Mutagenesis and its Testing Methods Review Article *O.S. Vivekanandan
Transcription
Mutagenesis and its Testing Methods Review Article *O.S. Vivekanandan
Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online SAMANTHI Mutagenesis and its Testing Methods *O.S. Vivekanandan Dept. of Biotechnology/ Bioinformatics, Vels University, Pallavaram, Chennai – 600 117, India Abstract Mutations are changes in the genetic makeup that can either be small or large, can result in a changed phenotypic expression that can be neutral, beneficial or harmful to the organism. Mutations can be spontaneous or deliberately induced the later having several applications including for industrial biotechnology. Understanding mutagenesis is important for obtaining an insight into the complex gene behavior/function mechanisms. Mutation detection and quantification is enhanced to a great extent by the technological advancements in the cytogenetic and molecular techniques. In this review, the types of mutations and the historical perspectives of mutation analysis are discussed. Also, the various types of mutations, numbering twenty five, including the somatic, germinal and morphological mutations are described. Mutation screening and analysis methods vary in accordance to the nature of mutations and the type of sample material. Here, fourteen different mutagenesis screening methods which can be applied for a variety of samples including plant, animal and malignant tissues are reviewed and discussed. Key words: Mutations, history of mutation research, mutagenesis, mutation types, mutation detection. Introduction Mutations are the genetic alterations either induced or spontaneous in genetic material. Evolutionary advance has been evinced in the study from the identification of the phenomenon itself, technological innovations for its detection both in vivo and in vitro, in selected test systems and general populations. The study of induced mutations had its beginning more than 75 years ago, with the work of Herman Muller (1928), who developed a method for the recognition of mutations that are induced by X-ray in Drosophila. Chemical mutagenesis has received a major thrust during the past decade following 1) the observation of a close association between mutagenecity and carcinogenecity, 2) the amount of exposure of human system to the multitude of chemicals in every day. In recent year's studies in mutation, research entered a new era due to advances made in the screening techniques. This has lead to a significant advancement in the study of chemical mutagenesis. This has warranted undertaking a survey of available literature on mutagenesis. nature, rather than having been small and continuous, may well have been large and discontinuous. de Vries (1900) called these large effects. The mutation theory proposed by de Vries (1900) has formed an alternative to the Theory of Natural Selection put forward by Darwin. de Vries was working with the evening primrose (Oenothera lamarkiana) in which new and strikingly different types of plants occasionally appeared breeding true to the new type. On the basis of this work, that new species would originate as a result of large discontinuous variations or mutations rather than from the gradual accumulation of numerous small hereditary differences in size, shape, color, etc., by natural selection. However, his theory turned to be based on a variety of changes in the genome of Oenothera, including tetraploidy, trisomics, reciprocal translocations and balanced lethal systems. However, these hereditary changes did not represent genetic mutations even though they breed true and remain distinct from parental type. These spurious recombinant mutants in Oenothera are the results of a unique situation not to be found in all species and therefore they cannot serve as a general mechanism for evolution. The mutation research dates back to 1791 when Setch Wright noticed a Norwegian lamb with unequal short legs in his flock of normal legged sheep. Wright thought that it would be worthwhile having a whole flock of short-legged sheep, which could not get over the low stone fence and damage the crop in the adjacent fields. In the successive generations, this trait was transferred and a breed was developed where all sheep had short legs. This character resulted from a change in the hereditary material that occurred in a particular cell. This will be carried in all cells descending from the parent cells. The point mutation was discovered at a time when the science of genetics did not even have its birth. The short legged sheep are known as Ancon breed. Mutation is an unequal phenomenon of interest in the history of science. Throughout the 20th century, mutations have been at the heart of science of heredity. The place of mutants in the history of genetics has been underestimated due to the induction of mutations often entitled a mode of enquiry that included altering the environment partly by means of new tools like radium, X-ray and chemicals. The effect of mutations may be great, or may be so small that refined statistical or genetic methods are needed to detect the difference between mutant types. The field of mutagenesis started in the year 1953, when the structure of DNA was known. The early use of nitrous acid and hydroxylamine as mutagens in eukaryotes, Historical Perspective Received: September 2014 Accepted: September 2014 *Corresponding Author Email:[email protected] In the late 19th century, prior to the discovery of Mendal's work, de Vries and others had put forth a theory, that hereditary changes in 07 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online initiated induced mutagenesis. This lead to the development of methods for the metabolic activation of mutagens by microsomal preparations and the selection of a mutant tester set for the qualitative characterization of the mutagenic activity of chemicals. Today, DNA sequencing has replaced the use of diagnostic mutagens, but studies of this kind formed the foundation of molecular mutation research Genesis of Mutation Research The term mutation is derived from a Latin word 'Mutare' (to change), which was used earlier to describe the changes in hereditary material. During early 1900, investigators in Netherlands (de Vries, 1901) and rediscovered the works of George Mendal. The growth of new science formed the framework for the eventual inquiry into the nature of gene. These scientific innovations prompted to know how the external factors induce changes in the natural genetic order. Most of the early work in this new line of research took place in Europe. Charles Darwin, in his early work on the “Origin of Species by Natural Selection” (1859) used the term 'mutation' to describe the production of variation in organisms. The term mutation was then used widely in the scientific literature. It was difficult to determine when the term mutation was first used in relation to the field of genetics and modern biology. This new word was used by Hugo de Vries during 1886, to denote the appearance of variation in the plant evening primrose (Oenothera lamarkiana) (de Vries 1900 a, 1900 b). Latter, he used this term as the key title word in his volume “The Mutation Theories” in which he gave an elaborate description on the production of morphological changes observed in Oenothera (de Vries, 1901). During 1901, de Vries has proposed, that knowledge on principles of mutation will certainly, in