efflux (microbiology)

All microorganisms, with a few exceptions, have highly conserved DNA sequences in their genome that are transcribed and translated to efflux pumps. Efflux pumps are capable of moving a variety of different toxic compounds out of cells, such as antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals, bacterial metabolites and neurotransmitters via active efflux, which is vital part for xenobiotic metabolism. This active efflux mechanism is responsible for various types of resistance to bacterial pathogens within bacterial species - the most concerning being antibiotic resistance because microorganisms can have adapted efflux pumps to divert toxins out of the cytoplasm and into extracellular media.

Efflux systems function via an energy-dependent mechanism (active transport) to pump out unwanted toxic substances through specific efflux pumps. Some efflux systems are drug-specific, whereas others may accommodate multiple drugs with small multidrug resistance (SMR) transporters.

Efflux pumps are proteinaceous transporters localized in the cytoplasmic membrane of all kinds of cells. They are active transporters, meaning that they require a source of chemical energy to perform their function. Some are primary active transporters utilizing adenosine triphosphate hydrolysis as a source of energy, whereas others are secondary active transporters (uniporters, symporters, or antiporters) in which transport is coupled to an electrochemical potential difference created by pumping hydrogen or sodium ions into the cell. (W)

Protein TolC, the outer membrane component of a tripartite efflux pump in Escherichia coli.

AcrB, the other component of pump, Escherichia coli.

embryo

An embryo is the early stage of development of a multicellular organism. In general, in organisms that reproduce sexually, embryonic development is the part of the life cycle that begins just after fertilization and continues through the formation of body structures, such as tissues and organs. Each embryo starts development as a zygote, a single cell resulting from the fusion of gametes (i.e. fertilization of a female egg cell by a male sperm cell). In the first stages of embryonic development, a single-celled zygote undergoes many rapid cell divisions, called cleavage, to form a blastula, which looks similar to a ball of cells. Next, the cells in a blastula-stage embryo start rearranging themselves into layers in a process called gastrulation. These layers will each give rise to different parts of the developing multicellular organism, such as the nervous system, connective tissue, and organs.

A newly developing human is typically referred to as an embryo until the ninth week after conception, when it is then referred to as a fetus. In other multicellular organisms, the word “embryo” can be used more broadly to any early developmental or life cycle stage prior to birth or hatching. (W)

A male human embryo, seven weeks old or nine weeks' gestational age.

embryonic development

In developmental biology, embryonic development, also known as embryogenesis, is the development of an embryo. Embryonic development starts with the fertilization of an egg cell (ovum) by a sperm cell, (spermatozoon). Once fertilized, the ovum becomes a single diploid cell known as a zygote. The zygote undergoes mitotic divisions with no significant growth (a process known as cleavage) and cellular differentiation, leading to development of a multicellular embryo. In mammals, the term refers chiefly to the early stages of prenatal development, whereas the terms fetus and fetal development describe later stages. (W)

Diagram of stages of embryo development to a larval and adult stage.

Cell divisions (cleavage). First stages of division of mammalian embryo. Semidiagrammatic. (From a drawing by Allen Thomson.) z.p. Zona striata. p.gl. Polar bodies. a. Two-cell stage. b. Four-cell stage. c. Eight-cell stage. d, e. Morula stage.

In philosophy, systems theory, science, and art, emergence occurs when an entity is observed to have properties its parts do not have on their own. These properties or behaviors emerge only when the parts interact in a wider whole. For example, smooth forward motion emerges when a bicycle and its rider interoperate, but neither part can produce the behavior on their own.

Emergence plays a central role in theories of integrative levels and of complex systems. For instance, the phenomenon of life as studied in biology is an emergent property of chemistry, and psychological phenomena emerge from the neurobiological phenomena of living things.

In philosophy, theories that emphasize emergent properties have been called emergentism. Almost all accounts of emergentism include a form of epistemic or ontological irreducibility to the lower levels. (w)

The formation of complex symmetrical and fractal patterns in snowflakes exemplifies emergence in a physical system.

Emergent evolution was the hypothesis that, in the course of evolution, some entirely new properties, such as mind and consciousness, appear at certain critical points, usually because of an unpredictable rearrangement of the already existing entities. The term was originated by the psychologist C. Lloyd Morgan in 1922 in his Gifford Lectures at St. Andrews, which would later be published as the 1923 book Emergent Evolution.

