DNA Typing and Genetic Mapping - Assignment Example

Running Head: FORENSIC BIOLOGY Name: University: Course: Tutor: Date of Submission QUESTION ONE DNA profiling also termed as DNA testing, DNA typing or genetic fingerprinting can be described as technique used in forensic science and normally it is usually used by forensic scientists in identifying individuals as per their respective DNA profiles. Normally the DNA profiles are usually recorded in sets of numbers which in really sense reflect a particular individual’s DNA makeup and sometimes it’s used to identify the identity of an individual (Edwards & Hammond, 2004). This technique therefore is used to identify individuals of the same species through the use of their DNA samples by scientists. The first process is Restriction fragment length polymorphism (RFLP) where a double stranded DNA is obtained from blood or semen after which is cut into small fragments by varying length of enzymes. The fragments are thereafter separated depending on the size through the process of electrophoresis through which fragments of the same length are transferred to a nylon membrane. Once this done the segments are matched up through radioactively process where only labeled DNA segments hence enabling only identical fragments to stick together. The excess DNA fragments are washed away and an x-ray is taken of the remaining segments of DNA. The main aim of this process is to give the actual picture of what the labeled fragments were in the original sample. The second technique is Short tandem repeat profiling (STR) where an enzyme is normally used to replicate many copies of very small and tiny sections of the DNA.The DNA fragments are cut into small pieces and afterwards separated through the process of electrophoresis. Once the DNA fragments have been separated they are visualized with a specific silver stain through the process of polymerase chain reaction. Through this process the DNA is split, replicated resulting into more DNA fragments. The reaction is usually submitted to kinetic control mechanisms. CSF1PO THO1 TPOX vWA Frequency Allele Frequency Allele Frequency Allele Frequency 0.000 5 0.007 6 0.002 11 0.000 0.002 6 0.237 7 0.000 12 0.000 0.002 7 0.148 8 0.528 13 0.000 0.033 8 0.117 9 0.093 14 0.131 0.249 9 0.155 10 0.056 15 0.082 0.309 9.3 0.331 11 0.284 16 0.211 0.330 10 0.005 12 0.037 17 0.265 0.060 11 0.000 13 0.000 18 0.202 0.014 All 1.000 All 1.000 19 0.087 0.000 20 0.021 1.000 21 0.000 All 1.000 The allele 5 at the locus CSF1PO was observed at a frequency of 0.000 times in a population Therefore it is reasonable to estimate that there is a chance p=0.00 that any particular CSF1PO allele, selected at random, would be 5. Similarly, the chance is about q=0.002 for a random CSP1PO allele to be 6. Prior to typing the suspect, if we an assumption that the suspect here is not the donor of the evidence then we can think of him as someone who received a CSF1PO allele at random from each of his parents. The chance to receive 0.000 from his mother and 0.002 from his father is therefore pq, and to receive 6 from mother and 5 from father is another pq, so the probability to be 5,6 by chance is 2pq. Hence about 16% of people have the 5,6 genotype at the CSF1PO locus. The calculations for the THO1 and vWA loci are similar, and taking them into account whittles the overall chance for a random person to have the combined genotype from 4% down to about 1/0000. Given the fact that at TPOX locus both alleles are the same then only one term will be used thus pp or p2, which represent a probability of 28% of people with same TPOX genotype. b) Outline the stages involved in DNA profiling, including the name, purpose and process of each stage. According to studies the following are believed to be the stages of DNA profiling: Stage 1: DNA EXTRACTION This is the first stage in DNA profiling and it involves the separation of DNA from other organic and non-organic components of the sample by the forensic scientists. The separation technique depends on the type of sample and here the cells are normally broken down to release DNA. .At this point the Lab Technicians usually extract DNA from the nucleus of cells which are usually present in the samples collected for DNA analysis such as human hair, tissue, bone or blood and fluids. After collecting the DNA samples the next step is to wash them with specific chemicals and through this process unwanted cellular materials are removed leaving the sample with required chemicals that can be important for DNA profiling. Once the Sample has been washed then the next step is to isolate the samples which in normally cases take about one to four hours according to the size of the sample or sample type. The last step is to extract the DNA from the samples and once the DNA has been extracted a number of methods or techniques are thereafter used to develop a DNA profile. In circumstances where only a small amount of DNA is obtained from the