future enable the production of artificial mutation in plants, that is, the creation of better varieties of plants and animals. Auerbach (1976) used the term mutation to describe the changes in quality, quantity and arrangement of genes. During the early years of 1905, the idea of using chemicals to induce mutations began to intrigue investigators. Franz Wolff (1909) and Elizabeth Schiemann (1912), who independently conducted mutation experiments with bacteria and Fungi (Bacillus prodigious and Aspergillus niger) using various oxidizing agents. Many interesting discoveries were being made in the field of genetics in the first three decades of twentieth century. These findings had stimulated, thinking about the artificial induction of mutations. Muller (1928) has showed unequivocally that radiation is a mutagen. He has also developed the concept of 'mutation rate'. This has prompted many researchers to initiate the studies to determine the mutagenecity of chemical compounds. It was finally established that chemicals could induce heritable mutations. Auerbach and Robson (1946) established that chemical warfare agent mustard gas was mutagenic on Drosophila sp. Late in the 1940's, the relationship between mutagenesis and carcinogenesis also began to intrigue some investigators. There is a danger of producing mutations in somatic cells by radiation, which may result in cancers, leukemia etc., in mitotically dividing tissue. SAMANTHI The New Dimensions The genetic toxicology begins its new chapter during 1950's. Barthelmess (1956) had been interested in the mutagenecity of chemicals and had collaborated many publications on this subject. The results of research in genetics within the last two decades call for increased consideration of possible cytogenetic side effects and their consequences in organisms exposed to toxicants. Joshuva (1962) began his studies on the hazardous chemicals to the germ cells of man. During 1950's there was an issue of whether routine toxicity testing should include assays for mutagenecity before approval of the common chemicals that are put to human use. Auerbach (1960) stated that more and more chemicals are used in therapeutics, food processing and other industries; the testing of substances for mutagenic ability will become a necessary protective measures. During 1960's a concern was developed to detect the hazards of chemicals on human health, not only for the present generation but also for those yet unborn. Although it is clearly desirable that mutation research should be carried out on a wide range of organisms as possible, extrapolation to man can be made with the most confidence where they are derived from work with a mammal. The mouse is the mammal offering the most advantages for genetical studies, in addition, a great many mutants are known and the linkage map is fairly well worked out. The most productive method has been derived on mouse system is the specific-locus method that help in assessing the genetic hazards of chemical and physical agents (mutagens). The technique also helps to elucidate the nature of mutation process. The environmental mutagenic society (EMS) had its origin during 1968 headed by Hollaender at USA. The objectives outlined are the encouragement of interest in potential hazard of mutagens in human environment, publication on methodologies of mutagenecity testing, publication of newsletter and formation of register of chemicals tested for mutagenecity in particular system. Thus, officially born EMS has prompted the initiation of staring such societies in other countries. In India, the Environmental Mutagenic Society on India (EMSI) was first started by Dr.Sundram at BARC, Mumbai. This society got affiliation with the EMS of USA. The dedication and hard work of the scientists has provided an excellent list of hazardous chemicals which can induce mutagenesis in human population. Kinds of Mutation - a glimpse Mutation occurs more frequently in large group of genes, which are converted into large chromosomes than in smaller groups, therefore, mutations could occur at random. The mutation process only a mechanical loss or dimination of the gene by deletion of chromosomal material or an increase of the gene may lead to reverse mutations. The gene is an 'ultra microscopic particle'. A large cell contain thousands of genes, a change in a single invisible one of these molecules can profoundly affect the physical and chemical properties and result in new gene composition. The gene molecules are also found to some extent in mitochondria and chloroplast (Muller, 1947). Mutations may either spontaneous or induced; 08 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online accordingly they are termed as spontaneous mutations and induced mutations respectively. The change in genome involving chromosome parts, whole chromosome or whole chromosome sets are called chromosomal mutations or chromosomal aberrations. The chromosomal mutations are proved to be of great significance in applied biology, agricultural, animal husbandry and medicine. The point mutations refer to alterations of single base pairs of DNA to a small number of adjacent base pairs. The point mutations are classified as intragenic suppressor mutations, extragenic suppressor mutations, missence suppressor mutations, frame shift mutations and physical suppressor mutations (Anthony et al., 2000). Spontaneous Mutation Mutations enhance spontaneous induction of chromosome breaks and somatic chromosome mutations. Spontaneous mutation occurs during cell division. Mutagenic damage produced by alkylating agents may get converted to mutant DNA sequences. These chemicals also induce sex linked lethal and somatic reversions in Drosophila. Ahuja and Dhayal (2007) reported that petal spotted spontaneous mutants of four species were identified from the populations of Gossypium hirsutum having three different genotypes. These mutants were found to have some desirable morphological and fiber technological characters. This might be possible as a result of mutation of pigmentation but also other traits. Transgenic cell lines are also useful to analyse the relation between gene mutations and chromosome aberrations. Spontaneous mutations are frequent in meiotic cells, through a process of recombination and are caused by inherent instability in gene expressions. Forward mutations are change away and reverse mutations are change to the wild type allele. These mutations lead to the loss of function of a gene or to new function. The forward mutation is the single nucleotide pair substitution at DNA level or at protein level. I. At DNA Level 1. Transition Atransition is the replacement of a base by another base of the same chemical category. For e.g. purine replaced by purine, pyrimidine is replaced by pyrimidine. 2. Transversion A transversion is the opposite category of the transition, where a base of chemical category is replaced by another base of different chemical category. For e.g. purine is replaced by pyrimidine, pyrimidine replaced by purine. 3. Addition or Deletion Mutation This is a type of mutation where a single base pair addition, deletion or substitution leads to degeneration of the code and existence of translational or termination codons. II. At protein Level 4. Silent substitution Mutation SAMANTHI The mutation changes are coded for an amino acid into another codon for the same amino acid. The alteration of AAA to AAG is not detected and both code for the same amino acid lycine. These alterations are the silent mutation. 