macrophage

Macrophages (abbreviated as Mφ, MΦ or MP) (Greek: large eaters, from Greek μακρός (makrós) = large, φαγεῖν (phagein) = to eat) are a type of white blood cell of the immune system that engulfs and digests cellular debris, foreign substances, microbes, cancer cells, and anything else that does not have the type of proteins specific to healthy body cells on its surface in a process called phagocytosis.

These large phagocytes are found in essentially all tissues, where they patrol for potential pathogens by amoeboid movement. They take various forms (with various names) throughout the body (e.g., histiocytes, Kupffer cells, alveolar macrophages, microglia, and others), but all are part of the mononuclear phagocyte system. Besides phagocytosis, they play a critical role in nonspecific defense (innate immunity) and also help initiate specific defense mechanisms (adaptive immunity) by recruiting other immune cells such as lymphocytes. For example, they are important as antigen presenters to T cells. In humans, dysfunctional macrophages cause severe diseases such as chronic granulomatous disease that result in frequent infections.

Macrophages were first discovered by Élie Metchnikoff, a Russian zoologist, in 1884. (W)

A macrophage of a mouse forming two processes to phagocytize two smaller particles, possibly pathogens.

Steps of a macrophage ingesting a pathogen: a. Ingestion through phagocytosis, a phagosome is formed b. The fusion of lysosomes with the phagosome creates a phagolysosome; the pathogen is broken down by enzymes c. Waste material is expelled or assimilated (the latter not pictured) Parts: 1. Pathogens 2. Phagosome 3. Lysosomes 4. Waste material 5. Cytoplasm 6. Cell membrane.

mast cell

A mast cell (also known as a mastocyte or a labrocyte) is a migrant cell of connective tissue that contains many granules rich in histamine and heparin. Specifically, it is a type of granulocyte derived from the myeloid stem cell that is a part of the immune and neuroimmune systems. Mast cells were discovered by Paul Ehrlich in 1877. Although best known for their role in allergy and anaphylaxis, mast cells play an important protective role as well, being intimately involved in wound healing, angiogenesis, immune tolerance, defense against pathogens, and vascular permeability in brain tumours.

The mast cell is very similar in both appearance and function to the basophil, another type of white blood cell. Although mast cells were once thought to be tissue resident basophils, it has been shown that the two cells develop from different hematopoietic lineages and thus cannot be the same cells. (W)

Mast cells. Photo of cultured mast cells at 100X using an oil immersion lens and an olympus digital camera. The cells are stained with Tol Blue, and might appear slightly degranulated as they were activated using an artificial antigen during the course of an experiment.

The role of mast cells in the development of allergy.. Mast cells are involved in allergy. Allergies such as pollen allergy are related to the antibody known as IgE. Like other antibodies, each IgE antibody is specific; one acts against oak pollen, another against ragweed.

meiosis

Meiosis (from Greek μείωσις, meiosis, meaning "lessening") is a special type of cell division of germ cells in sexually-reproducing organisms used to produce the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately result in four cells with only one copy of each paternal and maternal chromosome (haploid). Additionally, prior to the division, genetic material from the paternal and maternal copies of each chromosome is crossed over, creating new combinations of code on each chromosome. Later on, during fertilisation, the haploid cells produced by meiosis from a male and female will fuse to create a cell with two copies of each chromosome again, the zygote. (W)

In meiosis, the chromosome or chromosomes duplicate (during interphase) and homologous chromosomes exchange genetic information (chromosomal crossover) during the first division, called meiosis I. The daughter cells divide again in meiosis II, splitting up sister chromatids to form haploid gametes. Two gametes fuse during fertilization, creating a diploid cell with a complete set of paired chromosomes.

Diagram of the meiotic phases 🔎

membrane contact site

Membrane contact sites (MCS) are close appositions between two organelles. Ultrastructural studies typically reveal an intermembrane distance in the order of the size of a single protein, as small as 10 nm or wider, with no clear upper limit. These zones of apposition are highly conserved in evolution. These sites are thought to be important to facilitate signalling, and they promote the passage of small molecules, including ions, lipids and (discovered later) reactive oxygen species. MCS are important in the function of the endoplasmic reticulum (ER), since this is the major site of lipid synthesis within cells. The ER makes close contact with many organelles, including mitochondria, Golgi, endosomes, lysosomes, peroxisomes, chloroplasts and the plasma membrane. Both mitochondria and sorting endosomes undergo major rearrangements leading to fission where they contact the ER. Sites of close apposition can also form between most of these organelles most pairwise combinations. First mentions of these contact sites can be found in papers published in the late 1950s mainly visualized using electron microscopy (EM) techniques. Copeland and Dalton described them as “highly specialized tubular form of endoplasmic reticulum in association with the mitochondria and apparently in turn, with the vascular border of the cell”.(W)

membrane topology

Topology is the branch of mathematics that deals with loop, knots, compartments and connectivities. The cell membrane (and endomembrane system) goes through various transformations, so membrane system has its topological features.

It is said that the Lumens of the endoplasmic reticulum and Golgi apparatus, are topologically equivalent to the exterior of the cell. This results into protein sorting and protein trafficking. Those portions of polypeptide chains that are located into the inner surface of Endoplasmic reticulum, ends up getting exposed to the cell surface. The assymmetry in biological membrane's two leaflet, such as composition of lipids, proteins, glycolipids etc. are related to membrane topology. (W)

Endomembrane system might look complex but it maintains a definite membrane topology.

Group I and II transmembrane proteins have opposite final topologies. Group I proteins have the N terminus on the far side and C terminus on the cytosolic side. Group II proteins have the C terminus on the far side and N terminus in the cytosol. However final topology not the only criterion for defining transmembrane protein groups, rather location of topogenic determinants and mechanism of assembly is considered in the classification. Group I and II transmembrane proteins have opposite orientations. Group I proteins have the N terminus on the far side and C terminus on the cytosolic side. Group II proteins have the C terminus on the far side and N terminus in the cytosol. Adapted from Genes IX by Benjamin Lewin. (W)

membrane vesicle trafficking

Membrane vesicle trafficking in eukaryotic animal cells involves movement of important biochemical signal molecules from synthesis-and-packaging locations in the Golgi body to specific 'release' locations on the inside of the plasma membrane of the secretory cell, in the form of Golgi membrane-bound micro-sized vesicles, termed membrane vesicles (MVs). In this process, the 'packed' cellular products are released/secreted outside the cell across its plasma membrane. However, this vesicular membrane is retained and recycled by the secretory cells. This phenomenon has a key role in synaptic neurotransmission, endocrine secretion, mucous secretion, granular-product secretion by neutrophils, etc. The scientists behind this discovery were awarded Nobel prize for the year 2013. In the prokaryotic gram-negative bacterial cells, membrane vesicle trafficking is mediated via bacterial outer membrane bounded nano-sized vesicles, called bacterial outer membrane vesicles (OMVs). In this case, however, the OMV membrane is secreted as well, along with OMV-contents to outside the secretion-active bacterium. This phenomenon has a key role in host-pathogen interactions, endotoxic shock in patients, invasion and infection of animals/plants, inter-species bacterial competition, quorum sensing, exocytosis, etc. (W)

Here a vesicle forms as cargo, receptors and coat proteins gather. The vesicle then buds outwards and breaks free into the cytoplasm. The vesicle is moved towards its target location then docks and fuses.

memory T cell

Memory T cells are a subset of T lymphocytes that might have some of the same functions as memory B cells. Their lineage is unclear. (W)

On-Off-On model: 1. After the naive T cell (N) encounters an antigen it becomes activated and begins to proliferate (divide) into many clones or daughter cells. 2. Some of the T cell clones will differentiate into effector T cells (E) that will perform the function of that cell (e.g. produce cytokines in the case of helper T cells or invoke cell killing in the case of cytotoxic T cells). 3. Some of the cells will form memory T cells (M) that will survive in an inactive state in the host for a long period of time until they re-encounter the same antigen and reactivate.

Developmental differentiation model: In this model, memory T cells generate effector T cells, not the other way around.

Mendelian inheritance

Mendelian inheritance is a type of biological inheritance that follows the principles originally proposed by Gregor Mendel in 1865 and 1866, re-discovered in 1900 and popularized by William Bateson. These principles were initially controversial. When Mendel's theories were integrated with the Boveri–Sutton chromosome theory of inheritance by Thomas Hunt Morgan in 1915, they became the core of classical genetics. Ronald Fisher combined these ideas with the theory of natural selection in his 1930 book The Genetical Theory of Natural Selection, putting evolution onto a mathematical footing and forming the basis for population genetics within the modern evolutionary synthesis. (W)

Gregor Mendel, the Moravian Augustinian monk who founded the modern science of genetics.

Myosotis: Colour and distribution of colours are inherited independently.

P-Generation and F1-Generation: The dominant allele for purple-red flower hides the phenotypic effect of the recessive allele for white flowers. F2-Generation: The recessive trait from the P-Generation phenotypically reappears in the individuals that are homozygous with the recessive genetic trait. Cross of two different homozygous parents as P-generation: In the F1-generation all plants have the same heterozygous genotype and the dominant flower colour in the phenotype.

In other words, there is both an endogenous metabolome and an exogenous metabolome. The endogenous metabolome can be further subdivided to include a "primary" and a "secondary" metabolome (particularly when referring to plant or microbial metabolomes). A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function. Secondary metabolites may include pigments, antibiotics or waste products derived from partially metabolized xenobiotics. The study of the metabolome is called metabolomics. (W)

General schema showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome) .

metabolism

Metabolism (from Greek: μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. (The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary metabolism or intermediate metabolism).

Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration); or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy. (W)

Simplified view of the cellular metabolism.

A diagram depicting a large set of human metabolic pathways (L) 🔎

Microbiota are "ecological communities of commensal, symbiotic and pathogenic microorganisms" found in and on all multicellular organisms studied to date from plants to animals. Microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host. The synonymous term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves.

The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genetic characteristics, sometimes collectively referred to as a holobiont.

All plants and animals, from simple life forms to humans, live in close association with microbial organisms. Several advances have driven the perception of microbiomes, including:

• the ability to perform genomic and gene expression analyses of single cells and of entire microbial communities in the disciplines of metagenomics and metatranscriptomics
• databases accessible to researchers across multiple disciplines
• methods of mathematical analysis suitable for complex data sets

Biologists have come to appreciate that microbes make up an important part of an organism's phenotype, far beyond the occasional symbiotic case study. (W)

A micelle or micella (plural micelles or micellae, respectively) is an aggregate (or supramolecular assembly) of surfactant molecules dispersed in a liquid colloid. A typical micelle in aqueous solution forms an aggregate with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single-tail regions in the micelle centre.

