedures such as utilizing, organisms for the production of novel drugs or employing stem cells to, replace/regenerate injured tissues and possibly regenerate whole organs. It, could simply be called medical biotechnology., • Green biotechnology: Green biotechnology applies to agriculture and involves, such processes as the development of pest-resistant grains and the accelerated, evolution of disease-resistant animals., • Blue biotechnology: Blue biotechnology, rarely mentioned, encompasses, processes in the marine and aquatic environments, such as controlling the, proliferation of noxious water-borne organisms., • White biotechnology: White (also called gray) biotechnology involves industrial processes such as the production of new chemicals or the development of, new fuels for vehicles., , 1-5

Page 7 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.1. Fourteen-month-old genetically engineered (‘biotech’) salmon (left) and standard salmon (right)., , A distinction is made between ‘non-gene biotechnology’ and ‘gene biotechnology’:, • Non-gene biotechnology: Non-gene biotechnology works with whole cells, tissues, or even individual organisms. Non-gene biotechnology is the more popular, practice, involving plant tissue culture, hybrid seed production, microbial, fermentation, production of hybridoma antibodies and immunochemistry., • Gene biotechnology: Gene biotechnology deals with genes, the transfer of, genes from one organism to another and genetic engineering., Biotechnology, like other advanced technologies, has the potential for misuse. Concern, about this has led to efforts by some groups to enact legislation restricting or banning, certain processes or programs, such as human cloning and embryonic stem cell, research. There is also concern that if biotechnological processes are used by groups, with nefarious intent, the end result could be biological warfare. Apart from their, beneficial applications, biotechnological principles also have the potential for destruction, the best example of which is bioterrorism. A representation of the potential, pitfalls of biotechnology in fiction can be found in the novel Frankenstein [18, 19]. In, this science fiction story, the character of Frankenstein has created a human life which, becomes a monster; this monster becomes the cause of the destruction of Frankenstein,, the creator of human life. The real-life changes that can be brought about by, biotechnology can easily be seen in figure 1.1, illustrating a 14-month-old genetically, engineered (‘biotech’) salmon (left) and a standard salmon (right)., , 1.3 Biotechnology and its various stages of development, It is well known that the technical application of biological material is considered to be, biotechnology. To understand how biotechnology works it is important to think about, the starting point or material for biotechnology processes. Generally, biotechnology, utilizes living material or biological products to generate new products for use in, various medical, agricultural, pharmaceutical and environmental applications. The, ultimate goal of biotechnology is to benefit humanity by, for example, the production of, resistant crops, vegetables, recombinant proteins, higher milk-producing animals, etc., Different developmental stages have taken place in biotechnology to meet the, various needs of humans at the time. Its development was principally based on, observations, and the application of these observations to practical scenarios. Owing, to the evolution of new technologies and a better understanding of various principles, of life science, the complexity of biotechnology has increased. Table 1.1 gives, 1-6

Page 8 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Table 1.1. Historical events in biotechnology., , Periods of biotechnology, history, Pre-1800, (Early applications and, speculation), , Events, 6000 BC, Yeast was utilized to prepare beer (Sumerians and Babylonians)., 4000 BC, In Egypt, a process was discovered to prepare leavened bread by, means of yeast., 420 BC, Greek philosopher Socrates (470–399 BC) hypothesized on the similar, characteristics between parents and their offspring., 320 BC, Greek philosopher Aristotle (384–322 BC) theorized that all, inheritance originates from the father., 1000 AD, Hindus recognized that some illnesses may ‘run in the family’. At the, same time, the theory of abiogenesis, or spontaneous generation based, on the idea that organisms arise from non-living matter, developed., According to this theory maggots could develop from horse hair., 1630, William Harvey explained that plants and animals are similar in their, reproduction, i.e. they reproduce sexually., 1660–1675, Marcello Malpighi (1628–1694) investigated blood circulation in, capillaries using a microscope and found that the brain is connected, to the spinal cord by bundles of fibers which form the nervous, system [20, 21]., 1673, Antonie van Leeuwenhoek (1632–1723) was the first researcher to, explain micro-organisms such as protozoa and bacteria, and also, identify that these micro-organisms play an active role in, fermentation., 1701, Giacomo Pylarini found that the deliberate administration of, smallpox could prevent its occurrence later in life, especially in, children. Later, this procedure was termed ‘vaccination’ and a, process that uses cowpox instead of smallpox was established as the, most reliable treatment [22, 23]., , 1800–1900, (Significant advances in, basic understanding), , 1809, Nicolas Appert invent a technique using heat to can and sterilize food., (Continued), , 1-7

Page 9 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1827, In the field of heredity, there had long been a hunt for the so-called, mammalian egg. It had proved elusive, however, in 1827 the first, report of canine eggs offered a basic clue to major breakthroughs in, reproduction, at first in lower animals, 1850, Ignaz Semmelweis utilized epidemiological examinations to suggest, the theory that puerperal fever could be transmitted from mother to, mother by physicians. He also suggested that all physicians should, wash their hands after investigating each patient. For this, suggestion he was criticized by medical professionals and ultimately, lost his employment., 1856, Carl Ludwig discovered a procedure for keeping animal organs alive, under in vitro conditions. This was done by supplying blood to them., In contrast to the concepts of Justus von Liebig, Pasteur (1822–1895), suggested that microbes are responsible for fermentation., 1859, Charles Darwin (1809–1882) speculated that animal populations adapt, their forms to eventually best utilize the surroundings, a process he, described as ‘natural selection’. During his stay in the Galapagos, Islands, he saw how the finches’ beaks on each island were adapted, for the environment, especially regarding food sources., 1863, Pasteur discovered the method of pasteurization. In this method he, heated wine enough to inactivate microbes (that would otherwise, convert the ‘vin’ to ‘vin aigre’ or ‘sour wine’) and realized that this, procedure did not affect the flavor of the wine [26]., Heinrich Anton de Bary established that a fungus was responsible for, potato blight. A major challenge for researchers during this period, was to differentiate whether a microbe was responsible for this or, whether it was the outcome of a disease., 1865, Mendel (1822–1884) suggested the laws of heredity to the National, Scientific Society (Brunn, Austria). Mendel anticipated that, imperceptible core units of information were responsible for, noticeable characteristics. He called these ‘factors’, which were later, called genes (units that were inherited by one generation from its, parents). The research done by Mendel was overlooked and not, acknowledged due to Darwin’s more sensational publication five, years earlier, until 1900 when Hugo de Vries, Erich von Tschermak, and Carl Correns supported Mendel’s mechanism of heredity., , 1-8

Page 10 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1868, Casimir Joseph Davaine cured plants suffering from bacterial, infection by a novel heat treatment. While working in a hospital,, Johannes Friedrich Miescher separated nuclein (a compound made, of nucleic acid) from pus cells. These pus cells were derived from, waste bandages [24]., 1870, Walther Flemming discovered mitosis [25]., 1871, During the period 1873–76 interest in DNA research began. DNA, was initially derived from the sperm of trout (found in the river, Rhine). During this period Koch investigated anthrax and explored, certain techniques to identify, culture and stain micro-organisms., He also took images of them which were later supported by Gram,, Cohn and Weigart [26]., 1880, While working on fowl cholera, Louis Pasteur explored weakened, (attenuated) strains of micro-organisms that might not be virulent, but could nevertheless potentially prevent healthy individuals, against severe forms of a similar disease [26]., 1881, Koch explained techniques for harvesting bacterial colonies on potato, slices, gelatin and agar medium [26]. For the isolation of pure culture, and for distinguishing the nutrients needed for genetic mutations, the, agar technique was one of the most common methods. Thomas D, Brock considered this breakthrough as the single most important, discovery in the development of microbiology., During the same period Pasteur explored the application of the, attenuation process in the production of vaccines against certain, bacterial pathogens, e.g. fowl cholera and anthrax; this was an, early stage in immunology which led to the exploration of areas, such as preventive medicine [26]., 1884, Koch established his ‘claims’ for assessing whether a microbe or, another agent is responsible for disease., During the same period Pasteur established a rabies vaccine [26]., Gram described the differential staining technique for cellular, peptidoglycan-containing bacteria now known as Gram staining [27]., Mendel passed away after 41 years of predominantly investigating the, heredity ‘factors’ of pea plants. He did not receive any technical, support during his lifetime, but said before his death, ‘My time will, come’ [28], (Continued), , 1-9

Page 11 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1900–1953, (Genetics:converging on, DNA), , 1900: Mendel’s work finally took on importance, Mendel’s work had given birth to genetic science. It was revived again, by three researchers, de Vries, von Tschermak and Correns, who were, working on the application of original work done by Mendel [29]., 1902: Human genetics is born, Sutton found that chromosomes (paired) contain certain elements which, are transferred from one generation to another. During this transfer,, traits are transported through carriers called chromosomes. He also, advised that Mendel’s ‘factors’ are sited on chromosomes [30]., 1905: X and Y chromosomes related to gender, Edmund Beecher Wilson and Nettie Stevens shared the same idea of, separating X and Y chromosomes for the determination of sex. They, also demonstrated that a single Y chromosome determines maleness,, while two copies of the X chromosome decide femaleness [31]., 1905–1908, William Bateson and R C Punnett, along with other researchers, found, that several genes alter or modify the action of other genes [32]., 1906, Paul Erlich also investigated atoxyl compounds and discovered the, important features of Salvarsan (the first chemotherapeutic agent) [33]., 1907, Thomas Hunt Morgan started his investigation into fruit flies that, would reveal that chromosomes have a defined role in heredity;, additionally, he discovered mutation theory. This resulted in an, understanding of the basic concepts and mechanisms of heredity [34]., 1909: Mendel’s laws to animals, Wilhelm Johannsen used the word ‘gene’ to mean the carrier/transporter, of heredity. He also coined the terms ‘genotype’ and ‘phenotype’; the, genotype is the genetic composition/establishment of an organism,, whereas the phenotype describes the actual organism or its, morphological characteristics, resulting from a blend of the genotype, and a range of external/environmental factors [35]., 1910: Basis of modern genetics, Morgan also demonstrated that carriers of genetic information, called, asor genes, are present on chromosomes, creating the basis for, modern genetics. This work later assisted him in utilizing, Drosophila fruit flies to examine heredity [36]., 1911, During the same period Morgan established the separation of certain, inherited features that are generally linked to the separation/, breaking of chromosomes during the process of cell division. He, also investigated the mapping of the genetic sites present on the, chromosomes of the fruit fly [36]., , 1-10

Page 12 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1912, Crystallography era: William Lawrence Bragg discovered the, application of x-rays in the determination of the molecular, structure of crystalline substances [37]., 1918, Herbert M Evans stated (mistakenly) that human genetic material is, made up of 48 chromosomes [38]., 1924: Eugenics in the United States, Several US diplomats, encouraged by the eugenics movement,, accepted the US Immigration Act (1924), limiting the admission of, illiterate refugees from Southern and Eastern Europe on the basis, of their alleged genetic inferiority., 1926, Morgan published The Theory of the Gene.’ This was based on Mendelian, genetics (breeding investigations and optical microscopy) [36]., Hermann Joseph Muller discovered that x-rays are responsible for, genetic mutations in fruit flies taking place 1500 times faster than, under normal conditions. This innovation offered researchers and, scientists a procedure to induce mutations. Later, various mutagens, were explored to understand the complexity behind different, genotypes [39]., 1928, Frederick Griffiths observed the ‘transforming principle’ in which a, rough type of bacterium is transformed to a smooth type when a, mysterious ‘transforming element’ from the smooth type is present., After 16 years, Oswald Theodore Avery discovered that, ‘transforming element’ to be DNA [40]., Alexander Fleming studied an old culture of bacteria infected with fungal, growth and found that it did not show any bacterial growth in a radius, surrounding a piece of mold (fungi) in a petri dish. This breakthrough, gave birth to the antibiotics era or penicillin age, and penicillin was, accessible to patients 15 years later for therapeutic use [41]., 1938, Proteins and DNA were studied by means of x-rays. This was the, dawn of a new age of crystallography in which large molecular, weight complex proteins can be studied by x-rays., The term ‘molecular biology’ was coined., 1941: One gene, one enzyme, George Wells Beadle and Edward L Tatum examined Neurospora, crassa, a mold that usually invades and grows on bread, and proposed, ‘one gene, one enzyme’ theory: each gene encodes for or is translated, into an enzyme to accomplish tasks within an organism [40]., (Continued), , 1-11