samples and it cannot be enough for effective development of a DNA profile then it can be enlarged through the use of polymerase chain reaction (PCR) Stage 2: DNA QUANTITATION This is the second stage and at this stage the DNA obtained in the first stage is chopped or cut into very tiny and small fragments through the use of restriction enzymes which leads to a thousands restriction fragments having different shapes and sizes . A particular restriction enzyme normally cuts the DNA at a specified base sequence after which several tests are run on the chopped DNA fragments to deduce the quantity of DNA present in the sample obtained. Once the amount of DNA present in a particular sample has been established the next step is to make estimates through a clear comparison between the samples in relation to the standards of established quantities of DNA(Gill , 2003). Usually the scientists have a target of an amount of DNA that is usually equivalent to one nanogram and this process usually takes up to approximately two hours. In situations where insufficient quantities of DNA are obtained then, the first step may be repeated. Normally the process of DNA quantitation is usually carried out with an aim of improving amplification efficiency, obtaining balanced profiles, effective data interpretation, cost effectiveness, to reduce the presence of artifacts, to reduce instances of data re-analysis and to preserve the sample and date as well as data obtained for future (Gill , 2003). Stage 3: PCR AMPLIFICATION of MULTIPLE STR MARKERS At this stage various chemicals are added to the sample with an aim of allowing given specific DNA fragments obtained in stage two to multiple into more fragments. At this stage the Lab Technicians usually targets thirteen DNA locations which are normally used for examination by a device which cycles in rounds of 28-32 though heating and cooling process. The fragments are thereafter subjected to Polymerase Chain Reaction (PCR) which roughly takes about three hours for the process to end. After this the fragments are thereafter isolated according to size through a process known as gel electrophoresis. During this process shorter DNA fragments tends to move faster than the longer fragments .After this process, the DNA fragments are then injected into wells then an electric current is applied along the gel. At this stage the DNA is usually charged negatively hence being attracted to the positive end gel. To obtain a fluorescent image, a radioactive material is usually added to the DNA fragments Stage 4:  GENOTYPING At this stage fragment division DNA pattern is analyzed and the PCR products are then separated and detected. Additionally, a genetic analyzer is later on used to record images of the DNA segments as it flows through the small tube. During the process the results are then recorded which tend to apply as spikes which are very much related to the EKG chart. A computer is then used to record the results after which the data is analyzed in relations to the required standards. The numbers usually correlate with each other the one of the 13 specific locations labeled in the PCR represents the specific individual DNA profile (Gill , 2003). Stage 5:  COMPARISON OF RESULTS Once the DNA profile has been established then a DNA expert undertakes the initiative of reviewing the DNA profile obtained through genotyping with an aim of determining whether the match with other samples. Incase of a match then it clearly shows that DNA was contributed by a particular individual and in case of a non-match then it clearly evident that an individual is excluded as the donor. Once all the results are in place the last step is the interpretation of the results which usually may take less than an hour and in most cases it relies heavily on the quality of the sample being tested (Gill , 2003). c) Outline and explain the qualities of DNA that have made it such an important tool for human identification. DNA is perceived as a unique molecule which actually contains all the genetic information regarding a particular person and one individual has her or his DNA made up of approximately three billion building blocks referred to as nucleotides or bases. DNA is the molecule that contains all the genetic information of an individual. One person's DNA is perceived as a chemical code which is usually found in the cells of every person’s body hence each individual has a different DNA from the other person except for identical twins. Given its unique character DNA is as an effective tool of in analyzing the crime scene. DNA fragments can be easily connected through the use of ligation enzymes, and the process of DNA fragments ligating is very much important in the sense that researchers can use various DNA fragments from different sources to develop a recombinant DNA. Recombinant DNA is very much essential in plasmids and in most cases its usually associated to the genetically modified organisms. DNA becomes much