1.
Chromosome
–
A chromosome is a DNA molecule with part or all of the genetic material of an organism. Prokaryotes usually have one single circular chromosome, whereas most eukaryotes are diploid, chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes, a nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around it. Chromatin fiber, together with associated proteins is known as chromatin, chromatin is present in most cells, with a few exceptions, for example, red blood cells. Occurring only in the nucleus of cells, chromatin contains the vast majority of DNA, except for a small amount inherited maternally. Chromosomes are normally visible under a microscope only when the cell is undergoing the metaphase of cell division. Before this happens every chromosome is copied once, and the copy is joined to the original by a centromere resulting in an X-shaped structure, the original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, in this highly condensed form chromosomes are easiest to distinguish and study. In prokaryotic cells, chromatin occurs free-floating in cytoplasm, as these cells lack organelles, the main information-carrying macromolecule is a single piece of coiled double-helix DNA, containing many genes, regulatory elements and other noncoding DNA. The DNA-bound macromolecules are proteins that serve to package the DNA, chromosomes vary widely between different organisms. Some species such as certain bacteria also contain plasmids or other extrachromosomal DNA and these are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. Chromosomal recombination during meiosis and subsequent sexual reproduction plays a significant role in genetic diversity. In prokaryotes and viruses, the DNA is often densely packed and organized, in the case of archaea, by homologs to eukaryotic histones, small circular genomes called plasmids are often found in bacteria and also in mitochondria and chloroplasts, reflecting their bacterial origins. Some use the term chromosome in a sense, to refer to the individualized portions of chromatin in cells. However, others use the concept in a sense, to refer to the individualized portions of chromatin during cell division. The word chromosome comes from the Greek χρῶμα and σῶμα, describing their strong staining by particular dyes, schleiden, Virchow and Bütschli were among the first scientists who recognized the structures now so familiar to everyone as chromosomes. The term was coined by von Waldeyer-Hartz, referring to the term chromatin, in a series of experiments beginning in the mid-1880s, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were the continuity of chromosomes and the individuality of chromosomes and it is the second of these principles that was so original
2.
Organelle
–
In cell biology, an organelle is a specialized subunit within a cell that has a specific function. Individual organelles are usually enclosed within their own lipid bilayers. The name organelle comes from the idea that these structures are to cells what an organ is to the body, organelles are identified by microscopy, and can also be purified by cell fractionation. There are many types of organelles, particularly in eukaryotic cells, while prokaryotes do not possess organelles per se, some do contain protein-based bacterial microcompartments, which are thought to act as primitive organelles. In biology organs are defined as confined functional units within an organism, the analogy of bodily organs to microscopic cellular substructures is obvious, as from even early works, authors of respective textbooks rarely elaborate on the distinction between the two. In the 1830s, Félix Dujardin refuted Ehrenberg theory which said that microorganims have the organs of multicellular animals. Credited as the first to use a diminutive of organ for cellular structures was German zoologist Karl August Möbius, under this definition, there would only be two broad classes of organelles, mitochondria plastids. Other organelles are also suggested to have endosymbiotic origins, but do not contain their own DNA, under the more restricted definition of membrane-bound structures, some parts of the cell do not qualify as organelles. Nevertheless, the use of organelle to refer to non-membrane bound structures such as ribosomes is common and this has led some texts to delineate between membrane-bound and non-membrane bound organelles. The larger organelles, such as the nucleus and vacuoles, are visible with the light microscope. They were among the first biological discoveries made after the invention of the microscope, not all eukaryotic cells have each of the organelles listed below. Exceptional organisms have cells that do not include some organelles that might otherwise be considered universal to eukaryotes, there are also occasional exceptions to the number of membranes surrounding organelles, listed in the tables below. In addition, the number of organelles of each type found in a given cell varies depending upon the function of that cell. This idea is supported in the Endosymbiotic theory, in the past, they were often viewed as having little internal organization, but slowly, details are emerging about prokaryotic internal structures. However, more recent research has revealed that at least some prokaryotes have microcompartments such as carboxysomes and these subcellular compartments are 100–200 nm in diameter and are enclosed by a shell of proteins. The function of a protein is correlated with the organelle in which it resides. CoRR Hypothesis Ejectosome Endosymbiotic theory Organelle biogenesis Membrane vesicle trafficking Host-pathogen interface Tree of Life project, Eukaryotes
3.
Mother
–
A mother is the female parent of a child. Mothers are women who inhabit or perform the role of bearing some relation to their children, thus, dependent on the context, women can be considered mothers by virtue of having given birth, by raising their child, supplying their ovum for fertilisation, or some combination thereof. Such conditions provide a way of delineating the concept of motherhood, women who meet the third and first categories usually fall under the terms birth mother or biological mother, regardless of whether the individual in question goes on to parent their child. Accordingly, a woman who meets only the condition may be considered an adoptive mother. The above concepts defining the role of mother are neither exhaustive nor universal, as any definition of mother may differ based on how social, cultural, and religious roles are defined. The parallel conditions and terms for males, those who are fathers do not, by definition, Mother and fatherhood are not limited to those who are or have parented. Women who are pregnant may be referred to as expectant mothers or mothers-to-be, the modern English word is from Middle English moder, from Old English mōdor, from Proto-Germanic *mōdēr, from Proto-Indo-European *méh₂tēr. Other cognates include Latin māter, Greek μήτηρ, Common Slavic *mati, Persian مادر, biological motherhood for humans, as in other mammals, occurs when a pregnant female gestates a fertilized ovum. Typically a fetus develops from the zygote, resulting in an embryo. Gestation occurs in the uterus until the fetus is sufficiently developed to be born. In humans, gestation is often around 9 months in duration, after which the woman experiences labor and this is not always the case, however, as some babies are born prematurely, late, or in the case of stillbirth, do not survive gestation. Usually, once the baby is born, the mother produces milk via the lactation process, the mothers breast milk is the source of antibodies for the infants immune system and commonly the sole source of nutrition for the first year or more of the childs life. Mother can often apply to an other than the biological parent. This is commonly either a mother or a stepmother. The term othermother or other mother is used in some contexts for women who provide care for a child not biologically their own in addition to the childs primary mother. Adoption, in forms, has been practiced throughout history. Modern systems of adoption, arising in the 20th century, tend to be governed by comprehensive statutes, in recent decades, international adoptions have become more and more common. Adoption in the United States is common and relatively easy from a point of view
4.
Offspring
–
In biology, offspring are the young born of living organisms, produced either by a single organism or, in the case of sexual reproduction, two organisms. Collective offspring may be known as a brood or progeny in a general way. This can refer to a set of offspring, such as the chicks hatched from one clutch of eggs, or to all the offspring. Human offspring are referred to as children, male children are sons, offspring can occur after mating or after artificial insemination. Offspring contains many parts and properties that are precise and accurate in what they consist of, and what they define. As the offspring of a new species, also known as a child or f1 generation, consist of genes of the father and the mother, each of these offspring contains numerous genes which have coding for specific tasks and properties. Males and females contribute equally to the genotypes of their offspring, in which gametes fuse and form. An important aspect of the formation of the parent offspring is the chromosome, depending on which genes are dominantly expressed in the gene will result in the sex of the offspring. The female will give an X chromosome, whereas the male, depending on the situation. If a male offspring is produced, the gene will consist of an X, if two X chromosomes are expressed and produced, it produces a female offspring. Cloning is the production of an offspring which represents the identical genes as its parent, reproductive cloning begins with the removal of the nucleus from an egg, which holds the genetic material. In order to clone an organ, a cell is to be produced. A common misconception of cloning is that it produces a copy of the parent being cloned. Cloning copies the DNA/genes of the parent and then creates a genetic duplicate, the clone will not be a similar copy as he or she will grow up in different surroundings from the clone and may encounter different opportunities and experiences. Although mostly positive, cloning also faces some setbacks in terms of ethics, though cell division and DNA replication is a vital part of survival, there are many steps involved and mutations can occur with permanent change in an organisms and their offsprings DNA. Lineal descendant kinship and descent Clutch size Infanticide Litter Parent-offspring conflict Parental investment
5.
Egg cell
–
The egg cell, or ovum, is the female reproductive cell in oogamous organisms. The egg cell is not capable of active movement. When egg and sperm fuse, a cell is formed. Karl Ernst von Baer discovered the mammalian ovum in 1827, the fusion of spermatozoa with ova was observed by Oskar Hertwig in 1876. In animals, egg cells are known as ova. The term ovule is used for the young ovum of an animal, in vertebrates, ova are produced by female gonads called ovaries a number of ova are present at birth in mammals and mature via oogenesis. White et al. disproved the longstanding dogma that all of the ova are produced before birth, the team from the Vincent Center for Reproductive Biology, Massachusetts, Boston could prove that oocyte fromation takes place in ovaries of reproductive-age women. This report challenged a fundamental belief, held since the 1950s, in all mammals the ovum is fertilized inside the female body. The human ova grow from primitive germ cells that are embedded in the substance of the ovaries, each of them divides repeatedly to give secretions of the uterine glands, ultimately forming a blastocyst. The ovum is one of the largest cells in the human body, the human ovum measures approximately 0.12 mm in diameter. Ooplasm is the yolk of the ovum, a substance at its center, which contains its nucleus, named the germinal vesicle. Mammalian ova contain only an amount of the nutritive yolk. In contrast, bird eggs contain enough to supply the chick with nutriment throughout the period of incubation. In the oviparous animals the ova develop protective layers and pass through the oviduct to the outside of the body and they are fertilized by male sperm either inside the female body, or outside. After fertilization, an embryo develops, nourished by nutrients contained in the egg and it then hatches from the egg, outside the mothers body. See egg for a discussion of eggs of oviparous animals, the egg cells cytoplasm and mitochondria are the sole means the egg is able to reproduce by mitosis and eventually form a blastocyst after fertilization. Some fish, reptiles and many use this technique. Nearly all land plants have alternating diploid and haploid generations, gametes are produced by the gametophyte, which is the haploid generation
6.