5. Non-Sense Mutation These types of mutations have a considerable effect on the function of proteins. The codon from one amino acid is replaced by translation or termination of a codon. It was identified that the HOX AB nonsense mutations in a family with hand – foot genetical syndrome. The stop codon truncates and eliminates or reduces the ability of the protein to bind DNA . 6. Null Mutation This type of mutations are otherwise called nothing mutations. That is in or close to active site of a protein leading to lack of function. This completely abolishes the activity of the gene. 7. Missense Mutation or Synonymous Mutation The codon for one amino acid is replaced by a codon for another amino acid resulting with a substitution of a chemically similar amino acid. This type of mutation has a less severe effect on the function and structure of proteins. 8. Frame shift Mutation Non-sense mutations lead to the premature termination of translation. They have considerable effect on protein function. The lesions are called frame shift mutations. Acridine derivatives, the mutagens induce mutation by suppressing CNG base sequence and results frame shift mutations at these regions. The frame site mutations influenced by T4 DNA polymerase. This plays a variety of role in the metabolic events leading to frame shift mutations by transitions and transversions. The target into for these mutations is the G-C base pairs. Bhatia et al., (2007), detected that a single base change in the putative promoter region of one of the clinical isolates of Mycobacterium tuberculosis that behaves like a gain - of function mutations. Frame shift mutations cause drastic consequences for the protein by adding or removing one or several base sequences. This results with a shift in the frame of DNA base pairs. The carcinogenesis is proven frame shift mutagen. 9. Point Mutation / Gene Mutation Point mutation refers to alteration of single base pairs of DNA or to small number adjacent base pairs. Point mutations are classified into intragenic suppressor mutations, missense suppressor mutations, frame shift suppressor mutations and physiological suppressor mutations. Induction of point mutation in somatic cells in culture can be as quantitative as in microbial systems because a large number of cells are easily obtainable. The data on somatic mutation in mammalian cell cultures both spontaneous and induced will be of particular value when they are compared with the data on mutation frequencies at the same or different loci in vitro somatic mutations itself may play an important role in development, oncology, immune mechanisms and aging. Point mutations affecting the Uid R regulatory gene were sought to investigate the regulation of Uid A. the binding of the regulatory molecule may facilitate the binding of 09 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online the other one in a cooperative process. The Uid R - d mutations do not modify Uxu AB operon expression in a wild type strain contrary to the behavior of Ux UR – d mutations (Curlas Blanco et al, 1986). Gene mutation result in the synthesis of defective enzymes, which have lost their catalyst properties totally or partially. If the enzyme loses its activity, the biochemical reaction leading to the formation of a product may be absent. The product may be a metabolic, needed for growth and hence has to be added from outside. This addition may activate the mutational effect (Sulochana Das, 1981). The 'S' gene region of hepatitis B virus is responsible for the expression of surface antigens and includes the determinant region. The kinds of point mutations were identified within 'S' region. High rate mutations were found in chronic hepatitis patients and their family members (Mehnet Ozaslam et al, 2007). The cause for portal hypertension in Indian populations is due to G 20210 prothrombin gene mutation (Sanjay Sharma et al, 2006). The point mutation in DNA binding domain of mex R gene could be one of the factors contributing to the possible drug resistance in patients having Cornell keratitis (Suman et al, 2006). Mutations in genes trigger cell death and premature ageing disorder. This may also lead to the lung disorders in youngsters. The modified purines, a- amino purines and b- N-hydroxy amino purines are known to cause point mutations in prokaryotes. The vibration in space vehicles is also responsible for inducing point mutations. It causes G-C to A-Tmutations. 10. Somatic Mutations Somatic mutations are not passed on to progeny. Mutations in somatic cells have an impact on the well-being and survival of individuals. Somatic mutations in genes would help to regulate the cell cycle may lead to cancer mutations occur in a special type of genes called proto-oncogenes, resulting from one progenitor cell is called a clone. This is linked with mutagenesis. The external and internal factors mutate the spindle formation induce gene or spindle formation repressor gene. This leads to abnormal proliferation of somatic cells resulting in cancer. 11. Germinal Mutations Germinal mutations occur in germ cells, play an active role in the determination of sex. These mutants are expressed only in the male descendants. The sudden appearance of a novel phenotype in a pedigree where there is no such previous records of such novel appearance is determined through germinal mutations. 12. Morphological Mutations Morphological mutations will affect the outwardly visible properties like color, shape and size of an organism. 13. Lethal Mutations New lethal mutations are recognized by their effects on the survival of organisms. a) Dominant Mutations A dominant mutations offer the great advantage of appearing in the SAMANTHI generation immediately after mutational event, in contrast to recessive, which may be delayed for many generations. b) Dominant lethal Mutations A dominant lethal mutation (DL) is the one, which kills an individual heterozygous for it, carrying it in a single dose. The dominant will have arisen in egg or sperm prior to fertilization and could kill the zygote during development. The primary genetic lesion responsible for dominant lethal mutation is chromosome breakage. The assay can be used to study the problems of interacting both synergetic and antagonistic between known mutagens. In Drsophila melanogaster, ethylmethane sulfonate induced X- linked temperature sensitive lethal and semi-lethal mutants. The temperature sensitive at 15 loci affect the fidelity of mitotic chromosomal behavior in Drosophila (David Smith et al, 1985). The dominant lethal egg may die and disappear without a trace. The uterine tumor kills the placental cell after mitosis or after the implantation of the fertilized egg. There is a potentiality for not developing the process of differentiation that is necessary to produce a fetus. The late fetal death results in subnormal size, and posses restricted development in structures. 14. Conditional Mutations Based on the environmental conditions mutations may be a) restrictive-occurs in certain environment b) permissive-occurs in different environment. 15. Biochemical Mutations Biochemical mutations are identified by the loss or change of some biochemical function of the cells. This will lead to the development and expression of inborn errors of metabolism. Many such losses in function of mutation are found to be recessive and some are dominant. 