Page 13 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1943, The Rockefeller Foundation (New York) collaborated with the, Mexican government to start the Mexican Agricultural Program, [42]. This was the first step toward plant breeding at a global level., 1943–1953, Cortisone (17α,21-dihydroxypregn-4-ene-3,11,20-trione), a pregnane, (21-carbon) steroid hormone, was first produced in great amounts., Cortisone is considered as the first biotech product., 1944, Selman Abraham Waksman (a Ukrainian-American researcher), explored streptomycin, an active antibiotic against TB., 1945, The United Nations Food and Agriculture Organization was, established in Quebec, Canada, with the objective of encouraging, agricultural practices., 1945–1950, For the first time, animal cell cultures were harvested in laboratories,, giving birth to the field of animal tissue culture., 1947, Barbara McClintock first demonstrated ‘transposable elements’, known as ‘jumping genes’ with the capability to move (or jump), from one site on the genome to another site. Scientific society did, not welcome the implications of her discovery at the time [44]., 1950, Erwin Chargaff discovered that the same levels of adenine and, thymine are present in DNA, as are the same levels of guanine and, cytosine [45]. These associations were later named ‘Chargaff’s, rules’. Later, Chargaff’s rules functioned as an important principle, for James Watson and Francis Crick in measuring different models, for the structure of DNA., DNA research, science, explodes (1953–1976), , 1953–1976: Expanding the boundaries of DNA research, The discovery of the structure of DNA finally resulted in an explosion, of research into molecular biology and genetics, providing the, resources for biotechnology development., 1953, The journal Nature published Watson and Crick’s article based on, unfolding the double-helix structure of DNA., 1953, Based on his technical exposure George Otto Gey developed the HeLa, human cell line. Cells taken from cancer patient Henrietta Lacks, (who died in 1951) became the first immortal human cells and were, cultured to develop a polio vaccine., , 1-12

Page 14 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1957: Central dogma of DNA—how DNA makes a protein, Crick and Gamov studied ‘central dogma’, demonstrating how DNA, functions to construct protein [47]., 1959, François Jacob and Jacques Lucien Monod documented the veracity, of gene-based regulation. They explained gene mapping with, mappable control functions sited on the chromosome in the DNA, sequence which they later named the ‘repressor’ and ‘operon’ [48]., 1962, Watson and Crick were awarded the Nobel Prize in Physiology or, Medicine with Maurice Wilkins. Disappointingly, Rosalind, Franklin, who actually contributed to the discovery of the doublehelical structure of DNA, died before this date, and Nobel Prize, conventions do not permit a prize to be awarded posthumously [49]., 1966: Genetic code cracked, The genetic code was explored by several researchers. Marshall, Warren Nirenberg, J Heinrich Matthaei and S Ochoa reported that, a genetic sequence of three nucleotide bases (called codons) decides, each of 20 amino acids [50]., 1967, Arthur Kornberg reported a study using single-stranded natural viral, DNA to assemble 5300 nucleotide building blocks, and at the same, time his Stanford group synthesized viral DNA [50]., 1970: Oncogenes, Virologists Peter H Duesberg and Peter K Vogt identified the first, oncogene in a virus. This gene can be utilized to study various, human cancers [51], 1972: First recombinant DNA molecule, Paul Berg, a biochemist, utilized a restriction enzyme to cut DNA into, fragments. He employed a ligase enzyme to join two DNA strands, concurrently to form a hybrid circular molecule. This was the first, recombinant DNA (rDNA) molecule synthesized., 1972: NIH guidelines for rDNA, Berg and other researchers at the National Institutes of Health (NIH), worked hard to establish guidelines to sanction the strategy for, DNA splicing. Their concerns resulted in the Asilomar Conference, (1975)., 1973: Ames test, Bruce Nathan Ames, a biochemist at UC Berkeley, developed an, investigation to distinguish chemicals that damage DNA. Later, the, Ames test became extensively used to identify cancer-causing, substances [40]., (Continued), , 1-13

Page 15 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1975: rDNA moritorium, A global meeting was held in Asilomar, California, with the objective, of approving guidelines regulating rDNA experimentation. All the, scientists involved discussed the development of ‘safe’ bacteria and, plasmids., 1976: More about oncogenes, J Michael Bishop and Harold Varmus at the University of California,, San Francisco (UCSF) established that cancer-causing genes called, oncogenes become visible on animal chromosomes, and, modifications in their structure or expression can result in, metastatic growth [53]., 1976: Release of NIH guidelines, The NIH released the first set of guidelines for rDNA experimentation., Later, these guidelines restricted several types of trials., 1977–present (modern, biotechnology), , 1977–present: The dawn of biotech, With the advent of genetic engineering it was possible to produce human, protein in bacteria for the first time. Biotech-based organizations, started focusing more on the applications of genetic engineering. In, 1978, Herbert W Boyer at UCSF synthesized synthetic human insulin, by introducing the insulin gene into the bacterium Escherichia coli, [54]. This breakthrough opened the gateway for further developments, in DNA sequencing and cloning techniques., 1977, Genentech Inc. was the first organization to achieve the synthesis of a, human protein (somatostatin) in a bacterium. Somatostatin is a, human growth hormone (hGH)-releasing inhibitory factor. A, synthetic, recombinant gene was for the first time employed to, clone a protein. Several researchers believed that this was the, beginning of the age of modern biotechnology [55]., 1978: Recombinant insulin, Genentech Inc. announced that its laboratory had achieved the, synthesis of human insulin using rDNA technology [55]., 1980: Patents allowed, The US Supreme Court granted that genetically modified living, organisms could be patented. According to a Supreme Court, decision (1980) the Exxon oil company was allowed to patent an, oil-eating micro-organism., Kary Mullis and other researchers at UC Berkeley, California,, established a tool for multiplying DNA sequences in vitro using the, polymerase chain reaction (PCR) [56]., 1982: Site-directed mutagenesis, Genentech Inc. signed an agreement from the US Food and Drug, Administration (FDA) to further market genetically engineered, , 1-14

Page 16 : Introduction to Pharmaceutical Biotechnology, Volume 1, , human insulin. In 1982 the FDA allowed the first genetically, engineered drug in the form of human insulin produced by bacteria., Michael Smith at the University of British Columbia, Vancouver,, established a procedure for producing precise amino acid changes, anywhere in a protein., 1983: Site-directed mutagenesis, Eli Lilly obtained a license to make and sell insulin., 1985, During this period genetic fingerprinting stepped into the court room., Cal Bio produced a gene by a cloning method that encodes human, lung surfactant protein, an important step toward reducing, premature birth complications., For the first time, genetically modified plants that resistant to insects,, viruses and bacteria were examined., The NIH published guidelines for performing experiments in gene, therapy on humans., 1986, Chiron Corp. obtained FDA approval for the production of the first, recombinant vaccine for hepatitis., A genetically modified crop (the tobacco plant) was allowed by the, Environmental Protection Agency (EPA)., 1987, Calgene Inc. obtained a patent for the tomato polygalacturonase, DNA sequence, which was later used to synthesize an antisense, RNA sequence that can further extend the shelf life of fruit., 1988, Harvard molecular geneticists Philip Leder and Timothy A Stewart, were granted the first patent based on a genetically modified animal, (a mouse that is highly susceptible to breast cancer) [57]., 1990, UCSF and Stanford University achieved their 100th rDNA patent, license. At the end of the 1991 financial year, both organizations, had received $40 million from the patent., 1990: Patents and money, The first gene-based treatment was performed on a four-year-old girl, suffering from an immunological disorder known as adenosine, deaminase deficiency (ADA) deficiency. Gene therapy emerged,, however ethical concerns surrounding gene therapy were highly, debated., Commencement of the Human Genome Project, with the global, objective to plot all of the genes in the human body. The expected, cost was $13 billion., (Continued), , 1-15

Page 17 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Michael Crichton’s novel Jurassic Park was released, in which, bioengineered dinosaurs wander in a paleontological theme park;, the project goes wrong, with deadly outcomes., 1992, The US Army started taking blood and tissue samples from all new, employees as part of a ‘genetic dog-tag’. This course of action was, intended for better identification of soldiers killed in battle., 1993, Researcher Kary Mullis won the Nobel Prize in Chemistry for, inventing the tool of PCR [58]., 1996, A groundbreakingly efficient diagnostic biosensor test allowed for the, first time the instant detection of the toxic strain of E. coli (strain, 0157:H7), the bacteria responsible for several food poisoning, outbreaks. The possibility of its use against anthrax and other, bioterrorism agents was also assessed., The discovery of a gene linked to Parkinson’s disease offered, researchers a significant new chance for the determination of the, cause of, and potential treatments for, the incapacitating, neurological disorder., Reports showed that there were public concerns about research into, the human genome and gene therapy, with a combination of fear, and mistrust., 1997, Researchers at the Roslin Institute in Scotland announced that they, had cloned a sheep called Dolly from the cell of an adult ewe. Dolly, was the first mammal cloned by a technique called nuclear transfer, technology. Nuclear transfer allows the introduction of complete, genetic material from one cell into another enucleated unfertilized, egg cell., 1998, A group of researchers succeeded in culturing embryonic stem cells.A, number of researchers at Japan’s Kinki University cloned eight, identical calves by means of cells taken from a single adult cow.A, rough draft of the human genome map was created, presenting the, sites of more than 30 000 genes., 1999, A fatal neurological disease called bovine spongiform encephalopathy, (BSE), also known as mad cow disease, that spread from cattle to, humans, was diagnosed by a new medical diagnostic examination, that facilitated the quick detection of BSE/Creutzfeldt–Jakob, disease (CJD)., , 1-16

Page 18 : Introduction to Pharmaceutical Biotechnology, Volume 1, , a breakdown of historical events in biotechnology. The development of biotechnology can be divided into broad stages or categories, including:, • Ancient biotechnology (8000–4000 BC): Early history as related to food and, shelter; includes domestication of animals., • Classical biotechnology (2000 BC; 1800–1900 AD): Built on ancient biotechnology; fermentation promotes food production and medicine., • 1900–1953: Genetics., • 1953–1976: DNA research, science explodes., • Modern biotechnology (1977): Manipulates genetic information in organisms; genetic engineering; various technologies enable us to improve crop, yield and food quality in agriculture and to produce a broader array of, products in industries., 1.3.1 Old and new biotechnology, While the word biotechnology is of recent origin, the discipline itself is very old. To, produce wine, vinegar, curd, leavened bread, etc, humans began employing microorganisms as early as 5000 BC. These processes were commonly employed at a, domestic scale and have become such an integral part of normal food processing, methods that we may even hesitate to refer to them as biotechnology. Such, processes, based on the natural capabilities of micro-organisms, are commonly, considered to be ‘old’ biotechnology., 1.3.2 Ancient biotechnology (pre-1800), In the period before the year 1800, some events that were based on common, observations about nature can be categorized as biotechnological developments., Three important basic needs of human civilization are food, clothes and shelter. In, the ancient era the paucity of food led to the domestication of food products,, formally called ‘agriculture’. During ancient times humans understood the importance of water, light and other requirements for the optimal growth of food plants, and the domestication of different wild animals, which helped them improve their, living conditions and satisfy their hunger. The domestication of wild animals was the, beginning of the observation, understanding and applications of animal breeding., This initial period of the evolution of farming led to another development in, methods for food preservation and storage. The utilization of cold caves or pots (in, the form of leather bags and clay jars) to preserve food for long-term storage began., After discovering the basic facts behind the domestication of food crops and wild, animals, human beings moved on to other new inventions such as curd, cheese, etc., Cheese can be considered to be one of the first direct products (or by-products) of, biotechnology, since it was prepared by adding rennet (an enzyme found in the, stomachs of calves) to sour milk. This is only possible when milk is exposed to, microbes (although there was no understanding of this at that time). Among all, microbial strains, yeast is one of the oldest microbes to have been exploited by, humans for their benefit. This primitive microbe has long been employed for the, production of alcoholic beverages such as whiskey, wine, beer, etc. Among the oldest, 1-17

Page 19 : Introduction to Pharmaceutical Biotechnology, Volume 1, , preservatives, vinegar has a significant importance because of its low pH and, potential in preventing the growth of certain microbes, which means it can be used, successfully in food preservation. These discoveries and their significance allowed, people to work on further improvement of the processes involved. However, while, processes such as the decomposition of debris or other materials, which was later, called fermentation, were powerful tools to improve their living conditions, people, were ignorant of the principles behind them., Among the most primitive examples of crossbreeding for the benefit of humans is the, mule. Man started using mules for transportation, carrying loads and farming,, before the days of tractors or trucks. Mules are comparatively easier to obtain than, hinnies (the offspring of a male horse and a female donkey). Mules and hinnies both, have 63 chromosomes, unlike the horse (64) and the donkey (62). Some of the, processes and products developed in the ancient period are described in table 1.2., Table 1.2. Biotechnological processes and products developed in the ancient period., , Process or product, developed, , Events that contributed to its development, , Domestication, , • Food supplies were often seasonal. In winter, food supplies could, become quite low., • People came up with ways of capturing fish and small animals., • 15 000 years ago, large animals were difficult to catch., • People may only have had meat when they found a dead animal., • Domestication most likely began 11 000–12 000 years ago in the Middle, East., • It involved the adaptation of organisms so they could be cultured., • Seen by scientists as the beginning of biotechnology., • Cattle, goats and sheep were the earliest domesticated food animals., , Food preservation, , • People knew that some foods rotted, while others changed form and, continued to be good to eat., • Foods stored in a cool cave did not spoil as quickly., • Foods heated by fire also did not spoil as quickly., • Immersion in sour liquids prevented food decay., • Food was stored in bags of leather or jars of clay., • Fermentation occurs if certain micro-organisms are present, it creates, an acid condition that slows or prevents spoilage., , Cheese, , •, •, •, •, , One of the first food products made through biotechnology., Strains of bacteria were added to milk, resulting in sour milk., An enzyme called ‘rennet’ was added., Rennet comes from the lining of the stomachs of calves. It is genetically, engineered today., • Not all cheese is made from rennet., • It may have been first developed by nomadic tribes in Asia some 4000, years ago., , 1-18