The hypothesis was widely criticized for providing no mechanism to how entirely new properties emerge, and for its historical roots in teleology. (w)

In philosophy, emergentism is the belief in emergence, particularly as it involves consciousness and the philosophy of mind, and as it contrasts with and also does not contrast with reductionism. A property of a system is said to be emergent if it is a new outcome of some other properties of the system and their interaction, while it is itself different from them. Emergent properties are not identical with, reducible to, or deducible from the other properties. The different ways in which this independence requirement can be satisfied lead to variant types of emergence. (W)

emperipolesis

Emperipolesis is the presence of an intact cell within the cytoplasm of another cell. It is derived from Greek (en is inside, peripoleomai is go round). Emperipolesis is an uncommon biological process, and can be physiological or pathological.

It is related to peripolesis, which is the attachment of one cell to another.

Emperipolesis is unlike phagocytosis, in which the engulfed cell is killed by the lysosomal enzymes of the macrophage. Instead, the engulfed cell remains viable within the other, and can exit at any time without causing structural or functional abnormalities in either cell. (W)

Micrograph showing emperipolesis in a case of Rosai-Dorfman disease. H&E stain. Very high magnification micrograph showing emperipolesis in a lymph node affected by Rosai-Dorfman disease, also known as sinus histiocytosis with massive lymphadenopathy. H&E stain. Emperipolesis is phagocytosis of whole cells. It is not specific for Rosai-Dorfman disease. See also Image:Rosai-Dorfman disease - very high mag.jpg - uncropped version of this image .

Emperipolesis: a band neutrophil inside a megakaryocyte (Wright-Giemsa, 100x, oil).

Emperipolesis in Rosai-Dorfman disease highlighted by S-100 staining. LYMPH NODES-SPLEEN: ROSAI-DORFMAN DISEASE: EXTRANODAL These large histiocytes staining strongly for S-100 protein clearly show the presence of lymphocytes within cytoplasmic vacuoles.

Emperipolesis: Megakaryocyte containing a segmented neutrophil, stained with a May-Grünwald Giemsa stain. Megakaryocyte containing a segmented neutrophil. Image taken from a bone marrow aspirate slide, stained with a May-Grünwald Giemsa stain.

endocytosis

Endocytosis is a cellular process in which substances are brought into the cell. The material to be internalized is surrounded by an area of cell membrane, which then buds off inside the cell to form a vesicle containing the ingested material. Endocytosis includes pinocytosis (cell drinking) and phagocytosis (cell eating). It is a form of active transport. (W)

The different types of endocytosis. Endocytosis is a process whereby cells absorb material (molecules such as proteins) from the outside by engulfing it with their cell membrane. It is used by all cells of the body because most substances important to them are polar and consist of big molecules, and thus cannot pass through the hydrophobic plasma membrane.

From L to R: Phagocytosis, Pinocytosis, Receptor-mediated endocytosis.

The endomembrane system is composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell. These membranes divide the cell into functional and structural compartments, or organelles. In eukaryotes the organelles of the endomembrane system include: the nuclear membrane, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, endosomes, and plasma (cell) membrane among others. The system is defined more accurately as the set of membranes that form a single functional and developmental unit, either being connected directly, or exchanging material through vesicle transport. Importantly, the endomembrane system does not include the membranes of chloroplasts or mitochondria, but might have evolved from the latter (see below: Evolution). (W)

Detail of the endomembrane system and its components.

1 Nucleus 2 Nuclear pore 3 Rough endoplasmic reticulum (RER) 4 Smooth endoplasmic reticulum (SER) 5 Ribosome on the rough ER 6 Proteins that are transported 7 Transport vesicle 8 Golgi apparatus 9 Cis face of the Golgi apparatus 10 Trans face of the Golgi apparatus 11 Cisternae of the Golgi apparatus.

Detailed illustration of the plasma membrane. Including the structure of a phospholipid.

endocrine system

The endocrine system is a chemical messenger system comprising feedback loops of the hormones released by internal glands of an organism directly into the circulatory system, regulating distant target organs. In humans, the major endocrine glands are the thyroid gland and the adrenal glands. In vertebrates, the hypothalamus is the neural control center for all endocrine systems. The study of the endocrine system and its disorders is known as endocrinology. Endocrinology is a branch of internal medicine.

A number of glands that signal each other in sequence are usually referred to as an axis, such as the hypothalamic-pituitary-adrenal axis. In addition to the specialized endocrine organs mentioned above, many other organs that are part of other body systems have secondary endocrine functions, including bone, kidneys, liver, heart and gonads. For example, the kidney secretes the endocrine hormone erythropoietin. Hormones can be amino acid complexes, steroids, eicosanoids, leukotrienes, or prostaglandins. (W)

Text____.