more useful in this case as researchers can use circular DNA developed fragments which contain few genes together with plasmids, through the insertion of plasmids into bacteria to amplify the initially inserted circular DNA fragments (Gill , 2003). It is easy to manipulate and Magnify small amounts of DNA through the process of polymerase chain reaction (PCR) and through this process various specific sequences related to DNA are easily isolated hence changing the targeted regions of DNA.Since this process is very much effective in magnifying small amount of DNA, it is used to identify various kinds of DNA sequence present in a sample. It is very easy to determine the various sequences of nucleotides found in DNA fragments through the process of DNA sequencing hence through this process various scientists are able to determine the molecular sequences related to certain diseases in the body. DNA can be easily manipulated in the laboratories through the use of restriction enzymes which in most cases the enzymes help in cutting down the DNA into specific fragments at a specific interval producing conventional fragments which are normally visualized through the process of gel electrophoresis that eventually separates the fragments according to their length and size. DNA Profiling in an effective tool in solving crimes as the patterns of the DNA Profile obtained is usually matched between that of the suspect and the victim and in situations where the profile matches with that of the suspect the results are used as strong evidence to show that the suspect was present at the crime scene. Though the DNA profile may match it does not necessary prove the suspected that he or she committed the crime.DNA Profiling can solve crimes. When the profile doesn’t relate to suspect match, then he or she is excluded from the case. DNA analysis or profiling can be used in solving medical problems.DNA profiles are normally used to identify the paternity of a particular individual whether he or she is a parent of the child or not (Gill , 2003)t. A particular child paternal father or maternal mother is usually established through the use of Paternity suits, Inheritance cases and Immigration cases. Through the comparison of a DNA profile that belongs to a particular mother as well as her child then it clear to determine whether she is the mother of the child or not through the analysis of DNA fragments SECTION B Question 2 a) Outline the structure of DNA and explain how it is used in Forensic Investigations. Use a diagram to illustrate your answer The structure of DNA contains the following components deoxyribose (a sugar molecule), a phosphate group (a phosphorous, P atom surrounded by oxygen, O atoms), and a nitrogen-Containing base 4 nitrogen-containing bases namely adenine, guanine, thymine and cytosine Exploring a DNA chain The sugars in the backbone The DNA backbone is essential seen as a repeated prototype of sugar groups as well as phosphate group(Sullivan & Robertson, 1992). . The term DNA means deoxyribonucleic acid which is a clear implication that DNA structure also contains a particular sugar known as Deoxyribose which actually is seen as a modification of another form of sugar known as ribose. Ribose acts as the backbone sugar of RNA, which is termed as ribonucleic acid. The diagram of Ribose is as below Source: http://marysbridge.com/Documents/Ch10.pdf This diagram does not cointain carbon atoms hence ribose is seen as a molecule.When ribose loses an oxygen atom it becomes Deoxyribose which implies that it is de-oxy as shown in the diagram below Source: http://marysbridge.com/Documents/Ch10.pdf. The other part of DNA structure is phosphate group which actually is seen as an attached sugar molecule that cointains five carbons and hydgrogen atoms –OH as shown in the picture below. Source: http://marysbridge.com/Documents/Ch10.pdf. The last part of the DNA structure is nucleotide which in really sense contains four complex organic bases namely cytosine (C), thymine (T), adenine (A) and guanine (G). Source: http://marysbridge.com/Documents/Ch10.pdf. How DNA is used in Forensic investigations DNA is perceived as a chemical code which is usually found in the cells of every person’s body hence each individual has a different DNA from the other person. Given it’s unique character of DNA it as an effective tool of in analyzing the crime scene. In forensic analysis it’s a process which actually involves the testing of various regions of a particular individual’s DNA (Sullivan & Robertson, 1992). There two common types of DNA profiling techniques used in Forensic investigations. The first process is Restriction fragment length polymorphism (RFLP) where a double stranded DNA is obtained from blood or semen after which is cut into small fragments by varying length of enzymes. The fragments are thereafter separated depending on the size through the process of electrophoresis through which fragments of the same length are