This phase is caused by the packing behavior of single-tail lipids in a bilayer. The difficulty filling all the volume of the interior of a bilayer, while accommodating the area per head group forced on the molecule by the hydration of the lipid head group, leads to the formation of the micelle. This type of micelle is known as a normal-phase micelle (oil-in-water micelle). Inverse micelles have the head groups at the centre with the tails extending out (water-in-oil micelle).

Micelles are approximately spherical in shape. Other phases, including shapes such as ellipsoids, cylinders, and bilayers, are also possible. The shape and size of a micelle are a function of the molecular geometry of its surfactant molecules and solution conditions such as surfactant concentration, temperature, pH, and ionic strength. The process of forming micelles is known as micellisation and forms part of the phase behaviour of many lipids according to their polymorphism. (W)

. Scheme of a micelle formed by phospholipids in an aqueous solution.

microfilament

Microfilaments, also called actin filaments, are protein filaments in the cytoplasm of eukaryotic cells that form part of the cytoskeleton. They are primarily composed of polymers of actin, but are modified by and interact with numerous other proteins in the cell. Microfilaments are usually about 7 nm in diameter and made up of two strands of actin. Microfilament functions include cytokinesis, amoeboid movement, cell motility, changes in cell shape, endocytosis and exocytosis, cell contractility, and mechanical stability. Microfilaments are flexible and relatively strong, resisting buckling by multi-piconewton compressive forces and filament fracture by nanonewton tensile forces. In inducing cell motility, one end of the actin filament elongates while the other end contracts, presumably by myosin II molecular motors. Additionally, they function as part of actomyosin-driven contractile molecular motors, wherein the thin filaments serve as tensile platforms for myosin's ATP-dependent pulling action in muscle contraction and pseudopod advancement. Microfilaments have a tough, flexible framework which helps the cell in movement.(W)

Actin cytoskeleton of mouse embryo fibroblasts, stained with Fluorescein isothiocyanate-phalloidin.

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.

The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. The scientific study of microorganisms began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax. (W)

A cluster of Escherichia coli bacteria magnified 10,000 times.

microtubule

Microtubules are polymers of tubulin that form part of the cytoskeleton and provide structure and shape to eukaryotic cells. Microtubules can grow as long as 50 micrometres and are highly dynamic. The outer diameter of a microtubule is between 23 and 27 nm while the inner diameter is between 11 and 15 nm. They are formed by the polymerization of a dimer of two globular proteins, alpha and beta tubulin into protofilaments that can then associate laterally to form a hollow tube, the microtubule. The most common form of a microtubule consists of 13 protofilaments in the tubular arrangement. (W)

Microtubule and tubulin metrics.

minicircle

Minicircles are small (~4kb) circular replicons. They occur naturally in some eukaryotic organelle genomes. In the mitochondria-derived kinetoplast of trypanosomes, minicircles encode guide RNAs for RNA editing. In Amphidinium, the chloroplast genome is made of minicircles that encode chloroplast proteins. (W)

Minicircle preparation from a parental plasmid. The parental plasmid contains two recombinase target sites (black half arrows). Recombination between these sites generates the desired minicircle (bottom right) together with the miniplasmid (bottom left). The hook on the red minicircle-insert stands for a scaffold-matrix attachment region ( S/MAR-Element), which allows for autonomous replication in the recipient cell.

Components of a typical animal cell: Nucleolus Nucleus Ribosome (little dots) Vesicle Rough endoplasmic reticulum Golgi apparatus (or, Golgi body) Cytoskeleton Smooth endoplasmic reticulum Mitochondrion Vacuole Cytosol (fluid that contains organelles, comprising the cytoplasm) Lysosome Centrosome Cell membrane

The mitochondrion (plural mitochondria) is a semi autonomous double-membrane-bound organelle found in most eukaryotic organisms. Some cells in some multicellular organisms may, however, lack mitochondria (for example, mature mammalian red blood cells). A number of unicellular organisms, such as microsporidia, parabasalids, and diplomonads, have also reduced or transformed their mitochondria into other structures. To date, only one eukaryote, Monocercomonoides, is known to have completely lost its mitochondria, and one multicellular organism, Henneguya salminicola, is known to have retained mitochondrion-related organelles in association with a complete loss of their mitochondrial genome. (W)

Mitochondrion ultrastructure (interactive diagram) A mitochondrion has a double membrane; the inner one contains its chemiosmotic apparatus and has deep grooves which increase its surface area. While commonly depicted as an "orange sausage with a blob inside of it" (like it is here), mitochondria can take many shapes and their intermembrane space is quite thin.

One model for the origin of mitochondria and plastids (L) 🔎

mitogen

A mitogen is a peptide or small protein that induces a cell to begin cell division: mitosis. Mitogenesis is the induction (triggering) of mitosis, typically via a mitogen. The mechanism of action of a mitogen is that it triggers signal transduction pathways involving mitogen-activated protein kinase (MAPK), leading to mitosis. (W)

mitosis

In cell biology, mitosis is a part of the cell cycle,in which, replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which the total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA is replicated) and is often followed by telophase and cytokinesis; which divides the cytoplasm, organelles and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of Mitosis all together define the mitotic (M) phase of an animal cell cycle—the division of the mother cell into two daughter cells genetically identical to each other. (W)

Mitosis in an animal cell (phases ordered counter-clockwise) 🔎

molecular evolution

Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes. (W)

The process of recombination involves the breakage and rejoining of parental chromosomes (M, F). This results in the generation of chromosomes (C1, C2) that share DNA from both parents.

monocyte

Monocytes are a type of leukocyte, or white blood cell. They are the largest type of leukocyte and can differentiate into macrophages and myeloid lineage dendritic cells. As a part of the vertebrate innate immune system monocytes also influence the process of adaptive immunity. There are at least three subclasses of monocytes in human blood based on their phenotypic receptors. (W)

Micrograph of Giemsa-stained monocytes.

3D Rendering of a monocyte.

A scanning electron microscope (SEM) image of normal circulating human blood. One can see red blood cells, several knobby white blood cells including lymphocytes, a monocyte, a neutrophil, and many small disc-shaped platelets. This is a scanning electron microscope image from normal circulating human blood. One can see red blood cells, several white blood cells including lymphocytes, a monocyte, a neutrophil, and many small disc-shaped platelets. Red cells are nonnucleated and contain hemoglobin, an important protein that contains iron and allows the cell to carry oxygen to other parts of the body. They also carry carbon dioxide away from peripheral tissue to the lungs where it can be exhaled. The infection-fighting white blood cells are classified in two main groups: granular and agranular. All blood cells are formed in the bone marrow. There are two types of agranulocytes: lymphocytes, which fight disease by producing antibodies and thus destroying foreign material, and monocytes. Platelets are tiny cells formed in bone marrow and are necessary for blood clotting. Type: Black & White Print.

Reference ranges for blood tests of white blood cells, comparing monocyte amount (shown in green) with other cells.

morphogen

A morphogen is a substance whose non-uniform distribution governs the pattern of tissue development in the process of morphogenesis or pattern formation, one of the core processes of developmental biology, establishing positions of the various specialized cell types within a tissue. More specifically, a morphogen is a signaling molecule that acts directly on cells to produce specific cellular responses depending on its local concentration.

Typically, morphogens are produced by source cells and diffuse through surrounding tissues in an embryo during early development, such that concentration gradients are set up. These gradients drive the process of differentiation of unspecialised stem cells into different cell types, ultimately forming all the tissues and organs of the body. The control of morphogenesis is a central element in evolutionary developmental biology (evo-devo). (W)

morphogenesis

Morphogenesis (from the Greek morphê shape and genesis creation, literally "the generation of form") is the biological process that causes a cell, tissue or organism to develop its shape. It is one of three fundamental aspects of developmental biology along with the control of tissue growth and patterning of cellular differentiation.

The process controls the organized spatial distribution of cells during the embryonic development of an organism. Morphogenesis can take place also in a mature organism, such as in the normal maintenance of tissue homeostasis by stem cells or in regeneration of tissues after damage. Cancer is an example of highly abnormal and pathological tissue morphogenesis. Morphogenesis also describes the development of unicellular life forms that do not have an embryonic stage in their life cycle. Morphogenesis is essential for the evolution of a new forms.

Morphogenesis is a mechanical process involving forces that generate mechanical stress, strain, and movement of cells, and can be induced by genetic programs according to the spatial patterning of cells within tissues. (W)

Morphogenesis is controlled by a "toolkit" of genes which switch development on and off at precise times and places. Here, gap genes in the fruit fly are switched on by genes such as bicoid, setting up stripes which create the body's segmental form..

In biology, a mutation is an alteration in the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes can be of either DNA or RNA. Mutations result from errors during DNA replication, mitosis, and meiosis or other types of damage to DNA (such as pyrimidine dimers that may be caused by exposure to radiation or carcinogens), which then may undergo error-prone repair (especially microhomology-mediated end joining) or cause an error during other forms of repair or else may cause an error during replication (translesion synthesis). Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.

Mutations may or may not produce discernible changes in the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution, cancer, and the development of the immune system, including junctional diversity. Mutation is the ultimate source of all genetic variation, providing the raw material on which evolutionary forces such as natural selection can act. (W)

The mycobiome, mycobiota, or fungal microbiome, is the fungal community in and on an organism.

There is a low abundance of fungi associated with most human body sites, such as the gastrointestinal tract, where fungi typically compose just 0.001 - 0.1% of the microbial community. However, fungi compose a significant fraction of the microbiome at some locations, such as the ear canal.

The mycobiome is relevant to human physiology as fungi may be important in maintaining microbial community structure, metabolic function, and immune-priming. Mutualism between humans and fungi is not yet well understood, and there is much to be learned about how fungi interact with the nonfungal constituents of the microbiome. (W)

Mycobiota (plural noun, no singular) are a group of all the fungi present in a particular geographic region (e.g. "the mycobiota of Ireland") or habitat type (e.g. "the mycobiota of cocoa").

Mycobiota exist on the surface and in the gastrointestinal system of humans. There are as many as sixty-six genera and 184 species in the gastrointestinal tract of healthy people. Most of these are in the Candida genera.