Page 20 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Yeast, , •, •, •, •, •, , Vinegar, , •, •, •, •, , Fermentation, , • Process in which yeast enzymes chemically change compounds into, alcohol., • In making vinegar the first product of fermentation is alcohol., • In ancient times, this likely happened by accident., • Advancements occurred in the 1800s and early 1900s., , Fermenters, , • Allowed better control, especially with vinegar., • New products such as glycerol, acetone and citric acid resulted., , Antibiotics, , •, •, •, •, •, •, •, , Long used in food preparation and preservation., Used in bread baking., Produces a gas in the dough causing the dough to rise., Used in fermented products such as vinegar., Ethanol production require the use of yeast in at least one stage of, production., , Used in pickling., Keeps foods from spoiling., Juices and extracts from fruits and grains can be fermented., Biblical references to wine indicate the use of fermentation some 3000, years ago., • Ancient product used to preserve food., , First drug produced by microbes., Used in both human and veterinary medicine., Use of fermentation hastened the development of antibiotics., Penicillin was developed in the late 1920s., Introduced in the 1940s as a drug used to combat bacterial infections., Many kinds are available today., Limitations in their use keep disease-producing organisms from developing immunity to antibiotics., • Some disease organisms are now resistant to certain antibiotics., , 1.3.3 Classical biotechnology, Classical biotechnology is the second phase of the development of biotechnology., This stage existed from 1800 to almost the middle of the twentieth century. In the, classical era different observations started pouring in, supported by scientific, evidence. These observations made it possible to solve the puzzles of biotechnology., Each and every observation has made its own contribution in furthering the, exploration of new discoveries. The fundamental idea of the transfer of genetic, information from one generation to another forms the core of biotechnology., Information on the transfer of genetic information was first deciphered by Gregor, John Mendel (1822–1884), an Austrian Augustinian monk. Mendel presented his, ideas on the laws of inheritance to the Natural Science Society in Brunn, Austria., He first observed the transfer of genetic information in a plant, Pisum sativum,, commonly known as the pea plant [59]. Moreover, Mendel also hypothesized, , 1-19

Page 21 : Introduction to Pharmaceutical Biotechnology, Volume 1, , that an invisible internal unit of information accounted for observable traits., These ‘factors’, later called genes, were passed from one generation to the next., Nevertheless, the sad part of his story is that Mendel failed to receive due, acknowledgment for his invention for almost 34 years after his death, when other, scientists such as Hugo de Vries, Erich von Tschermak and Carl Correns validated, his work in 1900. The main reason why Mendel’s discovery remained overlooked for, such long time was that in the same period Charles Darwin’s theory of evolution was, so overwhelming that it overshadowed the implications of the work done by Mendel., During this time the nucleus in cells was discovered [59], and Fredrich Miescher, a, Swiss biologist, reported the existence of nuclein, a compound that consisted of, nucleic acid that he had extracted from pus cells, i.e. white blood cells [59]. These, two discoveries gave germination to the DNA era, which became the basis of, modern molecular biology, the discovery of DNA as a genetic material and the role, of DNA in the transfer of genetic information. Meanwhile the bacterial propagation, method was first proposed by Robert Koch (1881), a German physician, who, described the bacterial colonies growing on potato slices (the first ever solid medium), [59]. While working on the cause behind the solidification of jelly, Walter Hesse (one, of the co-workers in Koch’s laboratory) discovered the nutrient agar, the most, acceptable and useful medium for obtaining pure microbial cultures, as well as for, their identification [59]. He discovered agar when he asked his wife what kept the, jelly solid even at high temperatures in summer. She said it was agar, and since then, the nutrient has been used for microbial cultures. Heinrich Wilhelm Gottfried von, Waldeyer-Hartz, a German scientist in the nineteenth century, coined the term, ‘chromosome’ for an organized structure of DNA and protein present in cells or a, single piece of coiled DNA containing many genes, regulatory elements and other, nucleotide sequences [59]. Among various other prominent discoveries during this, period, vaccinations against smallpox and rabies were developed by Edward Jenner,, a British physician, and Louis Pasteur, a French biologist, respectively. The, development of biological sciences seemed to be reaching an exponential phase., During this period the principle of genetics in inheritance was redefined by T H, Morgan. He showed inheritance, and the role of chromosomes in inheritance, using, fruit flies (Drosophila melanogaster). Later, in 1926, this work was published in, Morgan’s book The Theory of the Gene. Prior to Morgan’s 1909 work, the term, ‘gene’ had already been coined by Wilhelm Johannsen (1857–1927). He described, the gene as the carrier of heredity. Afterwards Johannsen coined the terms, ‘genotype’ to describe the genetic constitution of an organism, and ‘phenotype’ to, describe the actual organism. After this exploration genetics started gaining, importance. This led to the beginning of the eugenics movement in the USA, (1924). At the same time, Alexander Fleming, a British physician, discovered, antibiotics when he observed that one micro-organism can be used to kill another, micro-organism. The basic idea behind it was a true representation of the ‘divide and, rule’ policy of humans. He noticed that all bacteria (Staphylococci) died when a, mold was growing in a petri dish. Afterwards he discovered penicillin, the, antibacterial toxin from the mold P. notatum, which could be used against many, infectious diseases. He wrote ‘When I woke up just after dawn on September 28,, 1-20

Page 22 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1928, I certainly didn’t plan to revolutionize all medicine by discovering the world’s, first antibiotic, or bacteria killer’ [15]. He also concluded that vaccines and, antibiotics would turn out to be the best saviors of humanity: ‘Can we attribute, these two discoveries for the ever increasing population as well the ever ageing, population of the world?’, 1.3.4 Modern biotechnology, A major obstacle to scientific discoveries was the Second World War. After the war,, some essential discoveries were explored. These discoveries form the basis for modern, biotechnology and have brought this field to its current status. Some of the prominent, events of the modern age of biotechnology are highlighted in table 1.3., Table 1.3. Historical and current events that form the basis of modern biotechnology., , Year, , Discoveries, The 1950s, , 1952, , • George Otto Gey created a continuous cell line taken from a human cervical, carcinoma. This cell line, known as HeLa, is still used in therapeutic research., , 1953, , • Watson and Crick explored DNA as a genetic material, and discovered its, structure, called the double-helix., , 1954, , • Joseph Murray carried out the first kidney transplant between identical twins., , 1957, , • Scientists revealed that sickle-cell anemia occurs due to an alteration in a single, amino acid in hemoglobin cells., , 1958, , • Arthur Kornberg created DNA in a test tube for the first time. The first mechanical, protein sequencer, the Moore–Stein amino acid analyzer, is developed., , 1960, , The 1960s, • A French researcher discovered messenger RNA (mRNA)., , 1961, , • François Jacob and Jacques Monad demonstrated the concept of Operon., , 1962, , • Osamu Shimomura explored the green fluorescent protein in the jellyfish Aequorea, victoria. He afterward developed it into a technique for examining formerly, invisible cellular processes [60]., , 1963, , • Samuel Katz and John F Enders developed the first vaccine for measles [61]., , 1963, , • Autonomous groups in the USA, Germany and China produced insulin, a, pancreatic hormone., , 1964, , • The existence of reverse transcriptase was predicted., , 1967–71, , • Maurice Hilleman made the first American vaccine for mumps [62]., • The first vaccine for rubella was developed., • Rubella was combined with the measles and mumps vaccines to yield the measles/, mumps/rubella (MMR) vaccine., , 1968, , • How the arrangement of nucleotides in nucleic acids regulates the cell’s synthesis of, proteins was discovered., (Continued), , 1-21

Page 23 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1970, , The 1970s, • Restriction enzymes were discovered., , 1972, , • DNA ligases, which join DNA fragments together, were used for the first time., • The DNA composition of humans was discovered to be 99% similar to that of, chimpanzees and gorillas., • The purified enzyme reverse transcriptase was first employed to prepare complementary DNA from purified messenger RNA in a test tube., , 1973, , • Stanley Cohen and Herbert Boyer used bacterial genes to perform the first, successful rDNA experiment [63]., • Sir Edwin Mellor Southern developed a blotting technique for DNA called the, Southern blot., , 1974, , • The NIH formed a Recombinant DNA Advisory Committee to supervise recombinant genetic research., • The first vaccine for chicken pox was developed in Japan., , 1975, , • Colony hybridization and Southern blotting were explored for identifying specific, DNA sequences., • The first monoclonal antibodies were prepared., • César Milstein, Georges Jean Franz Kohler and Niels Kaj Jerne explored the, monoclonal antibody technique by fusing immortal tumor cells with antibodyproducing B-lymphocyte cells to generate hybridomas that constantly produce, identical antibodies., , 1975, , • The theory of cytoplasmic hybridization was proposed, and the first ever monoclonal antibodies were synthesized., , 1976, , • The NIH published the first guidelines for rDNA research., • Molecular hybridization was employed for the prenatal diagnosis of alpha, thalassemia. Yeast genes were expressed in E. coli bacteria., , 1977, , • Procedures were developed to swiftly sequence long sections of DNA. Genetically, engineered bacteria were employed to manufacture the human growth protein, somatostatin, marking the first time a synthetic recombinant gene was employed to, clone a protein. Several believed this to be the arrival of the ‘age of biotechnology’., • R Austrian et al at the University of Pennsylvania developed the first vaccine for, pneumonia [65]., , 1978, , • Boyer synthesized the human insulin gene (i.e. a synthetic version of it) and inserted, it into the bacterium E. coli, allowing the bacterium to produce human insulin., • Louise Brown, the first test-tube baby, was born in the UK. The first vaccine for, meningococcal meningitis was developed., , 1980, , The 1980s, • According to US Supreme Court, genetically altered life forms could be patented,, creating vast possibilities for commercially exploiting genetic engineering., • The first patent of this nature was awarded to the Exxon oil company to patent an, oil-eating micro-organism, which would afterward be employed in the 1989 cleanup, of the Exxon oil spill at Prince William Sound, Alaska. S Cohen and D H Boyer, received a US patent for gene cloning., • The first automatic gene machine was developed in California., , 1-22

Page 24 : Introduction to Pharmaceutical Biotechnology, Volume 1, , • Launch of Amgen, which would grow to become the world’s largest biotechnology, medicines company., 1981, , • Baruch Blumberg and Irving Millman developed the first vaccine for hepatitis B [66]., • Researchers in Switzerland cloned mice., • The first transgenic animals were produced by transforming genes from other, animals into mice., , 1982, , • The FDA supported the first recombinant protein., , 1983, , • Luc Montagnier of the Pasteur Institute in Paris isolated the AIDS virus., • Kary Mullis discovered the polymerase chain reaction (PCR), a technique for, multiplying DNA sequences., • PCR was identified as the most innovative molecular biology technique. The FDA, sanctioned a monoclonal antibody-based diagnostic analysis to identify Chlamydia, trachomatis., • The first artificial chromosome was produced and the first genetic markers for, specific inherited diseases were discovered., , 1984, , • The DNA fingerprinting technique was discovered. When a restrictive enzyme is, applied to DNA from various individuals, the ensuing sets of fragments sometimes vary, noticeably from one person to the next. Such differences in DNA are called restriction, fragment length polymorphisms and are particularly helpful in genetic investigations., • The first genetically engineered vaccine was discovered for hepatitis B. The whole, genome of the human immunodeficiency virus (HIV) virus was cloned and, sequenced., , 1985, , • Genetic fingerprinting stepped into the courtroom., • Genentech became the first biotechnology organization to launch its own biopharmaceutical product., • Genetically engineered plants resistant to viruses, insects and bacteria were fieldtested for the first time., • Cloning of the gene that encodes human lung surfactant protein was achieved. This, was a major step toward reducing premature birth problems., • The NIH sanctioned guidelines for executing trials of gene therapy on humans., , 1986, , • Peter G Schultz from UC Berkeley explained how to conjugate antibodies and, enzymes (abzymes) to create therapeutics [67]., • The automated DNA sequencer was discovered in California. The FDA sanctioned, the first monoclonal antibody treatment to fight kidney transplant rejection., • The FDA sanctioned the first biotech-derived interferon drugs to treat cancer., Drugs to treat Kaposi’s sarcoma, a complication of AIDS, were discovered., • The FDA sanctioned the first genetically engineered human vaccine to avert, hepatitis B., , 1987, , • The FDA sanctioned a genetically engineered tissue plasminogen activator to treat, heart attacks., • Maynard Olson and colleagues at Washington University discovered yeast artificial, chromosomes, which are expression vectors for large proteins., • Reverse transcription and the PCR were linked to augment messenger RNA, sequences. DNA microarray technology, the use of a set of various DNAs in, arrays for expression outline, was first explained., (Continued), , 1-23

