Instruct: Given a question, retrieve documents that can help answer the question.
Query: What is within a nucleus of a cell?
In cell biology, the cytoplasm is all of the material within a cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The main components of the cytoplasm are cytosol – a gel-like substance, the organelles – the cell's internal sub-structures, and various cytoplasmic inclusions. The cytoplasm is about 80% water and usually colorless.
Cell theory led biologists to re-envision individual organisms as interdependent assemblages of individual cells. Scientists in the rising field of cytology, armed with increasingly powerful microscopes and new staining methods, soon found that even single cells were far more complex than the homogeneous fluid-filled chambers described by earlier microscopists. Robert Brown had described the nucleus in 1831, and by the end of the 19th century cytologists identified many of the key cell components: chromosomes, centrosomes mitochondria, chloroplasts, and other structures made visible through staining. Between 1874 and 1884 Walther Flemming described the discrete stages of mitosis, showing that they were not artifacts of staining but occurred in living cells, and moreover, that chromosomes doubled in number just before the cell divided and a daughter cell was produced. Much of the research on cell reproduction came together in August Weismann's theory of heredity: he identified the nucleus (in particular chromosomes) as the hereditary material, proposed the distinction between somatic cells and germ cells (arguing that chromosome number must be halved for germ cells, a precursor to the concept of meiosis), and adopted Hugo de Vries's theory of pangenes. Weismannism was extremely influential, especially in the new field of experimental embryology.
The physical properties of the cytoplasm have been contested in recent years. It remains uncertain how the varied components of the cytoplasm interact to allow movement of particles and organelles while maintaining the cell’s structure. The flow of cytoplasmic components plays an important role in many cellular functions which are dependent on the permeability of the cytoplasm. An example of such function is cell signalling, a process which is dependent on the manner in which signaling molecules are allowed to diffuse across the cell. While small signaling molecules like calcium ions are able to diffuse with ease, larger molecules and subcellular structures often require aid in moving through the cytoplasm. The irregular dynamics of such particles have given rise to various theories on the nature of the cytoplasm.
Protein is a nutrient needed by the human body for growth and maintenance. Aside from water, proteins are the most abundant kind of molecules in the body. Protein can be found in all cells of the body and is the major structural component of all cells in the body, especially muscle. This also includes body organs, hair and skin. Proteins are also used in membranes, such as glycoproteins. When broken down into amino acids, they are used as precursors to nucleic acid, co-enzymes, hormones, immune response, cellular repair, and other molecules essential for life. Additionally, protein is needed to form blood cells.
In the absence of hormone, estrogen receptors are largely located in the cytosol. Hormone binding to the receptor triggers a number of events starting with migration of the receptor from the cytosol into the nucleus, dimerization of the receptor, and subsequent binding of the receptor dimer to specific sequences of DNA known as hormone response elements. The DNA/receptor complex then recruits other proteins that are responsible for the transcription of downstream DNA into mRNA and finally protein that results in a change in cell function. Estrogen receptors also occur within the cell nucleus, and both estrogen receptor subtypes have a DNA-binding domain and can function as transcription factors to regulate the production of proteins.
In biology, cell theory is the historic scientific theory, now universally accepted, that living organisms are made up of cells, that they are the basic structural/organizational unit of all organisms, and that all cells come from pre-existing cells. Cells are the basic unit of structure in all organisms and also the basic unit of reproduction. With continual improvements made to microscopes over time, magnification technology advanced enough to discover cells in the 17th century. This discovery is largely attributed to Robert Hooke, and began the scientific study of cells, also known as cell biology. Over a century later, many debates about cells began amongst scientists. Most of these debates involved the nature of cellular regeneration, and the idea of cells as a fundamental unit of life. Cell theory was eventually formulated in 1839. This is usually credited to Matthias Schleiden and Theodor Schwann. However, many other scientists like Rudolf Virchow contributed to the theory. It was an important step in the movement away from spontaneous generation.
Nucleons sit at the boundary where particle physics and nuclear physics overlap. Particle physics, particularly quantum chromodynamics, provides the fundamental equations that explain the properties of quarks and of the strong interaction. These equations explain quantitatively how quarks can bind together into protons and neutrons (and all the other hadrons). However, when multiple nucleons are assembled into an atomic nucleus (nuclide), these fundamental equations become too difficult to solve directly (see lattice QCD). Instead, nuclides are studied within nuclear physics, which studies nu and their interactions by approximations and models, such as the nuclear shell model. These models can successfully exp nuclide properties, as for example, whether or not a particular nuclide undergoes radioactive decay.