Though found to be present on the skin and in the gi tract in healthy individuals, the normal resident mycobiota can become pathogenic in those who are immunocompromized. Such multispecies infections lead to higher mortalities. In addition hospital-acquired infections by C. albicans have become a cause of major health concerns. A high mortality rate of 40-60% is associated with systemic infection. The best-studied of these are Candida species due to their ability to become pathogenic in immunocompromised and even in healthy hosts. Yeasts are also present on the skin, such as Malassezia species, where they consume oils secreted from the sebaceous glands. Pityrosporum (Malassezia) ovale, which is lipid-dependent and found only on humans. P. ovale was later divided into two species, P. ovale and P. orbiculare, but current sources consider these terms to refer to a single species of fungus, with M. furfur the preferred name. (W)

Staphylococcus aureus.

Escherichia coli.

myelin

Myelin is a lipid-rich (fatty) substance that surrounds nerve cell axons (the nervous system's "wires") to insulate them and increase the rate at which electrical impulses (called action potentials) are passed along the axon. The myelinated axon can be likened to an electrical wire (the axon) with insulating material (myelin) around it. However, unlike the plastic covering on an electrical wire, myelin does not form a single long sheath over the entire length of the axon. Rather, each myelin sheath insulates the axon over a single long section and, in general, each axon comprises multiple long myelinated sections separated from each other by short myelin sheath-gaps called nodes of Ranvier.

Myelin is formed in the central nervous system (CNS; brain, spinal cord and optic nerve) by glial cells called oligodendrocytes and in the peripheral nervous system (PNS) by glial cells called Schwann cells. In the CNS, axons carry electrical signals from one nerve cell body to another. In the PNS, axons carry signals to muscles and glands or from sensory organs such as the skin. Each myelin sheath is formed by the concentric wrapping of an oligodendrocyte (CNS) or Schwann cell (PNS) process (a limb-like extension from the cell body) around the axon. Myelin reduces the capacitance of the axonal membrane. On a molecular level, in the internodes it increases the distance between extracellular and intracellular ions, reducing the accumulation of charges. The discontinuous structure of the myelin sheath results in saltatory conduction, whereby the action potential "jumps" from one node of Ranvier, over a long myelinated stretch of the axon called the internode, before "recharging" at the next node of Ranvier, and so on, until it reaches the axon terminal. Nodes of Ranvier are the short (c. 1 micron) unmyelinated regions of the axon between adjacent long (c. 0.2 mm – >1 mm) myelinated internodes. Once it reaches the axon terminal, this electrical signal provokes the release of a chemical message or neurotransmitter that binds to receptors on the adjacent post-synaptic cell (e.g., nerve cell in the CNS or muscle cell in the PNS) at specialised regions called synapses.

This "insulating" role for myelin is essential for normal motor function (i.e. movement such as walking), sensory function (e.g. hearing, seeing or feeling the sensation of pain) and cognition (e.g. acquiring and recalling knowledge), as demonstrated by the consequences of disorders that affect it, such as the genetically determined leukodystrophies; the acquired inflammatory demyelinating disorder, multiple sclerosis; and the inflammatory demyelinating peripheral neuropathies. Due to its high prevalence, multiple sclerosis, which specifically affects the central nervous system (brain, spinal cord and optic nerve), is the best known disorder of myelin. (W)

Neuron description.

A neuron cell diagram, cropped to show oligodendrocyte and myelin sheath.

Transmission electron micrograph of a cross-section of a myelinated PNS axon, generated at the Electron Microscopy Facility at Trinity College, Hartford, Connecticut. Transmission electron micrograph of a myelinated axon. The myelin layer (concentric) surrounds the axon of a neurone, showing cytoplasmathic organs inside. Generated and deposited into the public domain by the Electron Microscopy Facility at Trinity College.

myelin-associated glycoprotein

Myelin-associated glycoprotein (MAG, Siglec-4) is a type 1 transmembrane protein glycoprotein localized in periaxonal Schwann cell and oligodendrocyte membranes, where it plays a role in glial-axonal interactions. MAG is a member of the SIGLEC family of proteins and is a functional ligand of the NOGO-66 receptor, NgR. MAG is believed to be involved in myelination during nerve regeneration in the PNS and is vital for the long-term survival of the myelinated axons following myelinogenesis. In the CNS MAG is one of three main myelin-associated inhibitors of axonal regeneration after injury, making it an important protein for future research on neurogenesis in the CNS. (W)

Chromosome 19 (human). MAG. Identifiers Aliases MAG, GMA, S-SIGLEC-4A, SIGLEC4A, SPG75, myelin associated glycoprotein External IDs OMIM: 159460 MGI: 96912 HomoloGene: 1771 GeneCards: MAG

Chromosome 19 (human). Based on Ensembl's GRCh38.p10 ideogram. Numerical raw data for human chromosome of assembly GRCh38.p3 (shown below) is available at NCBI's Genome Decoration Page.. Human chromosome 19. G-banding ideogram in resolution 850 bphs. (W) . Band 19q13.12 Start 35,292,125 bp End 35,313,807 bp

myelinogenesis

Myelinogenesis is generally the proliferation of myelin sheaths in the nervous system, and specifically the progressive myelination of nerve axon fibers in the central nervous system. This is a non-simultaneous process that occurs primarily postnatally in mammalian species, beginning in the embryo during the midst of early development and finishing after birth. (W)

Nerve myelination.

1. Axon 2. Nucleus of Schwann Cell 3. Schwann Cell 4. Myelin Sheath 5. Neurilemma. A myelin sheath is a protective band made up of proteins and fatty acids that surrounds the nerves like that on the spinal cord. It is formed by myelinating Schwann cells that wrap around the axon. The Schwann cells do not only create the myelin sheath, but also help protect the axon. The myelin sheath’s purpose is to allow the impulses from nerve cells to transmit quicker and fluently. It also prevents charges from leaking out of the nerves. 1. Axon 2. Nucleus of Schwann Cell 3. Schwann Cell 4. Myelin Sheath 5. Neurilemma. (W)

Neuron with oligodendrocyte and myelin sheath. A neuron cell diagram, cropped to show oligodendrocyte and myelin sheath..

naive T cell

A naive T cell (Th0 cell) is a T cell that has differentiated in bone marrow, and successfully undergone the positive and negative processes of central selection in the thymus. Among these are the naive forms of helper T cells (CD4+) and cytotoxic T cells (CD8+). A naive T cell is considered immature and, unlike activated or memory T cells, has not encountered its cognate antigen within the periphery. (W)

natural killer cell

A NK Cell, it has a similar appearance to the other lymphocytes with which it acts together and has a common origin.

Natural killer cells, also known as NK cells or large granular lymphocytes (LGL), are a type of cytotoxic lymphocyte critical to the innate immune system. The role of NK cells is analogous to that of cytotoxic T cells in the vertebrate adaptive immune response. NK cells provide rapid responses to virus-infected cells, acting at around 3 days after infection, and respond to tumor formation. Typically, immune cells detect the major histocompatibility complex (MHC) presented on infected cell surfaces, triggering cytokine release, causing the death of the infected cell by lysis or apoptosis. NK cells are unique, however, as they have the ability to recognize and kill stressed cells in the absence of antibodies and MHC, allowing for a much faster immune reaction. They were named "natural killers" because of the notion that they do not require activation to kill cells that are missing "self" markers of MHC class 1. This role is especially important because harmful cells that are missing MHC I markers cannot be detected and destroyed by other immune cells, such as T lymphocyte cells. (W)

natural killer T cell

Natural killer T (NKT) cells are a heterogeneous group of T cells that share properties of both T cells and natural killer cells. Many of these cells recognize the non-polymorphic CD1d molecule, an antigen-presenting molecule that binds self and foreign lipids and glycolipids. They constitute only approximately 1% of all peripheral blood T cells. Natural killer T cells should neither be confused with natural killer cells nor killer T cells (cytotoxic T cells). (W)

nephron

The nephron is the microscopic structural and functional unit of the kidney. It is composed of a renal corpuscle and a renal tubule. The renal corpuscle consists of a tuft of capillaries called a glomerulus and an encompassing Bowman's capsule. The renal tubule extends from the capsule. The capsule and tubule are connected and are composed of epithelial cells with a lumen. A healthy adult has 1 to 1.5 million nephrons in each kidney. Blood is filtered as it passes through three layers: the endothelial cells of the capillary wall, its basement membrane, and between the foot processes of the podocytes of the lining of the capsule. The tubule has adjacent peritubular capillaries that run between the descending and ascending portions of the tubule. As the fluid from the capsule flows down into the tubule, it is processed by the epithelial cells lining the tubule: water is reabsorbed and substances are exchanged (some are added, others are removed); first with the interstitial fluid outside the tubules, and then into the plasma in the adjacent peritubular capillaries through the endothelial cells lining that capillary. This process regulates the volume of body fluid as well as levels of many body substances. At the end of the tubule, the remaining fluid—urine—exits: it is composed of water, metabolic waste, and toxins. (W)

This is an image of a kidney nephron and its structure..

A neural circuit is a population of neurons interconnected by synapses to carry out a specific function when activated. Neural circuits interconnect to one another to form large scale brain networks. Biological neural networks have inspired the design of artificial neural networks, but artificial neural networks are usually not strict copies of their biological counterparts. (W)

neurogenesis

Neurogenesis is the process by which nervous system cells, the neurons, are produced by neural stem cells (NSCs). It occurs in all species of animals except the porifera (sponges) and placozoans. Types of NSCs include neuroepithelial cells (NECs), radial glial cells (RGCs), basal progenitors (BPs), intermediate neuronal precursors (INPs), subventricular zone astrocytes, and subgranular zone radial astrocytes, among others.