Page 25 : Introduction to Pharmaceutical Biotechnology, Volume 1, , • The collection of DNA was used to recognize genes whose expression is altered by, interferon., • The FDA sanctioned a diagnostic serum tumor marker test for ovarian cancer., 1988, , • Congress financed the Human Genome Project, a huge international attempt to, map and sequence the human genetic code as well as the genomes of other species., • The first contract between two organizations with parallel patents for crosslicensing of biotech products occurred and became the example., , 1989, , • The FDA sanctioned Amgen’s first biologically derived human therapeutic., • Oil-eating bacteria were employed to clear up the Exxon Valdez oil spill., • A gene responsible for cystic fibrosis was explored., , 1990, , The 1990s, • The first nationally sanctioned gene therapy treatment was executed effectively on a, four-year-old girl suffering from an immune disorder called adenosine deaminase, deficiency., • The Human Genome Project was launched., • The FDA approved the first hepatitis C antibody test, which helped to guarantee, the purity of blood bank products., • The FDA sanctioned a bioengineered form of the protein interferon gamma to treat, chronic granulomatous disease., • The FDA sanctioned a modified enzyme for enzyme replacement therapy to treat, severe combined immunodeficiency disease. It was the first successful application of, enzyme replacement therapy for an inherited disease., , 1992, , • The US Army accumulated blood and tissue tests from all new recruits as part of a, genetic dog-tag plan intended to achieve better recognition of soldiers killed in, combat., • The FDA sanctioned the first genetically engineered blood-clotting factor—a, recombinant protein used to treat hemophilia A., • The FDA sanctioned a recombinant protein to treat renal cell cancer. American, and British researchers revealed a technique for analyzing embryos in vitro for, genetic abnormalities, e.g. cystic fibrosis and hemophilia., , 1993, , • The FDA approved a recombinant protein to treat multiple sclerosis—marking the, first new multiple sclerosis treatment in 20 years., • A global research team, led by Daniel Cohen from the Center for the Study of, Human Polymorphisms, Paris, created a rough map of all 23 pairs of human, chromosomes., • Two minor trade organizations merged together to form the Biotechnology, Industry Organization, an international biotechnology support group., , 1994, , • The FDA sanctioned a recombinant protein to deal with growth hormone (GH), deficiency., • Mary-Claire King at UC Berkeley explored the first breast cancer gene, BRCA1, [68]. The FDA sanctioned a modified enzyme to deal with Gaucher’s disease., • A number of genes, human and otherwise, were identified and their functions, explained. These comprised: Ob, a gene inclining to obesity; BCR, a breast cancer, receptiveness gene; BCL-2, a gene linked to apoptosis (programmed cell death);, Hedgehog genes (named because of their shape), which synthesize proteins that, , 1-24

Page 26 : Introduction to Pharmaceutical Biotechnology, Volume 1, , direct cell differentiation in complex organisms; and Vpr, a gene regulating the, reproduction of the HIV virus., • Genetic linkage studies recognized the role of genes in a variety of disorders,, including bipolar disorder, cerulean cataracts, melanoma, dyslexia, prostate cancer,, thyroid cancer, hearing loss, sudden infant death syndrome and dwarfism., • The FDA sanctioned a genetically engineered description of human DNase, which, breaks down protein accretion in the lungs of cystic fibrosis patients. This, corresponded to the first new therapeutic drug for treating cystic fibrosis., 1995, , • The first baboon-to-human bone marrow transplant was executed on an AIDS, patient., • The first vaccine for hepatitis A was explored., • The NIH, the US Army and the Centers for Disease Control and Prevention were, considerably involved in the growth and clinical testing of the vaccine., • Researchers at the Institute for Genomic Research completed the first full gene, sequence of a living organism for the bacterium Haemophilus influenzae., • A European study group determined a genetic defect that turned out to be the most, frequent cause of deafness., , 1996, , • Researchers at the Department of Biochemistry at Stanford University and, Affymetrix developed the gene chip, a small glass or silica microchip that contains, thousands of individual genes that can be examined simultaneously. This symbolized a scientific breakthrough in gene expression and DNA sequencing technology., • Research groups sequenced the complete genome of a complex organism,, Saccharomyces cerevisiae, otherwise known as baker’s yeast. The accomplishment, symbolizes the entire sequencing of the largest genome to date. A novel, economic, diagnostic biosensor test was developed to hasten the detection of a toxic strain of, E. coli, the bacteria responsible for several food-poisoning outbreaks., , 1997, , • The first human artificial chromosome was discovered., • A mixture of natural and synthetic DNA was used to synthesize a genetic cassette, that could possibly be adapted and employed in gene therapy., • The FDA sanctioned a recombinant follicle stimulating hormone to deal with, infertility., • The FDA permitted the first bloodless HIV-antibody analysis, which used cells, from patients’ gums. Researchers at the Institute for Genomic Research sequenced, the entire genome of the Lyme disease pathogen, Borrelia burgdorferi, along with, the genome for the organism associated with stomach ulcers, Helicobacter pylori., • Researchers at the University of Wisconsin–Madison sequenced the E. coli genome., • The FDA permitted the first therapeutic antibody to treat cancer in the USA. It was, employed for patients with non-Hodgkin’s lymphoma., , 1998, , • Human skin was created in the laboratory for the first time., • Two research groups cultured embryonic stem cells., • Embryonic stem cells were employed to regenerate tissue and produce disorders, mimicking diseases., • Researchers at the Sanger Institute in the UK and at the Washington University, School of Medicine in St Louis, USA, sequenced the first whole animal genome for, the Caenorhabditis elegans worm., (Continued), , 1-25

Page 27 : Introduction to Pharmaceutical Biotechnology, Volume 1, , • A rough draft of the human genome map was created, displaying the sites of more, than 30 000 genes., • The first vaccine for Lyme disease was discovered., • The FDA sanctioned a novel monoclonal antibody to treat Crohn’s disease., • A monoclonal antibody therapy employed against breast cancer had positive, outcomes, indicating a new age of management based on the molecular targeting, of tumor cells., • Support for using the HER2 inhibitor for the management of breast cancer in, patients who had tested positive for the HER2 mutation brought personalized, medicine to oncology., , 2000, , The 2000s, Har Gobind Khorana synthesized DNA in a test tube [59]., Kary Mullis added value to Har Gobind Khorana’s findings by amplifying DNA in a, test tube, to create a thousand times more than the original amount of DNA [59]., Sir Ian Wilmut cloned an adult sheep and called the cloned sheep ‘Dolly’ [59]., Craig Venter sequenced the human genome; the first publicly accessible genomes, would later be those of James Watson and Ventor., Researchers at Celera Genomics and the Human Genome Project successfully, completed a rough draft of the human genome [59]., , 2001, , The journals Science and Nature reported the human genome sequence, making it, feasible for researchers all over the world to start investigating innovative, treatments for diseases that have genetic origins, e.g. heart disease, cancer,, Parkinson’s and Alzheimer’s., , 2002, , An era of very rapid shotgun sequencing of major genomes was completed. Included, were the mouse, chimpanzee, dog and hundreds of other species., , 2003, , Celera and the NIH successfully finished the sequencing of the human genome., , 2004, , The FDA supported the first monoclonal antibody (i.e. antiangiogenic, inhibiting, blood vessel formation or angiogenesis) for cancer therapy., The FDA approved a DNA microarray analysis system, which helped in selecting, medications for different conditions. This was a significant step toward modified, medicine., , 2006, , The FDA sanctioned a recombinant vaccine against human papillomavirus, which, causes genital warts and cervical cancer., Researchers established the three-dimensional (3D) structure of HIV, which causes AIDS., , 2007, , Researchers discovered how to use human skin cells to produce embryonic stem cells., , 2008, , Venter replicated a bacterium’s genetic structure completely from laboratory, chemicals, taking a step nearer to generating the world’s first living artificial, organism [59]., , 2008, , Japanese chemists developed the first DNA molecule made nearly entirely of artificial, parts. The finding could be used in areas of gene therapy., , 1-26

Page 28 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 2009, , Former US President Barack Obama signed an administrative order releasing national, funding for broader research on embryonic stem cells., Scientists identified three new genes connected with Alzheimer’s disease, paving the, way for possible new diagnostics and therapeutics., Geron commenced the first FDA approved clinical trial by means of embryonic stem, cells., , 2010, , The FDA sanctioned a modified prostate cancer medicine that improves a patient’s, immune cells to distinguish and attack cancer cells., The FDA sanctioned an osteoporosis treatment that was one of the first medicines, based on genomic investigations., Craig Venter showed that a synthetic genome could duplicate alone., , 2011, , A trachea developed from stem cells was transplanted into a human recipient.Progress, in 3D printing technology resulted in ‘skin-printing’., The FDA sanctioned the first cord blood therapy to be employed in hematopoietic, stem cell transplantation protocols in patients with disorders influencing the, hematopoietic system., , 2012, , The FDA issued draft regulations for biosimilar drugs., , In the modern era, researchers had almost all the basic tools available to them for, their applications. With these tools the majority of basic concepts were elucidated,, which fast-forwarded the path to important scientific discoveries. These studies and, discoveries have unlimited implications and applications. Conclusively, biotechnology has brought humanity to this level of comfort; looking ahead, the next question, is, where will it take us? Biotechnology has both beneficial and destructive potential., It is we who should now decide how to use this technology to help humanity rather, than to destroy it., , 1.4 Scope and importance of biotechnology, Biotechnology is the science of the controlled application of biological agents for, beneficial use. Since biotechnology is not an independent discipline, its well-known, integration with allied fields such as biochemistry, molecular biology and microbiology facilitates the technological application of biological agents. Therefore,, modern biotechnology has developed as a science with enormous potential for, human welfare in areas ranging from food processing to human health and, environmental protection. The major significance of this field of science in different, fields will be evident from the following examples., 1.4.1 Biotechnology in medicine, One of the major areas in biotechnology is the medical sector. This is the field in, which most of the research is taking place and several breakthroughs have been, made. It is also the area that raises the highest number of ethical and legal issues., 1-27

Page 29 : Introduction to Pharmaceutical Biotechnology, Volume 1, , The scope of biotechnology in medicine is to utilize techniques in living systems to, produce therapeutic proteins, which are usually called biopharmaceuticals or, recombinant proteins. Products such as monoclonal antibodies, DNA and RNA, probes are produced for the diagnosis of various diseases. Additionally, therapeutic, protein-based drugs such as insulin and interferon have been synthesized with, bacteria for the treatment of human diseases. As previously mentioned, the use of, biotechnology in the field of medicine is also known as ‘red’ biotechnology. It deals, with many major and minor aspects of human life, from making medicines more, effective in terms of cost and efficiency, to tackling one of the most difficult branches, of medicine, curing genetic diseases. Red biotechnology covers various potential, medicines for diseases such as cancer and AIDS. It can be divided into four main, areas: biopharmaceuticals, gene therapy, pharmacogenomics and genetic testing., As described above, red biotechnology deals with production of medicinal drugs, that can be proteins (including antibodies that fight infection) or nucleic acids (DNA, or RNA). There is no involvement of chemicals in the synthesis process since they, are derived from micro-organisms which synthesize them naturally. The first, approved product for therapeutic use was biosynthetic ‘human’ insulin made via, rDNA technology. Human insulin replaced the pig insulin that had been previously, used and revolutionized the industry with its success. This human insulin, sometimes, called rHI, or the trade name Humulin, was developed by Genentech but licensed to, Eli Lilly and Company, which manufactured and marketed the product starting in, 1982., The second major field of red biotechnology is gene therapy, which deals with the, diagnosis and treatment of genetic diseases and some other diseases such as cancer., This therapy encompasses the manipulation of genes and the correction of defective, genes. During this process genes are inserted, deleted or modified. One of the most, common forms of gene therapy is the incorporation of functional genes into an, unspecified genomic location in order to replace a mutated and dysfunctional gene., Pharmacogenomics and genetic testing both use techniques of red biotechnology, that are individual-specific. In pharmacogenomics the genetic information of the, individual is derived, and drugs are developed that can be inserted into that, particular individual, whereas in genetic testing different tests are conducted among, family members to determine genetic diseases, sex and carrier screening. It can also, be used in paternity disputes. Monoclonal antibodies, DNA and RNA probes are, used for the diagnosis of various diseases and valuable drugs such as insulin and, interferon have been synthesized by bacteria for the treatment of human diseases., DNA fingerprinting is utilized for the identification of parents and criminals. The, development of recombinant vaccines for diseases such as human hepatitis B using, genetically engineered microbes is one of the list of notable achievements., 1.4.2 Industrial biotechnology, Industrial biotechnology was established for the large-scale production of alcohol, and antibiotics by micro-organisms. Currently, various pharmaceutical drugs and, chemicals such as lactic acid, glycerine, etc, are being produced by genetic, , 1-28