Human mitochondrial genetics
–
Human mitochondrial genetics is the study of the genetics of human mitochondrial DNA. The human mitochondrial genome is the entirety of information contained in human mitochondria. Mitochondria are small structures in cells that generate energy for the cell to use, Mitochondrial DNA is not transmitted through nuclear DNA. In humans, as in most multicellular organisms, mitochondrial DNA is inherited only from the mothers ovum, there are theories, however, that paternal mtDNA transmission in humans can occur under certain circumstances. Mitochondrial inheritance is therefore non-Mendelian, as Mendelian inheritance presumes that half the material of a fertilized egg derives from each parent. Eighty percent of mitochondrial DNA codes for mitochondrial RNA, and therefore most mitochondrial DNA mutations lead to functional problems, which may be manifested as muscle disorders. Because they provide 30 molecules of ATP per glucose molecule in contrast to the 2 ATP molecules produced by glycolysis, the mitochondrial diseases are genetic disorders carried in mitochondrial DNA, or nuclear DNA coding for mitochondrial components. Slight problems with any one of the enzymes used by the mitochondria can be devastating to the cell. In humans, mitochondrial DNA forms closed circular molecules that contain 16,569, DNA base pairs, each human mitochondrion contains, on average, approximately 5 such mtDNA molecules, with the quantity ranging between 1 and 15. Each human cell contains approximately 100 mitochondria, giving a number of mtDNA molecules per human cell of approximately 500. Mitochondrial genetic mutations that occur in the nuclear DNA can occur in any of the chromosomes, mutations inherited through the chromosomes can be autosomal dominant or recessive and can also be sex-linked dominant or recessive. Chromosomal inheritance follows normal Mendelian laws, despite the fact that the phenotype of the disease may be masked, because of the complex ways in which mitochondrial and nuclear DNA communicate and interact, even seemingly simple inheritance is hard to diagnose. A mutation in chromosomal DNA may change a protein that regulates the production of another protein in the mitochondria or the cytoplasm. Mitochondrial genome mutations are passed on 100% of the time from mother to all her offspring, so, if a female has a mitochondrial trait, all offspring inherit it. However, if a male has a trait, no offspring inherit it. In a few cases, some mitochondria or a mitochondrion from the cell enters the oocyte. Genes in the mitochondrial genome are as follows. It was originally believed that the mitochondrial genome contained only 13 protein-coding genes
7.
Immunogold labelling
–
Immunogold labeling or Immunogold staining is a staining technique used in electron microscopy. Gold is used for its electron density which increases electron scatter to give high contrast dark spots. First used in 1971, immunogold labeling has been applied to both electron microscopy and scanning electron microscopy, as well as brightfield microscopy. The labeling technique can be adapted to distinguish multiple objects by using differently-sized gold particles, Immunogold labeling can introduce artifacts, as the gold particles reside some distance from the labelled object and very thin sectioning is required during sample preparation. Immunogold labeling was first used in 1971 by Faulk and Taylor to identify Salmonella antigens and it was first applied in transmission electron microscopy and was especially useful in highlighting proteins found in low densities, such as some cell surface antigens. As the resolution of scanning electron microscopy increased, so too did the need for nanoparticle-sized labels such as immunogold, in 1975, Horisberger and coworkers successfully visualised gold nanoparticles with a diameter of less than 30 nm and this soon became an established SEM technique. First, a section of the sample is cut, often using a microtome. Various other stages of preparation may then take place. The prepared sample is incubated with a specific antibody designed to bind the molecule of interest. Next, an antibody which has gold particles attached is added. Gold can also be attached to protein A or protein G instead of a secondary antibody, the electron-dense gold particle can now be seen under an electron microscope as a black dot, indirectly labeling the molecule of interest. Immunogold labeling can be used to more than one target simultaneously. This can be achieved in electron microscopy by using two different-sized gold particles, an extension of this method used three different sized gold particles to track the localisation of regulatory peptides. A more complex method of multi-site labeling involves labeling opposite sides of an antigenic site separately, although immunogold labeling is typically used for transmission electron microscopy, when the gold is silver-enhanced it can be seen using brightfield microscopy. The silver enhancement increases the size, also making scanning electron microscopy possible. In order to produce the gold particles, colloidal gold particles are placed in an acidic enhancing solution containing silver ions. Gold particles then act as a site and silver is deposited onto the particle. An example of the application of silver-enhanced immunogold labeling was in the identification of the pathogen Erwinia amylovora, an inherent limitation to the immunogold technique is that the gold particle is around 15-30 nm away from the site to which the primary antibody is bound
8.
DNA
–
Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
9.
Mitochondrion
–
The mitochondrion is a double membrane-bound organelle found in all eukaryotic organisms. Some cells in multicellular organisms may however lack them. A number of organisms, such as microsporidia, parabasalids. To date, only one eukaryote, Monocercomonoides, is known to have completely lost its mitochondria, the word mitochondrion comes from the Greek μίτος, mitos, thread, and χονδρίον, chondrion, granule or grain-like. Mitochondria generate most of the supply of adenosine triphosphate, used as a source of chemical energy. Mitochondria are commonly between 0.75 and 3 μm in diameter but vary considerably in size and structure, unless specifically stained, they are not visible. Mitochondrial biogenesis is in turn temporally coordinated with these cellular processes, Mitochondria have been implicated in several human diseases, including mitochondrial disorders, cardiac dysfunction, heart failure and autism. The number of mitochondria in a cell can vary widely by organism, tissue, for instance, red blood cells have no mitochondria, whereas liver cells can have more than 2000, The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the space, the inner membrane. Although most of a cells DNA is contained in the cell nucleus, mitochondrial proteins vary depending on the tissue and the species. In humans,615 distinct types of protein have been identified from cardiac mitochondria, the mitochondrial proteome is thought to be dynamically regulated. The first observations of structures that probably represented mitochondria were published in the 1840s. Richard Altmann, in 1890, established them as cell organelles, the term mitochondria was coined by Carl Benda in 1898. Leonor Michaelis discovered that Janus green can be used as a stain for mitochondria in 1900. Benjamin F. Kingsbury, in 1912, first related them with cell respiration, in 1913, particles from extracts of guinea-pig liver were linked to respiration by Otto Heinrich Warburg, which he called grana. Warburg and Heinrich Otto Wieland, who had postulated a similar particle mechanism. It was not until 1925, when David Keilin discovered cytochromes, in the following years, the mechanism behind cellular respiration was further elaborated, although its link to the mitochondria was not known. The introduction of tissue fractionation by Albert Claude allowed mitochondria to be isolated from other cell fractions, in 1946, he concluded that cytochrome oxidase and other enzymes responsible for the respiratory chain were isolated to the mitchondria
10.
Eukaryote
–
A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
11.
Adenosine triphosphate
–
Adenosine triphosphate is a nucleotide, also called a nucleoside triphosphate, is a small molecule used in cells as a coenzyme. It is often referred to as the unit of currency of intracellular energy transfer. ATP transports chemical energy within cells for metabolism, most cellular functions need energy in order to be carried out, synthesis of proteins, synthesis of membranes, movement of the cell, cellular division, transport of various solutes etc. The ATP is the molecule that carries energy to the place where the energy is needed, when ATP breaks into ADP and Pi, the breakdown of the last covalent link of phosphate liberates energy that is used in reactions where it is needed. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three mechanisms of ATP biosynthesis. Metabolic processes that use ATP as an energy source convert it back into its precursors, ATP is therefore continuously recycled in organisms, the human body, which on average contains only 250 grams of ATP, turns over its own body weight equivalent in ATP each day. ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and it is also used by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP. The ratio between ATP and AMP is used as a way for a cell to sense how much energy is available and control the metabolic pathways that produce and consume ATP. Apart from its roles in signaling and energy metabolism, ATP is also incorporated into nucleic acids by polymerases in the process of transcription, ATP is the neurotransmitter believed to signal the sense of taste. The structure of this consists of a purine base attached by the 9′ nitrogen atom to the 1′ carbon atom of a pentose sugar. Three phosphate groups are attached at the 5′ carbon atom of the pentose sugar and it is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. When ATP is used in DNA synthesis, the sugar is first converted to deoxyribose by ribonucleotide reductase. ATP was discovered in 1929 by Karl Lohmann, and independently by Cyrus Fiske and Yellapragada Subbarow of Harvard Medical School and it was proposed to be the intermediary molecule between energy-yielding and energy-requiring reactions in cells by Fritz Albert Lipmann in 1941. It was first artificially synthesized by Alexander Todd in 1948, ATP consists of adenosine – composed of an adenine ring and a ribose sugar – and three phosphate groups. The phosphoryl groups, starting with the group closest to the ribose, are referred to as the alpha, beta, consequently, it is closely related to the adenosine nucleotide, a monomer of RNA. ATP is highly soluble in water and is stable in solutions between pH6.8 and 7.4, but is rapidly hydrolysed at extreme pH. Consequently, ATP is best stored as an anhydrous salt, ATP is an unstable molecule in unbuffered water, in which it hydrolyses to ADP and phosphate. This is because the strength of the bonds between the groups in ATP is less than the strength of the hydrogen bonds, between its products, and water
12.