In eukaryotes, DNA is organized with the help of histones into compact particles called nucleosomes, where sequences of about 147 DNA base pairs make ~1.65 turns around histone protein octamers. DNA within nucleosomes is inaccessible to many transcription factors. Some transcription factors, so-called pioneering factors are still able to bind their DNA binding sites on the nucleosomal DNA. For most other transcription factors, the nucleosome should be actively unwound by molecular motors such as chromatin remodelers. Alternatively, the nucleosome can be partially unwrapped by thermal fluctuations, allowing temporary access to the transcription factor binding site. In many cases, a transcription factor needs to compete for binding to its DNA binding site with other transcription factors and histones or non-histone chromatin proteins. Pairs of transcription factors and other proteins can play antagonistic roles (activator versus repressor) in the regulation of the same gene.
In eukaryotes, the enzymes in this electron transport system use the energy released from the oxidation of NADH to pump protons across the inner membrane of the mitochondrion. This causes protons to build up in the intermembrane space, and generates an electrochemical gradient across the membrane. The energy stored in this potential is then used by ATP synthase to produce ATP. Oxidative phosphorylation in the eukaryotic mitochondrion is the best-understood example of this process. The mitochondrion is present in almost all eukaryotes, with the exception of anaerobic protozoa such as "Trichomonas vaginalis" that instead reduce protons to hydrogen in a remnant mitochondrion called a hydrogenosome.
The cytosolic, intermembrane space, compartment has a water content of 3.8 μl/mg protein, while the mitochondrial matrix 0.8 μl/mg protein. It is not known how mitochondria maintain osmotic balance across the inner mitochondrial membrane, although the membrane contains aquaporins that are believed to be conduits for regulated water transport. Mitochondrial matrix has a pH of about 7.8. Mitochondrial DNA was discovered by Nash and Margit in 1963. One to many double stranded mainly circular DNA is present in mitochondrial matrix. Mitochondrial DNA is 1% of total DNA of a cell. It is rich in Guanine and Cytosine content. Mitochondria of mammals have 55s ribosomes.
Mitochondria, as a major energy factory of the cell, was previously a free-living prokaryote that invades the eukaryotic cells by the endosymbiosis theory, which gained acceptance around the 1970s. Under this theory, symbiotic organelles gradually transferred their genes to the eukaryotic genome, implying that mtDNA was gradually integrated into the nuclear genome. Despite the metabolic alterations and functional adaptations in the host eukaryotes, circular mitochondrial DNA is contained within the organelles. Containing 37 genes, mitochondrial DNA has an essential role in the production of necessary compounds, such as required enzymes for the proper function of mitochondria. Specifically, it has been suggested that certain genes (such as the genes for cytochrome oxidase subunits I and II) within the organelle are necessary to regulate redox balance throughout membrane-associated electron transport chains. These parts of the mitochondrial genome have been reported to be the most frequently employed. Mitochondria is not the only location within which the cell mtDNA, mitochondrial DNA, can be found; sometimes transfer of mitochondrial DNA from organelles to the nucleus can occur; the evidence of such translocation has been seen through the comparison of mitochondrial DNA sequence with the genome sequence of the counterparts. The integration and recombination of cytoplasmic mtDNA into the nuclear DNA is called Nuclear Mitochondrial DNA, which is abbreviated as NUMT.
The possible presence of organelle DNA inside the nuclear genome was suggested after finding of homologous structure to the mitochondrial DNA, which was shortly after the discovery of the presence of an independent DNA within the organelles in 1967. This topic stayed untouched until the 1980s. Initial evidence that DNA could move among cell compartments came when fragments of chloroplast DNA were found in the maize mitochondrial genome with the help of cross-hybridization, between chloroplast and mitochondrial DNA, and physical mapping of homologous regions. After this initial observation, Ellis coined the name "promiscuous DNA" in order to signify the transfer of DNA intracellularly from one organelle to the other and is the presence of organelle DNA in multiple cellular compartments. This is not only an important discovery on its own, but is also highly informative and helpful for understanding the evolutionary process and the time period different occurrence might take place. The searching for mtDNA in nuclear DNA continued until 1994 when the recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat was reported. This is the time that NUMT was coined to designate the large stretches of mitochondrial DNA in the genome.
