Instruct: Given a question, retrieve documents that answer the question.
Query: What is cytoplasm made off?
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.[1]
Cytoplasmic determinants are special molecules which play a very important role during oocyte maturation, in the female's ovary. During this period of time, some regions of the cytoplasm accumulate some of these cytoplasmic determinants, whose distribution is thus very heterogenic. They play a major role in the development of the embryo's organs. Each type of cell is determined by a particular determinant or group of determinants. Thus, all the organs of the future embryo are distributed and operating well thanks to the right position of the cytoplasmic determinants. The action of the determinants on the blastomeres is one of the most important ones. During the segmentation, cytoplasmic determinants are distributed among the blastomeres, at different times depending on the species and on the type of determinant. Therefore, the daughter cells resulting from the first divisions are totipotent : they can, independently, lead to a complete individual. That is not possible after the cytoplasmic determinants have been distributed in the differentiated blastomeres.
The entire cell contains several cytoplasmic domains with each domain having a nucleus and a few chloroplasts. Cytoplasmic domains are interconnected by cytoplasmic "bridges" that are supported by microtubules. The peripheral cytoplasm (whose membrane is overlaid by the cell wall), is only about 40 nm thick.
Male sterility can arise spontaneously via mutations in nuclear genes and/or cytoplasmic genes. Male sterility is easy to detect because a large number of pollen grains are produced. Pollen grains can be assayed through staining techniques (carmine, lactophenol or iodine). 
Male sterility can be either cytoplasmic or cytoplasmic–genetic. In this case, the trigger for CMS is in the extranuclear genome - (mitochondria or chloroplast). The extranuclear genome is only maternally inherited. Manifestation of male sterility in CMS may be controlled either entirely by cytoplasmic factors or by interactions between cytoplasmic factors and nuclear factors.
Amoeboid movement Cytoplasmic streaming Protoplasm, a general term for cytoplasm Syncytium
Newer information has begun to suggest that the HSP60 found in the mitochondria differs from that of the cytoplasm. With respect to the amino acid sequence, the cytoplasmic HSP60 has an N-terminal sequence not found in the mitochondrial protein. In gel electrophoresis analysis, significant differences were found in the migration of cytoplasmic and mitochondrial HSP60. The cytoplasmic HSP60 contains a signal sequence of 26 amino acids on the N terminus. This sequence is highly degenerate and is capable of folding into amphiphilic helix. Antibodies against HSP60 targeted both the mitochondrial and cytoplasmic form. Nonetheless, antibodies against the signal sequence targeted only the cytoplasmic form. Under normal physiological condition, both are found in relatively equal concentrations. In times of stress or high need of HSP60 in either the cytoplasm or the mitochondria, the cell is capable for compensating by increasing the presence of HSP60 in one compartment and decreasing its concentration in the opposite compartment.
The cytoplasm of the egg not only determines cell fate, but also determines the dorsal/ventral axis. The cytoplasm in the vegetal pole specifies this axis and removing this cytoplasm leads to a loss of axis information. The yellow cytoplasm specifies the anterior/posterior axis. When the yellow cytoplasm moves to the posterior of the egg to become posterior vegetal cytoplasm (PVC), the anterior/posterior axis is specified. Removal of the PVC leads to a loss of the axis while transplantation to the anterior reverses the axis.
Cytoplasmic flows created through osmotic pressure gradients flow longitudinally along the fungal hyphae and crash into the end causing growth. It has been demonstrated that the greater pressure at the hyphal tip corresponds to faster growth rates. Longer hyphae have greater pressure differences along their length allowing for faster cytoplasmic flow rates and larger pressures at the hyphal tip. This is why longer hyphae grow faster than shorter ones. Tip growth increases as cytoplasmic flow rate increases over a 24 hour period until a max rate of 1 micron/second growth rate is observed. Off shoots from the main hyphae are shorter and have slower cytoplasmic flow rates and correspondingly slower growth rates.
There has been research examining the motion of cytoplasmic particles independent of the nature of the cytoplasm. In such an alternative approach, the aggregate random forces within the cell caused by motor proteins explain the non-Brownian motion of cytoplasmic constituents.[11]
The Mg ion tends to bind only weakly to proteins ("K" ≤ 10) and this can be exploited by the cell to switch enzymatic activity on and off by changes in the local concentration of Mg. Although the concentration of free cytoplasmic Mg is on the order of 1 mmol/L, the total Mg content of animal cells is 30 mmol/L and in plants the content of leaf endodermal cells has been measured at values as high as 100 mmol/L (Stelzer "et al.", 1990), much of which buffered in storage compartments. The cytoplasmic concentration of free Mg is buffered by binding to chelators (e.g., ATP), but also, what is more important, by storage of Mg in intracellular compartments. The transport of Mg between intracellular compartments may be a major part of regulating enzyme activity. The interaction of Mg with proteins must also be considered for the transport of the ion across biological membranes.