Cell nucleus
–
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. Eukaryotes usually have a nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei. Cell nuclei contain most of the genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones. The genes within these chromosomes are the nuclear genome and are structured in such a way to promote cell function. The nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression—the nucleus is, therefore, because the nuclear membrane is impermeable to large molecules, nuclear pores are required to regulate nuclear transport of molecules across the envelope. The pores cross both nuclear membranes, providing a channel through which larger molecules must be transported by carrier proteins while allowing free movement of small molecules. Movement of large molecules such as proteins and RNA through the pores is required for gene expression and the maintenance of chromosomes. The best-known of these is the nucleolus, which is involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA, the nucleus was the first organelle to be discovered. What is most likely the oldest preserved drawing dates back to the early microscopist Antonie van Leeuwenhoek and he observed a lumen, the nucleus, in the red blood cells of salmon. Unlike mammalian red blood cells, those of other vertebrates still contain nuclei, the nucleus was also described by Franz Bauer in 1804 and in more detail in 1831 by Scottish botanist Robert Brown in a talk at the Linnean Society of London. Brown was studying orchids under microscope when he observed an opaque area and he did not suggest a potential function. In 1838, Matthias Schleiden proposed that the plays a role in generating cells. He believed that he had observed new cells assembling around cytoblasts, Franz Meyen was a strong opponent of this view, having already described cells multiplying by division and believing that many cells would have no nuclei. The function of the nucleus remained unclear, between 1877 and 1878, Oscar Hertwig published several studies on the fertilization of sea urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus. This was the first time it was suggested that an individual develops from a nucleated cell, therefore, the necessity of the sperm nucleus for fertilization was discussed for quite some time. However, Hertwig confirmed his observation in other groups, including amphibians. Eduard Strasburger produced the results for plants in 1884
13.
Plastid
–
The plastid is a major double-membrane organelle found, among others, in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell and they often contain pigments used in photosynthesis, and the types of pigments present can change or determine the cells color. They have an evolutionary origin and possess a double-stranded DNA molecule that is circular. Those plastids that contain chlorophyll can carry out photosynthesis, Plastids can also store products like starch and can synthesise fatty acids and terpenes, which can be used for producing energy and as raw material for the synthesis of other molecules. For example, the components of the plant cuticle and its epicuticular wax are synthesized by the cells from palmitic acid. All plastids are derived from proplastids, which are present in the regions of the plant. Proplastids and young chloroplasts commonly divide by fission, but more mature chloroplasts also have this capacity. In plants, plastids may differentiate into several forms, depending upon which function they play in the cell, each plastid creates multiple copies of a circular 75–250 kilobase plastome. The plastome contains about 100 genes encoding ribosomal and transfer ribonucleic acids as well as involved in photosynthesis. However, these only represent a small fraction of the total protein set-up necessary to build and maintain the structure. Plastid DNA exists as large protein-DNA complexes associated with the envelope membrane. Each nucleoid particle may contain more than 10 copies of the plastid DNA, the proplastid contains a single nucleoid located in the centre of the plastid. The developing plastid has many nucleoids, localized at the periphery of the plastid, during the development of proplastids to chloroplasts, and when plastids convert from one type to another, nucleoids change in morphology, size and location within the organelle. The remodelling of nucleoids is believed to occur by modifications to the composition, many plastids, particularly those responsible for photosynthesis, possess numerous internal membrane layers. In plant cells, long thin protuberances called stromules sometimes form and extend from the main body into the cytosol. Proteins, and presumably smaller molecules, can move within stromules, most cultured cells that are relatively large compared to other plant cells have very long and abundant stromules that extend to the cell periphery. In 2014, evidence of possible plastid genome loss was found in Rafflesia lagascae, a non-photosynthetic parasitic flowering plant, and in Polytomella, extensive searches for plastid genes in both Rafflesia and Polytomella yielded no results, however the conclusion that their plastomes are entirely missing is still controversial. Some scientists argue that plastid genome loss is unlikely since even non-photosynthetic plastids contain genes necessary to complete various biosynthetic pathways, in algae, the term leucoplast is used for all unpigmented plastids and their function differs from the leucoplasts of plants
14.
Chloroplast
–
Chloroplasts /ˈklɔːrəˌplæsts, -plɑːsts/ are organelles, specialized subunits, in plant and algal cells. Their discovery inside plant cells is usually credited to Julius von Sachs and they then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of functions, including fatty acid synthesis, much amino acid synthesis. The number of chloroplasts per cell varies from one, in algae, up to 100 in plants like Arabidopsis. A chloroplast is a type of known as a plastid. Other plastid types, such as the leucoplast and the chromoplast, contain little chlorophyll, chloroplasts are highly dynamic—they circulate and are moved around within plant cells, and occasionally pinch in two to reproduce. Their behavior is influenced by environmental factors like light color. Chloroplasts, like mitochondria, contain their own DNA, which is thought to be inherited from their ancestor—a photosynthetic cyanobacterium that was engulfed by a eukaryotic cell. Chloroplasts cannot be made by the plant cell and must be inherited by each cell during cell division. With one exception, all chloroplasts can probably be traced back to a single endosymbiotic event, despite this, chloroplasts can be found in an extremely wide set of organisms, some not even directly related to each other—a consequence of many secondary and even tertiary endosymbiotic events. The word chloroplast is derived from the Greek words chloros, which means green, and plastes, the first definitive description of a chloroplast was given by Hugo von Mohl in 1837 as discrete bodies within the green plant cell. In 1883, A. F. W. Schimper would name these bodies as chloroplastids, in 1884, Eduard Strasburger adopted the term chloroplasts. Chloroplasts are one of many types of organelles in the plant cell and they are considered to have originated from cyanobacteria through endosymbiosis—when a eukaryotic cell engulfed a photosynthesizing cyanobacterium that became a permanent resident in the cell. Mitochondria are thought to have come from an event, where an aerobic prokaryote was engulfed. This origin of chloroplasts was first suggested by the Russian biologist Konstantin Mereschkowski in 1905 after Andreas Schimper observed in 1883 that chloroplasts closely resemble cyanobacteria, chloroplasts are only found in plants, algae, and the amoeboid Paulinella chromatophora. Cyanobacteria are considered the ancestors of chloroplasts and they are sometimes called blue-green algae even though they are prokaryotes. They are a phylum of bacteria capable of carrying out photosynthesis. Cyanobacteria also contain a cell wall, which is thicker than in other gram-negative bacteria
15.
Gene
–
A gene is a locus of DNA which is made up of nucleotides and is the molecular unit of heredity. The transmission of genes to an offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes, genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions, genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypical traits, usage of the term having a gene typically refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection or survival of the fittest of the alleles, the concept of a gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. The existence of discrete inheritable units was first suggested by Gregor Mendel, from 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas, although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured the distinction between genotype and phenotype, charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles that would mix during reproduction, de Vries called these units pangenes, after Darwins 1868 pangenesis theory. In 1909 the Danish botanist Wilhelm Johannsen shortened the name to gene, advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the repository of genetic information by experiments in the 1940s to 1950s. In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination, collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. This dogma has since shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics, in 1972, Walter Fiers and his team at the University of Ghent were the first to determine the sequence of a gene, the gene for Bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing, an automated version of the Sanger method was used in early phases of the Human Genome Project. The theories developed in the 1930s and 1940s to integrate molecular genetics with Darwinian evolution are called the evolutionary synthesis
16.
Human genome
–
The human genome is the complete set of nucleic acid sequence for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. Human genomes include both protein-coding DNA genes and noncoding DNA, haploid human genomes, which are contained in germ cells consist of three billion DNA base pairs, while diploid genomes have twice the DNA content. The Human Genome Project produced the first complete sequences of human genomes, with the first draft sequence. The human genome was the first of all vertebrates to be completely sequenced, as of 2012, thousands of human genomes have been completely sequenced, and many more have been mapped at lower levels of resolution. The resulting data are used worldwide in biomedical science, anthropology, forensics, there is a widely held expectation that genomic studies will lead to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution. Although the sequence of the genome has been completely determined by DNA sequencing. There are an estimated 19, 000-20,000 human protein-coding genes, in June 2016, scientists formally announced HGP-Write, a plan to synthesize the human genome. The total length of the genome is over 3 billion base pairs. The genome is organized into 22 paired chromosomes, plus the X chromosome and, in males only and these are all large linear DNA molecules contained within the cell nucleus. The genome also includes the mitochondrial DNA, a small circular molecule present in each mitochondrion. Basic information about these molecules and their content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table. Chromosome lengths were estimated by multiplying the number of base pairs by 0.34 nanometers, variations are unique DNA sequence differences that have been identified in the individual human genome sequences analyzed by Ensembl as of December,2016. The number of identified variations is expected to increase as further personal genomes are sequenced and analyzed, in addition to the gene content shown in this table, a large number of non-expressed functional sequences have been identified throughout the human genome. Links open windows to the reference chromosome sequences in the EBI genome browser, small non-coding RNAs are RNAs of as many as 200 bases that do not have protein-coding potential. These include, microRNAs, or miRNAs, small nuclear RNAs, or snRNAs, long non-coding RNAs are RNA molecules longer than 200 bases that do not have protein-coding potential. Although the human genome has been sequenced for all practical purposes. A recent study noted more than 160 euchromatic gaps of which 50 gaps were closed, however, there are still numerous gaps in the heterochromatic parts of the genome which is much harder to sequence due to numerous repeats and other intractable sequence features. The content of the genome is commonly divided into coding and noncoding DNA sequences
17.
