Whole genome sequencing
Whole genome sequencing is ostensibly the process of determining the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. In practice, genome sequences that are nearly complete are called whole genome sequences. Whole genome sequencing has been used as a research tool, but is being introduced to clinics. In the future of personalized medicine, whole genome sequence data may be an important tool to guide therapeutic intervention; the tool of gene sequencing at SNP level is used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, hence may lay the foundation for predicting disease susceptibility and drug response. Whole genome sequencing should not be confused with DNA profiling, which only determines the likelihood that genetic material came from a particular individual or group, does not contain additional information on genetic relationships, origin or susceptibility to specific diseases.
In addition, whole genome sequencing should not be confused with methods that sequence specific subsets of the genome - such methods include whole exome sequencing or SNP genotyping. As of 2017 there were no complete genomes including humans. Between 4% to 9% of the human genome satellite DNA, had not been sequenced; the DNA sequencing methods used in the 1970s and 1980s were manual, for example Maxam-Gilbert sequencing and Sanger sequencing. The shift to more rapid, automated sequencing methods in the 1990s allowed for sequencing of whole genomes; the first organism to have its entire genome sequenced was Haemophilus influenzae in 1995. After it, the genomes of other bacteria and some archaea were first sequenced due to their small genome size. H. influenzae has a genome of 1,830,140 base pairs of DNA. In contrast, both unicellular and multicellular such as Amoeba dubia and humans have much larger genomes. Amoeba dubia has a genome of 700 billion nucleotide pairs spread across thousands of chromosomes.
Humans contain fewer nucleotide pairs than A. dubia however their genome size far outweighs the genome size of individual bacteria. The first bacterial and archaeal genomes, including that of H. influenzae, were sequenced by Shotgun sequencing. In 1996 the first eukaryotic genome was sequenced. S. cerevisiae, a model organism in biology has a genome of only around 12 million nucleotide pairs, was the first unicellular eukaryote to have its whole genome sequenced. The first multicellular eukaryote, animal, to have its whole genome sequenced was the nematode worm: Caenorhabditis elegans in 1998. Eukaryotic genomes are sequenced by several methods including Shotgun sequencing of short DNA fragments and sequencing of larger DNA clones from DNA libraries such as bacterial artificial chromosomes and yeast artificial chromosomes. In 1999, the entire DNA sequence of human chromosome 22, the shortest human autosome, was published. By the year 2000, the second animal and second invertebrate genome was sequenced - that of the fruit fly Drosophila melanogaster - a popular choice of model organism in experimental research.
The first plant genome - that of the model organism Arabidopsis thaliana - was fully sequenced by 2000. By 2001, a draft of the entire human genome sequence was published; the genome of the laboratory mouse Mus musculus was completed in 2002. In 2004, the Human Genome Project published an incomplete version of the human genome. Thousands of genomes have been wholly or sequenced. Any biological sample containing a full copy of the DNA—even a small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing; such samples may include saliva, epithelial cells, bone marrow, seeds, plant leaves, or anything else that has DNA-containing cells. The genome sequence of a single cell selected from a mixed population of cells can be determined using techniques of single cell genome sequencing; this has important advantages in environmental microbiology in cases where a single cell of a particular microorganism species can be isolated from a mixed population by microscopy on the basis of its morphological or other distinguishing characteristics.
In such cases the necessary steps of isolation and growth of the organism in culture may be omitted, thus allowing the sequencing of a much greater spectrum of organism genomes. Single cell genome sequencing is being tested as a method of preimplantation genetic diagnosis, wherein a cell from the embryo created by in vitro fertilization is taken and analyzed before embryo transfer into the uterus. After implantation, cell-free fetal DNA can be taken by simple venipuncture from the mother and used for whole genome sequencing of the fetus. Sequencing of nearly an entire human genome was first accomplished in 2000 through the use of shotgun sequencing technology. While full genome shotgun sequencing for small genomes was in use in 1979, broader application benefited from pairwise end sequencing, known colloquially as double-barrel shotgun sequencing; as sequencing projects began to take on longer and more complicated genomes, multiple groups began to realize that useful information could be obtained by sequencing both
Epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence. The Greek prefix epi- in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic basis for inheritance. Epigenetics most denotes changes that affect gene activity and expression, but can be used to describe any heritable phenotypic change; such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal development. The standard definition of epigenetics requires these alterations to be heritable, either in the progeny of cells or of organisms; the term refers to the changes themselves: functionally relevant changes to the genome that do not involve a change in the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA.