Neurogenesis is most active during embryonic development and is responsible for producing all the various types of neurons of the organism, but it continues throughout adult life in a variety of organisms. Once born, neurons do not divide (see mitosis), and many will live the lifespan of the animal. (W)

A neurosphere of neural stem cells in rat embryo spreads out into a single layer of cells. A) Neurosphere of subventricular zone cells after two days in culture. B) Shows the neurosphere at four days in culture and cells migrating away. C) Cells at the periphery of the neurosphere mostly having extending processes. Neural progenitor cells (small-size jpg version of Journal.pone.0001604.g001.png) : After forming a neurosphere, embryonic neural progenitor cells spread out into a monolayer. A. Neurosphere consisting of SVZ cells isolated at E15 that have aggregated in suspension after 2 days in culture. Scale bar: 100 µm. B. Neurosphere of SVZ cells derived at E15 that has attached to the floor of the culture flask after 4 days in culture. Note cells migrating away from the neurosphere. Scale bar: 100 µm. C. Cells at the periphery of neurospheres were chosen for electrophysiological recording. Most of the recorded cells extended processes. Arrows indicate the location of recording (left) and puffer (right) pipettes. Scale bar: 20 µm. (W)

neuroimmune system

The neuroimmune system is a system of structures and processes involving the biochemical and electrophysiological interactions between the nervous system and immune system which protect neurons from pathogens. It serves to protect neurons against disease by maintaining selectively permeable barriers (e.g., the blood–brain barrier and blood–cerebrospinal fluid barrier), mediating neuroinflammation and wound healing in damaged neurons, and mobilizing host defenses against pathogens.

The neuroimmune system and peripheral immune system are structurally distinct. Unlike the peripheral system, the neuroimmune system is composed primarily of glial cells; among all the hematopoietic cells of the immune system, only mast cells are normally present in the neuroimmune system. However, during a neuroimmune response, certain peripheral immune cells are able to cross various blood or fluid–brain barriers in order to respond to pathogens that have entered the brain. For example, there is evidence that following injury macrophages and T cells of the immune system migrate into the spinal cord. Production of immune cells of the complement system have also been documented as being created directly in the central nervous system. (W)

Follow this link to read the original description/caption in the review on glial modulators. Psychostimulants increase synaptic damage through direct actions on neurons and glia including both microglia and astroglia. Psychostimulants damage presynaptic terminals of neurons causing the production of reactive oxygen (ROS) and nitrogen (species), and the production of damage-associated molecular patterns (DAMPs) that trigger activation of pattern recognition receptors (PRRs), including Toll-like receptors (TLRs), NOD-like receptors (NLRs) and other PRRs associated with microglia, and to a lesser extent astroglia. Dopaminergic neurons are particularly vulnerable to methamphetamine, which disrupts dopamine transporter (DAT) and vesicular monoamine transporter 1 (VMAT2) function. Importantly, psychostimulants disrupt glial function directly by increasing intracellular Ca2+ concentration ([Ca2+]i), NF-κB transcriptional activity, and by activating sigma1-receptors (sigma1-R) and enzyme systems driving oxidative and nitrosative stress especially in microglia (and other cell types). Increases in NF-κB transcriptional activity result in the increased production of tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ), and interleukin-6 (IL-6) (among others) cytokines by microglia and to a lesser degree by astroglia. Psychostimulants also obstruct the buffering of extracellular glutamate by inhibiting excitatory amino acid transporters-1/2 (EAAT1/2) and the conversion of glutamate to glutamine by inhibiting glutamine synthetase, as well as limiting glucose metabolism in astrocytes. Collectively, neuronal damage combined with a heightened state of glial activation promotes positive microglial-astroglial, and neuronal-glial feedback that cause spiraling increases in neuroinflammation and neuronal injury. If unchecked, the cumulative insults result in lasting neurodegenerative changes. Modified and reprinted from reference (Hauser et al., 2012)—an “open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.5/), which permits unrestrictive use, distribution, and reproduction in any medium, provided the original work is properly cited.” This diagram depicts the neuroimmune mechanisms that mediate methamphetamine-induced neurodegeneration in the human brain. The NF-κB-mediated neuroimmune response to methamphetamine use which results in the increased permeability of the blood–brain barrier arises through its binding at and activation of sigma-1 receptors, the increased production of reactive oxygen species (ROS), reactive nitrogen species (RNS), and damage-associated molecular pattern molecules (DAMPs), the dysregulation of glutamate transporters (specifically, EAAT1 and EAAT2) and glucose metabolism, and excessive calcium influx in glial cells and dopamine neurons.

Different types of glial cells including microglia, astroglia and oligodendrocytes.

Withdrawal reflex.

neuromodulation

Neuromodulation is the physiological process by which a given neuron uses one or more chemicals to regulate diverse populations of neurons. Neuromodulators typically bind to metabotropic, G-protein coupled receptors (GPCRs) to initiate a second messenger signaling cascade that induces a broad, long-lasting signal. This modulation can last for hundreds of milliseconds to several minutes. Some of the effects of neuromodulators include: alter intrinsic firing activity, increase or decrease voltage-dependent currents, alter synaptic efficacy, increase bursting activity and reconfiguration of synaptic connectivity.

Major neuromodulators in the central nervous system include: dopamine, serotonin, acetylcholine, histamine, norepinephrine and several neuropeptides. Neuromodulators can be packaged into vesicles and released by neurons, secreted as hormones and delivered through the circulatory system. A neuromodulator can be conceptualized as a neurotransmitter that is not reabsorbed by the pre-synaptic neuron or broken down into a metabolite. Some neuromodulators end up spending a significant amount of time in the cerebrospinal fluid (CSF), influencing (or "modulating") the activity of several other neurons in the brain. (W)

A neuron, neurone or nerve cell, is an electrically excitable cell that communicates with other cells via specialized connections called synapses. It is the main component of nervous tissue in all animals except sponges and placozoa. Plants and fungi do not have nerve cells.

Neurons are typically classified into three types based on their function. Sensory neurons respond to stimuli such as touch, sound, or light that affect the cells of the sensory organs, and they send signals to the spinal cord or brain. Motor neurons receive signals from the brain and spinal cord to control everything from muscle contractions to glandular output. Interneurons connect neurons to other neurons within the same region of the brain or spinal cord. A group of connected neurons is called a neural circuit. (w)

Multipolar Neuron.

Diagram of the human nervous system. The relationship between the brain, spinal cord, and rest of the nerves in the body is demonstrated.

SMI32-stained pyramidal neurons in cerebral cortex.

Synaptic vesicles containing neurotransmitters.

Chemical synapse.

Guillain–Barré syndrome – demyelination.

neutrophil

METİN (W)

Neutrophil. 3D rendering of a neutrophil.

Neutrophil white blood cells (leukocytes) Neutrophils with segmented nuclei surrounded by erythrocytes and platelets. Intra-cellular granules are visible in the cytoplasm (Giemsa stained).

Neutrophil granulocyte migrates from the blood vessel to the matrix, secreting proteolytic enzymes, in order to dissolve intercellular connections (to the improvement of its mobility) and envelop bacteria through phagocytosis..

Reference ranges for blood tests of white blood cells, comparing neutrophil amount (shown in pink) with that of other cells.

Hypersegmented neutrophil.

HSC=Hematopoietic stem cell, Progenitor=Progenitor cell, L-blast=lymphoblast, Lymphocyte, Mo-blast=Monoblast, Monocyte, Myeloblast, Pro-M=Promyelocyte, Myelocyte, Meta-M=Metamyelocyte, Neutrophil, Eosinophil, Basophil, Pro-E=Proerythroblast, Baso-E=Basophilic erythroblast, poly-e=Polychromatic erythroblast, Ortho-E=orthochromatic erythroblast, Erythrocyte, Promegakaryocyte, megakaryocyte, Platelet.

Scanning electron micrograph of a neutrophil (yellow) phagocytosing anthrax bacilli (orange). Scale bar is 5 μm. Neutrophil engulfing anthrax bacteria, taken with a Leo 1550 scanning electron microscope. Scale bar is 5 micrometers. .

Micrograph showing several neutrophils during an acute inflammation.

Activity of neutrophil-killer and neutrophil-cager in NBT test.

Blood cell lineage.

More complete lineages. This diagram shows the hematopoiesis as it occurs in humans. It may look incomplete when rendered directly from WikiMedia. Reference list is found at: File:Hematopoiesis (human) diagram.png The morphological characteristics of the hematopoietic cells are shown as seen in a Wright’s stain, May-Giemsa stain or May-Grünwald-Giemsa stain. Alternative names of certain cells are indicated between parentheses. Certain cells may have more than one characteristic appearance. In these cases, more than one representation of the same cell has been included. Together, the monocyte and the lymphocytes comprise the agranulocytes, as opposed to the granulocytes (basophil, neurtophil and eosinophil) that are produced during granulopoiesis. B., N. and E. stand for Basophilic, Neutrophilic and Eosinophilic, respectively – as in Basophilic promyelocyte. For lymphocytes, the T and B are actual designations. [1] The polychromatic erythrocyte (reticulocyte) at the right shows its characteristic appearance when stained with methylene blue or Azure B. [2] The erythrocyte at the right is a more accurate representation of its appearance in reality when viewed through a microscope. [3] Other cells that arise from the monocyte: osteoclast, microglia (central nervous system), Langerhans cell (epidermis), Kupffer cell (liver). [4] For clarity, the T and B lymphocyte are split to better indicate that the plasma cell arises from the B-cell. Note that there is no difference in the appearance of B- and T-cells unless specific staining is applied.

noogenesis

Noogenesis is the emergence and evolution of intelligence. (W)

📥 Noogenesis (W)

The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes which in eukaryotic cells surrounds the nucleus, which encases the genetic material.

The nuclear envelope consists of two lipid bilayer membranes, an inner nuclear membrane, and an outer nuclear membrane. The space between the membranes is called the perinuclear space. It is usually about 20–40 nm wide. The outer nuclear membrane is continuous with the endoplasmic reticulum membrane. The nuclear envelope has many nuclear pores that allow materials to move between the cytosol and the nucleus. Intermediate filament proteins called lamins form a structure called the nuclear lamina on the inner aspect of the inner nuclear membrane and gives structural support to the nucleus. (W)

A comprehensive diagram of a human cell nucleus.

Nuclear pores crossing the nuclear envelope.

nuclear lamina

The nuclear lamina is a dense (~30 to 100 nm thick) fibrillar network inside the nucleus of most cells. It is composed of intermediate filaments and membrane associated proteins. Besides providing mechanical support, the nuclear lamina regulates important cellular events such as DNA replication and cell division. Additionally, it participates in chromatin organization and it anchors the nuclear pore complexes embedded in the nuclear envelope.

The nuclear lamina is associated with the inner face of the double bilayer nuclear envelope, whereas the outer face is continuous with the endoplasmic reticulum. The nuclear lamina is similar in structure to the nuclear matrix, but the latter extends throughout the nucleoplasm. (W)

Confocal microscopic analysis of dermal fibroblast in primary culture from a control (a and b) and the subject with HGPS (c and d). Labelling was performed with anti-lamin A/C antibodies. Note the presence of irregularly shaped nuclear envelopes in many of the subject's fibroblasts.