Page 30 : Introduction to Pharmaceutical Biotechnology, Volume 1, , engineering for better quality and quantity. Biotechnology has provided us with a, very efficient and economical technique for the production of a variety of, biochemicals, e.g. immobilized enzymes. Protein engineering is another important, area where existing proteins and enzymes are remodeled for a specific function or to, increase the efficiency of their function., 1.4.3 Biotechnology and the environment, Environmental problems such as pollution control, the depletion of natural, resources for non-renewable energy, conservation of biodiversity, etc, are being, dealt with using biotechnology. For example, bacteria are being utilized for the, detoxification of industrial effluents, to combat oil spills, for treatment of sewage, and for biogas production. Biopesticides offer an environmentally safer alternative, to chemical pesticides for control of insect pests and diseases., 1.4.4 Biotechnology and agriculture, Currently the potential of plant tissue culture is widely utilized for the rapid and, economic clonal multiplication of fruit and forest trees, for the production of virusfree genetic stock and planting material, as well as in the creation of novel genetic, variations through somaclonal variation. With the aid of rDNA technology, it has, now become possible to produce transgenic plants with desirable genes such as, herbicide resistance, disease resistance, increased shelf life, etc. Techniques such as, molecular breeding have been employed to accelerate the process of crop improvement. For instance, molecular markers, such as restriction fragment length polymorphism (RFLP), and simple sequence repeats (SSRs) provide potential tools for, the indirect selection of both qualitative and quantitative traits, and also for, studying genotypic diversity., , 1.5 Biotechnology techniques, Some of the basic tools that are frequently experimented with in biotechnology to, explore surrounding applications are listed in table 1.4., 1.5.1 Bioreactors, In earlier times bioreactors were used for centuries to make wine and beer. The, bioreactor is possibly the most important single piece of equipment used in, biotechnology. Bioreactors are the containers or vessels that allow biological, processes to take place under optimum conditions. These reactors, in controlled, environments, will yield a useful substance in large amounts., 1.5.2 Cell fusion, This technique involves the fusion of two cells to make a single cell that contains all, the genetic material of the original cells. So far, this technique has been employed to, create new plants by fusing cells from species that do not naturally hybridize (from a, cross-breed) and then generating whole plants from the fused cells., 1-29

Page 31 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Table 1.4. Basic techniques used in biotechnology., , Techniques, , Description, , Genetic engineering (rDNA), technology, , The use of cellular enzymes to manipulate DNA; transferring, DNA between unrelated organisms, , Protein engineering technology, , Used to improve existing/create novel proteins to make useful, products, , Antisense or RNAi technology, , Can block or decrease the production of certain proteins, , Cell and tissue culture, technology, , Growing cells/tissues under laboratory conditions to produce, an entire organism, or to produce new products, , Bioinformatics technology, , Computational analysis of biological data, e.g. sequence, analysis macromolecular structures, high-throughput, profiling data analysis, , Protein separation and, identification techniques, , Contour-clamped homogeneous electric field gel, electrophoresis, Agarose gel electrophoresis, Vertical pulse field gradient electrophoresis, Pulsed field electrophoresis, Polyacrylamide gel electrophoresis, Microarray, Isoelectric focusing, Field inversion gel electrophoresis, Two-dimensional (2D) gel electrophoresis, , Blotting techniques, , Nucleic acid blotting, Southern blot analysis, Protein blotting, Northern blot analysis, Dot blot technique, Autoradiography, , Sterilization techniques, , Steam sterilization, Ultraviolet sterilization, Flame sterilization, Filter sterilization, Dry sterilization, Chemical sterilization, Alcohol sterilization, , PCR-based techniques, , Single-nucleotide polymorphism, Targeted PCR and sequencing, SSRs or microsatellites, Sequence-targeted microsatellites, Sequence-related amplification polymorphism, Sequence-characterized amplified regions, Sequence-specified amplified polymorphism, Selective amplification of microsatellite polymorphic loci, , 1-30

Page 32 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Retrotransposon-based markers, Retrotransposon microsatellite-amplified polymorphism, Retrotransposon-based insertional polymorphism, Random amplified polymorphic DNA, Random amplified microsatellite polymorphism, Microsatellite-directed PCR: unanchored primers, Microsatellite-directed PCR: anchored primers, Inter-retro transposon amplified polymorphism, DNA amplification fingerprinting, Cleaved amplified polymorphic sequences, Arbitrarily fragmented length polymorphism, Gene transfer techniques, , Chemical methods, • Calcium phosphate co-precipitation, • Polycation-DMSO technique, • PEG-mediated transformation, • DEAE-dextran procedure, Physical methods, • Ultrasound-mediated gene transformation, • Silicon carbide fiber-mediated transformation, • Microinjection, • Macroinjection, • Liposome-mediated method, • Electroporation, • Biolistics/particle bombardment/microprojectile, • Virus-mediated gene transfer, • Bacteria-mediated gene transfer, • Agrobacterium-mediated gene transfer, , Miscellaneous techniques, , Protoplast fusion techniques, transposon tagging in, heterologous species, techniques used for single-cell cultures, (Bergmann cell plating technique), immobilization, techniques, artificial seed technology, chromosome, elimination techniques, rDNA technology,, spectrophotometry (quantitation, enzyme kinetics), nucleic, acid purification and molecular weight determinations, cell, separation methods, protein separation and quantitation,, liquid scintillation (double label) counting, autoradiography, (cellular and gross), restriction enzyme mapping, gene, expression and oligonucleotide synthesis, , 1.5.3 Liposome-based delivery, Liposomes are microscopic spherical structures that develop when lipids form a, suspension in water. These spherical vesicles arrange themselves so as to generate a, tiny space inside the center of the liposome. Such space can potentially be exploited, to deliver/transport another substance, such as a drug. Liposomes have important, , 1-31

Page 33 : Introduction to Pharmaceutical Biotechnology, Volume 1, , applications in biotechnology since they may offer novel means of transporting, certain drugs to particular parts of the body across the biological membranes, e.g., peptides could be encapsulated in liposomes and transported across biological, membranes., 1.5.4 Cell or tissue culture, This technique allows the growth and division of individual cells in a bath of sterile,, nutritive fluid which often contains hormones and growth substances. This method, is used extensively in biological laboratories, for example, in cancer research, plant, breeding and routine analysis of chromosome karyotopes. The whole process is, conducted in an in vitro environment by providing a suitable culture medium that, contains a mixture of nutrients either in solid form or in liquid form., 1.5.5 Genetic engineering, The basis of genetic engineering is the alteration of genetic material (hereditary, material) or the combination of genes in an organism. By modifying the organism,, genetic researchers give the organism and its descendants different traits. This, technology was practiced in earlier times by breeding plants and animals to produce, favorable combinations of genes. By using this technology, ‘genetic engineers’ have, produced most of the economically important varieties of flowers, vegetables, grains,, cows, horses, dogs and cats. During the 1970s and 1980s, researchers established, ways to isolate individual genes and reintroduce them into cells or into plants,, animals or other organisms., 1.5.6 DNA fingerprinting, DNA fingerprinting is a technique that is employed for identifying the components, of DNA (the material of the genes) that are unique to a particular individual., Variations in DNA among different individuals can be used for identification, purposes. This small section of the DNA of an organism uniquely distinguishes that, particular organism from all others. Such varying bits of genetic material take the, form of sequences of DNA called mini-satellites, which are repeated several times., The number of repetitions of mini-satellites per region of a gene can vary enormously, between unrelated individuals., 1.5.7 Cloning, The method of production of identical animals, plants or micro-organisms from a, single individual is known as cloning. In other words, it is a process by which an, organism is derived from a single parent through non-sexual reproduction. Cloning, is gifted in nature to those organisms that reproduce asexually and produce their, own clones, e.g. plants, micro-organisms and simple animals such as corals., However, mammals reproduce sexually, and cannot clone naturally since the, descendant of a mammal inherits its genetic material not from one parent but half, from each parent. Hence, the offspring produced is never an identical copy of either, 1-32

Page 34 : Introduction to Pharmaceutical Biotechnology, Volume 1, , of its parents. In nature, clones from mammals are confined to the production of, identical twins., 1.5.8 Artificial insemination and ET technology, Development in the study of embryology, urology and urogenitology has led to, progress in the area dealing with artificial insemination. Artificial insemination, allows the artificial introduction of semen into the reproductive tract of a female, animal, and is extensively used in breeding animals, such as sheep and cattle. Males, with dominant and desirable hereditary traits/characteristics are selected for semen, collection. Collected semen from males with desirable traits can be frozen and, transported long distances to fertilize female animals. Artificial insemination is also, employed to help women who wish to conceive where normal conception is not, possible., 1.5.9 Stem cell technology, With the advancement of biotechnology, it is now possible to utilize the potential, of stem cells for beneficial purposes. Stem cells are undifferentiated and can, mitotically divide to create mature functional cells, e.g. bone marrow stem cells, can give rise to the entire range of immune system blood cells. Stem cells are found, in most organisms, but are usually found in multicellular organisms. In 1908, Alexander Maksimov coined the term ‘stem cell’, and later stem cell research work, was continued by Canadian scientists Ernest A McCulloch and James E Till in the, 1960s. During this period two extensive types of mammalian stem cells were, discovered: embryonic stem cells that are isolated from the inner cell mass of, blastocysts, and adult stem cells that are found in adult tissues. During the, development of embryos, stem cells can differentiate into all of the specialized, embryonic tissues whereas in adult organisms, stem cells and progenitor cells act as, a repair system for the body, replenishing specialized cells, but also maintaining, the normal turnover of regenerative organs, such as blood, skin or intestinal, tissues. Current research utilizes highly plastic adult stem cells from a variety of, sources, including umbilical cord blood and bone marrow, for various medical, therapies. Advancements in therapeutic cloning allow the development of embryonic cell lines and autologous embryonic stem cells more conveniently and offer, promising candidates for future therapies., The classical definition of a stem cell requires that it possesses two properties:, • Self-renewal or the ability to go through numerous cycles of cell division, while maintaining an undifferentiated state., • Potency or the capacity to differentiate into specialized cell types. Stem cells, can be of the following types:, - Totipotent (in other words, omnipotent) stem cells can differentiate into, any kind of cell type. Such cells can construct a complete, viable,, organism. They are produced from the fusion of an egg and sperm cell., - Pluripotent stem cells come from totipotent cells and can differentiate, into almost all cells, i.e. cells derived from any of the three germ layers., 1-33

Page 35 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Pluripotent adult stem cells are rare and usually small in number but can, originate in a number of tissues including umbilical cord blood. In mice,, pluripotent stem cells are directly produced from adult fibroblast, cultures. Regrettably, mice do not live long with stem cell organs., Most adult stem cells are lineage-restricted (multipotent) and are, normally referred to by their tissue origin., - Multipotent stem cells can differentiate into a number of cells, however, only into those of a closely connected family of cells. Multipotent stem, cells are also originated in amniotic fluid. These stem cells are very, active, expand broadly without feeders and are not tumorigenic., Amniotic stem cells are multipotent and can differentiate into cells of, osteogenic, myogenic, endothelial, adipogenic, hepatic and also neuronal, lines., - Oligopotent stem cells can be distinguished into only a few cells, such as, lymphoid or myeloid stem cells., - Unipotent cells can offer only one cell type, their own; but they have the, property of self-renewal., The potential of stem cells can be demonstrated in vitro by means of methods such as, clonogenic assays, in which single cells are characterized by their ability to differentiate and self-renew. Also, stem cells can be isolated based on a distinctive set of, cell surface markers. However, in vitro culture conditions can alter the behavior of, cells, making it unclear whether the cells will behave in a similar manner in vivo., Considerable debate exists as to whether some proposed adult cell populations are, truly stem cells. The term ‘adult stem cell’ refers to any cell which is found in a, developed organism that has the properties of a stem cell. Also known as somatic, stem cells and germline (giving rise to gametes) stem cells, they can be found in, children, as well as adults. Adult stem cell treatments have been successfully used for, many years to treat leukemia and related bone/blood cancers through bone marrow, transplants. Adult stem cells are also used in veterinary medicine to treat tendon and, ligament injuries in horses. Stem cell transplantation was first used in the treatment, of blood disorders and it was a breakthrough. Conventionally known as bone, marrow transplantation, the stem cells responsible for the production of blood cells, reside in the bone marrow, a special tissue inside the cavity of the bones. The blood, cells originate in the bone marrow from a parent cell or the ‘stem cell’. The blood, stem cell is given simply as an intravenous infusion like a blood transfusion. The, stem cells will automatically find their way home to the bone marrow. They will, replace the patient’s diseased marrow to give healthy blood cells. The best donors, would be siblings of the patient, a twin or extended family members. Unrelated, donors may also be used., , 1.6 Applications of biotechnology, The enormous potential of biotechnology is exploited to yield high therapeutic, compounds (table 1.5)., , 1-34