Recently it has been proposed that the cytoplasm behaves like a glass-forming liquid approaching the glass transition.[9] 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).[9] 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.[9]
The ooplasm consists of the cytoplasm of the ordinary animal cell with its spongioplasm and hyaloplasm, often called the "formative yolk"; and the "nutritive yolk" or "deutoplasm", made of rounded granules of fatty and albuminoid substances imbedded in the cytoplasm.
In addition to the already illustrated structural differences between cytoplasmic and mitochondrial HSP60, there are marked functional differences. Studies have suggested that HSP60 plays a key role in preventing apoptosis in the cytoplasm. The cytoplasmic HSP60 forms a complex with proteins responsible for apoptosis and regulates the activity of these proteins. The cytoplasmic version is also involved in immune response and cancer. These two aspects will be elaborated on later. Extremely recent investigations have begun to suggest a regulatory correlation between HSP60 and the glycolytic enzyme, 6-phosphofructokinase-1. Although not much information is available, cytoplasmic HSP60 concentrations have influenced the expression of 6-phosphofructokinase in glycolysis. Despite these marked differences between the cytoplasmic and mitochondrial form, experimental analysis has shown that the cell is quickly capable of moving cytoplasmic HSP60 into the mitochondria if environmental conditions demand a higher presence of mitochondrial HSP60.
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.[7] 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.[8] 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.[9] The irregular dynamics of such particles have given rise to various theories on the nature of the cytoplasm.
The combined structure of XPO5, RanGTP, and pre-miRNA is known as the ternary complex. Once the ternary complex is formed, it diffuses through a nuclear pore complex into the cytoplasm, transporting pre-miRNA into the cytoplasm in the process. Once in the cytoplasm, RanGAP hydrolyzes GTP to GDP, causing a conformational change that releases the pre-miRNA into the cytoplasm.
Berkeley bodies are organelles unique to the yeast cell "Saccharomyces cerevisiae", with a secretory mutation in the genes sec7 and sec14. The function of the organelle lies in the CTV (cytoplasm to vacuole targeting) pathway, which is a transport pathway for certain vacuolar hydrolases to be degenerated. The Berkeley body acts as the transport medium from the cytoplasm to the vacuole within this pathway. Studies have shown that Berkeley bodies share structural similarities with autophagosomes, which are involved in autophagy.
The organelle consists of two enclosed membranes forming an enclosed lumen, which contains cytoplasm. It is formed by vesicles budding off the Golgi apparatus or the endoplasmic reticulum. They were discovered in 1980 by Novick and Schekman, of the Department of Biochemistry, University of California, Berkeley.
The presence of Döhle bodies in mature and immature neutrophils on a blood smear can be normal if they are present only in small numbers. They are also normally more abundant in cats and horses. Döhle bodies are intra-cytoplasmic structures composed of agglutinated ribosomes; they will increase in number with inflammation and increased granulocytopoiesis. If there are many neutrophils in the bloodstream containing Döhle bodies, these can be referred to as toxic neutrophils. Toxic neutrophils can also correspond to neutrophils that possess a more basophilic cytoplasm, basophilic granulation (infrequently observed), or cytoplasmic vacuoles in addition to one of the preceding cytoplasmic changes. Döhle bodies, cytoplasmic basophilia and cytoplasmic granulation all reflect "defects" in cell production and maturation during active granulocytopoiesis. Just like a left shift, the presence of toxic neutrophils suggests increased granulocytopoiesis. However, in a freshly prepared blood smear, the presence of vacuolation in addition to toxic neutrophils, reflects endotoxemia resulting in autolysis of neutrophils. This autodigestion is responsible for the cytoplasmic vacuolation. It is the single toxic change that does not result from the "manufacturing" process.
There has long been evidence that the cytoplasm behaves like a sol-gel.[10] It is thought that the component molecules and structures of the cytoplasm behave at times like a disordered colloidal solution (sol) and at other times like an integrated network, forming a solid mass (gel). This theory thus proposes that the cytoplasm exists in distinct fluid and solid phases depending on the level of interaction between cytoplasmic components, which may explain the differential dynamics of different particles observed moving through the cytoplasm.
