Forensic Immunology: Phylogenesis - Essay Example

Running Head: FORENSIC IMMUNOLOGY Forensic Immunology Name Institution Date Introduction Phylogenesis can be termed as the chain of events responsible for the species’, genus’, tribe’s, race’s, or organ’s evolutionary development as well as their history .This also applies to the organism’s higher taxonomic grouping. The word philogenetics has its origin from the Greek words phyle/phylon meaning race or tribe and geneticos meaning birth- related therefore Philogenetics involves studying how the different groups of organisms are related (for instance populations and species) using data that gives molecular sequence and the data matrices of the morphology. Phylogenetics is therefore the scientific discipline which is concerned with description as well as reconstruction of genetic relationship patterns among higher taxa and species. The phylogenetic trees have a greater convenience in representation of life’s evolutionary history visually. The diagrams show organisms’ inferred relationship and speciation events’ order leading from common ancestors to the diversified descendants. Phylogenetics is the scientific discipline concerned with describing and reconstructing the patterns of genetic relationships among species and among higher taxa. Phylogenetic trees are a convenient way of visually representing the evolutionary history of life. The idea of tree having both roots and branches was taken from the early idea that there is progression of life from lower (which is older) to higher (which is recent) form thereby forming the term family tree. These diagrams illustrate the inferred relationships between organisms and the order of speciation events that led from earlier common ancestors to their diversified descendants. The trees have various parts with nodes representing the taxonomic units, like organisms, common ancestors, species, genus, population or even the taxonomic group that is higher. Since branches link nodes uniquely, they are a representation of the genetical relationships while their pattern gives the tree its topology. The scaled trees have branch lengths proportional to given biological property that is vital ,for instance the number of transformations of the amino acids in the protein phylogeny nodes. These trees are either rooted or otherwise. The rooted ones contain a special node which is termed as the root representing the tree’s common ancestor of the taxa therefore making the trees directional, considering that the taxa have their evolution from he roots. The unrooted trees on the other hand just show relationships only with no common ancestor reference. Phylogenetic analysis is important in tracing the genes with known roles and comparing how they are related with the ones that don’t have their roles known so as to be able to predict the functions of the unknown genes. This is the basis of drug discovery (Branca 2002; Wu 2002).It also acts as the epidemiology’s standard part considering its application in identifying the disease reservoirs and detailed tracking of disease transmission. These principles may also be crucial in tracking the bioweapons’ source (Cummings and Relman 2002). The Phylogenetic analysis is also vital in pathogen –tracking crucial in selecting vaccines which are appropriate for specific regions (Gaschen et al. 2002).it applies the ribotyping technique in organism identification or tracing its relative that it is closest related to by mapping to the tree of life its ribosomal RNA.This is applicable even where other methods can not reorganize or culture the organism. Both ribotypying as well as other genotyping methods have been influential in identifying infectious agents of disease in people that have been previously unknown (Bull and Wichman 2001; Relman 1999).These analysis are as well crucial in the determination of protein folds considering that Considering that common ancestors have proteins that retain their folds (Benner 2001). Phylogenetics applies Phylogenetic methods in showing tree phylogenies. These methods include the cladistic methods where the taxa get grouped in to hierarchies that are nested, with their determination being by derived organism characters that are shared. There is also the Phenetic method where clustering as well as the classification of organisms is based on the identical character number shared basing on general similarity. Maximum parsimony is also another method where the tree that describes the data best is the one which reduces data conflict amount. There is also the Maximum likelihood method, which is a statistical technique that is both effective and robust and applied in every field of science. As opposed to the parsimony, this technique uses character conflict in a given amount to find phylogenic trees. The distance matrix methods have high computational speeds hence making them very popular in phylogeny inferring (Nei &Kumar 2000, Ch. 6). Every distance method changes the character data in to a pairwise distance matrix, where every distance has a possible taxa pairing in the study. Other methods include the Bayesian inference method, Quartets method, Artificial intelligence and genetic alogarithms method, and invariants method which is also termed as the evolutionary parsimony method. There have been tests carried out to