16. Gain-of -function mutations During these mutations, a kind of new phenotype is produced due to a dominant allele. Mutant genes are used as the probes to disassemble the constituent part of a biological function and to examine their working and interactions (Anthony et al, 2007). 17. Insertional Mutations This method relies on the fact of the exogenous DNA inserted randomly into the genome, can produce mutations if inserted fragment interrupts a gene or its regulatory sequences (Alberts et al, 2002). 18. Chromosomal Mutations The changes in genome involving chromosomal parts, whole chromosomes or chromosome sets are called chromosomal aberration or chromosomal mutations; this is of great significance in applied science. The history of chromosomal mutations can be traced back to 1947, when Auerbach and Robson induced mutational changes in Drosophila by using nitrogen mustered. In India, Swaminathan (1950) used the chemical agent in the improvement of crop plants. 19. X - linked Recessive Mutations If a new mutation occurs in a 'X' chromosome, the chances are 2:1 that it occurs in a female, since she has two 'X' chromosomes. If the mutation occurs in males and the trait is very rare so that the possibility of his wife being a carrier can be regulated, the mutant 10 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online phenotype has virtually no chance of being exposed until the grand children generations. Ashadevi et al, (2005) studied two-eye color and two using mutants in Drosophila species. The x- linked mutations were identified on the typical criss-cross patterns of inheritance of the phenotypes. 20. Autosomal Recession Mutation A recessive autosomal mutant will be expressed only if it is transmitted in gametes from both parents 21. De novo Mutations A new mutation that was not inherited from either parent is called de novo mutation. These mutations, where the effects are not influencing the fitness of an individual, can accumulate due to genetic drift. Mutation is the mechanism upon which natural selection acts, providing the advantages, new traits or disadvantageous traits that die out with weaker organisms. Homeotic mutants are useful in understanding morphogenesis – development and the interplay of environment and genotype. In one example of such mutants, the mosquito proboscis labella are modified. These mosquitoes are not able to pierce skin and obtain blood from the mammalian host (Thomas et al, 1971). 22. Para-mutation Para-mutation is an interaction between alleles that lead to direct the heritable change, at the locus with higher frequency and sometimes invariability within the time span of a generation. The first instance of para-mutation leading to the irregular allelic interaction as observed in rabbit ear region, in Pissum sativum and also at 'R' locus in maize (Alexander Brink, 1973). 23. Mitochondrial Mutations Human ageing depend on the decline of respiratory function heading to the increased production of reaction oxygen species (ROS) and free radicals on mitochondria due to enhanced electron lack of the respiratory chain recently it has been shown that mitochondrion due to enhanced electron lack of the respiratory chain. Recently it has been shown that mitochondrial mutations are also influencing human ageing. The oxidative modification and mutation of mitochondrial DNA (mtDNA) were found to increase exponentially with age in human and animal tissue. Mitochondrial mutations can lead to various syndromes such as CPEO (Chronic progressive external ophthalmoplesia), KSS (Kears-Sayre Syndrome), MERRF (Myoclonic Epilepsy with ragged red fibers), MELAS (Mitochondrial encepahalomyopathy, lactic Acidosis and stroke – like episodes), NARP (Neuropathy, Ataxia and Retinitis Pigmentosa), MNGIE (Myoneurogastro intestinal disorder and encephalopathy), recurrent myoglobinuria due to coenzyme Q 10 deficiency etc., and affecting major organs. Parkinson's and Alzheimer's diseases can also be caused by mtDNA mutations. Recent reports showed that somatic and homoplastic mutations in mtDNA causing multiple neonatal deaths. The mt DNA mutation disease might be caused only when the bearer is exposed to an environmental toxin like amino glycoside induced ototoxicity. The Leigh syndrome is due to the basal ganglionic lesions caused by variations in mitochondrial and nuclear gene. A novel homoplasmic T11984 C missense mutation occurs in ND4 gene, which replaces a SAMANTHI highly conserved amino acid tyrosine with histidine. This mutation alters the secondary structures of ND4 sub unit. Mutation at the DFNBI locus which encode connexin 26 (CX 26) and connexin 30 (CX30), proteins respectively, are main cause for sporadic and familial non-syndromic hearing impairment in many populations. Specific mtDNA mutations have been found to be associated with non-syndromic hearing impairment. Deletion and three point mutations in mtDNA are found to be the cause for these mutations. Oxidative stress is a condition established due to an imbalance between antioxidant levels and reactive oxygen species in variety of diseases like diabetes, cancer, ageing, Alzhmeir, anthrosclerosis, rheumatoid arthritis, multiple sclerosis, muscular dystrophy, cancer, etc., Recently male sterility is also attributed to this condition, might be due to the damage of mitochondrial and DNA (mutation) in the spermatozoa. The excess reaction oxygen species (ROS) and low antioxidant levels in the semen might cause mitochondrial DNA mutations and vice versa in oligoasthenozoospermia men. This result in impairing the fertilizing capacity of spermatozoa (Kunal et al, 2009) Mitochondrial DNA is known for high mutation rates caused by lack of protective histones, inefficient DNA repair systems and continuous exposure to mutagenic effects and oxygen radicals. It was suggested that the extent of mitochondrial DNA mutations might be useful in the prognosis of cancer outcome/and/or the response to certain therapies. The presence of mutations correlated with Human Papilloma virus infection in the patients suffering from cervical carcinoma. Mutations in either mtDNA or nuclear gene encoding oxidative phosphorylation may lead to clinical disorders like mitochondrial encephalomyopathies in pediatric patients. The study will be useful in genetic diagnosis and counseling of mitochondrial disease in men in India. A novel nonsense mutation (CH994T) in the mitochondrial ND 4 gene, which replaces threonine with isoleucine, was observed in all of the oligoastheno zoospermic men but not in any of the normo zoospermic fertile men (Deepa selvi et al, 2006). 24. Cataract Mutation The specific locus mutations, dominant cataract mutations, protein change mutations and enzyme activity mutation are affected by certain physical and chemical factors. 