Disintegration of the cytoplasm, pyknosis of the nuclei, and karyolysis of the nuclei of scattered transitional cells may be seen in urine from healthy individuals as well as in urine containing malignant cells. Cells with an attached tag of partially preserved cytoplasm were initially described by Papanicolaou and are sometimes called comet or decoy cells. They may have some of the characteristics of malignancy, and it is therefore important that they be recognized for what they are.
The bacterial cell is surrounded by a cell membrane which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. Unlike eukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells. However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalize aspects of bacterial metabolism, such as the carboxysome. Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division.
As FDV is a reovirus its genome is also made of dsRNA. The genome is linear and made up of ten segments, consisting of 27000-30500 base pairs. There are at least six structural proteins coded for in the genome. Replication occurs in the host cell cytoplasm or cytoplasmic viroplasma.
Two of the other, less frequently employed uses of FLIP are to determine how proteins are shuttled from the Cytoplasm to the Nucleus and then determine the rate at which this shuttling occurs. To determine what portions are involved and when in the shuttling process they are involved, continuous scans are observed. The sooner a part of the cytoplasm is used in the shuttling process, the more rapidly it experiences complete loss of fluorescence. The resulting image of this process should be a completely photobleached cytoplasm. If the cell also participates in nuclear export from the nucleus to the cytoplasm, photobleaching will also occur in the nucleus.
While CMS is controlled by an extranuclear genome, nuclear genes may have the capability to restore fertility. When nuclear restoration of fertility genes ("Rf") is available for a CMS system in any crop, it is cytoplasmic–genetic male sterility; the sterility is manifested by the influence of both nuclear (with Mendelian inheritance) and cytoplasmic (maternally inherited) genes. There are also restorers of fertility ("Rf") genes that are distinct from genetic male sterility genes. The "Rf" genes have no expression of their own unless the sterile cytoplasm is present. "Rf" genes are required to restore fertility in S cytoplasm that causes sterility. Thus plants with N cytoplasm are fertile and S cytoplasm with genotype "Rf"- leads to fertiles while S cytoplasm with "rfrf" produces only male steriles. Another feature of these systems is that "Rf" mutations ("i.e.", mutations to "rf" or no fertility restoration) are frequent, so that N cytoplasm with "Rfrf" is best for stable fertility.
In many animal cells, centrioles and spindles keep nuclei centered within a cell for mitotic, meiotic, and other processes. Without such a centering mechanism, disease and death can result. While mouse oocytes do have centrioles, they play no role in nucleus positioning, yet, the nucleus of the oocyte maintains a central position. This is a result of cytoplasmic streaming. Microfilaments, independent of microtubules and myosin 2, form a mesh network throughout the cell. Nuclei, positioned in non-centered cell locations, have been demonstrated to migrate distances greater than 25 microns to the cell center. They will do this without going off course by more than 6 microns when the network is present. This network of microfilaments has organelles bound to it by the myosin Vb molecule. Cytoplasmic fluid is entrained by the motion of these organelles, however, no pattern of directionality is associated with the movement of the cytoplasm. In fact, the motion has been demonstrated to fulfill Brownian motion characteristics. For this reason, there is some debate as to whether this should be called cytoplasmic streaming. Nonetheless, directional movement of organelles does result from this situation. Since the cytoplasm fills the cell, it is geometrically arranged into the shape of a sphere. As the radius of a sphere increases, surface area increases. Further, the motion in any given direction is proportional to the surface area. So thinking of the cell as a series of concentric spheres, it is clear that spheres with larger radii produce a greater amount of movement than spheres with smaller radii. Thus, the movement toward the center is greater than the movement away from the center, and net movement pushing the nucleus towards a central cellular location exists. In other words, the random motion of the cytoplasmic particles create a net force toward the center of the cell. Additionally, the increased motion with the cytoplasm reduces cytoplasmic viscosity allowing the nucleus to move more easily within the cell. These two factors of the cytoplasmic streaming center the nucleus in the oocyte cell.
"Neurospora crassa" is a multicellular fungus with many off shooting hyphae. Cells can be up to 10 cm long, and are separated by a small septum. Small holes in the septum allow cytoplasm and cytoplasmic contents to flow from cell to cell. Osmotic pressure gradients occur through the length of the cell to drive this cytoplasmic flow. Flows contribute to growth and the formation of cellular subcompartments.