determine the validity of Phylogenetic methods in reliably showing the phylogenies .they have undergone empirical tests especially in situations where there is knowledge of the true phylogeny with certainty, since there was direct observation. For instance there was propagation as well as splitting of bacteriophage T7 sequentially with mutagen being present, where there was tracking of every lineage out of 135,135 trees that were possibly phylogenetic, the tree that was true had been determined perfectly by the methods of Phylogenetics in blind analysis. There was the use of five different methods, but still each of them chose the tree that was correct ( Hillis et al.1992 ). Still in a different study, there was the use of 24 mice strains with known genealogical relationship and the cladistic analysis gave almost equal results to the phylogeny of the strains known (Atchely and Fitch 1991). There was also application of Phylogenetic analysis in predicting retrospectively the human influenza A virus’ right evolutionary tree more than 4/5 of the time during the flue season from 1983-1994(Bush et al)..There was also the use of AIDS virus sequence which was 111 modem HIV-1 sequence in 1998 in the Phylogenetic analysis in order to predict the viral ancestor’s nucleotide sequence where they descended from. The result matched closely, with great statistical probability, the very HIV sequence of the ancestors which is present in the HIV-1 seropositive sample of the African plasma whose collection and archive was in Congo in the year 1959 (Zhu et al.1998 ). For long period, science and technology has been very influential in investigating and developing new ideas that have impacted the world to a larger extent. Phylogenetic methods have been instrumental in investigating the origin of many things while giving reasons for their development and functions, Phylogenetics have also deeply investigated the immune system ,which is the major determinant of resistivity to microbes and has been deeply studied including its functions ,structure, blood banking, organ transplanting, function disorders, and immunization. These results have been used to establish the origin of bioweapons and also establishing the relationship between various viral transmission species. Viruses as natural bio-weapons According to the medical science, the instability of the genome is a greatly undesired feature considering that it is the source of the malignant cell alterations, autoimmunity, spontaneous abortion and also the emerging as well as the re-emerging of viruses that are new. Though the advantages of this instability are many compared to the disadvantages, this is in addition to the ability of the DNA/RNA sequence that is emitted to act as biological weapons naturally against any concurrent species or predators. This may also be the source of the positive selective pressure which helps in supporting the evolutionary features’ conservation like the instability of the genome as well as the ability it has in emitting its sequences. Viruses have been known to attack hosts frequently. It is also probable that the original source of various viruses that that attack both insects as well as mammals come from the arthropods like the flaviviridae; as well as the production of viruses that cause infections to insects as well a as plants and animals like the Rabdoviridae and also the Reoviridae.For instance the mammalian picorna viruses are quite identical both structurally as well as genetically to various small RNA insect viruses and also about two viruses of plants. Since the viruses of insects are very diverse compared to the viruses of mammals, their origin is attributed to a particular insect that depended on plants or mammals for food during the evolutionary process. Most viruses that attack the human population are frequently zoonozis.Even though animals are considered the greatest source of pathogenic viruses that frequently attack human beings. The viruses are easily disseminated to human beings because of the way human beings live which creates a higher probability of new virus transmission from the animals (hosts) to people. The rodents as well as the arthropods also cause virus transmission from a species to the next, with their role as vectors is being increased in urban milieu.Otheranimals,mostly primates are a representation of the virus sources that are potentially pathogenic to people especially considering the new or re-emerging extremely virulent as well as dangerous disease- causing viruses like the Marburg, syndrome of the Hantavirus lung ,Ebola, Congo Crimean hemorrhagic fever, Korean haerrmohagic disease,SARS-Co virus and more so HIV1 and also HIV2 ( Clewley, 1995). HIV is a great human problem since it is the cause of Acquired Immune Deficiency Syndrome (AIDS) .It is a retrovirus with double RNA genomes that are single stranded and which have lengths of about 11 kilobases within a virion.just like the other retroviruses, its replication happens through the intermediate stage of the RNA which is referred to as provirus, which always integrates in the DNA of the host thereby creating hardships in its eradication. The infection has three stages, with the first stage being the time when there is penetration of the infection to the host as well as its replication, it lasts for many