Phylogenetics
–
In biology, phylogenetics /ˌfaɪloʊdʒəˈnɛtɪks, -lə-/ is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, the result of these analyses is a phylogeny – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a tree can be living organisms or fossils. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, taxonomy is the classification, identification and naming of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline, usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood, and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed, prior to 1990, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses, the term phylogeny derives from the German Phylogenie, introduced by Haeckel in 1866, and the Darwinian approach to classification became known as the phyletic approach. During the late 19th century, Ernst Haeckels recapitulation theory, or biogenetic fundamental law, was widely accepted, but this theory has long been rejected. O. See, Huerta-Cepas, Jaime, Dopazo, Joaquín, Gabaldón, ETE, A python Environment for Tree Exploration. PhylomeDB, A public database hosting thousands of gene phylogenies ranging many different species, See, Huerta-Cepas, J. Capella-Gutierrez, S. Pryszcz, L. P. Denisov, I. Kormes, D. Marcet-Houben, M. Gabaldón, T. PhylomeDB v3.0, An expanding repository of genome-wide collections of trees, alignments, lents, N. H. Cifuentes, O. E. Carpi, A. Teaching the Process of Molecular Phylogeny and Systematics, A Multi-Part Inquiry-Based Exercise
18.
Evolution
–
Evolution is change in the heritable characteristics of biological populations over successive generations. Evolutionary processes give rise to biodiversity at every level of organisation, including the levels of species, individual organisms. In July 2016, scientists reported identifying a set of 355 genes from the LUCA of all living on Earth. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, existing patterns of biodiversity have been shaped both by speciation and by extinction. More than 99 percent of all species that lived on Earth are estimated to be extinct. Estimates of Earths current species range from 10 to 14 million, more recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described. In the mid-19th century, Charles Darwin formulated the theory of evolution by natural selection. This teleonomy is the quality whereby the process of natural selection creates and preserves traits that are fitted for the functional roles they perform. The processes by which the changes occur, from one generation to another, are called evolutionary processes or mechanisms, the four most widely recognized evolutionary processes are natural selection, genetic drift, mutation and gene migration. Natural selection and genetic drift sort variation, mutation and gene migration create variation, consequences of selection can include meiotic drive, nonrandom mating and genetic hitchhiking. In the early 20th century the modern evolutionary synthesis integrated classical genetics with Darwins theory of evolution by natural selection through the discipline of population genetics, the importance of natural selection as a cause of evolution was accepted into other branches of biology. Moreover, previously held notions about evolution, such as orthogenesis, evolutionism, evolutionary computation, a sub-field of artificial intelligence, involves the application of Darwinian principles to problems in computer science. The proposal that one type of organism could descend from another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander, such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura, in contrast to these materialistic views, Aristotelianism considered all natural things as actualisations of fixed natural possibilities, known as forms. This was part of a teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. In the 17th century, the new method of modern science rejected the Aristotelian approach, however, this new approach was slow to take root in the biological sciences, the last bastion of the concept of fixed natural types. The biological classification introduced by Carl Linnaeus in 1735 explicitly recognized the nature of species relationships. Other naturalists of this time speculated on the change of species over time according to natural laws
19.
Anthropology
–
Anthropology is the study of various aspects of humans within past and present societies. Social anthropology and cultural anthropology study the norms and values of societies, linguistic anthropology studies how language affects social life. Biological or physical anthropology studies the development of humans. The abstract noun anthropology is first attested in reference to history and its present use first appeared in Renaissance Germany in the works of Magnus Hundt and Otto Casmann. Their New Latin anthropologia derived from the forms of the Greek words ánthrōpos and lógos. It began to be used in English, possibly via French anthropologie, various short-lived organizations of anthropologists had already been formed. The Société Ethnologique de Paris, the first to use Ethnology, was formed in 1839 and its members were primarily anti-slavery activists. When slavery was abolished in France in 1848 the Société was abandoned and these anthropologists of the times were liberal, anti-slavery, and pro-human-rights activists. Anthropology and many other current fields are the results of the comparative methods developed in the earlier 19th century. For them, the publication of Charles Darwins On the Origin of Species was the epiphany of everything they had begun to suspect, Darwin himself arrived at his conclusions through comparison of species he had seen in agronomy and in the wild. Darwin and Wallace unveiled evolution in the late 1850s, there was an immediate rush to bring it into the social sciences. When he read Darwin he became a convert to Transformisme. His definition now became the study of the group, considered as a whole, in its details. Broca, being what today would be called a neurosurgeon, had taken an interest in the pathology of speech and he wanted to localize the difference between man and the other animals, which appeared to reside in speech. He discovered the speech center of the brain, today called Brocas area after him. The title was translated as The Anthropology of Primitive Peoples. The last two volumes were published posthumously, Waitz defined anthropology as the science of the nature of man. By nature he meant matter animated by the Divine breath, i. e. he was an animist and he stresses that the data of comparison must be empirical, gathered by experimentation
20.
Biogeography
–
Biogeography is the study of the distribution of species and ecosystems in geographic space and through time. Organisms and biological communities often vary in a regular fashion along geographic gradients of latitude, elevation, isolation, phytogeography is the branch of biogeography that studies the distribution of plants. Zoogeography is the branch that studies distribution of animals, Biogeography is an integrative field of inquiry that unites concepts and information from ecology, evolutionary biology, geology, and physical geography. The short-term interactions within a habitat and species of organisms describe the application of biogeography. Historical biogeography describes the long-term, evolutionary periods of time for broader classifications of organisms, early scientists, beginning with Carl Linnaeus, contributed theories to the contributions of the development of biogeography as a science. Beginning in the century, Europeans explored the world and discovered the biodiversity of life. Linnaeus initiated the ways to classify organisms through his exploration of undiscovered territories, the patterns of species distribution across geographical areas can usually be explained through a combination of historical factors such as, speciation, extinction, continental drift, and glaciation. Through observing the distribution of species, we can see associated variations in sea level, river routes, habitat. Additionally, this science considers the constraints of landmass areas and isolation. As writer David Quammen put it. biogeography does more than ask Which species, and, what is sometimes more crucial, Why not. Modern biogeography often employs the use of Geographic Information Systems, to understand the factors affecting organism distribution, often mathematical models and GIS are employed to solve ecological problems that have a spatial aspect to them. Biogeography is most keenly observed on the worlds islands and these habitats are often much more manageable areas of study because they are more condensed than larger ecosystems on the mainland. They can then apply their understanding to similar but more complex mainland habitats, Islands are very diverse in their biomes, ranging from the tropical to arctic climates. This diversity in habitat allows for a range of species study in different parts of the world. One scientist who recognized the importance of geographic locations was Charles Darwin. Two chapters in On the Origin of Species were devoted to geographical distribution, the first discoveries that contributed to the development of biogeography as a science began in the mid-18th century, as Europeans explored the world and discovered the biodiversity of life. During the 18th century most views on the world were shaped around religion and for many natural theologists, Carl Linnaeus, in the mid-18th century, initiated the ways to classify organisms through his exploration of undiscovered territories. When he noticed that species were not as perpetual as he believed, when Noah’s ark landed on Mount Ararat and the waters receded, the animals dispersed throughout different elevations on the mountain
21.
Bacteria
–
Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
22.
Symbiogenesis
–
It holds that the organelles distinguishing eukaryote cells evolved through symbiosis of individual single-celled prokaryotes.5 billion years ago. In more detail, mitochondria appear to be related to Rickettsiales proteobacteria, in 1918 the French scientist Paul Portier published Les Symbiotes in which he claimed that the mitochondria originated from a symbiosis process. Ivan Wallin extended the idea of an origin to mitochondria in the 1920s. The Russian botanist Boris Kozo-Polyansky was the first to explain the theory in terms of Darwinian evolution, in his 1924 book Symbiogenesis, A New Principle of Evolution he wrote, The theory of symbiogenesis is a theory of selection relying on the phenomenon of symbiosis. These theories were dismissed or ignored. The theory was advanced and substantiated with evidence by Lynn Margulis in a 1967 paper. This last idea has not received much acceptance, because flagella lack DNA, according to Margulis and Dorion Sagan, Life did not take over the globe by combat, but by networking. The possibility that peroxisomes may have an endosymbiotic origin has also been considered, christian de Duve proposed that they may have been the first endosymbionts, allowing cells to withstand growing amounts of free molecular oxygen in the Earths atmosphere. However, it now appears that they may be formed de novo, the endosymbiotic theory is considered to be a type of saltational evolution. According to Keeling and Archibald, the way to distinguish organelles from endosymbionts is by their reduced genome sizes. As an endosymbiont evolves into an organelle, most of their genes are transferred to the host cell genome, the host cell and organelle need to develop a transport mechanism that enables transfer back of the protein products needed by the organelle but now manufactured by the cell. Cyanobacteria and α-proteobacteria are the most closely related free-living organisms to plastids, both cyanobacteria and α-proteobacteria maintain a large genome encoding thousands of proteins. Plastids and mitochondria exhibit a reduction in genome size when compared to their bacterial relatives. Nowack and her colleagues performed gene sequencing on the chromatophore and found that only 867 proteins were encoded by these photosynthetic cells, comparisons with their closest free living cyanobacteria of the genus Synechococcus revealed that chromatophores underwent a drastic genome shrinkage. Thus, these chromatophores were found to be non-functional for organelle-specific purposes when compared to mitochondria and this distinction could have promoted the early evolution of photosynthetic organelles. The loss of autonomy, that is, the loss of many genes from endosymbionts. Taking into account the entire original endosymbiont genome, there are three possible fates for genes over evolutionary time. The loss of autonomy and integration of the endosymbiont with its host can be attributed to nuclear gene transfer
23.