Page 36 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Table 1.5. List of biotechnological products explored from 1938 to 1998., , Year, 1938, 1940–1945, 1943–1953, 1977, , 1978, 1982, 1986, 1986, 1987, 1990, , 1994, 1994, 1994, , 1998, , Product, Howard Florey/Ernst Chain, Oxford University, England, isolated penicillin., Large-scale production of penicillin., Cortisone first manufactured in large amounts., Genentech produced somatostatin (human GH-releasing inhibitory factor),, manufactured in bacteria. A recombinant gene was used to clone a protein for the, first time., Harvard researchers produced rat insulin by rDNA., The FDA approved genetically engineered human insulin., Orthoclone OKT3 (Muromonab-CD3) approved for reversal of kidney transplant, rejection., First recombinant vaccine approved—hepatitis., Genentech obtained approval for rt-PA (tissue plasminogen activator) for heart, attacks., Actimmune (interferon 1b) approved for chronic granulomatous disease., Adagen (adenosine deaminase) approved for severe combined immunodeficiency, disease., First genetically engineered food, the Flavr Savr tomato, was approved., Genentech’s Nutropin was approved (GH deficiency)., Centocor’s ReoPro approved for patients undergoing balloon angioplasty., Genzyme’s Ceredase/Cerezyme was approved for Gaucher’s disease (inherited, metabolic disease)., Recombinant GM-CSF was approved (chemotherapy induced neutropenia)., Centocor’s Remicade was approved (monoclonal antibody for Crohn’s disease)., , 1.6.1 Basic applications of biotechnology, There are numerous established applications of biotechnology that are segregated, according to their respective defined areas, as shown in table 1.6., 1.6.2 Most common applications, Some of the most common applications of biotechnology are highlighted below., 1.6.2.1 Cloning, The term cloning describes a number of different processes that can be used to, produce genetically identical copies of a biological entity. The copied material,, which has the same genetic make-up as the original, is referred to as a clone. Various, historical events that led to the development of cloning are listed in table 1.7., , 1-35

Page 37 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Table 1.6. Applications of biotechnology in different areas., , Area, , Applications, , Plant biotechnology, , Transgenic plants, production of secondary metabolite,, production of pathogen-free plants or crop improvement,, production of herbicide-resistant crops, pest-resistant (‘Bt, concept’ pest-resistant transgenic) plants, drought resistance,, flood resistance, salt tolerance, high-yielding GM crops,, nitrogen fixing ability, acidity and salinity tolerance, in vitro, germplasm conservation, genetic variability, in vitro, pollination, induction of haploidy, somatic hybridization,, genetic transformation, molecular pharming, somatic, embryogenesis, organogenesis, phytoremediation, in vitro, plant germplasm conservation, mutant selection, somaclonal, variation, plant genome analysis, hybrid seeds, artificial seeds, , Animal biotechnology, , Biopharmaceuticals: Production of hormones, growth factors,, interferons, enzymes, recombinant proteins, vaccines, blood, components, oligonucleotides, transcription factor-based, drugs, oligonucleotides, Antibiotics, Replacement therapies: Lack of production of normal substances, (factor VIII—missing in hemophilia, insulin), Diagnostics: antibodies, biosensors, PCR, therapeutics, vaccines,, medical research tools, human genome research, development, of biosensors, IVF, ET, Gene therapy, Stem cell therapy, Animal tissue culture: Cell, tissue and organ culture, Gene cloning: rDNA technology, genetic engineering, transgenic, animals, antibiotics, DNA markers, animal husbandry,, xenotransplantation, medical biotechnology, Therapeutics: Natural products such as from the foxglove, (Digitalis, heart conditions) and yew tree (cancer agent, taxol), for breast and ovarian cancers, endogenous therapeutic agents, i.e. proteins produced by the body that can be replicated by, genetically engineering, tPA—tissue plasminogen factor, (dissolves blood clots), biopharmaceuticals (drug or vaccine, developed through biotechnology), therapeutants, i.e. products, used to maintain health or prevent disease, biopharming, i.e., production of pharmaceuticals in cultured organisms, certain, blood-derived products needed in human medicine can be, produced in the milk of goats, Biopolymers and medical devices: natural substances useful as, medical devices: hyaluronate, an elastic, plastic-like substance used, to treat arthritis, prevent post-surgical scarring in cataract surgery,, used for drug delivery, adhesive substances to replace stitches, , 1-36

Page 38 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Designer drugs: Using computer modeling to design drugs, without the lab-protein structure, Evolutionary and ecological genomics: Finding genes associated, with ecological traits and evolutionary diversification., Common goals are health and productivity, Agricultural biotechnology, , The applications of animal biotechnology, crop biotechnology,, horticultural biotechnology, tree biotechnology, food, processing, plant biotechnology (photosynthesis improvers,, bio-fertilizers, stress-resistant crops and plants, bio-insecticides, and biopesticides), food biotechnology, Food: Increased milk production, leaner meat in pork, growth, hormones in farm-raised fish that result in earlier market-ready fish, Pharmaceuticals: Animals engineered to produce human proteins, for drugs, including insulin and vaccines, Breeding disease tolerance, exact copies of desired stock,, increased yields, Health: Micro-organisms introduced into feed for beneficial, purposes, diagnostics for disease and pregnancy detection,, animals engineered to produce organs suitable for, transplantation into humans, , Environmental biotechnology, , Environmental monitoring: Diagnosis of environmental, problems via biotechnology, Waste management: Bioremediation is the use of microbes to, break down organic molecules or environmental pollutants, Pollution prevention: Renewable resources, biodegradable, products, alternative energy sources, , Fuel and fodder, , Provides a clean and renewable alternative to traditional fossil, fuels, the burning of which contributes to global warming, Tissue culture technique offers rapid afforestation of degraded, forests and regeneration of green cover, Biotechnology could play an important role in three ways in the, productivity of biomass, Can be used to generate methane, , Industrial biotechnology, , Metabolite production (acetone, butanol, alcohol, antibiotics,, enzymes, vitamins, organic acids), anaerobic digestion (for, methane production), waste treatment (both organic and, industrial), production of bio-control agents, fermentation of, food products, bio-based fuel and energy, industrial, microbiology, biotechnology in the galvanizing industry,, recovery of metals and minerals, bioethanol, bioconversion of, synthesized gas to liquid fuels such as methanol, using bacteria, to remove byproducts, pulp and paper, sugars from starches,, animal feed, food, textiles and leather, pharmaceuticals, an, enzymatic process for producing antibiotics, (Continued), , 1-37

Page 39 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Table 1.6. (Continued ), , Area, , Applications, , Aquatic biotechnology, , Aquaculture, restoring and protecting marine ecosystems,, improving seafood quality, environmental remediation, marine, byproducts for human health, biomaterial and bioprocessing,, marine molecular biotechnology, , Table 1.7. The timeline of cloning., , Year, , Cloning event, , 1885, 1901, , First ever display of artificial embryo twinning., Cloning hypothesized: Hans Spemann splits a two-celled newt embryo into two, parts, effectively producing two larvae. (Later, in 1938, Spemann hypothesized, that animals could be cloned by fusing an embryo with an egg cell.), Artificial embryo twinning in a vertebrate achieved., It was found that the cell nucleus regulates embryonic development., First thriving nuclear transfer (frog)., Nuclear transfer from a differentiated cell (frog)., Term ‘clone’ coined: John Burdon Sanderson Haldane used ‘clone’ in his speech on, the biological potential for the human species over the next ten thousand years., First cloned fish: Tong Dizhou, an embryologist from China, developed the world’s, first cloned fish by incorporating the DNA from a cell of a male carp into an egg, from a female carp., Stanley Norman Cohen and Herbert Boyer discovered the tool of DNA cloning,, which copies genes to facilitate their transplantation between various biological, species., First mammalian embryo produced by nuclear transfer (rabbit)., First transgenic (genetically modified) mouse., Giant mouse created by transferring GH genes from a rat., First mammal produced by nuclear transfer (sheep)., First transgenic domestic animal, a pig., A sequence of transgenic mice developed carrying human genes., Nuclear transfer from an embryonic cell (cow)., Transgenic pig hearts made: researchers discover transgenic pig hearts that endure, up to 30 h when transplanted to baboons. The FDA sanctions the use of, transgenic pig livers as bridge organs for transplant candidates awaiting organs., Nuclear transfer from laboratory cells (sheep)., The birth of the first cloned animal, Dolly the sheep, was proclaimed., First primate engineered by embryonic cell nuclear transfer (rhesus monkey)., Cloning of a transgenic lamb (Polly) from cells engineered with a marker gene and a, human gene was announced. In this fashion, the genetic alteration of a lamb was, combined with the techniques of cloning, thereby generating animals that produce, a new protein., , 1902, 1928, 1952, 1958, 1963, 1963, , 1973, , 1975, 1980, 1982, 1984, 1985, 1987, 1987, 1995, , 1996, 1996, 1997, 1997, , 1-38

Page 40 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1997, 1998–1999, 2000, 2000, 2000, 2001, 2001, , 2001, 2001, , 2002, 2002, 2002, , 2003, , 2003, 2006, 2007, 2013, , Nuclear transfer from genetically engineered laboratory cells (sheep)., Additional mammals cloned by somatic cell nuclear transfer (mice, cows and goats)., First pigs cloned: PPL Therapeutics clones the first pigs, engineered to create organs, for human transplant., First transgenic pigs cloned: Infigen clones the first transgenic pigs, as a potential, source of organs and tissues for transplant for humans., The Raelian sect claimed it would clone a human within the year., Endangered animals cloned by somatic cell nuclear transfer., A patent was approved to the University of Missouri for a technology for cloning, mammals; the University then licensed the patent to Massachusetts company, Biotransplant. Critics were troubled since the patent application did not prohibit, humans, and specifically mentioned human eggs. Others challenged that the, patent was for just the process and not the product, although the patent says it, covers ‘cloned products’., Human clones banned in England: the Human Reproductive Cloning Act was, passed, barring the implanting of cloned embryos in the womb., Researchers produced the first clone of an endangered species: a type of Asian ox, known as a guar. Sadly, the baby guar, which had developed inside a surrogate, cow mother, died just a few days after its birth., US President Bush set up the Council on Bioethics to advise him on issues such as, stem cell research and cloning., Cloning to make body parts: Advanced Cell Technology proclaimed that cells from, cloned cow embryos were employed to cultivate kidney-like organs., CC (Carbon Copy), the first cloned pet: CC is not a phenotypic copy of the animal, she was cloned from. A number of people have expressed interest in having their, deceased pets cloned in the hope of getting a similar animal to replace the dead, one. But as demonstrated by CC the cloned cat, a clone may not turn out precisely, like the original pet whose DNA was employed to create the clone., Cloning approved for research purposes: the Kentucky House Judiciary Committee, banned reproductive cloning but permitted cloning for research purposes. The bill, would make the shipping or use of cloned embryos for reproductive purposes a, crime punishable by 10–20 years in prison, as well as requiring those conducting, cloning research to record it with the state Cabinet for Health Services 30 days, before commencement of research., An endangered type of ox, called the Banteg, was successfully cloned., A pig was developed to generate omega-3 fatty acids via the incorporation of a, roundworm gene., Primate (rhesus monkey) embryonic stem cells developed by somatic cell nuclear, transfer., Human embryonic stem cells developed by somatic cell nuclear transfer., , 1.6.2.1.1 Reproductive cloning, This involves constructing an egg using genetic material from another source. The, egg then develops into an embryo, before being planted in a female host’s uterus to, continue to develop. Reproductive cloning produces copies of whole animals., , 1-39

Page 41 : Introduction to Pharmaceutical Biotechnology, Volume 1, , 1.6.2.1.2 DNA/gene cloning, DNA cloning is a simpler method, whereby DNA is extracted from a host then, replicated using plasmids. Even individual genes can be cloned in this manner. Gene, cloning produces copies of genes or segments of DNA. A simple demonstration of, gene cloning is shown in figures 1.2 and 1.3., , Figure 1.2. Gene cloning for the production of pharmaceutical compounds., , Figure 1.3. rDNA, gene cloning and pharmaceutical production. In this mature and widely utilized, biotechnology, DNA can be cut at specific sequences using restriction enzymes. This creates DNA fragments, useful for gene cloning. Restriction enzymes are enzymes that cut DNA only at particular sequences. Different, restriction enzymes have different recognition sequences. This makes it possible to create a wide variety of, different gene fragments. Then, DNA cut by a restriction enzyme can be joined together in new ways. These, are known as rDNAs and they often are made of DNAs from different organisms. Ultimately this results in, new recombinant DNA with different sequences., , 1-40

Page 42 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.4. Therapeutic cloning from embryonic cells., , 1.6.2.1.3 Therapeutic cloning, This type of cloning is similar to reproductive cloning, except that stem cells are, extracted from the embryo and used to treat the host. This type of cloning has many, medical benefits for treating all sorts of diseases but is highly controversial because, of the destruction of the embryo following stem cell extraction. A simple demonstration of therapeutic cloning is shown in figure 1.4. Therapeutic cloning produces, embryonic stem cells for experiments aimed at creating tissues to replace injured or, diseased tissues. The inner cell mass (ICM) is the source of embryonic stem cells. The, embryo is destroyed by separating it into individual cells for the collection of ICM, cells. Stem cells are found in adults, but the most promising types of stem cells for, therapy are embryonic stem cells., In the context of cell replacement therapy, therapeutic cloning holds huge potential, for de novo organogenesis and the permanent treatment of incurable diseases such as, Parkinson’s disease, Duchenne muscular dystrophy and diabetes mellitus, as shown by, in vivo studies. Major obstacles obstructing advancement in therapeutic cloning are, tumorigenicity, epigenetic reprogramming, mitochondrial heteroplasmy, interspecies, pathogen transfer and low oocyte availability. Moreover, therapeutic cloning is also, often tied to ethical considerations concerning the source, destruction and moral, status of IVF embryos based on the argument of potential. Legislative and funding, issues also need to be addressed. Future considerations would include a distinction, between therapeutic and reproductive cloning in legislative formulations., 1.6.2.1.4 Applications, Reproductive cloning may enable researchers to make copies of animals with, potential benefits for the fields of medicine and agriculture. Since the announcement, of Dolly the sheep by Scottish researchers, other sheep have been genetically, modified to produce milk that contains a human protein essential for blood clotting., This research was conducted to derive the protein from the milk for humans whose, blood does not clot properly. This, along with many other studies, exemplifies the, , 1-41