Structure and function of the nuclear lamina. The nuclear lamina lies on the inner surface of the inner nuclear membrane (INM), where it serves to maintain nuclear stability, organize chromatin and bind nuclear pore complexes (NPCs) and a steadily growing list of nuclear envelope proteins (purple) and transcription factors (pink). Nuclear envelope proteins that are bound to the lamina include nesprin, emerin, lamina-associated proteins 1 and 2 (LAP1 and LAP2), the lamin B receptor (LBR) and MAN1. Transcription factors that bind to the lamina include the retinoblastoma transcriptional regulator (RB), germ cell-less (GCL), sterol response element binding protein (SREBP1), FOS and MOK2. Barrier to autointegration factor (BAF) is a chromatin-associated protein that also binds to the nuclear lamina and several of the aforementioned nuclear envelope proteins. Heterochromatin protein 1 (HP1) binds both chromatin and the LBR. ONM, outer nuclear membrane.

nuclear matrix

In biology, the nuclear matrix is the network of fibres found throughout the inside of a cell nucleus and is somewhat analogous to the cell cytoskeleton. In contrast to the cytoskeleton, however, the nuclear matrix has been proposed to be a dynamic structure. Along with the nuclear lamina, it aids in organizing the genetic information within the cell.

The exact function of this matrix is still disputed, and its very existence has been called into question. Evidence for such a structure was recognised as long ago as 1948 (Zbarskii and Debov), and consequently many proteins associated with the matrix have been discovered. The presence of intra-cellular proteins is common ground, and it is agreed that proteins such as the Scaffold, or Matrix Associated Proteins (SAR or MAR) have some role in the organisation of chromatins. There is evidence that the nuclear matrix is involved in regulation of gene expression in Arabidopsis thaliana. (W)

A nuclear pore is a part of a large complex of proteins, known as a nuclear pore complex that spans the nuclear envelope, which is the double membrane surrounding the eukaryotic cell nucleus. There are approximately 1,000 nuclear pore complexes (NPCs) in the nuclear envelope of a vertebrate cell, but it varies depending on cell type and the stage in the life cycle. The human nuclear pore complex (hNPC) is a 110 megadalton (MDa) structure. The proteins that make up the nuclear pore complex are known as nucleoporins; each NPC contains at least 456 individual protein molecules and is composed of 34 distinct nucleoporin proteins. About half of the nucleoporins typically contain solenoid protein domains—either an alpha solenoid or a beta-propeller fold, or in some cases both as separate structural domains. The other half show structural characteristics typical of "natively unfolded" or intrinsically disordered proteins, i.e. they are highly flexible proteins that lack ordered tertiary structure. These disordered proteins are the FG nucleoporins, so called because their amino-acid sequence contains many phenylalanine—glycine repeats. (W)

Diagram of human cell nucleus. Nuclear pore labeled at bottom left.

Labels: 1) Nuclear Envelope 2) Outer Ring 3)Spokes 4)Basket 5) Filaments.

nucleoid

The nucleoid (meaning nucleus-like) is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a prokaryote is circular, and its length is very large compared to the cell dimensions needing it to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. The length of a genome widely varies (generally at least a few million base pairs) and a cell may contain multiple copies of it.

There is not yet a high-resolution structure known of a bacterial nucleoid, however key features have been researched in Escherichia coli as a model organism. In E. coli, the chromosomal DNA is on average negatively supercoiled and folded into plectonemic loops, which are confined to different physical regions, and rarely diffuse into each other. These loops spatially organize into megabase-sized regions called macrodomains, within which DNA sites frequently interact, but between which interactions are rare. The condensed and spatially organized DNA forms a helical ellipsoid that is radially confined in the cell. The 3D structure of the DNA in the nuceoid appears to vary depending on conditions and is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent, influencing each other reciprocally. (W)

Formation of the Escherichia coli nucleoid A. An illustration of an open conformation of the circular genome of Escherichia coli. Arrows represent bi-directional DNA replication. The genetic position of the origin of bi-directional DNA replication (oriC) and the site of chromosome decatenation (dif) in the replication termination region (ter) are marked. Colors represent specific segments of DNA as discussed in C. B. An illustration of a random coil form adopted by the pure circular DNA of Escherichia coli at thermal equilibrium without supercoils and additional stabilizing factors. C. A cartoon of the chromosome of a newly born Escherichia coli cell. The genomic DNA is not only condensed by 1000-fold compared to its pure random coil form but is also spatially organized. oriC and dif are localized in the mid-cell, and specific regions of the DNA indicated by colors in A organize into spatially distinct domains. Six spatial domains have been identified in E. coli. Four domains (Ori, Ter, Left, and Right) are structured and two (NS-right and NS-left) are non-structured. The condensed and organized form of the DNA together with its associated proteins and RNAs is called nucleoid..

nucleolus organizer region

Nucleolus organizer regions (NORs) are chromosomal regions crucial for the formation of the nucleolus. In humans, the NORs are located on the short arms of the acrocentric chromosomes 13, 14, 15, 21 and 22, the genes RNR1, RNR2, RNR3, RNR4, and RNR5 respectively. These regions code for 5.8S, 18S, and 28S ribosomal RNA. The NORs are "sandwiched" between the repetitive, heterochromatic DNA sequences of the centromeres and telomeres. The exact sequence of these regions is not included in the human reference genome as of 2016 or the GRCh38.p10 released January 6, 2017. On 28 February 2019, GRCh38.p13 was released, which added the NOR sequences for the short arms of chromosomes 13, 14, 15, 21, and 22. However, it is known that NORs contain tandem copies of ribosomal DNA (rDNA) genes. Some sequences of flanking sequences proximal and distal to NORs have been reported. The NORs of a loris have been reported to be highly variable. There are also DNA sequences related to rDNA that are on other chromosomes and may be involved in nucleoli formation. (W)

Silver-stained nucleolus organizer region (arrow) at the tip of a chromosome of the Gecko Lepidodactylus lugubris.

The location of NORs and the nucleolar cycle in human cells. (A) Schematic showing a human rDNA array expanded to show the pre-rRNA-coding sequences that are transcribed by RNA Pol I. The positions of mature rRNA-coding sequences, ETSs, and ITSs are indicated. (B) The locations of NORs on the acrocentric chromosome are indicated. The short arms, circled in red, are missing from the current genome draft GRCh38.p7. (C) During cell division, transcription ceases, and nucleoli disappear. NORs can be observed as achromatic gaps on DAPI-stained metaphase chromosomes due to undercondensation of rDNA (red dotted line). Silent NORs (solid red) fail to show this morphology and do not contribute to nucleolar formation. Transcription resumes in anaphase, and nucleoli form around individual active NORs. In most cell types, these then fuse, producing characteristic large nucleoli surrounded by heterochromatin. (L)

Similar to the cytoplasm of a cell, the nucleus contains nucleoplasm, also known as karyoplasm, or nucleus sap. The nucleoplasm is a type of protoplasm, and is enveloped by the nuclear envelope (also known as the nuclear membrane). The nucleoplasm includes the chromosomes and nucleolus. Many substances such as nucleotides (necessary for purposes such as DNA replication) and enzymes (which direct activities that take place in the nucleus) are dissolved in the nucleoplasm. The soluble, liquid portion of the nucleoplasm is called the nucleosol or nuclear hyaloplasm. (W)

The protoplasmic material of the nucleus including the nucleolus labelled as nucleoplasm.

nucleosome

A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteinsand resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4.

DNA must be compacted into nucleosomes to fit within the cell nucleus. In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome.

Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosome positions in the genome are not random, and it is important to know where each nucleosome is located because this determines the accessibility of the DNA to regulatory proteins. (W)

Basic units of chromatin structure.

Scheme of nucleosome organization.

The crystal structure of the nucleosome core particle (PDB: 1EQZ​).

An organ is a group of tissues with similar functions. Plant life and animal life rely on many organs that coexist in organ systems.

A given organ's tissues can be broadly categorized as parenchyma, the tissue peculiar to (or at least archetypal of) the organ and that does the organ's specialized job, and stroma, the tissues with supportive, structural, connective, or ancillary functions. For example, in a gland, the tissue that makes the hormones is the parenchyma, whereas the stroma includes the nerves that innervate the parenchyma, the blood vessels that oxygenate and nourish it and carry away its metabolic wastes, and the connective tissues that provide a suitable place for it to be situated and anchored. The main tissues that make up an organ tend to have common embryologic origins, such as arising from the same germ layer. Functionally related organs often cooperate to form whole organ systems. Organs exist in most multicellular organisms. In single-celled organisms such as bacteria, the functional analogue of an organ is known as an organelle. In plants, there are three main organs. A hollow organ is an internal organ that forms a hollow tube, or pouch such as the stomach, intestine, or bladder.

In the study of anatomy, the term viscus refers to an internal organ. Viscera is the plural form.

The number of organs in any organism depends on which precise definition of the term one uses. By one widely used definition, 79 organs have been identified in the human body. (W)

General schema showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome) .

Components of a typical animal cell: Nucleolus Nucleus Ribosome (little dots) Vesicle Rough endoplasmic reticulum Golgi apparatus (or, Golgi body) Cytoskeleton Smooth endoplasmic reticulum Mitochondrion Vacuole Cytosol (fluid that contains organelles, comprising the cytoplasm) Lysosome Centrosome Cell membrane

In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. Organelles are either separately enclosed within their own lipid bilayers (also called membrane-bound organelles) or are spatially distinct functional units without a surrounding lipid bilayer (non-membrane bound organelles). Although most organelles are functional units within cells, some functional units that extend outside of cells are often termed organelles, such as cilia, the flagellum and archaellum, and the trichocyst.