Mammal
–
Mammals are any vertebrates within the class Mammalia, a clade of endothermic amniotes distinguished from reptiles by the possession of a neocortex, hair, three middle ear bones and mammary glands. All female mammals nurse their young with milk, secreted from the mammary glands, Mammals include the largest animals on the planet, the great whales. The basic body type is a quadruped, but some mammals are adapted for life at sea, in the air, in trees. The largest group of mammals, the placentals, have a placenta, Mammals range in size from the 30–40 mm bumblebee bat to the 30-meter blue whale. With the exception of the five species of monotreme, all modern mammals give birth to live young, most mammals, including the six most species-rich orders, belong to the placental group. The largest orders are the rodents, bats and Soricomorpha, the next three biggest orders, depending on the biological classification scheme used, are the Primates, the Cetartiodactyla, and the Carnivora. Living mammals are divided into the Yinotheria and Theriiformes There are around 5450 species of mammal, in some classifications, extant mammals are divided into two subclasses, the Prototheria, that is, the order Monotremata, and the Theria, or the infraclasses Metatheria and Eutheria. The marsupials constitute the group of the Metatheria, and include all living metatherians as well as many extinct ones. Much of the changes reflect the advances of cladistic analysis and molecular genetics, findings from molecular genetics, for example, have prompted adopting new groups, such as the Afrotheria, and abandoning traditional groups, such as the Insectivora. The mammals represent the only living Synapsida, which together with the Sauropsida form the Amniota clade, the early synapsid mammalian ancestors were sphenacodont pelycosaurs, a group that produced the non-mammalian Dimetrodon. At the end of the Carboniferous period, this group diverged from the line that led to todays reptiles. Some mammals are intelligent, with some possessing large brains, self-awareness, Mammals can communicate and vocalize in several different ways, including the production of ultrasound, scent-marking, alarm signals, singing, and echolocation. Mammals can organize themselves into fission-fusion societies, harems, and hierarchies, most mammals are polygynous, but some can be monogamous or polyandrous. They provided, and continue to provide, power for transport and agriculture, as well as commodities such as meat, dairy products, wool. Mammals are hunted or raced for sport, and are used as model organisms in science, Mammals have been depicted in art since Palaeolithic times, and appear in literature, film, mythology, and religion. Defaunation of mammals is primarily driven by anthropogenic factors, such as poaching and habitat destruction, Mammal classification has been through several iterations since Carl Linnaeus initially defined the class. No classification system is accepted, McKenna & Bell and Wilson & Reader provide useful recent compendiums. Though field work gradually made Simpsons classification outdated, it remains the closest thing to a classification of mammals
24.
Animal
–
Animals are multicellular, eukaryotic organisms of the kingdom Animalia. The animal kingdom emerged as a clade within Apoikozoa as the group to the choanoflagellates. Animals are motile, meaning they can move spontaneously and independently at some point in their lives and their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later in their lives. All animals are heterotrophs, they must ingest other organisms or their products for sustenance, most known animal phyla appeared in the fossil record as marine species during the Cambrian explosion, about 542 million years ago. Animals can be divided broadly into vertebrates and invertebrates, vertebrates have a backbone or spine, and amount to less than five percent of all described animal species. They include fish, amphibians, reptiles, birds and mammals, the remaining animals are the invertebrates, which lack a backbone. These include molluscs, arthropods, annelids, nematodes, flatworms, cnidarians, ctenophores, the study of animals is called zoology. The word animal comes from the Latin animalis, meaning having breath, the biological definition of the word refers to all members of the kingdom Animalia, encompassing creatures as diverse as sponges, jellyfish, insects, and humans. Aristotle divided the world between animals and plants, and this was followed by Carl Linnaeus, in the first hierarchical classification. In Linnaeuss original scheme, the animals were one of three kingdoms, divided into the classes of Vermes, Insecta, Pisces, Amphibia, Aves, and Mammalia. Since then the last four have all been subsumed into a single phylum, in 1874, Ernst Haeckel divided the animal kingdom into two subkingdoms, Metazoa and Protozoa. The protozoa were later moved to the kingdom Protista, leaving only the metazoa, thus Metazoa is now considered a synonym of Animalia. Animals have several characteristics that set apart from other living things. Animals are eukaryotic and multicellular, which separates them from bacteria and they are heterotrophic, generally digesting food in an internal chamber, which separates them from plants and algae. They are also distinguished from plants, algae, and fungi by lacking cell walls. All animals are motile, if only at life stages. In most animals, embryos pass through a stage, which is a characteristic exclusive to animals. With a few exceptions, most notably the sponges and Placozoa and these include muscles, which are able to contract and control locomotion, and nerve tissues, which send and process signals
25.
Sperm
–
Sperm is the male reproductive cell and is derived from the Greek word sperma. In the types of reproduction known as anisogamy and its subtype oogamy. A uniflagellar sperm cell that is motile is referred to as a spermatozoon, Sperm cells cannot divide and have a limited life span, but after fusion with egg cells during fertilization, a new organism begins developing, starting as a totipotent zygote. The human sperm cell is haploid, so that its 23 chromosomes can join the 23 chromosomes of the egg to form a diploid cell. In mammals, sperm develops in the testicles and is released from the penis, the mammalian sperm cell consists of a head, neck, a midpiece and a tail. The head contains the nucleus with densely coiled chromatin fibres, surrounded anteriorly by an acrosome, the neck contains the sperm centriole. The midpiece has a central core with many mitochondria spiralled around it, used for ATP production for the journey through the female cervix, uterus. The tail or flagellum executes the lashing movements that propel the spermatocyte, although semen contains millions of sperm, the egg will admit only one. The other ones will die and be absorbed. The spermatozoa of animals are produced through spermatogenesis inside the gonads via meiotic division. The initial spermatozoon process takes around 70 days to complete, the spermatid stage is where the sperm develops the familiar tail. The next stage where it becomes fully mature takes around 60 days when it is called a spermatozoan, Sperm cells are carried out of the male body in a fluid known as semen. Human sperm cells can survive within the reproductive tract for more than 5 days post coitus. Semen is produced in the vesicles, prostate gland and urethral glands. In 2016 scientists at Nanjing Medical University claimed they had produced cells resembling mouse spermatids artificially from stem cells and they injected these spermatids into mouse eggs and produced pups. Sperm quantity and quality are the parameters in semen quality. Thus, in humans, it is a measure of fertility in a man, the genetic quality of sperm, as well as its volume and motility, all typically decrease with age. Human sperm cells are vulnerable to free radical attack and the generation of oxidative DNA damage
26.
Uniparental inheritance
–
Uniparental inheritance is a non-mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father and this phenomenon is most commonly observed in eukaryotic organelles such as mitochondria and chloroplasts. This is because such organelles contain their own DNA and are capable of independent mitotic replication that does not endure crossing over with the DNA from another parental type, although uniparental inheritance is the most common form of inheritance in organelles, there is increased evidence of diversity. Some studies found doubly uniparental inheritance and biparental transmission to exist in cells, evidence suggests that even when there is biparental inheritance, crossing-over doesnt always occur. Furthermore, there is evidence that the form of inheritance varied frequently over time. Uniparental inheritance can be divided into subtypes based on the pathway of inheritance. Not only are these organelles capable of independent DNA replication, translation, in the case of mitochondria, maternal inheritance is almost the exclusive form of inheritance. Even if they are not destroyed, the DNAs of different mitochondria rarely genetically recombine with one another, thus, mitochondria in most animals are inherited from the maternal type only. Like all other concepts, the discovery of uniparental inheritance stems from the days of an Augustinian priest known as Gregor Johann Mendel. The soon-to-be father of modern genetics spent his days conducting hybridization experiments on pea plants in his monasterys garden. During a period of seven years, Mendel cultivated and tested some 29,000 pea plants which led to him deducing the two famous generalizations known as Mendels Laws of Heredity. The first, the law of segregation, states that any individual produces gametes. The second, the law of independent assortment, states that alleles of different genes assort independently of one another during gamete formation. Although his work was published, it lay dormant until it was rediscovered in 1900 by Hugo de Vries and Carl Correns but it was not until 1909 that non-mendelian inheritance was even suggested. Carl Erich Correns and Erwin Baur, in separately conducted researches on Pelargonium and Mirabilis plants, soon after, the discoveries of uniparental and doubly uniparental inheritance came. Non-Mendelian inheritance Extranuclear inheritance Gregor Johann Mendel Mendelian inheritance Epigenetic inheritance Organelles
27.
Ubiquitin
–
Ubiquitin is a small regulatory protein that has been found in almost all tissues of eukaryotic organisms. It was discovered in 1975 in Israel by Gideon Goldstein and further characterized throughout the 1970s and 1980s, there are four genes in the human genome that produce ubiquitin, UBB, UBC, UBA52 and RPS27A. The addition of ubiquitin to a protein is called ubiquitination or ubiquitylation. The protein modifications can be either a single protein or a chain of ubiquitin. The ubiquitination bonds are formed with one of the seven lysine residues as well as the very N-terminal methionine from the ubiquitin molecule. These linking residues are represented by a K or M and a number, first, a ubiquitin molecule is bonded by its C-terminus to a specific lysine residue on the target protein. This process repeats several times, leading to the addition of several ubiquitins, the discovery that ubiquitin chains target proteins to the proteasome, which degrades and recycles proteins, was honored with the Nobel Prize in chemistry in 2004. Ubiquitin was first identified in 1975 as an 8.5 kDa protein of unknown function expressed in all eukaryotic cells, the ubiquitination system was initially characterised as an ATP-dependent proteolytic system present in cellular extracts. Multiple APF-1 molecules were linked to a substrate molecule by an isopeptide linkage. Soon after APF-1-protein conjugation was characterised, APF-1 was identified as ubiquitin, the carboxyl group of the C-terminal glycine residue of ubiquitin was identified as the moiety conjugated to substrate lysine residues. Ubiquitin is a protein that exists in all eukaryotic cells. It performs its functions through conjugation to a large range of target proteins. A variety of different modifications can occur, the ubiquitin protein itself consists of 76 amino acids and has a molecular mass of about 8.5 kDa. Key features include its C-terminal tail and the 7 lysine residues and it is highly conserved among eukaryotic species, Human and yeast ubiquitin share 96% sequence identity. Ubiquitin is encoded in mammals by 4 different genes, UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. The UBB and UBC genes code for polyubiquitin precursor proteins, no ubiquitin and ubiquitination machinery are known to exist in prokaryotes. However, ubiquitin is believed to have descended from prokaryotic proteins similar to ThiS or MoaD and these prokaryotic proteins, despite having little sequence identity, share the same protein fold. These proteins also share sulfur chemistry with ubiquitin, a similar system exists for ThiS, with its E1-like enzyme ThiF
28.