Page 43 : Introduction to Pharmaceutical Biotechnology, Volume 1, , possibilities of cloned animals for testing of new drugs and treatment strategies. The, main motivation for using cloned animals for drug testing is that they are all, genetically identical. This means their responses to the drugs should be uniform, rather than variable as seen in animals with different genetic make-ups., In 2008, the FDA decided that meat and milk from cloned animals, such as cattle,, pigs and goats, are as safe as those from non-cloned animals. This decision means, that researchers are now free to use cloning methods. These methods can be used to, make copies of animals with desirable agricultural traits, such as high milk, production or lean meat. However, because cloning is still very expensive, it will, likely take many years until food products from cloned animals actually appear in, supermarkets. Moreover, cloning can also be utilized to create clones to build, populations of endangered, or possibly even extinct, species of animals. During the, era of genetic engineering most of the research has been focused towards transgenesis using rDNA and cloning as a basic tool for the procurement and maximum, utilization of elite traits., 1.6.2.2 DNA fingerprinting, Different individuals carry different alleles. Most alleles useful for DNA fingerprinting, differ on the basis of the number of repetitive DNA sequences they contain. If DNA is, cut with a restriction enzyme that recognizes sites on either side of the region that, varies, DNA fragments of different sizes will be produced. A DNA fingerprint is made, by analyzing the sizes of DNA fragments produced from a number of different sites in, the genome that vary in length. The more common the length variation at a particular, site and the greater the number of sites analyzed, the more informative the fingerprint., A simple demonstration of DNA fingerprinting is illustrated in figure 1.5., The techniques used in DNA fingerprinting also have applications in paleontology, archaeology, various fields of biology and medical diagnostics. In biological, classification, it can help show evolutionary change and relationships on the, molecular level, and it has the advantage of being useable even when only very, small samples, such as tiny pieces of preserved tissue from extinct animals, are, available. In criminal investigations, the DNA fingerprint of a suspect’s blood or, other body material is compared to that of the evidence from the crime scene to see, how closely they match. The technique can also be used to establish paternity. DNA, fingerprinting is generally regarded as a reliable forensic tool when done properly,, but some scientists have called for wider sampling of human DNA to ensure that the, segments analyzed are indeed highly variable for all ethnic and racial groups. It is, possible to create false genetic samples and use them to misdirect forensic investigators, but if those samples have been produced using gene amplification, techniques they can be distinguished from normal DNA evidence., 1.6.2.2.1 Applications, Personal identification. This is the idea of keeping everyone’s DNA on a computer as, a bar code. This concept has been discussed and has been decided to be impractical, and very expensive. It is very unlikely to become a system in general use. Photo, identification cards and social security numbers, for instance, are much more, efficient methods of identification and are not likely to change., 1-42

Page 44 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.5. DNA fingerprinting. Step 1: A site is chosen with three alleles useful for DNA fingerprinting. DNA, fragments of different sizes will be produced by a restriction enzyme that cuts at the points shown by the, arrows. Step 2 to step 4: The DNA fragments are separated on the basis of size. The technique is gel, electrophoresis. Step 5: Separated DNA pieces are transferred on a membrane. Step 6: Six diploid genotypes, are present in the population, possible patterns for a single ‘gene’ with three alleles: in a standard DNA, fingerprint, about a dozen sites are analyzed, with each site having many possible alleles., , Paternity and maternity: This is also a well-known application of DNA fingerprinting. This is the test used to find out who is the father of a baby or child. Every, individual has a variable number tandem repeat (VNTR) pattern which is inherited, from their parents. The pattern in each individual is different but it is similar enough, to reconstruct the parents’ VNTR. This method can also be used to ascertain the real, biological parents of an adopted child or determine legal nationality. Individuals, should be careful when using a test like this because it may have surprising results, that could cause distress., Criminal identification and forensics. This is a very famous field of DNA fingerprinting. It has become popularly known because of the hit TV series CSI: Crime, Scene Investigation. It is a very important use of DNA fingerprinting because it can, prove an individual’s innocence or guilt of committing a crime. To be used, a sample, of DNA has to be obtained from the scene of the crime and matched with the suspect, in question. The two pieces of DNA are then compared through VNTR patterns., Diagnosis and cures for inherited diseases. DNA fingerprinting can also be used to, detect and cure genetically inherited diseases. Using DNA fingerprinting one can, detect genetic diseases such as cystic fibrosis, hemophilia, Huntington’s disease and, many others. If the disease is detected at an early age it can be treated and there is a, greater chance that it can be defeated. Some couples who are carriers of a disease, seek out genetic counsellors who can use a DNA fingerprint to help them understand, the risks of having an affected child and give them information and assistance. The, 1-43

Page 45 : Introduction to Pharmaceutical Biotechnology, Volume 1, , fingerprints can be used by researchers to look for patterns that specific diseases have, and try to figure out ways that they can cure them., 1.6.2.3 rDNA technology, Restriction enzymes are enzymes that cut DNA only at particular sequences, (figures 1.6 and 1.7). Different restriction enzymes have different recognition, sequences. This makes it possible to create a wide variety of different gene, fragments. To harness the power of rDNA technology, human insulin produced, by bacteria plasmids is used to replicate rDNA. Plasmids are small circles of DNA, found in bacteria which replicate independently of the bacterial chromosome. Pieces, , Figure 1.6. Role of restriction enzyme in rDNA technology., , 1-44

Page 46 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.7. rDNA technology. Step 1: Select specific strains of bacteria. Step 2: Isolate the plasmid from the, bacteria. Step 3: Cut with restriction enzyme. Step 1a: Isolate human cells containing GOI that codes for the, synthesis of protein of interest and grow in tissue culture. Step 2a: Isolate DNA from human cells, cut with same, restriction enzyme. Step 3a: Allow the insertion of GOI into plasmid to form recombinant plasmid. Step 4:, Transformation of plasmid in bacteria. Step 5: Allow to grow them on culture medium. Step 6: Multiple bacterial, clones are screened for their GOI expression to produce protein. Step 7: Allow mass propagation of the new, bacteria. Step 8: Isolate and purify human protein such as insulin and develop formulations such as Humulin., , of foreign DNA can be added within a plasmid to create a recombinant plasmid., Replication often produces 50–100 copies of a recombinant plasmid in each cell. The, route to the production of human insulin by bacteria is shown in figure 1.7., Genetically modified plants have generated a large amount of interest in recent, years and continue to do so. In spite of this, the general public remains largely, uninformed of what a genetically modified (GM) plant actually is or what merits and, demerits the technology has to offer, particularly with a view to the range of, applications for which it can be used. From the first generation of GM crops, two, major areas of concern have appeared, specifically danger to the environment and, hazards to human health. Since GM plants are steadily being established in the, European Union (EU) there is the possibility of increased public concern regarding, potential health issues. While it is now routine for the press to espouse ‘health, campaigns’, the information they publish is often unpredictable and unreliable, compared to the available scientific proof. It is essential to understand the rDNAtechnology-mediated production of transgenic plants (figure 1.8)., 1.6.2.4 Stem cell therapy, A stem cell is an undifferentiated, dividing cell that gives rise to a daughter cell like, itself and a daughter cell that becomes a specialized cell type (figure 1.9)., , 1-45

Page 47 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.8. rDNA technology-based production of transgenic plant., , Figure 1.9. Stem cell and its development., , 1.6.2.4.1 Applications, Stem cells can be used to study development, i.e. they may help us understand how a, complex organism develops from a fertilized egg. In the laboratory, scientists can, follow stem cells as they divide and become increasingly specialized, making skin,, 1-46

Page 48 : Introduction to Pharmaceutical Biotechnology, Volume 1, , bone, brain and other cell types. Identifying the signals and mechanisms that, determine whether a stem cell chooses to carry on replicating itself or differentiates, into a specialized cell type, and into which cell type, will help us understand what, controls normal development. Some of the most serious medical conditions, such as, cancer and birth defects, are due to abnormal cell division and differentiation. A, better understanding of the genetic and molecular controls of these processes may, yield information about how such diseases arise and suggest new strategies for, therapy. This is an important goal of stem cell research., Stem cells have the ability to replace damaged cells and treat disease. This, property is already used in the treatment of extensive burns, and to restore the blood, system in patients with leukemia and other blood disorders. Stem cells may also hold, the key to replacing cells lost in many other devastating diseases for which there are, currently no sustainable cures. Today, donated tissues and organs are often used to, replace damaged tissue, but the need for transplantable tissues and organs far, outweighs the available supply. Stem cells, if they can be directed to differentiate, into specific cell types, offer the possibility of a renewable source of replacement cells, and tissues to treat diseases including Parkinson’s, stroke, heart disease and diabetes., This prospect is an exciting one, but significant technical hurdles remain that will, only be overcome through years of intensive research., Stem cells can be used to study disease. In many cases it is difficult to obtain cells, that are damaged by a disease and to study them in detail. Stem cells, either carrying, the disease gene or engineered to contain disease genes, offer a viable alternative., Scientists could use stem cells to model disease processes in the laboratory, and, better understand what goes wrong., Stem cells could provide a resource for testing new medical treatments. New, medicines could be examined for safety on specialized cells generated in large, numbers from stem cell lines—reducing the requirement for animal testing. Various, types of cell lines are already used in this way. Cancer cell lines, for example, are, used to screen potential anti-tumor drugs., , 1.7 Biotech research: 2015–2016, There now follows an overview of the most recent discoveries in biotechnology., Genetic modification is an alternative for incorporating new traits or producing, elite varieties, particularly in crops and trees. These superior varieties of plants have, socio-economic and environmental advantages. However, complex and lengthy EU, protocols are delaying their introduction to the market [69]. Considering GM, development, scientist’s state that Europe has not acquired a leading position in the, global GM market and that Europe is lagging behind in worldwide GM developments, and they call for a more technically authentic decision-making process., In another study scientists have produced microbes that cannot ‘run away from, home’. Swarmbots are the microbes engineered by rDNA technology from, genetically engineered bacteria, and could be useful in various fields. Current reports, suggest a platform technology (microbial swarmbot) which employs a spatial, arrangement to regulate the growth dynamics of engineered bacteria. This scheme, , 1-47

Page 49 : Introduction to Pharmaceutical Biotechnology, Volume 1, , can stop GM organisms from escaping into the surrounding environment and, additionally it can often encourage colonies of bacteria to react to changes against, surrounding environment [70]., Current researchers have also discovered an effective method of gene transfer, which involves culturing and transfecting of cells with genetic material on an array, of carbon nanotubes. This innovation has overcome the drawbacks of other gene, editing techniques. In this study researchers were more focused on the structure of, regulatory sequences in DNA is packaged in a cell [71]., Recent transfection approaches have considerable limitations, as most of them, are time consuming, cytotoxic, have inefficient introduction of test molecules into, target cells and are limited by the size of the genetic cargo. Golshadi et al [71], developed a novel approach of inserting genes and biomolecules into tens of, thousands of mammalian cells. This was achieved using hollow carbon nanotubes,, manufactured by template-based nanofabrication processes, to achieve rapid highefficiency transfer with low cytotoxicity, which will ultimately overcome the, molecular weight limits of recent approaches. In addition to nucleic acids this, approach can be utilized to deliver drugs or proteins. We have hypothetically, demonstrated this approach in figure 1.10., Wrapping of histone by nuclear DNA to form nucleosomes limits the binding of, transcription factors to gene regulatory sequences. Iwafuchi et al used low and high, levels of micrococcal nuclease digestion to evaluate the nucleosomal configuration in, mouse liver and finally discovered that MNase-accessible nucleosomes are present, more at liver-specific enhancers than at promoters and ubiquitous enhancers, , Figure 1.10. Novel approach of incorporating nucleic acids in ten thousand mammalian cells [71]., , 1-48

Page 50 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.11. MNase-accessible nucleosomes to assess the nucleosome configuration in mouse liver [72]., , (figure 1.11). [72]. They have concluded that as pioneer factor FoxA displaces linker, histone H1, nucleosomes are not solely repressive to gene regulation when they are, retained with, and exposed by, pioneer factors [72]., In another study, a comprehensive molecular investigation (transcriptional, mapping of human embryo) of the embryo’s first week of development has been, carried out [73]. In this study transcriptional mapping of human embryo development, including the sequenced transcriptomes of 1529 individual cells from 88, human preimplantation embryos, are presented. They report that there are considerable differences in embryonic development between humans and mice., The Hydra (freshwater polyp) is capable of restructuring a complete creature, from any piece of its body. It has been observed that Hydra remains alive when all its, neurons have gone. Hydra constantly differentiate a sophisticated nervous system, made of interstitial stem cells. Wenger et al describe the impact of the loss of, neurogenesis in Hydra by performing transcriptomic profiling at five positions along, the body axis [74]. They have concluded from their study how epithelial cells alter, their genetic program by overexpressing a sequence of genes, of which some are, related to various nervous functions. These epithelial cells improve their sensing, ability when neurogenesis is compromised. This unknown plasticity may represent, the potential of epithelial-like cells in early Planulozoa development [74]., Schaumberg et al have taken genetic engineering to a more advanced level., Currently, various researchers a are developing modular, programmable genetic, circuits that control specific plant functions [75]. Plant synthetic biology ensures, 1-49