The name organelle comes from the idea that these structures are parts of cells, as organs are to the body, hence organelle, the suffix -elle being a diminutive. 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 intracellular organelles per se, some do contain protein-based bacterial microcompartments, which are thought to act as primitive prokaryotic organelles. Also, the prokaryotic flagellum which protrudes outside the cell, and its motor, as well as the largely extracellular pilus, are often spoken of as organelles. (W)

Eukaryotic organelles

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Eukaryotic cells are structurally complex, and by definition are organized, in part, by interior compartments that are themselves enclosed by lipid membranes that resemble the outermost cell membrane. The larger organelles, such as the nucleus and vacuoles, are easily visible with the light microscope. They were among the first biological discoveries made after the invention of the microscope. (W)

Prokaryotic organelles

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Prokaryotes are not as structurally complex as eukaryotes, and were once thought not to have any internal structures enclosed by lipid membranes. In the past, they were often viewed as having little internal organization, but slowly, details are emerging about prokaryotic internal structures. An early false turn was the idea developed in the 1970s that bacteria might contain membrane folds termed mesosomes, but these were later shown to be artifacts produced by the chemicals used to prepare the cells for electron microscopy.(W)

organism

Amoebae are single-celled eukaryotes.

In biology, an organism (from Greek: ὀργανισμός, organismos) is any individual entity that embodies the properties of life. It is a synonym for "life form".

Organisms are classified by taxonomy into groups such as multicellular animals, plants, and fungi; or unicellular microorganisms such as protists, bacteria, and archaea. All types of organisms are capable of reproduction, growth and development, maintenance, and some degree of response to stimuli. Humans, squids, mushrooms, and vascular plants are examples of multicellular organisms that differentiate specialized tissues and organs during development.

An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains – bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles (such as mitochondria in animals and plants and plastids in plants and algae, all generally considered to be derived from endosymbiotic bacteria). Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes.

Estimates on the number of Earth's current species range from 2 million to 1 trillion, of which over 1.7 million have been documented. More than 99% of all species, amounting to over five billion species, that ever lived are estimated to be extinct.

In 2016, a set of 355 genes from the last universal common ancestor (LUCA) of all organisms was identified. (W)

organogenesis

Organogenesis is the phase of embryonic development that starts at the end of gastrulation and continues until birth. During organogenesis, the three germ layers formed from gastrulation (the ectoderm, endoderm, and mesoderm) form the internal organs of the organism.

The cells of each of the three germ layers undergo differentiation, a process where less-specialized cells become more-specialized through the expression of a specific set of genes. Cell differentiation is driven by cell signaling cascades. Differentiation is influenced by extracellular signals such as growth factors that are exchanged to adjacent cells which is called juxtracrine signaling or to neighboring cells over short distances which is called paracrine signaling. Intracellular signals consist of a cell signaling itself (autocrine signaling), also play a role in organ formation. These signaling pathways allows for cell rearrangement and ensures that organs form at specific sites within the organism. The organogenesis process can be studied using embryos and organoids. (W)

The endoderm of vertebrates produces tissue within the lungs, thyroid, and pancreas. The mesoderm aids in the production of cardiac muscle, skeletal muscle, smooth muscle, tissues within the kidneys, and red blood cells. The ectoderm produces tissues within the epidermis and aids in the formation of neurons within the brain, and melanocytes.

Neural precursor cells fold and elongate to form the neural tube. Mesoderm cells condense to form a rod which will send out signals to redirect the ectoderm cells above. This fold along the neural tube sets up the vertebrate central nervous system. Development of the neural tube in human embryos (Prentiss-Arey). A. An early embryo (Keibel) B. at 2 mm. (Graf Spee) C. at 2 mm. (Mall) D. at 2.7 mm (Kollmann). This is a scan of Figure 6 of the book "The anatomy of the nervous system" by Stephen Walter Ranson, with the labels redrawn.

orthornavirae

Orthornavirae is a kingdom of viruses that have genomes made of ribonucleic acid (RNA) and which encode an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to replicate the genome. Viruses in this kingdom also share a number of characteristics involving evolution, including high rates of genetic mutations, recombinations, and reassortments. (W)

Taxonomy and replication strategies of RNA viruses. a Simplified taxonomy of the genome architecture of the RNA viruses described in this review. See main text for used abbreviations. b (+RNA virus) Infection with a +RNA virus—as exemplified here with a CoV-like virion—releases a single-stranded RNA genome into the cytoplasm (1) [81, 173, 174]. (2) Translation of the 5′-terminal open-reading frame of the genome produces the viral replicase. (3) This multi-enzyme complex includes RdRp activity (orange) and associates with intracellular membranes before −RNA synthesis commences. Newly synthesised −RNAs are subsequently used to produce new +RNAs (4), which are typically capped (yellow) and polyadenylated (polyA). (Retrovirus) HIV-1 genomes are packaged as ssRNA in virions. When the ssRNA is released (1) a cDNA copy is synthesised by the RT (2). The RNA is next degraded by the intrinsic RNase H activity in the RT (3) and the single stranded cDNA converted to dsDNA (4). The dsDNA is imported in the nucleus (5) for integration into the host’s genetic material. (−RNA virus) (1) As illustrated here with an IAV-like particle, infection with an −RNA virus releases a viral RNA genome that is associated with a viral polymerase (orange) and nucleoprotein (green). (2) In the case of non-segmented −RNA viruses, these complexes support transcription to produce viral mRNAs or cRNAs. (3) Viral mRNAs are next translated and new viral proteins complex with cRNAs to synthesise new vRNAs. (5) The vRNA-containing complexes of some segmented −RNA viruses are imported into the nucleus of the host cell, where (6) the RdRp produces mRNAs or cRNAs. (7) mRNAs are transported to the cytoplasm, while cRNAs are bound by new viral proteins to form cRNPs for −RNA synthesis. (dsRNA virus) Fully duplexed RNA genomes lack cap and polyA elements. (1) The RdRp (orange), therefore, transcribes the viral genome inside the capsid of the virion (blue and red), so viral mRNAs can be (2) released into the cytoplasm as illustrated here with a rotavirus-like virion. In the cytoplasm the mRNA is translated (3) or replicated by newly synthesised viral RdRps (4). (W)

Phylogenetic tree with phylum branches highlighted. Negarnaviricota (brown), Duplornaviricota (green), Kitrinoviricota (pink), Pisuviricota (blue), and Lenarviricota (yellow). Phylogeny of RNA virus RNA-dependent RNA polymerases (RdRps) and reverse transcriptases (RTs): the main branches (branches 1 to 5). Each branch represents collapsed sequences of the corresponding set of RdRps. The 5 main branches discussed in the text are labeled accordingly. The bootstrap support values obtained by the indicated numerator/denominator calculations are shown for each internal branch. LTR, long-terminal repeat.

osmoregulation

Osmoregulation is the active regulation of the osmotic pressure of an organism's body fluids, detected by osmoreceptors, to maintain the homeostasis of the organism's water content; that is, it maintains the fluid balance and the concentration of electrolytes (salts in solution which in this case is represented by body fluid) to keep the body fluids from becoming too diluted or concentrated. Osmotic pressure is a measure of the tendency of water to move into one solution from another by osmosis. The higher the osmotic pressure of a solution, the more water tends to move into it. Pressure must be exerted on the hypertonic side of a selectively permeable membrane to prevent diffusion of water by osmosis from the side containing pure water.

Organisms in aquatic and terrestrial environments must maintain the right concentration of solutes and amount of water in their body fluids; this involves excretion (getting rid of metabolic nitrogen wastes and other substances such as hormones that would be toxic if allowed to accumulate in the blood) through organs such as the skin and the kidneys. (W)

Movement of water and ions in freshwater fish.

Movement of water and ions in saltwater fish.

Osmosis is the spontaneous net movement of solvent molecules through a selectively permeable membrane into a region of higher solute concentration, in the direction that tends to equalize the solute concentrations on the two sides. It may also be used to describe a physical process in which any solvent moves across a selectively permeable membrane (permeable to the solvent, but not the solute) separating two solutions of different concentrations. Osmosis can be made to do work. Osmotic pressure is defined as the external pressure required to be applied so that there is no net movement of solvent across the membrane. Osmotic pressure is a colligative property, meaning that the osmotic pressure depends on the molar concentration of the solute but not on its identity.

Osmosis is a vital process in biological systems, as biological membranes are semipermeable. In general, these membranes are impermeable to large and polar molecules, such as ions, proteins, and polysaccharides, while being permeable to non-polar or hydrophobic molecules like lipids as well as to small molecules like oxygen, carbon dioxide, nitrogen, and nitric oxide. Permeability depends on solubility, charge, or chemistry, as well as solute size. Water molecules travel through the plasma membrane, tonoplast membrane (vacuole) or protoplast by diffusing across the phospholipid bilayer via aquaporins (small transmembrane proteins similar to those responsible for facilitated diffusion and ion channels). Osmosis provides the primary means by which water is transported into and out of cells. The turgor pressure of a cell is largely maintained by osmosis across the cell membrane between the cell interior and its relatively hypotonic environment. (W)

The process of osmosis over a semi-permeable membrane. The blue dots represent particles driving the osmotic gradient. Caption: Osmosis is the diffusion of water through a semipermeable membrane down its concentration gradient. If a membrane is permeable to water, though not to a solute, water will equalize its own concentration by diffusing to the side of lower water concentration (and thus the side of higher solute concentration). In the beaker on the left, the solution on the right side of the membrane is hypertonic. URL:https://cnx.org/contents/FPtK1zmh@8.108:q2X995E3@12/The-Cell-Membrane Version 8.25 from the Textbook OpenStax Anatomy and Physiology Published May 18, 2016 The factual accuracy of this file is disputed. See Talk page, --Burkhard--Burkhard (talk) 16:53, 14 November 2016 (UTC) .

Effect of different solutions on blood cells.. Osmotic pressure is the hydrostatic pressure produced by a solution in a space divided by a differentially permeable membrane due to a differential in the concentrations of solute.

Micrographs of osmotic pressure on red blood cells (RBC). Human erythrocytes (red blood cells) viewed by phase contrast light microscopy. Three conditions are shown: hypertonic conditions (where the erythrocytes contract and appear "spiky"), isotonic conditions (where the erythrocytes appear normal) and hypotonic conditions (where the etrythrocytes expand and become more round).

Plant cell under different environments. In biology, turgor pressure or turgidity is the pressure of the cell contents against the cell wall, in plant cells, determined by the water content of the vacuole, resulting from osmotic pressure.

osmotic shock

Osmotic shock or osmotic stress is physiologic dysfunction caused by a sudden change in the solute concentration around a cell, which causes a rapid change in the movement of water across its cell membrane. Under conditions of high concentrations of either salts, substrates or any solute in the supernatant, water is drawn out of the cells through osmosis. This also inhibits the transport of substrates and cofactors into the cell thus “shocking” the cell. Alternatively, at low concentrations of solutes, water enters the cell in large amounts, causing it to swell and either burst or undergo apoptosis.