These epigenetic changes may last through cell divisions for the duration of the cell's life, may last for multiple generations though they do not involve changes in the underlying DNA sequence of the organism. One example of an epigenetic change in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become differentiated cells. In other words, as a single fertilized egg cell – the zygote – continues to divide, the resulting daughter cells change into all the different cell types in an organism, including neurons, muscle cells, endothelium of blood vessels, etc. by activating some genes while inhibiting the expression of others. Some phenomena not heritable have been described as epigenetic. For example, the term epigenetic has been used to describe any modification of chromosomal regions histone modifications, whether or not these changes are heritable or associated with a phenotype.
The consensus definition now requires a trait to be heritable. The term epigenetics in its contemporary usage emerged in the 1990s, but for some years has been used in somewhat variable meanings. A consensus definition of the concept of epigenetic trait as "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence" was formulated at a Cold Spring Harbor meeting in 2008, although alternate definitions that include non-heritable traits are still being used; the term epigenesis has a generic meaning "extra growth". It has been used in English since the 17th century. From the generic meaning, the associated adjective epigenetic, C. H. Waddington coined the term epigenetics in 1942 as pertaining to epigenesis, in parallel to Valentin Haecker's'phenogenetics'. Epigenesis in the context of the biology of that period referred to the differentiation of cells from their initial totipotent state in embryonic development; when Waddington coined the term, the physical nature of genes and their role in heredity was not known.
Waddington held that cell fates were established in development much as a marble rolls down to the point of lowest local elevation. Waddington suggested visualising increasing irreversibility of cell type differentiation as ridges rising between the valleys where the marbles are travelling. In recent times Waddington's notion of the epigenetic landscape has been rigorously formalized in the context of the systems dynamics state approach to the study of cell-fate. Cell-fate determination is predicted to exhibit certain dynamics, such as attractor-convergence or oscillatory; the term "epigenetic" has been used in developmental psychology to describe psychological development as the result of an ongoing, bi-directional interchange between heredity and the environment. Interactivist ideas of development have been discussed in various forms and under various names throughout the 19th and 20th centuries. An early version was proposed, among the founding statements in embryology, by Karl Ernst von Baer and popularized by Ernst Haeckel.
A radical epigenetic view was developed by Paul Wintrebert. Another variation, probabilistic epigenesis, was presented by Gilbert Gottlieb in 2003; this view encompasses all of the possible developing factors on an organism and how they not only influence the organism and each other, but how the organism influences its own development. The developmental psychologist Erik Erikson wrote of an epigenetic principle in his book Identity: Youth and Crisis, encompassing the notion that we develop through an unfolding of our personality in predetermined stages, that our environment and surrounding culture influence how we progress through these stages; this biological unfolding in relation to our socio-cultural settings is done in stages of psychosocial development, where "progress through each stage is in part determined by our success, or lack of success, in all the previous stages." Robin Holliday defined epigenetics as "the study of the mechanisms of temporal and spatial control of gene activity during the development of complex organisms."
Thus epigenetic can be used to describe anything other than DNA s
A microRNA is a small non-coding RNA molecule found in plants and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression. MiRNAs function via base-pairing with complementary sequences within mRNA molecules; as a result, these mRNA molecules are silenced, by one or more of the following processes: Cleavage of the mRNA strand into two pieces, Destabilization of the mRNA through shortening of its poly tail, Less efficient translation of the mRNA into proteins by ribosomes.miRNAs resemble the small interfering RNAs of the RNA interference pathway, except miRNAs derive from regions of RNA transcripts that fold back on themselves to form short hairpins, whereas siRNAs derive from longer regions of double-stranded RNA. The human genome may encode over 1900 miRNAs, although more recent analysis indicates that the number is closer to 600.miRNAs are abundant in many mammalian cell types and appear to target about 60% of the genes of humans and other mammals.