weeks. The second stage is the symptomatic one where there is duration of few months. The third stage is where the immune system of the host is overwhelmed and therefore is in a bad state after several years of the replication of the virus ending up in the development of AIDS. The most crucial aspect to be considered in HIV is the fact that it infects the immune system cells. It had its first description in 1981when some men were recognized as having Kaporsi’s sarcoma cancer and also pneumonia which came from pneumocystis carinii fungus infection. It was immediately discovered that these conditions came as a result of the immune dysfunction, therefore making patients have little resistance to the infections. Even though there was an earlier recognition of the immune deficiency syndrome, the AIDS was a so unique because it was spreading very first and the mortality due to it was fully effective. After two years, the agent that causes it, a retrovirus termed as the human immunodeficiency virus (HIV) was separated from a French patient suffering from AIDS. Therefore it was later realized that there were two types of HIV in the population of human beings. The major infections in the world come from the HIV-1, with a little population of west-Africans getting infections from a related virus which is HIV-2.even though the infection of AIDS was initially found in men who were gay, it soon became clear that the disease was also able to be spread via various body fluids with the most global transmission being via heterosexual intercourse. Since HIV was discovered, its spreading has been very radical (Montagnier, 1998). In the year 2000, over 36000000 individuals all over the world had the HIV infection, with new infections being more than 14000 every day, many of these patients being children. It also causes a higher mortality rate considering its death toll cumulatively which is over 22000000.The most affected place is the sub-Saharan Africa which represents 70% of total HIV infections, with the adults’ average prevalence in some countries reaching 25%. HIV is assumed to be descended from the simian immunodeficiency virus (SIV).Some of these simian immunodeficiency viruses resemble HIV1 and HIV2 for instance the simian immunodeficiency virus which are present in sooty mangabey monkey (SIVsm) which is also commonly referred to as the green monkey, indigenous to western Africa. The HIV strain that is more virulent, the HIV 1, had a great difficulty in placing, until recently. Its counterpart that was very close to it, the simian immunodeficiency virus, was identified and known as infecting the chimpanzees (CIVcpz), it had great differences with HIV.Apart from this, a chimpanzee’s frozen tissue was reported to be having a simian virus (SIVcpz) that almost resembled the HIV1. The chimpanzees trace their origin to a subgroup referred to as the pan troglodytes that were previously common in the west-central Africa, hence giving evidence to the researchers that they were the actual HIV-1 source; later the virus crossed species to people. It could also not be assumed that the chimpanzees were originally the HIV 1reservoir considering that they have rare chances of getting infections from the SIVcpz.it is also assumed that the wild chimps received simultaneous infections from two simian immunodeficiency viruses (SIVs) with ‘viral sex’ producing an additional virus having abilities of infecting people and also causing AIDS. There was also the discovery of the chimp virus as the amalgam of the red-capped mangabey’s SIV as well as the greater spot-nosed monkey’s virus. There is an assumption that hybridization happened inside the chimps having both SIV strains after killing two monkey species that were small. The hypothesis on the evolution of HIV from SIV has its basis on the various resemblances in the two viruses, mostly at their genetic level. The viruses are genetically similar as well as having their transmission in the same way. The difference is that as HIV causes AIDS in people, so do SIV to monkeys. Since both of the SIV as well as the HIV are found in blood, the belief of HIV getting in human beings through the blood of monkeys, possibly via drinking monkeys’ blood or eating their raw flesh, has been greatly supported. Interspecies sexual transmission is also among the causes. Examining the origin of HIV The human immunodeficiency virus has been very devastating therefore there have been various suggestions about its origins. The Phylogenetic methods have been applied in the estimation of the date of the previous HIV common ancestor using Phylogenetic tree which is a scientific illustration representing Phylogenetic analysis results. These show the way various HIV strains are related, in a pictorial form. The virologists of HIV use the Phylogenetic trees in identifying the HIV relations since these trees are based on the idea that transformations take place through common ancestor’s splitting. Phylogenesis has been used in estimating the date of previous HIV-1 common ancestor .the attempts that were carried out were obstructed by limitation of the sequence data of HIV-1 which antedate HIV-1 discovery in 1983.the computations as well are also very intensive creating difficulty in deriving time scale that was reliable or HIV-I molecular evolution at population level. There