All organisms have mechanisms to respond to osmotic shock, with sensors and signal transduction networks providing information to the cell about the osmolarity of its surroundings; these signals activate responses to deal with extreme conditions. Although single-celled organisms are more vulnerable to osmotic shock, since they are directly exposed to their environment, cells in large animals such as mammals still suffer these stresses under some conditions. Current research also suggests that osmotic stress in cells and tissues may significantly contribute to many human diseases.

In eukaryotes, calcium acts as one of the primary regulators of osmotic stress. Intracellular calcium levels rise during hypo-osmotic and hyper-osmotic stresses. (W)

osteoclast

An osteoclast (from Ancient Greek ὀστέον (osteon) 'bone', and κλαστός (clastos) 'broken') is a type of bone cell that breaks down bone tissue. This function is critical in the maintenance, repair, and remodelling of bones of the vertebral skeleton. The osteoclast disassembles and digests the composite of hydrated protein and mineral at a molecular level by secreting acid and a collagenase, a process known as bone resorption. This process also helps regulate the level of blood calcium. (W)

Bone structure - Bone degrading cells - Osteoclasts.

Osteoclast displaying many nuclei within its "foamy" cytoplasm. Osteoclast.

osteocyte

An osteocyte, a star-shaped type of bone cell, is the most commonly found cell in mature bone tissue, and can live as long as the organism itself. The adult human body has about 42 billion of them. Osteocytes do not divide and have an average half life of 25 years. They are derived from osteoprogenitor cells, some of which differentiate into active osteoblasts. Osteoblasts/osteocytes develop in mesenchyme.

In mature bones, osteocytes and their processes reside inside spaces called lacunae (Latin for a pit) and canaliculi, respectively. Osteocytes are simply osteoblasts trapped in the matrix that they secrete. They are networked to each other via long cytoplasmic extensions that occupy tiny canals called canaliculi, which are used for exchange of nutrients and waste through gap junctions.

Although osteocytes have reduced synthetic activity and (like osteoblasts) are not capable of mitotic division, they are actively involved in the routine turnover of bony matrix, through various mechanosensory mechanisms. They destroy bone through a rapid, transient (relative to osteoclasts) mechanism called osteocytic osteolysis. Hydroxyapatite, calcium carbonate and calcium phosphate is deposited around the cell. (W)

Bone structure - Bone cells - Osteocytes.

Diagram depicting transverse section of the fibula (decalcified) at a magnification of x250 (vectorized version).

An osteocyte in rat bone exposed by resin cast etching.

P element

P elements are transposable elements that were discovered in Drosophila as the causative agents of genetic traits called hybrid dysgenesis. The transposon is responsible for the P trait of the P element and it is found only in wild flies. They are also found in many other eukaryotes.

The P element encodes for the protein P transposase. Unlike laboratory strain females, wild type females are thought also to express an inhibitor to P transposase function, from the very same element. This inhibitor reduces the disruption to the genome caused by the P elements, allowing fertile progeny. Evidence for this comes from crosses of laboratory females (which lack P transposase inhibitor) with wild type males (which have P elements). In the absence of the inhibitor, the P elements can proliferate throughout the genome, disrupting many genes and killing progeny.

P elements are commonly used as mutagenic agents in genetic experiments with Drosophila. One advantage of this approach is that the mutations are easy to locate. In hybrid dysgenesis, one strain of Drosophila mates with another strain of Drosophila producing hybrid offspring and causing chromosomal damage known to be dysgenic. Hybrid dysgenesis requires a contribution from both parents. For example, in the P-M system, where the P strain contributes paternally and M strain contributes maternally, dysgenesis can occur. The reverse cross, with M cytotype father and P mother, produces normal offspring, as it crosses in a P x P or M x M manner. P male chromosomes can cause dysgenesis when crossed with an M female. (W)

paracellular transport

Paracellular transport refers to the transfer of substances across an epithelium by passing through the intercellular space between the cells. It is in contrast to transcellular transport, where the substances travel through the cell, passing through both the apical membrane and basolateral membrane.

The distinction has particular significance in renal physiology and intestinal physiology. Transcellular transport often involves energy expenditure whereas paracellular transport is unmediated and passive down a concentration gradient. Paracellular transport also has the benefit that absorption rate is matched to load because it has no transporters that can be saturated. (W)

In biology, a pathogen (Greek: πάθος pathos "suffering", "passion" and -γενής -genēs "producer of") in the oldest and broadest sense, is anything that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ. .(W)

phage ecology

Bacteriophages (phages), potentially the most numerous "organisms" on Earth, are the viruses of bacteria (more generally, of prokaryotes). Phage ecology is the study of the interaction of bacteriophages with their environments. (W)

phagemid

A phagemid or phasmid is a DNA-based cloning vector, which has both bacteriophage and plasmid properties. These vectors carry, in addition to the origin of plasmid replication, an origin of replication derived from bacteriophage. Unlike commonly used plasmids, phagemid vectors differ by having the ability to be packaged into the capsid of a bacteriophage, due to their having a genetic sequence that signals for packaging. Phagemids are used in a variety of biotechnology applications; for example, they can be used in a molecular biology technique called "Phage Display".(W)

phagocyte

Phagocytes are cells that protect the body by ingesting harmful foreign particles, bacteria, and dead or dying cells. Their name comes from the Greek phagein, "to eat" or "devour", and "-cyte", the suffix in biology denoting "cell", from the Greek kutos, "hollow vessel". They are essential for fighting infections and for subsequent immunity. Phagocytes are important throughout the animal kingdom and are highly developed within vertebrates. One litre of human blood contains about six billion phagocytes. They were discovered in 1882 by Ilya Ilyich Mechnikov while he was studying starfish larvae. Mechnikov was awarded the 1908 Nobel Prize in Physiology or Medicine for his discovery. Phagocytes occur in many species; some amoebae behave like macrophage phagocytes, which suggests that phagocytes appeared early in the evolution of life. (W)

Scanning electron micrograph of a neutrophil phagocytosing anthrax bacilli (orange).

Phagocytosis in three steps: 1. Unbound phagocyte surface receptors do not trigger phagocytosis. 2. Binding of receptors causes them to cluster. 3. Phagocytosis is triggered and the particle is taken up by the phagocyte.

Macrophages have special receptors that enhance phagocytosis (not to scale).

Simplified diagram of the phagocytosis and destruction of a bacterial cell.

Micrograph of Gram-stained pus showing Neisseria gonorrhoeae bacteria inside phagocytes and their relative sizes. This low-resolution photomicrograph reveals the histopathology in an acute case of gonococcal urethritis using Gram-stain technique. This slide is used to demonstrate the non-random distribution of gonococci among polymorphonuclear neutrophils. Note that there are both intracellular and extracellular bacteria in the field of view. (CDC) Higher resolution image (25.71 MB) available at PHIL..

Apoptosis—phagocytes clear fragments of dead cells from the body.

A schematic diagram of the presentation of foreign peptides by MHC 1 molecules. Simplified diagram of cytoplasmic protein degradation by the proteasome, transport into endoplasmic reticulum by TAP complex, loading on MHC class I, and transport to the surface for presentation.

Phagocytes derive from stem cells in the bone marrow.

Neutrophils move from the blood to the site of infection. Neutrophil granulocyte migrates from the blood vessel to the matrix, secreting proteolytic enzymes, in order to dissolve intercellular connections (for improvement of its mobility) and envelop bacteria through Phagocytosis.

Monocytes in blood (Giemsa stain).

Neutrophils with a segmented nuclei surrounded by erythrocytes, the intra-cellular granules are visible in the cytoplasm (Giemsa stained).

A dendritic cell. A screen clip from a video included in the journal article “Environmental Dimensionality Controls the Interaction of Phagocytes with the Pathogenic Fungi Aspergillus fumigatus and Candida albicans” A well resolved dendritic cell drags a conidium through a distance of up to 9 μm. The conidium, however, is not phagocytosed by the cell.

Cells of Staphylococcus aureus bacteria: the large, stringy capsules protect the organisms from attack by phagocytes.

Rickettsia are small bacteria—here stained red—that grow in the cytoplasm of non-professional phagocytes.. Gimenez stain of tick hemolymph cells infected with Rickettsia rickettsii, the causative agent of Rocky Mountain spotted fever. R. rickettsii is a small bacterium that grows inside the cells of its hosts. These bacteria range in size from 0.2 x 0.5 micrometers to 0.3 x 2.0 micrometers. They are difficult to see in tissues by using routine histologic stains and generally require the use of special staining methods. The genus Rickettsia is included in the bacterial tribe Rickettsieae, family Rickettsiaceae, and order Rickettsiales. This genus includes many other species of bacteria associated with human disease, including those in the spotted fever group and in the typhus group.

Leishmania tropica amastigotes (arrows) in a macrophage from skin.

phagocytosis (gözeyutarlığı)

Phagocytosis (from Ancient Greek φαγεῖν(phagein) 'to eat', and κύτος, (kytos) 'cell') is the process by which a cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis.

In a multicellular organism's immune system, phagocytosis is a major mechanism used to remove pathogens and cell debris. The ingested material is then digested in the phagosome. Bacteria, dead tissue cells, and small mineral particles are all examples of objects that may be phagocytized. Some protozoa use phagocytosis as means to obtain nutrients. (W)

Overview of phagocytosis.

The engulfing of a pathogen by a phagocyte.

Phagocytosis versus exocytosis. Phagocytosis and exocytosis can play an important role in nonspecific immune response. In phagocytosis, involving the destruction of pathogens, the pathogens are surrounded and then engulfed through endocytosis. The vacuole then forms and closes around the pathogens. In exocytosis, the lysosome and vacuole fuse together which allows enzymes to destroy pathogens. Debris from the pathogens is then released from the cell.

Scanning electron micrograph of a phagocyte (yellow, right) phagocytosing anthrax bacilli (orange, left). Neutrophil engulfing anthrax bacteria, taken with a Leo 1550 scanning electron microscope. Scale bar is 5 micrometers.