Up to now, the whole genomes of many eukaryotes, both vertebrate, and invertebrate, have been sequenced and NUMT was observed in the nuclear genome of various organisms, including yeast, "Podospora", sea urchin, locust, honey bee, "Tribolium", rat, maize, rice, and primates. In Plasmodium, "Anopheles gambiae", and "Aedes aegypti" mosquitoes NUMT can barely be detected. In contrast, the conserved fragments of NUMT have now few were identified in genome data for "Ciona intestinalis", "Neurospora crassa", "Schizosaccharomyces pombe", "Caenorhabditis elegans", "Drosophila melanogaster", and "Rattus norvegicus". Antunes and Ramos were found the presence of NUMT in the fish genome for the first time in 2005 using of BLASTN, MAFFT, very vigorous genome mappings, and phylogenic analysis. Across the animal kingdom, "Apis mellifera", from phylum "Arthropoda", and "Hydra magnipapillata", from phylum "Cnidaria", are respectively the first and second animals with the highest ratio of NUMTs to the total size of the nuclear genome while "Monodelphis Domestica", or Gray short-tailed opossum, is the record holder for NUMT frequency among vertebrates. Similar to animals, NUMTs are abundant in the plants and the longest NUMT fragment known so far, a 620-kb partially duplicated insertion of the 367-kb mtDNA of "Arabidopsis thaliana", was reported.
The ova, which are the female sex cells, are much larger than the sperm and are normally formed within the ovaries of the fetus before its birth. They are mostly fixed in location within the ovary until their transit to the uterus, and contain nutrients for the later zygote and embryo. Over a regular interval, in response to hormonal signals, a process of oogenesis matures one ovum which is released and sent down the Fallopian tube. If not fertilized, this egg is released through menstruation in humans and other great apes, and reabsorbed in other mammals in the estrus cycle.
Nuclear physics is the field of physics that studies the constituents and interactions of atomic nuclei. The most commonly known applications of nuclear physics are nuclear power generation and nuclear weapons technology, but the research has provided application in many fields, including those in nuclear medicine and magnetic resonance imaging, ion implantation in materials engineering, and radiocarbon dating in geology and archaeology.
Recently it has been proposed that the cytoplasm behaves like a glass-forming liquid approaching the glass transition. In this theory, the greater the concentration of cytoplasmic components, the less the cytoplasm behaves like a liquid and the more it behaves as a solid glass, freezing larger cytoplasmic components in place (it is thought that the cell's metabolic activity is able to fluidize the cytoplasm to allow the movement of such larger cytoplasmic components). A cell's ability to vitrify in the absence of metabolic activity, as in dormant periods, may be beneficial as a defence strategy. A solid glass cytoplasm would freeze subcellular structures in place, preventing damage, while allowing the transmission of very small proteins and metabolites, helping to kickstart growth upon the cell's revival from dormancy.
Microglia are a collective type of neuroglia (glial cell) located throughout the brain and spinal cord., found to have 9 distinct subtypes with different functions, appearance, and presence. Microglia account for 10–15% of all cells found within the brain. As the resident macrophage cells, they act as the first and main form of active immune defense in the central nervous system (CNS). Microglia (and other neuroglia including astrocytes) are distributed in large non-overlapping regions throughout the CNS. Microglia are key cells in overall brain maintenance—they are constantly scavenging the CNS for plaques, damaged or unnecessary neurons and synapses, and infectious agents. Since these processes must be efficient to prevent potentially fatal damage, microglia are extremely sensitive to even small pathological changes in the CNS. This sensitivity is achieved in part by the presence of unique potassium channels that respond to even small changes in extracellular potassium.
It groups all experimental data relevant for nuclear physics and nuclear applications. It includes a large number of physical quantities, like scattering and reaction cross sections (which are generally functions of energy and angle), nuclear structure and nuclear decay parameters, etc. It can involve neutrons, protons, deuterons, alpha particles, and virtually all nuclear isotopes which can be handled in a laboratory.
The scientific study of the nervous system increased significantly during the second half of the twentieth century, principally due to advances in molecular biology, electrophysiology, and computational neuroscience. This has allowed neuroscientists to study the nervous system in all its aspects: how it is structured, how it works, how it develops, how it malfunctions, and how it can be changed. For example, it has become possible to understand, in much detail, the complex processes occurring within a single neuron. Neurons are cells specialized for communication. They are able to communicate with neurons and other cell types through specialized junctions called synapses, at which electrical or electrochemical signals can be transmitted from one cell to another. Many neurons extrude a long thin filament of axoplasm called an axon, which may extend to distant parts of the body and are capable of rapidly carrying electrical signals, influencing the activity of other neurons, muscles, or glands at their termination points. A nervous system emerges from the assemblage of neurons that are connected to each other.