Page 51 : Introduction to Pharmaceutical Biotechnology, Volume 1, , enormous scientific benefits, containing the possible advancement of a sustainable, bio-based economy by the prognostic design of synthetic gene circuits. These circuits, are generated from quantitatively characterized genetic parts; nevertheless, this, approach has considerable obstacles in work with plants as it requires time for stable, transformation. Schaumberg co-workers described the quantitative characterization, of genetic parts and circuits for plant synthetic biology, describing how genetic, circuits control specific plant functions [75]., Another breakthrough was based on the determination of microbial growth using, GM fluorescing E. coli cells. This approach works in a similar way to the method, that is adopted to determine population levels of animals in the particular environments [76]. The growth dynamics of microbes is characteristically determined after, observing them directly, or when death is rare. In mammalian gut microbiota,, neither of these conditions holds, thus typical tactics cannot exactly determine the, microbial growth under an in vivo environment. To determine microbial growth, dynamics, Myhrvold et al explored a novel approach, by using distributed cell, division counting (DCDC), that uses the precise segregation at cell division of, genetically encoded fluorescent particles [76]. DCDC can allow the measurement of, microbial growth during antibiotic therapy, gut dysbiosis, infection, or other, situations relevant to human health. GM fluorescing E. coli measures gastrointestinal microbe growth rates (the population) that lives inside mammalian, gastrointestinal tracts., Another major breakthrough was achieved in the field of optogenetics, in, regulating the movement of proteins. Protein regulation in eukaryotes is a very, complex process. One of the key mechanisms for protein regulation is active, nucleocytoplasmic transport. LEXY is a potential optogenetic toolbox with various, applications in synthetic and cell biology. With the help of optogenetic tools it is, possible to control the import of nuclear protein and several reports are already, available on this. Optogenetics is the approach to control well-defined events within, specific cells of living tissue by using genetics and optics. In 2016 Niopek et al, for the, first time, evidenced an approach for spatiotemporal regulation of the export of a, tagged protein using a light-inducible nuclear export system (LEXY) [77]. In this, study light can be utilized to regulate the import/export of proteins from the cell, nucleus and also the activity of proteins in mammalian cells [77] (see figure 1.12)., Tissue engineering is an emerging area that has been attracting considerable, attention from researchers. In an effort to create artificial cartilage tissue, researchers, from Umea University have used cartilage cells from cow knee joints [78]. This novel, approach can be utilized to develop healthy cartilage tissue, and further researchers, could use the findings to develop a treatment, or cure, for osteoarthritis using stemcell-based tissue engineering. In this study, scientists have investigated how cells, (primary bovine chondrocytes), signaling molecules and the artificial support, material for the cartilage-like tissues (neotissues) can collectively work to encourage, tissue regeneration at an injured joint site. This approach offers treatment against, osteoarthritis by using healthy cartilage tissue which contains stem cells [78]. The, next breakthrough was made by researchers at the Harvard Wyss Institute for, Biologically Inspired Engineering and Harvard Medical School, which was based on, 1-50

Page 52 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.12. Application of optiogenetics in regulating the movement of proteins [77]., , R-bodies (retractable protein polymer) polymeric protein inclusions synthesized, inside the cytoplasm of bacteria. One of the most important features of these, proteins that they show structural variation at different pH. At high pH R-bodies, resemble a coil of ribbon whereas at lower pH they undergo a conformational, change and convert themselves into pointy hollow tubes. These hollow tubes are, capable of puncturing through membranes, rupturing the cell membrane and, releasing material present inside. This could offer applications in new drug delivery, and other applications in biotechnology and medicine [79]., Cellular reprogramming is an excellent approach to renew the capacity of selected, tissue to synthesize useful biochemicals inside the body. Scientists have invested, many years to replace the beta cells (insulin-producing pancreatic cells) that are lost, in diabetes. In 2016, Ariyachet et al showed the potential of antral stomach cells, (cells derived from the lower stomach) after reprogramming to produce functional, insulin-secreting cells [80]. In this study Ariyachet and co-workers separated tissue, from mice and after reprogramming cultured them into ‘mini-organs’. These miniorgans produced insulin when transplanted back into the animals under in vivo, conditions (see figure 1.13) [80]., In another study scientists have argued for the compulsory labeling of genetically, modified foods, which is essentially required to let the community, especially, consumers, to know what they are eating. This is based on a broad evaluation of, the global scientific and legal frameworks associated with genetically modified, organisms [81]. Certain producers and manufacturers are afraid of a negative, consumer response to GM labelled products., , 1-51

Page 53 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.13. Cellular reprogramming and development of mini-organs for the efficient production of, biochemicals [80]., , The CRISPR-Cas approach is often used for targeting, regulating, and editing, genomic sequences, it is a potential technique for producing genetically modified, animals. Yoshimi et al developed two new gene modification methods: lsODN (long, single-stranded oligodeoxynucleotide) and 2H2OP (two-hit two-oligo with plasmid)., These approaches use clustered, regularly interspaced, short palindromic repeats, (CRISPR) Cas systems (associated proteins) and single-stranded oligodeoxynucleotides (ssODN) [82]., Opiates have been used from historical times as pain-relieving agents and are, mainly derived from opium poppies. Modification of the alkaloid biosynthetic, pathway to increase the productivity of these alkaloids is difficult as regulation of, biosynthetic pathways in plants is complex. Therefore, current researchers used a, step-wise fermentation approach using engineered strains of E. coli to trigger the, production of thebaine up to a 300-fold increase. According to these researchers, this, enhancement is may be due to the presence of strong activity of enzymes related to, thebaine synthesis from (R)-reticuline in E. coli. These developments in opiate, production using genetically modified E. coli system signify a key step towards, alternative opiate production systems., Emerging novel proteins can be a lead source in the drug delivery industry. The, recent discovery of R-protein in the cytoplasm of bacteria that live inside Paramecia, (tiny aquatic organisms) can possibly be utilized to deliver drugs [84]. To understand, this phenomenon, it is essential to understand the role of R-bodies in Paramecia, as, shown in figure 1.14. Recently researchers have identified that the response of Rbodies present in Paramecia can be manipulated in a pH-dependent manner. These, , 1-52

Page 54 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.14. The role of R-bodies in Paramecia., , proteins are capable of selectively rupturing membrane compartments, thus may be, important for programming cellular compartmentalization [84]., Another work synthesized genetically encoded biosensors for intracellular concentration of a target metabolite. These biosensors are synthesized from transcription factors conjugated with a fluorescent substance to track product formation., By tracking pathways researchers are engineering microbes in highly creative, factories to produce products such as fine chemicals, therapeutics and biofuels [85]., Intestinal parasites infect more than one billion people worldwide, resulting in, malnutrition and developmental issues [86]. Currently two benzimidazoles and two, nicotinic acetylcholine receptor agonists are approved by the WHO. They are, available on the market, however, the development of resistant strains against these, agents urgently required new anthelminthics. Researchers made efforts to develop, Bacillus thuringiensis (Bt) crystal (Cry) proteins to treat intestinal nematode, infections in humans. Cry proteins have been considered as safe for humans. We, have used these proteins from over 50 years as crop insecticides., For the production of these insecticidal proteins (Bt proteins), researchers inserted, genes in the non-toxic bacteria Lactococcus lactis (figure 1.15). This can further help, in integration of this protein in to dairy products, or in the form of probiotics to, further deliver the protein to the intestines of affected people., Another major breakthrough in the year 2015 was that the Joint Research Centre, (JRC) developed a new database called the bioinformatics pipeline or JRC GMOAmplicons, which includes the more than 240 000 DNA sequences emerging in, GMOs [87]. This database will offer a complete source for the detection of DNA, target sequences and also assist in checking the presence of GMOs in food, feed and, the environment. This record is the broadest source of information available and can, , 1-53

Page 55 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Figure 1.15. Specific binding of Cry proteins derived from B. thuringiensis and expression of Bt protein gene in, L. lactis., , help in developing approaches for identifying GMOs in food and feed [88]. DiCarlo, et al, in their study ‘Safeguarding CRISPR-Cas9 gene drives in yeast’ described an, effective safeguarding mechanisms for working with gene drives and unveiled a firstof-its-kind approach for reversing the changes they spread [88]., It was observed that heat shock response is a type of stress which is important in, understanding the biogenesis and degradation of proteins inside the body and it is, equally important to understand cellular death [89]. It is well-known that aging can, increase the risk for protein conformational disease. It was observed that during the, onset of reproductive maturity HSR declines quickly. The suppression was because, of the increase in H3K27me3 marks at stress gene loci. In adult cells, genes start, aging by turning off cell stress responses [89]. These responses protect the cell by, keeping potential proteins folded and functional. During early maturity germ line, stem cells throw the switch and individual cells retain their reproductive capability, [89]. Based on similar work, Yang et al investigated the minimal set of gene, functions required to sustain life in E. coli. This study covers the set of genes required, to sustain life [90]. By using a comparative genomics-based core proteome, minimal, gene lists have been suggested., Embryonic stem cell development is an area of heightened attention today., Recently, several scientists discovered an approach to control embryonic stem cell, differentiation with the help of beams of light. This approach allows them to be, transformed into neurons in reaction to an accurate external sign. In another study,, the complete pathway of endocytosis was described by a team of researchers. In, particular, they studied how cells perform endocytosis by absorbing molecules which, can result in rapid embryonic healing. Considering this factor, the outcomes of the, study can be employed to design better treatments for wounds in adults [92]., , 1-54

Page 56 : Introduction to Pharmaceutical Biotechnology, Volume 1, , Researchers have engineered the cassava plant to offer higher levels of vitamin B6, in its storage roots and leaves. This could help guard millions of people in Africa, against serious deficiencies [93]., Several reports are available on target-based mutagenesis mediated by Cas9, (RNA-guided DNA endonuclease enzyme). Woo et al [94] reported genomic editing, in plants without insertion of foreign DNA into cells. They introduced the Cas9, protein to guide RNA into protoplasts of several plants and achieved targeted, mutagenesis at frequencies of up to 46%. This study may alleviate regulatory, concerns related to genetically modified plants, as the researchers used the Cas9, protein and did not insert foreign DNA., Several reports were published in 2012 and while it is not possible to describe all, of these, some promising research cannot be skipped, such as the research based on, the revolutionary tool for editing DNA (CRISPR), which could replace all medicine, , Figure 1.16. CRISPR technology. The virus incorporates DNA and inserts its DNA into the bacterial DNA,, where the bacterial immune response CRISPR identified this insertion and cut the DNA wherever an insertion, was made, and finally converted it back to healthy DNA., , 1-55

Page 57 : Introduction to Pharmaceutical Biotechnology, Volume 1, , with better treatments. This research was discovered by Jennifer A Doudna, a, biochemist at UC Berkeley, and her collaborator, Emmanuelle Charpentier of the, Helmholtz Centre., In general, CRISPR allows scientists to change DNA and it could allow scientists, to cure diseases. This technology came from a project studying how bacteria fight, against viruses. Some bacteria have an adaptive immune response called CRISPR, that allows then to detect viral DNA and destroy it (figure 1.16). One of the parts of, the CRISPR system, called Cas9, is able to seek out, cut and eventually degrade, viral DNA in a specific way. Doudna and colleagues realized that they could harness, its functions as a genetic engineering tool. Currently this technology is being used in, many parts of the world which Their work suggests that this tool will perhaps, fundamentally change both medicine and agriculture. A number of studies have, repaired defective DNA in mice, e.g. treating genetic disorders. Furthermore, plantbased researchers have used CRISPR to manipulate genes in crops, raising hopes, that it could lead to a better food supply. In 2014, MIT Technology Review called, CRISPR ‘the major biotech discovery of the century’ [95]., Now pharmaceutical companies are showing interest in taking CRISPR to the, next level to produce new drugs in the form of therapeutic proteins. Using CRISPRbased technology can create animal models, treat blood related disorders (easy to, deliver in the blood), correct mutations and have certain clinical applications which, will be seen in future. However, CRISPR technology raises many ethical issues, so, discussion continues on validation and safety concerns. In January 2016, Novartis, declared that it would be using Doudna’s CRISPR technology for its study into, cancer treatments. It intends to manipulate the genes of immune cells so that they, will attack tumors (figure 1.17). Microbes have been using CRISPR to alter their, , Figure 1.17. Out of thousands of studies in 2016, few headlines made such a remarkable contribution to, biotechnology., , 1-56

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