The endoplasmic reticulum (ER) is a type of organelle made up of two subunits – rough endoplasmic reticulum (RER), and smooth endoplasmic reticulum (SER). The endoplasmic reticulum is found in most eukaryotic cells and forms an interconnected network of flattened, membrane-enclosed sacs known as cisternae (in the RER), and tubular structures in the SER. The membranes of the ER are continuous with the outer nuclear membrane. The endoplasmic reticulum is not found in red blood cells, or spermatozoa. (W)

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

1 Nucleus 2 Nuclear pore 3 Rough endoplasmic reticulum (RER) 4 Smooth endoplasmic reticulum (SER) 5 Ribosome on the rough ER 6 Proteins that are transported 7 Transport vesicle 8 Golgi apparatus 9 Cis face of the Golgi apparatus 10 Trans face of the Golgi apparatus 11 Cisternae of the Golgi apparatus.

3D rendering of endoplasmic reticulum.

endosome

Endosomes are a collection of intracellular sorting organelles in eukaryotic cells. They are part of endocytic membrane transport pathway originating from the trans Golgi network. Molecules or ligands internalized from the plasma membrane can follow this pathway all the way to lysosomes for degradation or can be recycled back to the cell membrane in the endocytic cycle. Molecules are also transported to endosomes from the trans Golgi network and either continue to lysosomes or recycle back to the Golgi apparatus.

Endosomes can be classified as early, sorting, or late depending on their stage post internalization. Endosomes represent a major sorting compartment of the endomembrane system in cells.(W)

Electron micrograph of endosomes in human HeLa cells. Early endosomes (E - labeled for EGFR, 5 minutes after internalisation, and transferrin), late endosomes/MVBs (M) and lysosomes (L) are visible. Bar, 500 nm. Compartments of the endocytic pathway in HeLa cells. Early endosomes (E), late endosomes/MVBs (M), and lysosomes (L) are visible. Epidermal growth factor receptors (EGFR) and transferrin (Tf) are labelled in the early endosomes. Epidermal growth factor receptors are labelled with an antibody conjugated to 10 nm gold, applied to the cell surface. The cells were stimulated with EGF and allowed to internalize the receptors, bringing the gold with them. The image was taken 5 minutes after internalization, at which point most of the EGFR-gold has reached early endosomes (black dots, marked by arrowheads), but has not yet entered late endosomes or lysosomes. The cells are also loaded with transferrin conjugated to horseradish peroxidase (TfHRP). The HRP catalyses a reaction in the presence of DAB that produces a dark stain in the transferrin containing compartments in the image. HeLa cells were preincubated for 1 h in serum-free medium. For the final 30 minutes the cells were incubated with TfHRP. The cells were then incubated with EGF and anti-EGFR 10 nm gold-conjugated antibody for 30 minutes at 4°C, washed, and incubated at 37°C for a further 5 minutes, all in the presence of TfHRP. Arrowheads; anti-EGFR 10 nm gold. Dark content; cross linked TfHRP. Bar, 500 nm. Philips EM400 TEM Methods for cell fixation and preparation for electron microscopy can be found in the reference below. Briefly, cells were room temperature fixed, a DAB reaction was done, and the cells were osmium stained, dehydrated and embedded en face in epon. Related reference; Doyotte, A., Russell, M.R.G., Hopkins, C.R., Woodman, P.G. (2005) Depletion of TSG101 forms a mammalian ‘‘Class E’’ compartment: a multicisternal early endosome with multiple sorting defects. J. Cell Sci, 118:3003-3017. (W)

Diagram of the pathways that intersect endosomes in the endocytic pathway of animal cells. Examples of molecules that follow some of the pathways are shown, including receptors for EGF, transferrin, and lysosomal hydrolases. Recycling endosomes, and compartments and pathways found in more specialized cells, are not shown.. The endocytic pathway in animal cells. Endocytosed molecules from the cell surface are internalized to early endosomes. These then develop into late endosomes/multivesicular bodies (MVBs) by maturation; recycling molecules are removed, pH is lowered, lumenal vesicles form, and RAB5 is replaced with RAB7, making them competent for fusion with lysosomes. Fusion creates a hybrid, from which a lysosome is reformed. Molecules recycling to the plasma membrane can traffic via recycling endosomes (not shown). Molecules are also transported to/from the Golgi. More complicated pathways exist in specialized cells. Transferrin and its receptor cycle between the plasma membrane and (mainly) early endosomes. Transferrin releases its iron in the acidic endosome. EGF receptors that are activated by binding EGF, are downregulated by degradation in lysosomes. EGF binding stimulates ubiquitination of EGFRs and this targets them to the lysosome lumen, via lumenal vesicles. Mannose-6-phosphate receptors cycle between the Golgi and endosomes, releasing their cargo due to the low pH of the endosomes. (W).

epiboly

Epiboly describes one of the five major types of cell movements that occur in the Gastrulation stage of embryonic development of some organisms. Epibolic movement is the way in which a layer epithelial cells spreads. This can be achieved in multiple ways.