transferred to a nylon membrane. Once this done the segments are matched up through radioactively process where only labeled DNA segments hence enabling only identical fragments to stick together. The excess DNA fragments are washed away and an x-ray is taken of the remaining segments of DNA. The main aim of this process is to give the actual picture of what the labeled fragments were in the original sample. The second technique is Short tandem repeat profiling (STR) where an enzyme is normally used to replicate many copies of very small and tiny sections of the DNA.The DNA fragments are cut into small pieces and afterwards separated through the process of electrophoresis. Once the DNA fragments have been separated they are visualized with a specific silver stain through the process of polymerase chain reaction. Through this process the DNA is split, replicated resulting into more DNA fragments. The reaction is usually submitted to kinetic control mechanisms. b) Explain the following terms indicating how they are related to each other (i) Gene A gene can be termed as a unit of hereditary which consists of various sequences of DNA which actually leads to particular phenotype in an individual’s body. A gene therefore contains sequence of DNA that tends to occupy specific location on a chromosome hence determining the true characteristics of organisms in the body. Genes normally undergoes mutations in which the entire sequence of DNA changes. According to studies conducted by it indicates that genes usually achieve their effects through the direct protein synthesis and they are entirely composed of DNA, except in some virus which actually contain RNA instead. The genetic code is usually determined by the sequence of nitrogenous bases which are usually found along the DNA strand. (ii) Allele An allele is perceived to be an alternative form of a gene and it’s normally located at specific location on a specific chromosome. An allele therefore is seen as DNA codings which are used to determine various distinct traits of an individual that are usually inherited from parents to offspring’s. Organisms usually tend to have two kinds of alleles various traits and when they alleles combine together they are referred to as heterozygous where one allele becomes dominant over the other recessive. (iii) Polymorphism This a term which is used in biology to refer to the occurrence of various forms, stages, or types in an individual’s organisms as result of discontinuous genetic variation. Normally, this occurs in organisms of the same species as well as those with independent sexual variations. The most common example of polymorphism is perceived to be the separation higher organisms into male and female sexes. This implies that some forms of polymorphisms actually have no visible manifestations. Question 3 a) Outline the structure of hair, and explain the features of the hair that can be used to identify whether a hair is of human or animal origin. In the case of human hair, explain how the area of the body that originates from can be ascertained. Use diagrams to illustrate your answer. Hair Structure The hair usually composed of very strong structural proteins referred to as keratin and each strand of the hair usually consists of three layers namely; an innermost layer or medulla which is usually present only in very large and thick hairs. The other part is middle layer which is referred to as cortex in which it provides strength as well as color and texture to the hair. The last part is outermost layer which is normally referred to as cuticle and its seen to be a thin layer and colorless which actually serves the function of protection hence it’s the protector of the cortex (Sullivan & Robertson, 1992). Structure of the hair root Normally at the surface of the skin there is the hair root which has been enclosed within the hair follicle. At this point we have the dermal papilla which is usually receives bloodstream hence producing new hair. Dermal papilla is very crucial and important to hair growth since it is believed to contain receptors for male hormones as well as androgens. Androgens usually regulate hair growth as well as prevent hair loss. Hair Structure Source: Gill P, E. (2003) Feature distinguishing Human hair from animal hair. Hair follicle: This is considered as a small curved and deep buried fact of the scalp and its believed to be the point at which the hair normally starts to grow. At this point the hair follicle normally gets supplied with tiny blood vessels hence the blood passing through them in turn nourishes the growing regions. The body temperature that surrounds the hair follicle is usually not affected by cold nor hot weather. This is usually distinguished from the animal hair according to the rate at which the hair grows as animal hair grows faster depending on the amount of light they are exposed too. Image showing the hair follicle. Source: Edwards, A. , Hammond, T ( 2004). Hair Shaft: This is