Embryo
–
An embryo is an early stage of development of a multicellular diploid eukaryotic organism. In general, in organisms that reproduce sexually, an embryo develops from a zygote, the zygote possesses half the DNA of each of its two parents. In plants, animals, and some protists, the zygote will begin to divide by mitosis to produce a multicellular organism, the result of this process is an embryo. First attested in English in the mid-14c, the word embryon derives from Medieval Latin embryo, itself from Greek ἔμβρυον, lit. Young one, which is the neuter of ἔμβρυος, lit, growing in, from ἐν, in and βρύω, swell, be full, the proper Latinized form of the Greek term would be embryum. In animals, the development of the zygote into an embryo proceeds through specific stages of blastula, gastrula. The blastula stage typically features a fluid-filled cavity, the blastocoel, surrounded by a sphere or sheet of cells, in a placental mammal, an ovum is fertilized in a fallopian tube through which it travels into the uterus. An embryo is called a fetus at an advanced stage of development. In humans, this is from the week of gestation. During gastrulation the cells of the blastula undergo coordinated processes of cell division, invasion, in triploblastic organisms, the three germ layers are called endoderm, ectoderm, and mesoderm. The position and arrangement of the layers are highly species-specific, however. For example, in neurogenesis, a subpopulation of cells is set aside to become the brain, spinal cord. Modern developmental biology is extensively probing the molecular basis for every type of organogenesis, including angiogenesis, chondrogenesis, myogenesis, osteogenesis, and many others. In botany, a plant embryo is part of a seed, consisting of precursor tissues for the leaves, stem. Once the embryo begins to germinate — grow out from the seed — it is called a seedling, bryophytes and ferns also produce an embryo, but do not produce seeds. In these plants, the embryo begins its existence attached to the inside of the archegonium on a parental gametophyte from which the egg cell was generated, the structure and development of the rest of the embryo varies by group of plants. Once the embryo has expanded beyond the enclosing archegonium, it is no longer termed an embryo, embryos are used in various fields of research and in techniques of assisted reproductive technology. An egg may be fertilized in vitro and the embryo may be frozen for later use
29.
In vitro
–
In vitro studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. In contrast, in studies are those conducted in animals, including humans. In vitro studies are conducted using components of an organism that have been isolated from their biological surroundings, such as microorganisms, cells. For example, microrganisms or cells can be studied in artificial culture media, colloquially called test-tube experiments, these studies in biology, medicine, and their subdisciplines are traditionally done in test tubes, flasks, Petri dishes, etc. They now involve the range of techniques used in molecular biology. In contrast, studies conducted in living beings are called in vivo, polymerase chain reaction is a method for selective replication of specific DNA and RNA sequences in the test tube. Protein purification involves the isolation of a protein of interest from a complex mixture of proteins. In vitro fertilization is used to allow spermatozoa to fertilize eggs in a culture dish before implanting the resulting embryo or embryos into the uterus of the prospective mother and these ADME process parameters can then be integrated into so called physiologically based pharmacokinetic models or PBPK. In vitro studies permit a species-specific, simpler, more convenient, just as studies in whole animals more and more replace human trials, so are in vitro studies replacing studies in whole animals. This complexity makes it difficult to identify the interactions between individual components and to explore their basic biological functions, in vitro work simplifies the system under study, so the investigator can focus on a small number of components. Another advantage of in vitro methods is that cells can be studied without extrapolation from an experimental animals cellular response. Investigators doing in vitro work must be careful to avoid over-interpretation of their results, for example, scientists developing a new viral drug to treat an infection with a pathogenic virus may find that a candidate drug functions to prevent viral replication in an in vitro setting. However, before this drug is used in the clinic, it must progress through a series of in vivo trials to determine if it is safe and effective in intact organisms. Results obtained from in vitro experiments cannot usually be transposed, as is, building a consistent and reliable extrapolation procedure from in vitro results to in vivo is therefore extremely important. However, increasingly sophisticated in vitro experiments collect increasingly numerous, complex, mathematical models, such as systems biology models, are much needed here. In pharmacology, IVIVE can be used to approximate pharmacokinetics or pharmacodynamics and that indicates that extrapolating effects observed in vitro needs a quantitative model of in vivo PK. Physiologically based PK models are generally accepted to be central to the extrapolations, in these conditions, developing a simple PD model of the dose–response relationship observed in vitro, and transposing it without changes to predict in vivo effects is not enough
30.
Genetic genealogy
–
Genetic genealogy is the use of DNA testing in combination with traditional genealogy and traditional genealogical and historical records to infer relationships between individuals. Genetic genealogy involves the use of genealogical DNA testing to determine the level and this application of genetics became popular with family historians in the first decade of the 21st century, as tests became affordable. The tests have been promoted by groups, such as surname study groups, or regional genealogical groups. As of 2013 hundreds of thousands of people had been tested, as this field has developed, the aims of practitioners broadened, with many seeking knowledge of their ancestry beyond the recent centuries for which traditional pedigrees can be constructed. The investigation of surnames in genetics can be said to go back to George Darwin, in 1875, George Darwin used surnames to estimate the frequency of first-cousin marriages and calculated the expected incidence of marriage between people of the same surname. He arrived at a figure between 2. 25% and 4. 5% for cousin-marriage in the population of Great Britain, higher among the upper classes and lower among the general rural population. One famous study examined the lineage of descendants of Thomas Jefferson’s paternal line and male descendants of the freed slave. Bryan Sykes, a molecular biologist at Oxford University tested the new methodology in general surname research and his study of the Sykes surname obtained results by looking at four STR markers on the male chromosome. It pointed the way to becoming a valuable assistant in the service of genealogy. The first company to provide direct-to-consumer genetic DNA testing was the now defunct GeneTree, however, it did not offer multi-generational genealogy tests. In fall 2001, GeneTree sold its assets to Salt Lake City-based Sorenson Molecular Genealogy Foundation which originated in 1999, while in operation, SMGF provided free Y-Chromosome and mitochondrial DNA tests to thousands. Later, GeneTree returned to testing for genealogy in conjunction with the Sorenson parent company. In 2000, Family Tree DNA, founded by Bennett Greenspan and they initially offered eleven marker Y-Chromosome STR tests and HVR1 mitochondrial DNA tests. They originally tested in partnership with the University of Arizona, with the growing availability and affordability of genealogical DNA testing, genetic genealogy as a field grew rapidly. By 2003, the field of DNA testing of surnames was declared officially to have “arrived” in an article by Jobling, the number of firms offering tests, and the number of consumers ordering them, rose dramatically. The original Genographic Project was a research study launched in 2005 by the National Geographic Society and IBM, in partnership with the University of Arizona. In 2007, annual sales of genetic tests for all companies. The earliest test takers were customers most often those who started with a Y-Chromosome test to determine their fathers paternal ancestry and these men often took part in surname projects
31.
Y chromosome
–
The Y chromosome is one of two sex chromosomes in mammals, including humans, and many other animals. The other is the X chromosome, Y is the sex-determining chromosome in many species, since it is the presence or absence of Y that determines the male or female sex of offspring produced in sexual reproduction. In mammals, the Y chromosome contains the gene SRY, which triggers testis development, the DNA in the human Y chromosome is composed of about 59 million base pairs. The Y chromosome is passed only from father to son, with a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the human genome. To date, over 200 Y-linked genes have been identified, all Y-linked genes are expressed and hemizygous except in the cases of aneuploidy such as XYY syndrome or XXYY syndrome. The Y chromosome was identified as a sex-determining chromosome by Nettie Stevens at Bryn Mawr College in 1905 during a study of the mealworm Tenebrio molitor, edmund Beecher Wilson independently discovered the same mechanisms the same year. Stevens proposed that chromosomes always existed in pairs and that the Y chromosome was the pair of the X chromosome discovered in 1890 by Hermann Henking, Stevens named the chromosome Y simply to follow on from Henkings X alphabetically. The idea that the Y chromosome was named after its similarity in appearance to the letter Y is mistaken, all chromosomes normally appear as an amorphous blob under the microscope and only take on a well-defined shape during mitosis. This shape is vaguely X-shaped for all chromosomes and it is entirely coincidental that the Y chromosome, during mitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape. Most mammals have one pair of sex chromosomes in each cell. Males have one Y chromosome and one X chromosome, while females have two X chromosomes, in mammals, the Y chromosome contains a gene, SRY, which triggers embryonic development as a male. The Y chromosomes of humans and other mammals also contain other genes needed for normal sperm production, for example, the platypus relies on an XY sex-determination system based on five pairs of chromosomes. Among humans, some men have two Xs and a Y, or one X and two Ys, and some women have three Xs or a single X instead of a double X, there are other exceptions in which SRY is damaged, or copied to the X. For related phenomena, see Androgen insensitivity syndrome and Intersex, many ectothermic vertebrates have no sex chromosomes. If they have different sexes, sex is determined environmentally rather than genetically, for some of them, especially reptiles, sex depends on the incubation temperature, others are hermaphroditic. The chromosome with this became the Y chromosome, while the other member of the pair became the X chromosome. Over time, genes that were beneficial for males and harmful to females either developed on the Y chromosome or were acquired through the process of translocation, until recently, the X and Y chromosomes were thought to have diverged around 300 million years ago. The older estimate was based on reports that the platypus X chromosomes contained these sequences
32.