25. Coat Color Mutation in Animals Pioneering studies in this field were carried out at the return of the century by William Castle and two of his students. A series of manuscripts of 1917 and 1918 had showed that the coat color genetics was a useful way “to assist embryology and biochemistry in filling the links between germ cell and adult in specific cases”. Many coat color mutations are available, however a rudimentary knowledge of pigment chemistry and biochemistry provided a basis with which to interpret genetic interaction experiments. For example, it was remarked that there was a reciprocal and genetic relationship between black and yellow coat color in rabbits was due to the different alleles acting at the same locus. This has lead to the conclusion after 50 years of observation that the biochemical process responsible for determining whether hairs were black or yellow acted on a single substrate produced by the product of the albino rats. 11 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online During 1920's, systematic attempts were initiated at several research institutions to catalog and preserve different mutations and in addition to develop inbred, strains of animals so that the effects of different mutations could be studied on a constant genetic background. Most of the knowledge on coat color gene action has come from mice and other mammals have confirmed the principles behind coat color mutations. Many coat color mutations in mice and virtually all those in other mammals are of spontaneous origin. A special class of mutations at a small number of loci has been induced, experiments were designed to measure and characterize genotoxic effects of radiations and chemicals. In many research laboratories, experiments were designed to detect loss of function mutations at one of several different loci. In most mammals other than mice, a small number of loci have been recognized as coat color mutations. A temperature sensitive loss of function mutation in tyrosinase produces a distinctive phenotype known as the “Himalayan Mutations” in rabbits, mice or guinea pigs and also responsible for the characteristic appearance of Siamese coats. Coat color mutations are usually classified based on cellular/ and / or developmental processes that are disrupted, pigment cell differentiation/ migration/survival, biochemical synthesis of melanin intracellular trafficking membrane sorting of pigment granules or pigment type-switching. In mammals, melanin is a complex polymer, derived from oxidized derivatives of tyrosine, and is deposited with in sub cellular organelles called 'melanosomes'. Melanin synthesis requires a series of enzymes for different oxidation steps. A complete loss-of function for tyrosine leads to mutational effect. In mice, mutation in a large class of coat color genes produces a generalized pigment dilution, platelet storage pool deficiency and abnormal lysosomal trafficking. Mutations in several genes can alter pigment type-switching, including the agouti gene itself and melanocortin receptor gene, which encodes the receptor for agouti protein expressed on malanocytes. Most interesting group of coat color mutations are those that cause regular patterns of stripes or spots as in Zebras, Tigers, Leopards, or Giraffes. It is presumed that this is likely to be pheomelanin or eumelanin alternating with number of pigments. In human albinism refers to a generalized dilution or loss of pigmentation and is broadly grouped into conditions that affect eyes, skin and hair, approximately ten different genes were identified to mutate and cause albinism. Coat color variations are due to melanism pigment synthesis in house mice in Asia is described and found to be darker in humid habitats than those in drier habitats. The coat color variations might be due to the selective forces like bacterial degradations and thermoregulation (Lai et al, 2007). Evidence was provided that the expression of the aberrant coat color results from the action of an autosomal recessive mutation in Cheetahs (Acinonyx jubatus) (Van Aande and Arun Van Dyk, 1985). A. Structural changes in Chromosomes I. Changes in number of genes Deletion/ Deficiency A chemical agent induce two breaks in a chromosome may produce interstitial deletions (loss of segments). An intragenic deletion may SAMANTHI occur within a gene or mutagenic deletion will occur due to the breaks in two or several thousand genes. These deletions are responsible for tumor formation or lethal mutations (Anthony et al, 2000). Duplication A structural change in the chromosome produced due to the addition of an extra copy of some chromosome region. Duplications supply additional genetic material capable of evolving new functions. II. Changes in Gene Arrangement Insertion Two breaks occur in a chromosome, and rotate at 180° before rejoining with the two and fragments. Inversions do not change the overall amount of the genetic material, and in the phenotype. Inversion may be peracentric or pericentric. Translocations Two non-homologous chromosomes mutate by exchanging parts, the resulting rearrangements are called translocations. A segment from one chromosome is exchanged with a segment from another non-homologous chromosome. This kind of mutation is of great importance in agriculture since it helps to control insect pests. Reciprocal translocations are also seen in cancer cells Two schools of thought have come to explore the origin of chromosome rearrangements 1. Russian geneticist considered that rearrangements were “illegitimate cross - over” and were formed when two different chromosomes or regions of the same chromosome happened to lie in juxtaposition during the process of mutation. 2. The second school headed by Stadler, assumed that breakage always preceded rearrangement formation at any two broken ends. The target theory has remained a guiding principle in mutation research. The deletions are due to the removal of a piece of chromosome, which require two breaks. The origin of these deletions is still a puzzle. The oxygen modifies the types of deletions and modifies the target molecule and that act as a protective agent. Chromosomes number The aneuploids may be monosomics (2n-1), nullisomic, trisomics, double trisomics and tetrasomics. The trisomics are responsible for inducing human genetic disorder. 1. Loss or gain of a part of the chromosome set is called aneuploidy. 2. Loss or gain of a whole chromosome set is called euploidy. 3. Addition of one or more sets of chromosomes is called polyploidy. Polyploidy may be autopolyploids / allopolyploids Methods - Mutagenesis Screening The polyploidisation of colchicines in plants has provided an impetus for developing new avenues for research in mutagenesis. The initiation of investigations on this line of research on mutagenesis was systematically standardized and attempts were made to explore the properties of different mutagenic chemical agents. This was first made by Levan (1949) and his collaborators by applying a technique called Allium test. For animal materials, the mutagens are applied either through feeding or injecting or post – treatment cultures. The capacity of inducing chromosome breakage is a property of several chemical agents. Some of the mutagenic chemicals affect sulph-hydryl groups of proteins and others act through their influence on hydrogen bonds of nucleic acids. 