Trophozoites of Entamoeba histolytica with ingested erythrocytes. Trophozoites of Entamoeba histolytica with ingested erythrocytes (trichrome stain). The ingested erythrocytes appear as dark inclusions. Erythrophagocytosis is the only characteristic that can be used to differentiate morphologically E. histolytica from the nonpathogenic E. dispar. In these specimens, the parasite nuclei have the typical small, centrally located karyosome, and thin, uniform peripheral chromatin.

phagosome

In cell biology, a phagosome is a vesicle formed around a particle engulfed by a phagocyte via phagocytosis. Professional phagocytes include macrophages, neutrophils, and dendritic cells (DCs). A phagosome is formed by the fusion of the cell membrane around a microorganism, a senescent cell or an apoptotic cell. Phagosomes have membrane-bound proteins to recruit and fuse with lysosomes to form mature phagolysosomes. The lysosomes contain hydrolytic enzymes and reactive oxygen species (ROS) which kill and digest the pathogens. Phagosomes can also form in non-professional phagocytes, but they can only engulf a smaller range of particles, and do not contain ROS. The useful materials (e.g. amino acids) from the digested particles are moved into the cytosol, and waste is removed by exocytosis. Phagosome formation is crucial for tissue homeostasis and both innate and adaptive host defense against pathogens. (W)

Phagocytosis of a bacterium, showing the formation of phagosome and phagolysosome.

Phenotype (from Greek pheno-, meaning 'showing', and type, meaning 'type') is the term used in genetics for the composite observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological properties, its behavior, and the products of behavior. An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype, and the influence of environmental factors. Both factors may interact, further affecting phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype suggested that one can regard bird nests and other built structures such as caddis-fly larvae cases and beaver dams as "extended phenotypes". (W)

The shells of individuals within the bivalve mollusk species Donax variabilis show diverse coloration and patterning in their phenotypes.

photosynthesis

Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organisms' activities. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesis, from the Greek phōs (φῶς), "light", and sunthesis (σύνθεσις), "putting together". In most cases, oxygen is also released as a waste product. Most plants, most algae, and cyanobacteria perform photosynthesis; such organisms are called photoautotrophs. Photosynthesis is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. (W)

Photosynthesis changes sunlight into chemical energy, splits water to liberate O2, and fixes CO2 into sugar.

Phototrophs (Gr: φῶς, φωτός = light, τροϕή = nourishment) are organisms that carry out photon capture to produce complex organic compounds (such as carbohydrates) and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs often photosynthesize: they anabolically convert carbon dioxide into organic material to be utilized structurally, functionally, or as a source for later catabolic processes (e.g. in the form of starches, sugars and fats). All phototrophs either use electron transport chains or direct proton pumping to establish an electrochemical gradient which is utilized by ATP synthase, to provide the molecular energy currency for the cell. Phototrophs can be either autotrophs or heterotrophs. If their electron and hydrogen donors are inorganic compounds (e.g. Na₂S₂O₃, as in some purple sulfur bacteria, or H₂S, as in some green sulfur bacteria) they can be also called lithotrophs, and so, some photoautotrophs are also called photolithoautotrophs. Examples of phototroph organisms are: Rhodobacter capsulatus, Chromatium, Chlorobium etc. (W)

Terrestrial and aquatic phototrophs: plants grow on a fallen log floating in algae-rich water.

Flowchart to determine if a species is autotroph, heterotroph, or a subtype.

phylum

The hierarchy of biological classification's eight major taxonomic ranks. A kingdom contains one or more phyla. Intermediate minor rankings are not shown.

In biology, a phylum (plural: phyla) is a level of classification or taxonomic rank below kingdom and above class.Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts the terms as equivalent. Depending on definitions, the animal kingdom Animalia or Metazoa contains approximately 35 phyla; the plant kingdom Plantae contains about 14, and the fungus kingdom Fungi contains about 8 phyla. Current research in phylogenetics is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta.(W)

plasma cell

Plasma cells, also called plasma B cells, are white blood cells that originate in the bone marrow and secrete large quantities of proteins called antibodies in response to being presented specific substances called antigens. These antibodies are transported from the plasma cells by the blood plasma and the lymphatic system to the site of the target antigen (foreign substance), where they initiate its neutralization or destruction. B cells differentiate into plasma cells that produce antibody molecules closely modeled after the receptors of the precursor B cell. (W)

Micrograph of malignant plasma cells (plasmacytoma), many displaying characteristic "clockface nuclei", also seen in normal plasma cells. H&E stain. Micrograph of a plasmacytoma. H&E stain. The micrograph shows abundant (malignant) plasma cells with the occasional Mott cell, a plasma cell with intracytoplasmic Russell bodies (an eosinophilic uniformly staining membrane bound body which contains immunoglobulin). Other features of plasmacytomas (not apparent on the image) are: a prominent perinuclear hof (large Golgi bodies), and Dutcher bodies. Multiple myeloma (which is diagnosed using several clinical criteria) is, histologically, a plasmacytoma. Related images Uncropped. Cropped..

Plasma cell. Micrograph of a plasma cell with distinct clear perinuclear region of the cytoplasm, which contains large numbers of Golgi bodies. .

Plasma cells with Dutcher and Russell bodies (H&E, 100x, oil).

plasmid

A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that benefit the survival of the organism and confer selective advantage such as antibiotic resistance. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation.

Plasmids are considered replicons, units of DNA capable of replicating autonomously within a suitable host. However, plasmids, like viruses, are not generally classified as life. Plasmids are transmitted from one bacterium to another (even of another species) mostly through conjugation. This host-to-host transfer of genetic material is one mechanism of horizontal gene transfer, and plasmids are considered part of the mobilome. Unlike viruses, which encase their genetic material in a protective protein coat called a capsid, plasmids are "naked" DNA and do not encode genes necessary to encase the genetic material for transfer to a new host; however, some classes of plasmids encode the conjugative "sex" pilus necessary for their own transfer. The size of the plasmid varies from 1 to over 200 kbp, and the number of identical plasmids in a single cell can range anywhere from one to thousands under some circumstances. (W)

Illustration of a bacterium showing chromosomal DNA and plasmids (Not to scale). This image shows a line drawing of a bacterium with its chromosomal DNA and several plasmids within it. The bacterium is drawn as a large oval. Within the bacterium, small to medium size circles illustrate the plasmids, and one long thin closed line that intersects itself repeatedly illustrates the chromosomal DNA. (W)

There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas episomes, the lower example, can integrate into the host chromosome.

plasmolysis

Plasmolysis is the process in which cells lose water in a hypertonic solution. The reverse process, deplasmolysis or cytolysis, can occur if the cell is in a hypotonic solution resulting in a lower external osmotic pressure and a net flow of water into the cell. Through observation of plasmolysis and deplasmolysis, it is possible to determine the tonicity of the cell's environment as well as the rate solute molecules cross the cellular membrane. (W)

Before plasmolysis (top) and after (bottom). Epidermis cells of Rhoeo Discolor(Tradescantia); the vacuoles fill out the whole cell bodies. Size: Field of view ca. 450 µm .

Before plasmolysis (top) and after (bottom). Epidermis cells of Rhoeo Discolor (Tradescantia) after plasmolysis. The vacuoles (pink) have shrunk. Size: Field of view ca. 450 µm .

Plant cell undergoing Plasmolysis in a Hypertonic solution (x400 magnification).

Plant cell under different environments. In biology, turgor pressure or turgidity is the pressure of the cell contents against the cell wall, in plant cells, determined by the water content of the vacuole, resulting from osmotic pressure..

The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered endosymbiotic Cyanobacteria, related to the Gloeomargarita. Plastids were discovered and named by Ernst Haeckel, but A. F. W. Schimper was the first to provide a clear definition. Plastids are the site of manufacture and storage of important chemical compounds used by the cells of autotrophic eukaryotes. They often contain pigments used in photosynthesis, and the types of pigments in a plastid determine the cell's color. They have a common evolutionary origin and possess a double-stranded DNA molecule that is circular, like that of the circular chromosome of prokaryotic cells. (W)

Plant cells with visible chloroplasts.

ploidy

Ploidy is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Somatic cells, tissues, and individual organisms can be described according to the number of sets of chromosomes present (the "ploidy level"): monoploid (1 set), diploid (2 sets), triploid (3 sets), tetraploid (4 sets), pentaploid (5 sets), hexaploid (6 sets), heptaploid or septaploid (7 sets), etc. The generic term polyploid is often used to describe cells with three or more chromosome sets. (W)

A haploid set that consists of a single complete set of chromosomes (equal to the monoploid set), as shown in the picture above, must belong to a diploid species. If a haploid set consists of two sets, it must be of a tetraploid (four sets) species.

polyphage

Polyphage are genomic multimers of bacteriophage in which multiple viral particles are all encapsulated, one after the other, within the same set of coat proteins. This phenomenon is characteristic of filamentous phage. (W)

prokaryote

Comparison of eukaryotes vs. prokaryotes.

Diagram of the origin of life with the Eukaryotes appearing early, not derived from Prokaryotes, as proposed by Richard Egel in 2012. This view, one of many on the relative positions of Prokaryotes and Eukaryotes, implies that the universal common ancestor was relatively large and complex.

Phylogenetic ring showing the diversity of prokaryotes, and symbiogenetic origins of eukaryotes.

Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes

A protocell (or protobiont) is a self-organized, endogenously ordered, spherical collection of lipids proposed as a stepping-stone toward the origin of life. A central question in evolution is how simple protocells first arose and how they could differ in reproductive output, thus enabling the accumulation of novel biological emergences over time, i.e. biological evolution. Although a functional protocell has not yet been achieved in a laboratory setting, the goal to understand the process appears well within reach. (W)

The three main structures phospholipids form in solution; the liposome (a closed bilayer), the micelle and the bilayer. Cross section of the different structures that phospholipids can take in a aqueous solution. The circles are the hydrophilic heads and the wavy lines are the fatty acyl side chains.

Scheme of a micelle spontaneously formed by phospholipids in an aqueous solution.

This fluid lipid bilayer cross section is made up entirely of phosphatidylcholine..

Schematic showing two possible conformations of the lipids at the edge of a pore. In the top image the lipids have not rearranged, so the pore wall is hydrophobic. In the bottom image some of the lipid heads have bent over, so the pore wall is hydrophilic. Diagram of possible lipid arrangements at the edge of a pore through a lipid bilayer. (above) In the absence of any re-arrangement the pore walls will be hydrophobic since the alkane tails are exposed. (below) Some researchers believe that the lipids at the edge re-orient to line the pore wall with hydrophilic head groups..

Surfactant molecules arranged on an air – water interface.