Genealogical DNA test
–
A genealogical DNA test looks at a persons genome at specific locations for the purposes of determining ethnicity and genealogical relationships. Results give information about ethnic groups the tested may be descended from, in general, they do not give information about medical conditions or diseases. Several types of genealogical DNA tests are available, with each looking at a different part of the genome, taking a genealogical DNA test requires the submission of a DNA sample. The most common way to collect a DNA sample, which can be done by visiting a DNA test clinic or by ordering a home test through an independent DNA test supplier, is by a cheek-scraping. Other methods include spit-cups, mouthwash, and chewing gum, after collection, the sample is mailed to a testing lab. Some laboratories, such as FamilyTreeDNA, offer to store DNA samples for ease of future testing, there are three major types of genealogical DNA tests, Autosomal and X-DNA, Y-DNA and mtDNA. Autosomal tests look at Chromosomes 1-22 and X, the automsomes are inherited from both parents and all recent ancestors. The X-chromsome follows a special inheritance pattern. Ethnicity estimates are included with this sort of testing. Y-DNA looks at the Y-Chromosome, which is inherited father to son, mtDNA looks at the mitochondria, which is inherited from mother to child and so can be used to explore ones direct maternal line. Y-DNA and mtDNA cannot be used for ethnicity estimates, but can be used to find ones haplogroup, Autosomal DNA is the 22 pairs of chromosomes that do not contribute to sex. These are inherited exactly equally from both parents and roughly equally from grandparents to about 3x great-grand parents, inheritance is more random and unequal from more distant ancestors. Generally, a genealogical DNA test might test about 700,000 SNPs, like mtDNA and Y-DNA SNPs, autosomal SNPs are changes at a single point in genetic code. Therefore, the number of markers shared with a specific ancestor decreases by about half each generation, the major component of an autosomal DNA test is matching other individuals. Where two individuals share in common a number of consecutive SNPs, it can be projected that they share a segment of DNA at that part of their genomes. If the segment is longer than an amount set by the testing company. The unit for segments of DNA is the centimorgan, for comparison, a full human genome is about 6500 cMs. Most companies will show the customers how many cMs they share, some more distant cousins will not match at all Various advanced techniques and analysis can be done on this data. This includes features such as In-common/Shared Matches, Chromosome Browsers and Triangulation and this analysis is often required if DNA evidence is being used to prove or disprove a specific relationship
33.
Mitochondrial Eve
–
152 and 234 thousand years ago, a 2013 study cites a range of 99–148 thousand years ago. The male analog to the Mitochondrial Eve is the Y-chromosomal Adam, the inherited DNA in the male case is his nuclear Y chromosome rather than the mtDNA. Mitochondrial Eve and Y-chromosomal Adam need not have lived at the same time, the name Mitochondrial Eve alludes to biblical Eve. This has led to repeated misrepresentations or misconceptions in journalistic accounts on the topic, the title of Mitochondrial Eve is not permanently fixed to a single individual, but rather shifts forward in time over the course of human history as maternal lineages become extinct. Unlike her biblical namesake, she was not the living human female of her time. Using molecular clock methods in the late 1970s, Allan Wilson, Mark Stoneking, Rebecca L. Cann and it exhibited 0.02 substitution per base in a million years, which is 5-10 times faster than in nuclear DNA. Related work allowed for an analysis of the relationships among gorillas, chimpanzees. With data from 21 human individuals, Brown published the first estimate on the age of the mt-MRCA at 180,000 years ago. Using a larger, improved sample, Rebecca L. Cann concluded that it was possible to trace individual female lineages back hundreds of generations reaching the point of a common ancestor, early studies remained somewhat unconclusive, though. By 1985, data from the mtDNA of 145 women of different populations, after more than 40 revisions of the draft, the manuscript was submitted to Nature in late 1985 or early 1986 and published on 1 January 1987. The published conclusion was that all current human mtDNA originated from a population from Africa. The dating for Eve was a blow to the hypothesis, which was being controversially discussed at the time. The biblical connotation was very clear from the start, the accompanying research news in Nature had the title Out of the garden of Eden. Wilson himself preferred the term Lucky Mother and thought the use of the name Eve regrettable, but the concept of Eve caught on with the public and was repeated in a Newsweek cover story, and a cover story in Time on 26 January 1987. Shortly after the 1987 publication, criticism of its methodology and secondary conclusions was published, although the original research did have analytical limitations, the estimate on the age of the mt-MRCA has proven robust. More recent age estimates have remained consistent with the 140–200 kya estimate published in 1987, A2013 estimate dated Mitochondrial Eve to about 160 kya, another 2013 study reported the age of Mitochondrial Eve between 99 to 148 kya and that of the Y-MRCA between 120 and 156 kya. Without a DNA sample, it is not possible to reconstruct the genetic makeup of any individual who died very long ago. By analysing descendants DNA, however, parts of genomes are estimated by scientists
34.
Human
–
Modern humans are the only extant members of Hominina tribe, a branch of the tribe Hominini belonging to the family of great apes. Several of these hominins used fire, occupied much of Eurasia and they began to exhibit evidence of behavioral modernity around 50,000 years ago. In several waves of migration, anatomically modern humans ventured out of Africa, the spread of humans and their large and increasing population has had a profound impact on large areas of the environment and millions of native species worldwide. Humans are uniquely adept at utilizing systems of communication for self-expression and the exchange of ideas. Humans create complex structures composed of many cooperating and competing groups, from families. Social interactions between humans have established a wide variety of values, social norms, and rituals. These human societies subsequently expanded in size, establishing various forms of government, religion, today the global human population is estimated by the United Nations to be near 7.5 billion. In common usage, the word generally refers to the only extant species of the genus Homo—anatomically and behaviorally modern Homo sapiens. In scientific terms, the meanings of hominid and hominin have changed during the recent decades with advances in the discovery, there is also a distinction between anatomically modern humans and Archaic Homo sapiens, the earliest fossil members of the species. The English adjective human is a Middle English loanword from Old French humain, ultimately from Latin hūmānus, the words use as a noun dates to the 16th century. The native English term man can refer to the species generally, the species binomial Homo sapiens was coined by Carl Linnaeus in his 18th century work Systema Naturae. The generic name Homo is a learned 18th century derivation from Latin homō man, the species-name sapiens means wise or sapient. Note that the Latin word homo refers to humans of either gender, the genus Homo evolved and diverged from other hominins in Africa, after the human clade split from the chimpanzee lineage of the hominids branch of the primates. The closest living relatives of humans are chimpanzees and gorillas, with the sequencing of both the human and chimpanzee genome, current estimates of similarity between human and chimpanzee DNA sequences range between 95% and 99%. The gibbons and orangutans were the first groups to split from the leading to the humans. The splitting date between human and chimpanzee lineages is placed around 4–8 million years ago during the late Miocene epoch, during this split, chromosome 2 was formed from two other chromosomes, leaving humans with only 23 pairs of chromosomes, compared to 24 for the other apes. There is little evidence for the divergence of the gorilla, chimpanzee. Each of these species has been argued to be an ancestor of later hominins
35.
Microsatellite
–
A microsatellite is a tract of repetitive DNA in which certain DNA motifs are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within a genome, additionally. Microsatellites and their cousins, the minisatellites, together are classified as VNTR DNA. The name satellite refers to the observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying satellite layers of repetitive DNA. Microsatellites are often referred to as tandem repeats by forensic geneticists. They are widely used for DNA profiling in kinship analysis and in forensic identification and they are also used in genetic linkage analysis/marker assisted selection to locate a gene or a mutation responsible for a given trait or disease. Microsatellites are also used in genetics to measure levels of relatedness between subspecies, groups and individuals. A microsatellite is a tract of tandemly repeated DNA motifs that range in length from two to five nucleotides, and are typically repeated 5-50 times, for example, the sequence TATATATATA is a dinucleotide microsatellite, and GTCGTCGTCGTCGTC is a trinucleotide microsatellite. Repeat units of four and five nucleotides are referred to as tetra- and pentanucleotide motifs, microsatellites are distributed throughout the genome. Many are located in non-coding parts of the genome and therefore do not produce proteins, however they can also be located in regulatory regions. The telomeres at the ends of the chromosomes, thought to be involved in ageing/senescence, consist of repetitive DNA and they are thus classified as minisatellites, although insects for example have shorter repeat motifs in their telomeres which therefore could arguably be considered microsatellites. Unlike point mutations, which only a single nucleotide, microsatellite mutations lead to the gain or loss of an entire repeat unit. Thus, the rate at microsatellite loci is expected to differ from other mutation rates. The actual cause of mutations in microsatellites is debated, one proposed cause of such length changes is replication slippage, caused by mismatches between DNA strands while being replicated during meiosis. DNA polymerase, the responsible for reading DNA during replication, can slip while moving along the template strand. DNA polymerase slippage is more likely to occur when a sequence is replicated. Because microsatellites consist of repetitive sequences, DNA polymerase may make errors at a higher rate in these sequence regions. Several studies have found evidence that slippage is the cause of microsatellite mutations, typically, slippage in each microsatellite occurs about once per 1,000 generations
36.