Many miRNAs are evolutionarily conserved, which implies that they have important biological functions. For example, 90 families of miRNAs have been conserved since at least the common ancestor of mammals and fish, most of these conserved miRNAs have important functions, as shown by studies in which genes for one or more members of a family have been knocked out in mice; the first miRNA was discovered in the early 1990s. However, miRNAs were not recognized as a distinct class of biological regulators until the early 2000s. MiRNA research revealed different sets of miRNAs expressed in different cell types and tissues and multiple roles for miRNAs in plant and animal development and in many other biological processes. Aberrant miRNA expression are implicated in disease states. MiRNA-based therapies are under investigation; the first miRNA was discovered in 1993 including Lee and Feinbaum. However, additional insight into its mode of action required published work by Ruvkun's team, including Wightman and Ha.
These groups published back-to-back papers on the lin-4 gene, known to control the timing of C. elegans larval development by repressing the lin-14 gene. When Lee et al. isolated the lin-4 miRNA, they found that instead of producing an mRNA encoding a protein, it produced short non-coding RNAs, one of, a ~22-nucleotide RNA that contained sequences complementary to multiple sequences in the 3' UTR of the lin-14 mRNA. This complementarity was proposed to inhibit the translation of the lin-14 mRNA into the LIN-14 protein. At the time, the lin-4 small RNA was thought to be a nematode idiosyncrasy. In 2000, a second small RNA was characterized: let-7 RNA, which represses lin-41 to promote a developmental transition in C. elegans. The let-7 RNA was found to be conserved in many species, leading to the suggestion that let-7 RNA and additional "small temporal RNAs" might regulate the timing of development in diverse animals, including humans. A year the lin-4 and let-7 RNAs were found to be part of a large class of small RNAs present in C. elegans and human cells.
The many RNAs of this class resembled the lin-4 and let-7 RNAs, except their expression patterns were inconsistent with a role in regulating the timing of development. This suggested. At this point, researchers started using the term "microRNA" to refer to this class of small regulatory RNAs; the first human disease associated with deregulation of miRNAs was chronic lymphocytic leukemia. Under a standard nomenclature system, names are assigned to experimentally confirmed miRNAs before publication; the prefix "miR" is followed by a dash and a number, the latter indicating order of naming. For example, miR-124 was named and discovered prior to miR-456. A capitalized "miR-" refers to the mature form of the miRNA, while the uncapitalized "mir-" refers to the pre-miRNA and the pri-miRNA, "MIR" refers to the gene that encodes them.miRNAs with nearly identical sequences except for one or two nucleotides are annotated with an additional lower case letter. For example, miR-124a is related to miR-124b. Pre-miRNAs, pri-miRNAs and genes that lead to 100% identical mature miRNAs but that are located at different places in the genome are indicated with an additional dash-number suffix.
For example, the pre-miRNAs hsa-mir-194-1 and hsa-mir-194-2 lead to an identical mature miRNA but are from genes located in different genome regions. Species of origin is designated with a three-letter prefix, e.g. hsa-miR-124 is a human miRNA and oar-miR-124 is a sheep miRNA. Other common prefixes include'v' for viral and'd' for Drosophila miRNA; when two mature microRNAs originate from opposite arms of the same pre-miRNA and are found in similar amounts, they are denoted with a -3p or -5p suffix.. However, the mature microRNA found from one arm of the hairpin is much more abundant than that found from the other arm, in which case, an asterisk following the name indicates the mature species found at low levels from the opposite arm of a hairpin. For example, miR-124 and miR-124* share a pre-miRNA hairpin, but much more miR-124 is found in the cell. Plant miRNAs have near-perfect pairing with their mRNA targets, which induces gene repression through cleavage of the target transcripts. In contrast, animal miRNAs are able to recognize their target mRNAs by using as little as 6–8 nucleotides at the 5' end of the miRNA, not enough pair
Plasmodium falciparum is a unicellular protozoan parasite of humans, the deadliest species of Plasmodium that cause malaria in humans. It is transmitted through the bite of a female Anopheles mosquito, it is responsible for 50% of all malaria cases. It causes the disease's most dangerous form called falciparum malaria, it is therefore regarded as the deadliest parasite in humans, causing 435,000 deaths in 2017. It is associated with the development of blood cancer and is classified as Group 2A carcinogen; the species originated from the malarial parasite Laverania found in gorillas, around 10,000 years ago. Alphonse Laveran was the first to identify the parasite in 1880, named it Oscillaria malariae. Ronald Ross discovered its transmission by mosquito in 1897. Giovanni Battista Grassi elucidated the complete transmission from a female anopheline mosquito to humans in 1898. In 1897, William H. Welch created the name Plasmodium falciparum, which ICZN formally adopted in 1954. P. falciparum assumes several different forms during its life cycle.