is also the successful use of Phylogenetic calculations in estimating the period of the last common ancestor of HIV-I main group as 1931 (Korber et al, 2000). The Phylogenetic method used is based on the molecular clock assumption s signifying that the molecular transformation is the time’s linear function as well as the accumulation of substitutions depend on Poisson distribution, although there are limitations, for instance the variance of the evolutionary rates, the viral sequences average evolution rate in people is constant. However there is incorporation of the substitution’s different rates in the models of evolution between their bases, various site-specific evolution rates as well as different frequencies of the bases so as to accommodate all the factors in providing realistic estimation. There was also the application of a method that relaxed the strictness of the molecular clock assumption. Using the Phylogenetic tree that is rooted, the root-leaf distance has the time assigned ,therefore making the choice of the root, which acts a s a branching point where common ancestor lineage first diverges, is vital in timing. The root is actually considered as the ‘outgroups’ branch position, with the out-group specification as the sequence or even the sequence set which is external to the considered lineage. Therefore SIVcpz are considered an out group. The study realized that while applying out-group of SIVcpz ,there may be difference in the subtype which is dependent on the Phylogenetic method , the gene’s region put in to consideration, or may as well depend on whether there was the use of single as well as multiple use of out-group sequences. Using a different construction of out-group consisting of each subtype’s consensus sequence, there is avoidance of bias that originates from some clades being over-sampled. This also creates stable branch lengths. There is also another strategy of the out-group which holds in a fixed manner the found order of branching and the consensus out-group, as well as replacing the consensus out-group with SIVcpzUS sequence, then branch length re-optimization. The result is similar scores of likelihood to the SIVcpzUS- constructed trees as the starting out-group, showing that the position of the roots that are dependent on the sequence of the consensus and the ones from conventional method are compatible. After root construction, plotting the total length of the branch against the sampling year can be done with the Phylogenetic tree basis while assuming the evolution rate is constant or uniform. In t he linear relation that is inferred, there can be a backward projection in the estimation of zero branch length associated time, the ancestral sequence time. There are two factors that have been considered as influencing the estimation uncertainty, that is: the time for sampling has its recording to a one year precision, and HIV-1 provious can mostly get harbored and does not evolve for the time period extension in cells that are persistently infected, therefore the sampling of DNA done at a particular year may have their origin in the earlier years. When such effects are considered, there is construction of the method of bootstrap which gives confidence intervals (CIs) to about 95% on the estimation of the rate-of-evolution and timing, thereby giving the last common ancestor date of the HIV-1 M group as 1931( Schuh, 2009). In testing the validity, documented dates are mostly used. For instance with the first case of control as ZR.59 viral sequence, taken from sample of blood from the Democratic Republic of Congo in 1959.due to the construction of trees using the samples collected between 1980-2000,ZR.59 is earlier than these data therefore acting like a better control. These calculations bring the origin to about 1957, concurring with 1959 documentation date. Thai E subtype is as well another control, with its appearance first noted in Thailand’s northern part. Other documentations related to this have suggested a particular subtype E founder virus around 1986-1987 while the estimate date of their calculations being 1987. These analyses provide estimation of the year of HIV evolving from the SIVcpz.these estimations have suggestion that the ancestral sequence of the HIV-1 M group existed several years before the programs of vaccination. They also suggest that in 1957 there was full establishment of the various sub types. For the hypothesis of OPV t have consistency in analysis, more than nine viruses that are distinct genetically have to be differentiated in the chimpanzees before they get transmitted to human beings, then vaccine get it to the population of human beings, this is implausible. Therefore the Phylogenetic analysis indicates that ancestral sequence of HIV-1 M group came about around 1931.The analysis therefore has shown that the HIV virus was transmitted and not created. Conclusion The origin of various microorganisms have been of great concern to human beings since medieval times especially considering their disease causing properties, that they are very detrimental to health due to the severe consequences of their infections including loss of lives, causing disabilities among people, low work capacity, poor economic performance as well as impairments is a fact. 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