12 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online Physical and chemical structure of chromosomes Researches in the 19th and 20th centuries established that chromosomes bear the hereditary materials or 'genes' in a linear sequence of the permanent fibrous constitution. The chromosomes are the components of an eukaryotic and prokaryotic nucleus that are formed at the time of cell division. The chromomere hypothesis assumed that chromosome is composed of longitunally aligned chromatin granules joined by an achromatic thread. The chromonema hypothesis visualized a uniformly thick continuous structure in a chromosome, capable of spiralisation. Recent analysis showed that chromosomes are the continuous deoxy - nucleoprotein fiber in which condensed and decondensed segments may alternate. Most of the evidences, on ultra structure analysis of chromosomes indicate the presence of fibrils of 2-3 nm in diameter. Heterochromatic and euchromatic segments are characterized by different staining cycles in the different phases of growth and division. The centromere, secondary constriction regions, telomeric segments and other heterochromatic regions must fit in the molecular structure of the genophore, since they are the regions, which were differentiated functionally. The occurrence of divalent cations, histones and even lipids are often regarded as transverse incorporation. Chromosomes are the dynamic structure that has a major role in differentiation, development and control the reproduction of species. The precipitates of the pus cells were found to contain carbon, nitrogen, hydrogen, oxygen and phosphorous which are now known as DNA . The basic structural unit of chromatin called the 'nucleosome' was described by Roger Korenberg (1974). The nucleosomes are structurally complex in their organization. The DNA is wrapped around histones in nucleosome core particles and sealed by histone H1. Histone proteins lined to the linker DNA between nucleosome core particles. Nucleosome core particles contain 146 base pairs of DNA wrapped around histone core. Thus, the packaging of DNA with histones yields a chromatin fiber of a chromosome. The chromatin fibers are folded to form a compact structure in a chromosome. Adenine, thymine and guanine, cytosine rich DNA is wrapped around histones in nucleosome core particles and sealed by histones H1. Non-histone proteins are lined to the linker DNA between nucleosome core particles. Each chromosome will have a specialized unstained region called centromere or kinetochore. Recently, it was the showed that centric region also contain some amount of DNA. The chromosomes are formed during divisional phase of the cell cycle of a nucleus. Chromosome damage has been observed to be a reliable index of the measure of genetic damage to human. The Discovery of the fluorescent banding pattern in chromosomes has proved to be an effective tool in the identification through high-speed scanning devices. The chromosome does not follow a normal pattern of behavior in malignant cells. Vigorous research on the induction of chromosomal breakage, polyploidy and mutation by physical and chemical agents is being carried out in different parts of the world. Varied techniques are developed in the recent years to understand the different aspects of chromosomes and their role in mutations. The principles, applicability and drawbacks of these techniques are discussed by Sharma and Sharma (1980). Chromosomal aberrations are quantitatively, a significant class of mutational event for physical and chemical mutagenesis. It forms an SAMANTHI index for the study of mutational damage. The techniques employed in the study are short-term tissue culture, experiments on somatic cells and experiments on animals. The in vivo and in vitro productions of mutational changes are complex, since, the administration and absorption of the mutagenic chemical in the target cells. The compound may get detoxified in vivo by tissues. Before quantitative data derived in mutagenesis testing, the laboratory animals are used to make meaningful statements concerning man. However, more information is needed to 'bridge' these two species. It has been concluded that man is more sensitive as compared to the mouse for the production of interchanges by mutagens. Most of the chemicals tested are very specific in their time and mode of action (Kihlman, 1966) Pre – fixatives and fixatives. The cells are pre-treated with some specific chemicals for cleaning the cytoplasm, separating the middle lamella of a cell and bringing scattering of chromosomes through spindle inhibition during cell cycle and also to remove cell deposits. Acid and enzyme preparations are applied for cleaning cytoplasm and cell separation through digestion. Recently, Swaminathen and Natarajan (1957) have demonstrated that vegetable oils like sesamum oil brings scattering of chromosomes in metaphase. The pre-fixed cells are to be fixed in desired fixatives to kill the tissue without causing any distortion for the components. Some of the chemical fixatives are either lethal or decompose the cell components. Hence, the freezing method of fixatives was developed to minimize distortion of the tissue, least diffusion and no significant effect on the enzyme systems. In general, the fixatives are classified into non-metallic and metallic. After suitable fixation, the tissue is processed for further study. Different schedules are followed for serial sections and smear preparations. The microtomy is followed in order to show arrangement of cells in a tissue and sequence of stages in the divisional cycle. The procedure entails the operations like washing, dehydration, clearing, infiltration, embedding, microtome cutting, removal of sections and mounting on synthetic and natural resins. I. Plant Material 1. Mitotic Studies in Root Tip Cells A. Squash or Smear preparations The sectioning method has been largely replaced by smear or squash techniques. These methods are found to be of great advantage to bring about rapid and crucial observations. In smear, the cells are directly spread over a slide prior to fixation without any pretreatment to secure cell separation. Pollen mother cells in plants are the most convenient objects for smears. In squash, on the other hand, special treatments are needed for proper separation of individual cells. Then the cells are stained and squashed on a slide. b. Staining The structure and behavior of chromosomes can be studied only after they are stained by using 'vital' or 'non-vital' stains. The tissue retains the color due to chemical configuration called autochrome of the dye. The dyes are generally termed basic or acidic based on their chemical nature and behavior. In cytological studies, several types of mordents are used for proper stain adherence to the tissue. 13 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online c. Different Types of Staining Procedure The Feulgen reaction is the most effective with regard to chromosome staining. The chemistry of the staining has been worked out by different authors. There is a specific test for localizing DNAin situ. Carmine is another widely used dye for chromosome staining. Orcein dye was first employed as a chromosome stain by Lacour in 1941. The other stains such as chlorazol black, crystal violet, Haemotoxylin, Brazillin, Lacrmoid, Toluidine blue in different laboratories for specific study of the tissues. After staining the tissue, whether in the form of section or smear, is mounted on a suitable medium for observation. The mounting media such as balsam, euparal, lacto phenol, cedar wood oil, glycerin jelly etc., are used. 2. Mitotic Studies in Leaf Tips Sharma and Mookerjee (1955) gave a schedule for preparing leaf tip squash. The leaf tips are pre-treated with saturated aqueous solution of aesculine and is fixed in acetic ethanol mixture (1:1), stained in aceticorcein and squashed. 