Phylogeny
–
The taxa joined together in the tree are implied to have descended from a common ancestor. Phylogenetic trees are central to the field of phylogenetics, each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed, Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetic comparative methods. Unrooted trees illustrate only the relatedness of the nodes and do not require the ancestral root to be known or inferred. The idea of a tree of life arose from ancient notions of a progression from lower to higher forms of life. Charles Darwin also produced one of the first illustrations and crucially popularized the notion of a tree in his seminal book The Origin of Species. Over time, species classification has become static and more dynamic. A rooted phylogenetic tree is a tree with a unique node corresponding to the most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred, unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry, both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either labeled or unlabeled. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while a tree, sometimes called a tree shape. The last distinction is the most biologically relevant, it arises because there are places on an unrooted tree to put the root. For labeled bifurcating trees, there are,2 n −2. for n ≥2 total rooted trees and. 2 n −3. for n ≥3 total unrooted trees, among labeled bifurcating trees, the number of unrooted trees with n leaves is equal to the number of rooted trees with n −1 leaves. A dendrogram is a term for the diagrammatic representation of a phylogenetic tree. A cladogram is a phylogenetic tree formed using cladistic methods and this type of tree only represents a branching pattern, i. e. its branch spans do not represent time or relative amount of character change
37.
Phylogenetic tree
–
The taxa joined together in the tree are implied to have descended from a common ancestor. Phylogenetic trees are central to the field of phylogenetics, each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed, Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetic comparative methods. Unrooted trees illustrate only the relatedness of the nodes and do not require the ancestral root to be known or inferred. The idea of a tree of life arose from ancient notions of a progression from lower to higher forms of life. Charles Darwin also produced one of the first illustrations and crucially popularized the notion of a tree in his seminal book The Origin of Species. Over time, species classification has become static and more dynamic. A rooted phylogenetic tree is a tree with a unique node corresponding to the most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred, unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry, both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either labeled or unlabeled. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while a tree, sometimes called a tree shape. The last distinction is the most biologically relevant, it arises because there are places on an unrooted tree to put the root. For labeled bifurcating trees, there are,2 n −2. for n ≥2 total rooted trees and. 2 n −3. for n ≥3 total unrooted trees, among labeled bifurcating trees, the number of unrooted trees with n leaves is equal to the number of rooted trees with n −1 leaves. A dendrogram is a term for the diagrammatic representation of a phylogenetic tree. A cladogram is a phylogenetic tree formed using cladistic methods and this type of tree only represents a branching pattern, i. e. its branch spans do not represent time or relative amount of character change
38.
Heteroplasmy
–
Heteroplasmy is the presence of more than one type of organellar genome within a cell or individual. It is an important factor in considering the severity of mitochondrial diseases, because most eukaryotic cells contain many hundreds of mitochondria with hundreds of copies of mitochondrial DNA, it is common for mutations to affect only some mitochondria, leaving most unaffected. Although detrimental scenarios are well-studied, heteroplasmy can also be beneficial, for example, centenarians show a higher than average degree of heteroplasmy. Microheteroplasmy is present in most individuals and this refers to hundreds of independent mutations in one organism, with each mutation found in about 1–2% of all mitochondrial genomes. In order for heteroplasmy to occur, organelles must contain a genome and, in turn, in animals, mitochondria are the only organelles that contain their own genomes, so these organisms will only have mitochondrial heteroplasmy. In contrast, photosynthetic plants contain mitochondria and chloroplasts, each of which contains plastid genomes, therefore, plant heteroplasmy occurs in two dimensions. In 1909, while studying chloroplast genomes, Erwin Baur made the first observations about organelle inheritance patterns, organelle genome inheritance differs from nuclear genome, and this is illustrated by four violations of Mendels laws. During asexual reproduction, nuclear genes never segregate during cellular divisions and this is to ensure that each daughter cell gets a copy of every gene. However, organelle genes in heteroplasmic cells can segregate because they each have several copies of their genome and this may result in daughter cells with differential proportions of organelle genotypes. Mendel states that nuclear alleles always segregate during meiosis, however, organelle alleles may or may not do this. Nuclear genes are inherited from a combination of alleles from parents, making inheritance biparental. Conversely, organelle inheritance is uniparental, meaning the genes are all inherited from one parent, vegetative segregation, the random partitioning of cytoplasm, is a distinguishable characteristic of organelle heredity. During cell division, the organelles are divided equally, providing each cell with a random selection of plasmid genotypes. Uniparental inheritance refers to the fact that, in most organisms, however, this is not a general law. Many organisms that have the ability to differentiate maternal and paternal sexes will produce offspring with a mixture of maternal, paternal, animal populations of mitochondria avoid this buildup through a developmental process known as the mtDNA bottleneck. Cell-level selection may act to remove those cells with more mutant mtDNA. The mitochondrial bottleneck concept refers to the classic evolutionary term, which is used to explain an event that reduces and specifies a population and it was developed to describe why mitochondrial DNA in an embryo might be drastically different from that of its mother. When a large population of DNA is subsampled, each population will receive a slightly different proportion of mitochondrial genotypes
39.
Cellular noise
–
Cellular noise is random variability in quantities arising in cellular biology. For example, cells which are identical, even within the same tissue, are often observed to have different expression levels of proteins. These apparently random differences can have important biological and medical consequences, cellular noise was originally, and is still often, examined in the context of gene expression levels – either the concentration or copy number of the products of genes within and between cells. This measure is dimensionless, allowing a comparison of the importance of noise. Another quantity often used for convenience is the Fano factor. Cellular noise is often investigated in the framework of intrinsic and extrinsic noise, intrinsic noise refers to variation in identically-regulated quantities within a single cell, for example, the intra-cell variation in expression levels of two identically-controlled genes. Extrinsic noise refers to variation in identically-regulated quantities between different cells, for example, the variation in expression of a given gene. Intrinsic and extrinsic noise levels are compared in dual reporter studies. Note, These lists are illustrative, not exhaustive, and identification of sources is an active. Noise propagation, Low copy-number effects and diffusive dynamics result in each of the reactions in a cell occurring randomly. Stochasticity of reactions can be attenuated or amplified. Contribution each reaction makes to the variability in copy numbers can be quantified via Van Kampens system size expansion. Note, These lists are illustrative, not exhaustive, and identification of noise effects is an active, in particular, master equation treatments – where the probabilities P of observing a system in a state x at time t are linked through ODEs – have proved particularly fruitful. Numerically, the Gillespie algorithm or stochastic simulation algorithm is used to create realisations of stochastic cellular processes
40.
Paternal mtDNA transmission
–
In genetics, paternal mtDNA transmission and paternal mtDNA inheritance refer to the incidence of mitochondrial DNA being passed from a father to his offspring. Paternal mtDNA inheritance is observed in a proportion of species, in general. In contrast, mtDNA transmission from both parents occurs regularly in certain bivalves, paternal mtDNA inheritance in animals varies. For example, in Mytilidae mussels, paternal mtDNA is transmitted through the sperm, in testing 172 sheep, The Mitochondrial DNA from three lambs in two half-sib families were found to show paternal inheritance. An instance of paternal leakage resulted in a study on chickens, there has been evidences that paternal leakage is an integral part of the inheritance of Drosophila simulans. In human mitochondrial genetics, there is debate whether or not paternal mtDNA transmission is possible. Many studies hold that paternal mtDNA is never transmitted to offspring and this thought is central to mtDNA genealogical DNA testing and to the theory of mitochondrial Eve. The fact that mitochondrial DNA is maternally inherited enables researchers to trace maternal lineage far back in time, in sexual reproduction, paternal mitochondria found in the sperm are actively decomposed, thus preventing paternal leakage. Mitochondria in mammalian sperm are usually destroyed by the egg cell after fertilization, in 1999 it was reported that paternal sperm mitochondria are marked with ubiquitin to select them for later destruction inside the embryo. Some in vitro techniques, particularly intracytoplasmic sperm injection of a sperm into an oocyte. It is now understood that the tail of the sperm, which contains additional mtDNA and this had led to increased controversy about the fate of paternal mtDNA. Some sources state that so little paternal mtDNA is transmitted as to be negligible or that paternal mtDNA is so rarely transmitted as to be negligible, one study stated that about 1–2% of a persons mitochondria can be inherited from the father. The controversy about human paternal leakage was summed up in the 1996 study Misconceptions about mitochondria and mammalian fertilization, however, there has been only a single documented case of human paternal mitochondrial DNA transmission. According to the 2005 study More evidence for non-maternal inheritance of mitochondrial DNA. heteroplasmy is a newly discovered form of inheritance for mtDNA, heteroplasmy introduces slight statistical uncertainty in normal inheritance patterns. Some organisms, such as Cryptosporidium, have mitochondria with no DNA whatsoever, in plants, it has also been reported that mitochondria can occasionally be inherited from the father, e. g. in bananas. Some Conifers also show paternal inheritance of mitochondria, such as the coast redwood, y-chromosomal Adam Patrilineality Matrilineality Human mitochondrial genetics Human migration RecLOH List of genetic genealogy topics Marchington DR, Scott Brown MS, Lamb VK, et al. No evidence for paternal mtDNA transmission to offspring or extra-embryonic tissues after ICSI, sigurğardóttir S, Helgason A, Gulcher JR, Stefansson K, Donnelly P. The mutation rate in the human mtDNA control region, zeviani M, Di Donato S. Mitochondrial disorders
. PMID 15157274.
Media related to Mitochondrial DNA at Wikimedia Commons