Amino acids are organic compounds containing amine (-NH) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.
RNA is a biological macromolecule made of sugars and nitrogenous bases that plays a number of crucial roles in all living cells. There are several subtypes of RNA, with the most prominent in the cell being tRNA (transfer RNA), rRNA (ribosomal RNA), and mRNA (messenger RNA). All three of these are involved in the process of translation, with the most prominent species (~85%) of cellular RNA being rRNA. As a result, this is the most immediately visible species when RNA is analyzed via electrophoresis and is thus used for determining RNA quality (see Computation, below). rRNA comes in various sizes, with those in mammals belonging to the sizes 5S, 18S, and 28S. The 28S and 5S rRNAs form the large subunit and the 18S forms the small subunit of the ribosome, the molecular machinery responsible for synthesizing proteins.
Later artificial cells have ranged from hundred-micrometer to nanometer dimensions and can carry microorganisms, vaccines, genes, drugs, hormones and peptides. The first clinical use of artificial cells was in hemoperfusion by the encapsulation of activated charcoal.
NADH-coenzyme Q oxidoreductase, also known as "NADH dehydrogenase" or "complex I", is the first protein in the electron transport chain. Complex I is a giant enzyme with the mammalian complex I having 46 subunits and a molecular mass of about 1,000 kilodaltons (kDa). The structure is known in detail only from a bacterium; in most organisms the complex resembles a boot with a large "ball" poking out from the membrane into the mitochondrion. The genes that encode the individual proteins are contained in both the cell nucleus and the mitochondrial genome, as is the case for many enzymes present in the mitochondrion.
Unlike many nuclei within the central nervous system (CNS), the mesencephalic nucleus contains no chemical synapses but are electrically coupled. Neurons of this nucleus are unipolar cells that receive proprioceptive information from the mandible and send projections to the trigeminal motor nucleus to mediate monosynaptic jaw jerk reflexes. It is also the only structure in the CNS to contain first order sensory neurons, cell bodies of primary afferents in contact with the periphery, which are usually contained within ganglia (like the trigeminal ganglion). The mesencephalic nucleus can thus be considered functionally as a sensory ganglion embedded within the brainstem, making it neuroanatomically unique .
"Marteilia" has a very peculiar morphology. The outermost cell is the primary cell. Within the primary cell, there is a nucleus and between 3 and 16 secondary cells. Within a secondary cell, there is a nucleus and between 1 to 6 spores. Within each spore, there is a nucleus and another spore, which has yet another nucleus and spore within. This spore within a spore within a spore is termed a tricellular spore. "Marteilia" has tricellular spores where as the similar genera "Paramarteilia" and "Paramyxa" have bicellular and tetracellular spores respectively (Feist, Hine, Bateman, Stentiford, & Longshaw, 2009).
The nucleus of the cell lies between the anterior lobes of the chloroplast in parallel with the pyrenoid, and some species have developed anterior nuclear lobes. The nucleus is centrally located and is parallel with the flagellar depression and pyrenoid. Additionally, condensed chromatin can be viewed in the nucleus of certain species. See figure 1 for nuclear positioning within cells. The Golgi of "Tetraselmis" species has a distinct number of Golgi bodies usually within the range of 2-4, but species can have up to 8 or more. This is a reliable characteristic that is used to help classify species. Golgi bodies lie between the chloroplast and the basal bodies; cis-Golgi face the chloroplast and trans-Golgi face the basal bodies. Mitochondria are dispersed throughout the cytoplasm in no pattern. The cytoplasm may contain additional organelles and macromolecules such as lipid droplets, vacuoles, and lysosomes. Additionally, the starch produced by "Tetraselmis" is the same as those produced from land plants.
In neuroanatomy, a nucleus (plural form: nuclei) is a cluster of neurons in the central nervous system, located deep within the cerebral hemispheres and brainstem. The neurons in one nucleus usually have roughly similar connections and functions. Nuclei are connected to other nuclei by tracts, the bundles (fascicles) of axons (nerve fibers) extending from the cell bodies. A nucleus is one of the two most common forms of nerve cell organization, the other being layered structures such as the cerebral cortex or cerebellar cortex. In anatomical sections, a nucleus shows up as a region of gray matter, often bordered by white matter. The vertebrate brain contains hundreds of distinguishable nuclei, varying widely in shape and size. A nucleus may itself have a complex internal structure, with multiple types of neurons arranged in clumps (subnuclei) or layers.