considered to be a very important part of the hair structure and here it consists of three concentric layers namely the medulla which actually is the inner most layers hence does get affected by the human hair care products or processes. The other part is the middle layer which is called as cortex and it contains a particular pigment which tends to be changed through the process of dyeing, bleaching, perming and other processes (Jeffreys, 2003). The last part is the outer layer known as the cuticle which is usually made up of tiny overlapping scales and their work is to protect the cortex b) Choose two of the following techniques and critically evaluate their use in fibre analysis. Include an explanation of how the techniques work and identify the features of the fibre used for comparison for each technique A comparison microscope This is described as a technique used to analyze side-by-side specimens through the use of two connected microscopes which have been connected by an optical bridge. The results are usually divided into two windows hence enabling the two separate objects to be viewed together. This is usually done with an aim of preventing the situations where an observer actually relies on his memory while comparing the two objects during the process of fiber analysis under a particular given conventional microscope. Polarized Light Microscopy This where a polarized light microscope is usually used to observe as well as photograph the specimens which are normally visible as result of their primarily optically anisotropic character. In order to achieve this more effectively the microscope is usually equipped with a polarizer that has been positioned in the light path in front of the specimen and the analyzer (Jeffreys ,2003). This technique usually is capable of providing information on absorption color and optical boundaries between various minerals. Question 4 a) Define and explain the four types of blood stain found at crime scenes Passive bloodstains: These are blood stains which are usually created by the force of gravity. The other kind of blood stain is projected blood stains which usually occur when some form of energy has been transferred to the blood source. The third type of blood stain is transfer or contact blood stains where the stain is produced when the object with the blood actually comes into contact with a specific object or surface that does not contain have blood. The last type of blood stain is velocity or impact stains in which the stain is evaluated in terms of low, medium, and high velocity impact squatter. The variation in the velocity is usually used to describe the various amounts of energy that can be actually transferred to the blood source in a manner that create a stain in the end. Explain the four stages of blood stain analysis This involves the following stages The first step is the analysis of the weapon(s) did the perpetrator use? The second step is the determination of how many times the victim was actually hit, shot, stabbed, etc? The third step involves the determination of the position in which the victim was when the even occurred The four step involves the determination of the position of perpetrator during and after each event and here it also involves choosing one presumptive test for blood and explain how it functions Presumptive Blood screening This is usually perceived as a forensic test which is usually used to identify whether a particular blood is present in a certain material or not. The forensic investigators usually use some chemical luminal which helps in detecting the presence of blood in the sample. Normally there are various factors which affects presumptive test in cases where the investigator is confronted with several fluids at the crime to analyze at the scene of the incident. d) Using diagrams, explain the role of circular and teardrop bloodstains in establishing the number of impacts that must have been applied to cause a bloodstain pattern. These are usually referred to as high velocity impact spatter and they are usually produced when some objects traveling greater than 30m/s come in close contact with the source of blood. These stains are usually very small and approximately less than 1mm in diameter. The pattern of this squatter usually has a mist- like appearance and mostly these patterns are usually a result of gunshots or some explosives that could be caused by industrial machinery. Diagram showing blood pattern impact Source: Jeffreys , A. (2003). References Edwards A, & Hammond, T ( 2004). DNA typing and genetic mapping with trimeric and tetrameric repeats Am J Hum Gen 49: 746-756 Gill P, E. (2003) .Identification of the remains of the Romanov family by DNA analysis Nature genetics 6:130-135 Jeffreys , A. (2003). Individual-specific “fingerprints” of human DNA Nature 316:76-79 Sullivan K, & Robertson, J. (1992) Automated DNA profiling by fluorescent labelling of PCR products PCR Methods and Applications 2: 34-40 Read More