3. Pollen Grains The anthers were dissected from a young flower bud. They are smeared on a drop of acetic-carmine solution on a clean dry slide. Pollen mother cells are smeared for the study of meiotic chromosomes. The mitotic division in endosperm tissue can also be developed by acetic orcein squash method (Sharma and Varma, 1960). II. Animal Material The usual sources of materials are larval tails, ganglia and spermetogonial cells. These materials are sectioned through paraffin block preparations. The bone marrow cells of mammals were developed to study mitotic divisions in higher group of animals. Temporary squash / smear preparation were made from the testis of a male grasshopper for the study of meiotic chromosomes. Certain special technique, for the study of the differential nature of chromosome segments, was followed to study the special chromosomes, centromere, secondary constriction, heterochromatin, salivary gland chromosomes, lamp-brush chromosomes, polytene chromosomes, prochromosomes, pollen grains, embryo sac mother cells, endosperm and the study of nucleolus. The mitotic behavior of chromosomes in lower group of plants like algae and fungi were also studied through special techniques. Human leukocyte cultures were made to analyze the mutational behavior of chromosomes in man. Anomalies in the chromosome structure and variation in number can be studied through karyotype analysis. Buccal smears can also be made to study the mutational behavior of sex chromatin (Bar bodies). Chemical mutagens can be effectively administered to habrobracon aducts by aerosols, feeding, topical application and microinjection. Habrobracon eggs can be immersed in aqueous solution, which contain possible chemical mutagens. Mutational events like dominant lethal mutations, recessive lethal mutations and translocation can be measured in sperms, differing cell types during oogenesis of eggs. The habrobracon test is uniquely rapid and reliable for assaying dominant lethality. Studies with animal cells in tissue culture have shown that, as a rule, there appears to be a good SAMANTHI correlation between the chromosome breaking activities of chemicals in plant and animal cells. Although a chemical, which produce aberration in plant root tips usually, also does it in animal cells, the types of effect may vary in different two materials. For example, 5-bromo deoxy uridine, a thymidine analog induces chromosomal mutations in tissue culture of Chinese Hamster Ovary (CHO) cells, but does not cause any visible damage in the chromosomes of bean root tips (Hollaender, 1972). III. Mutation Analysis from Malignant Tissue The conspicuous features of cancer cells are the high frequency of mitotic divisions, chromosomal aberrations and numerical variations of chromosomes. The rapid advance in research on cancerous materials has been responsible for the development of several techniques for culturing malignant cells in vitro. The chromosome studies of these materials form the source of knowledge of the mutational changes in malignant tissues. IV. Chromosomal Banding Technique in Mutational Studies Human chromosome segments are analyzed through differential banding patterns of chromosomes. The technique has brought a revolution in the study of karyotype that permits precise identification of individual chromosome segments. This technique visualizes the molecular sequence of DNA and its mutational changes. V. Sister chromatid Exchanges (SCE) The SCE techniques demonstrate DNA segregation and give a uninemic interpretation of DNA organization within chromosomes. The technique permits the identification of the chromatids of each chromosome or the basis of differential staining intensities. These exchanges are either spontaneous or accelerated artificially. This method has been used in detecting in vivo exchanges in mammalian systems as a test environmental mutagens for studying chromosome structure, identifying active and inactive sex chromosomes and also DNA replication patterns in higher group of organisms exposed to a variety of mutagens. VI. Flowcytometry Flowcytometry provides a rapid sensitive and quantitative measurement of various testicular germ cell types. The information could provide an analysis on the ploidy nature of germ cells as induced by mutagens. Flowcytometry combines many advantages for rapid phenotypic and genotypic analysis of individual cells. Since, the DNA content of germ cell changes distinctly during the various steps of proliferation and transformation in spermatogenesis, DNA flow cytometry offers a method to monitor with relative ease such changes in dispersed testicular cells (Toppari et al, 1988). VII. Teratology The mutagenecity of chemical compound may also be assessed by teratogenecity assay in animal system. The foetotoxic effect of a mutagen may be evaluated through the induction of exposed pregnant animals (Wilson, 1965, and Gupta et al. 1978). The fetuses cleared and stained with Alizarin red - S stain. VIII. Micronucleus Test 14 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online Micronucleus test was developed in order to detect the structural chromosomal abnormalities in bone marrow cells of animal in vivo. The assay was introduced by Schimid (1975 & 1982). Micronuclei originate from chromatin, which lag during anaphase, indicating spindle disturbance. It is suitable for routine screening of mutagens and it may identify effects not covered by bacterial assays. This test is also able to identify inhibition of proliferation in the bone marrow by strong mutagens. IX. Sperm Head Abnormalities Mutations are influenced either by a physical or chemical agent in male germinal cells of men and animals. These agents induce damage in DNA and results with many abnormalities in the production of gametes namely the spermatozoids. The technique involves a series of steps and separating the cauda epididymis which is smeared to get spermatozoids. The techniques appear to give slightly more reproducible results than when an acute single dose is given; usually larger dose may be given over 5 days. X. Comet Assay The technique was first described by Singh et al (1988), gained popularity as a standard technique for evaluating the DNA damage/ repair. It involves the encapsulation of cells in a low-melting-point agarose suspension, lysis of cells in neutral or alkaline (pH > 13) conditions, and electrophoresis of the suspended lysed cells. This is followed by visual analysis with staining of DNA and calculating fluorescence to determine the extent of DNA damage. The comet assay and micro gel electrophoresis (MGE) were first introduced by Ostling and Johanson (1984). This is a neutral assay in which the lysis and electrophoresis were done under neutral conditions. Staining was done with acridine orange. The image obtained looked like a “comet” with a distinct head, comprising of intact DNA and a tail, consisting of damaged or broken pieces of DNA, hence the name comet assay was given. The assay can be performed on a variety of samples, which can be obtained as a single cell population e.g. Peripheral blood lymphocytes, nasal and buccal epithelium from clinically or occupationally exposed human population and for in vitro studies on cell lines e.g. CHO V 79, mouse lymphoma or cultured human lymphocytes and bone marrow cells. Both DNA and repair studies can be conducted. XI. Molecular assay in mutation detection The standard electrophoretic procedures could be combined with other methods, as they are developed and automated. It is possible to screen as many as ten different proteins. Once a variant type was found, the parents could be studied to see if it was inherited or was a new mutation. XII. Polymerase Chain Reaction (PCR) PCR based in vitro mutagenesis is an important tool that allows defined mutations to be made in vitro to cloned DNA. Prior to its conception, approaches focused on the generation of random mutation, such as those induced by radiation or chemicals. However, these methods did not allow mutations in a specific gene or chromosomal location to be investigated. PCR based in vitro mutagenesis, which is now commonly used in many laboratories SAMANTHI can provide critical information on the regulation of gene expression as well as protein structural function. 