The human-infective stage are sporozoites from the salivary gland of a mosquito. The sporozoites multiply in the liver to become merozoites; these merozoites invade the erythrocytes to form trophozoites and gametocytes, during which the symptoms of malaria are produced. In the mosquito, the gametocytes undergo sexual reproduction to a zygote. Ookinete forms oocyts from; as of the latest World Malaria Report of the World Health Organization, there were 219 million cases of malaria worldwide in 2017, up from 216 million cases in 2016. This resulted in an estimated 435,000 deaths; every malarial death is caused by P. falciparum, 93% of death occurs in Africa. Children under five years of age are most affected. In Sub-Saharan Africa, over 75% of cases were due to P. falciparum, whereas in most other malarial countries, less virulent plasmodial species predominate. Falciparum malaria was familiar to the ancient Greeks, who gave the general name πυρετός pyretós "fever". Hippocrates gave several descriptions on tertian quartan fever.
It was prevalent throughout the ancient Roman civilizations. It was the Romans who named the disease "malaria"—mala for bad, aria for air, as they believed that the disease was spread by contaminated air, or miasma. A German physician, Johann Friedrich Meckel, must have been the first to see P. falciparum but not knowing what it was. In 1847 he reported the presence of black pigment granules from the blood and spleen of a patient who died of malaria; the French Army physician Charles Louis Alphonse Laveran, while working at Bône Hospital identified the parasite as a causative pathogen of malaria in 1880. He presented his discovery before the French Academy of Medicine in Paris, published it in The Lancet, in 1881, he gave the scientific name Oscillaria malariae. But his discovery was received with skepticism because by that time leading physicians such as Theodor Albrecht Edwin Klebs and Corrado Tommasi-Crudeli claimed that they had discovered a bacterium as the pathogen of malaria. Laveran's discovery was accepted only after five years when Camillo Golgi confirmed the parasite using better microscope and staining technique.
Laveran was awarded the Nobel Prize in Medicine in 1907 for his work. In 1900, the Italian zoologist Giovanni Battista Grassi categorized Plasmodium species based on the timing of fever in the patient; the British physician Patrick Manson formulated the mosquito-malaria theory in 1894. His colleague Ronald Ross, a British Army surgeon, travelled to India to test the theory. Ross discovered in 1897; the next year, he demonstrated that a malarial parasite of birds could be transmitted by mosquitoes from one bird to another. Around the same time, Grassi demonstrated that P. falciparum was transmitted in humans only by female anopheline mosquito. Ross and Grassi were nominated for the Nobel Prize in Physiology or Medicine in 1902. Under controversial circumstances, only Ronald Ross was selected for the award. There was a long debate on the taxonomy, it was only in 1954 the International Commission on Zoological Nomenclature approved the binominal Plasmodium falciparum. The valid genus Plasmodium was created by two Italian physicians Ettore Marchiafava and Angelo Celli in 1885.
The species name was introduced by an American physician William Henry Welch in 1897. It is derived from the Latin falx, meaning "sickle" and parum meaning "like or equal to another". P. falciparum is now accepted to have evolved from Laverania species present in gorilla in Western Africa. Genetic diversity indicates; the closest relative of P. falciparum is P. praefalciparum, a parasite of gorillas, as supported by mitochondrial and nuclear DNA sequences. These two species are related to the chimpanzee parasite P. reichenowi, thought to be the closest relative of P. falciparum. P. falciparum was once thought to originate from a parasite of birds. Levels of genetic polymorphism are low within the P. falciparum genome compared to that of closely