1) Numerous strategies were developed to target defined region of DNA, including a. Base (s) substitution b. Deletion or insertion c. Chimeric gene generation d. Multiple site mutagenesis 2) The mega primer method and the quick change method, however, none of these approaches can be applied to all diverse mutagenesis; the methods using digestion with type Igs restriction enzymes and in vitro ligation, to generate mutations. This technique is applicable to diverse mutagenic purposes in molecular biology studies. A target gene is amplified in two separate PCR fragments by four PCR primers. This method is rapid and highly efficient and has been applied successfully to several different genes. This method is successful at generating mutations not only single site substitutions but also for multiple site substitutions, insertions, deletions, chimeragenesis and random mutagenesis. This method is also used for detecting the presence and diversity of low level mutations in human tumors with their potential prognostic value and their putative influence on the ability of tumors to resist during treatment and or metastasize (Hughes and Moody, 2007). XIII. The Host Mediated Assay The host-mediated assay is a simple technique that attempts to bridge the gap between in vitro microbial studies and definitive tests in mammals. This is a practical procedure for evaluating potential mutagenic agents in mammals. This is also, a valuable tool for characterizing mutagenic agents. The assay was developed to determine the ability of laboratory animals to either potentate or detoxify compounds concerning their mutagenecity. In addition to the studies in mammals, it is essential to conduct the in vitro assay. XIV. Mammalian cell culture There are four different methods for mutation selection in mammalian cell cultures. A. Mass selection method The method involves the expressing mass culture and extrinsic agents or specifically altered growth media. B. Lethal – Growth method Involves differential growth of mutants and non mutants cell and selection killing of growing non-mutant cells. C. Thymine less 'Death' method By the ' thymine less' death method a situation is created in which the parental cell die and the mutant cells do not grow but are able to stay alive in the selective environment. Thymidine deprivation does not lead to unbalanced growth and death in cells in which protein synthesis is also blocked. D. Replica plating method The procedure involves cloning of cells as micro cultures in plates and replication of the micro cultures with the replicator. A number of temperature sensitive mutants were isolated by the replica plating procedure. The capacity of inducing chromosome breakage is a property of several chemical agents. Some of the mutagenic chemicals effect sulphydryl groups of protein and others act through 15 THE SCITECH JOURNAL VOLUME 01 ISSUE 10 OCTOBER 2014 Review Article THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online their influence on hydrogen bonds of nucleic acids E. Molecular assay in assessing mutagenesis A variety of methods have been developed for introducing mutations into cloned genes, all of which involve the use of enzymes and chemicals that cleave, degrade or synthesize DNA. These mutations can be generated through either simple lestions or insertions or substitutions of single base, or systematic deletions, insertions or substitutions of clusters of bases. A systematic method can be used to generate a large number of deletions or insertions with in the general region of interest. These mutations are screened by fine – resolution restriction mapping and or DNA sequencing. Small deletions or insertions can be generated systematically either by partial digestion with pancreatic DNAase I, or by partial digestion with restriction enzymes. These methods have their own advantages and disadvantages. Several methods have been developed to generate sets of deletion mutants that back progressively more sequences from one and or the other of the target DNA. Out of these methods, the digestion with exonuclease III is proved to be an ideal method to analyse the molecular aspects of mutagenesis. Oligonucleotide mediated mutagenesis is used to add, delete or substitute nucleotides in a segment of DNA. The method can be used to alter individual codons in protein coding sequences or to generate defined changes in protein coding sequences or to generate defined changes in sequences that have a regulatory function. Oligonucleotides used to create deletions or insertions or to substitute two or more contiguous nucleotides. Restriction enzymes are used to recover the foreign DNA from the double standard replicating form of the recombinant bacteriophage genome that has been sequenced. Occasionally difficulties are encountered in obtaining a particular mutation. The nature of mutation, target sequence and vector are the encountered difficulties. X-ray diffraction of protein crystals and chemical modification of the side chains of the amino acids that form the primary sequence of protein and the two methods involved in the direct study, to understand the structure and function of a protein. The simplest method of localized random mutagenesis is to react a short fragment of double standard DNA with a chemical mutagen such as nitrous acid or hydroxylamine and to close the population of mutagenised fragments into a recombinant plasmid that carries the remainder of the wild - type gene. Another method in the molecular analysis of mutagenesis is the treatment of single standard DNA with chemicals that damage all four bases. Point mutations can be introduced into double standard DNA by incorporating base analysis with various types of DNA polymerases (Sambrook et al, 1989). Conclusion Understanding mutagenesis is important for unraveling the way genes function and behave. Mutations are important focus areas to study gene interactions and the factors affecting gene behavior. The advancements in technology in the detection methods have helped in studying mutagenesis and mutation induced changes with clarity. As mutations can be induced and targeted changes in the genes and gene sequences can be achieved, this area has tremendous potential SAMANTHI for direct beneficial applications References Alexander Brink R (1973), Paramutation. Ann.Rev.Genetics, 7: 129152. Anthony J.F, Griffiths, Jeffry H, Muller, David T, Suzuki, Richard C, Lewontin, William M, and Gebbert (2000), In: An Introduction of Genetic Analysis, Pub: W.h.Freeman, New York, pp: 463-493. Auerbach C (1976), In: “Mutation Research”. Pub: London:Champn And Hall, pp : 504. Auerbach C, Robson JM, (1947), The production of Mutations by chemical substances. Proc. R. Soci. 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