When undergoing epiboly, a monolayer of cells must undergo a physical change in shape in order to spread. Alternatively, multiple layers of cells can also undergo epiboly as the position of cells is changed or the cell layers undergo intercalation. While human embryos do not experience epiboly, this movement can be studied in sea urchins, tunicates, amphibians, and most commonly zebrafish. (W)

Epibolic movement of cells during gastrulation.

schematic of Zebrafish epiboly.

Cartoon of a 4-hour post fertilization zebrafish embryo, before the initiation of epiboly.

epigenetic clock

An epigenetic clock is a biochemical test that can be used to measure age. The test is based on DNA methylation levels. (W)

epigenetics in learning and memory

While the cellular and molecular mechanisms of learning and memory have long been a central focus of neuroscience, it is only in recent years that attention has turned to the epigenetic mechanisms behind the dynamic changes in gene transcription responsible for memory formation and maintenance. Epigenetic gene regulation often involves the physical marking (chemical modification) of DNA or associated proteins to cause or allow long-lasting changes in gene activity. Epigenetic mechanisms such as DNA methylation and histone modifications (methylation, acetylation, and deacetylation) have been shown to play an important role in learning and memory. (W)

Figure 1 HDAC inhibition enhances memory and synaptic plasticity through CREB:CBP. Figure adapted from Vecsey et al., (2007).

epithelial polarity

Cell polarity is a fundamental feature of many types of cells. Epithelial cells are one example of a polarized cell type, featuring distinct 'apical', 'lateral' and 'basal' plasma membrane domains. Epithelial cells connect to one another via their lateral membranes to form epithelial sheets that line cavities and surfaces throughout the animal body. Each plasma membrane domain has a distinct protein composition, giving them distinct properties and allowing directional transport of molecules across the epithelial sheet. How epithelial cells generate and maintain polarity remains unclear, but certain molecules have been found to play a key role. (W)

epithelium

Epithelium is one of the four basic types of animal tissue, along with connective tissue, muscle tissue and nervous tissue. It is a thin, continuous, protective layer of cells. Epithelial tissues line the outer surfaces of organs and blood vessels throughout the body, as well as the inner surfaces of cavities in many internal organs. An example is the epidermis, the outermost layer of the skin. (W)

Types of epithelium.

Escherichia coli

Escherichia coli, also known as E. coli is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but some serotypes (EPEC, ETEC etc.) can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls. The harmless strains are part of the normal microbiota of the gut, and can benefit their hosts by producing vitamin K2, (which helps blood to clot) and preventing colonisation of the intestine with pathogenic bacteria, having a symbiotic relationship. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards.

E. coli and other facultative anaerobes constitute about 0.1% of gut microbiota, and fecal–oral transmission is the major route through which pathogenic strains of the bacterium cause disease. Cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for many days and grow outside a host.

The bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon and energy. E. coli is the most widely studied prokaryotic model organism, and an important species in the fields of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA. Under favorable conditions, it takes as little as 20 minutes to reproduce. (W)

Low-temperature electron micrograph of a cluster of E. coli bacteria, magnified 10,000 times. Each individual bacterium is oblong shaped..

Model of successive binary fission in E. coli. Schematic diagram of the life cycle of Escherichia coli. Original caption During cell division, two new poles are formed, one in each of the progeny cells (new poles, shown in blue). The other ends of those cells were formed during a previous division (old poles, shown in red). (A) The number of divisions since each pole was formed is indicated by the number inside the pole. Using the number of divisions since the older pole of each cell was formed, it is possible to assign an age in divisions to that cell, as indicated. Similarly, cells that consecutively divided as a new pole are assigned a new pole age, based on the current, consecutive divisions as a new pole cell. (B) Time-lapse images of growing cells corresponding to the stages in (A). False color has been added to identify the poles.

A colony of E. coli growing. False color time-lapse video of E. coli colony growing on microscope slide. See the source for detailed growth conditions. Technical: Adapted from https://doi.org/10.1371/journal.pbio.0030045.sv001 . Added approximate scale bar based on the approximate length of 2.0 μm of E. coli bacteria. The original video is comprised of 114 frames, the first 40 taken at 4min intervals, the remaining 74 taken at 2min intervals. For this animation the first 40 frames were duplicated to 80 frames making the total frame count 154 and the framerate a constant 1 frame per 2 minutes.

Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound organelles. Eukaryotes belong to the domain Eukaryota or Eukarya. Their name comes from the Greek εὖ (eu, "well" or "good") and κάρυον (karyon, "nut" or "kernel"). Eukaryotic cells typically contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes. (W)

Eukaryotic cells are typically much larger than those of prokaryotes, having a volume of around 10,000 times greater than the prokaryotic cell. (W)

extracellular fluid

Extracellular fluid (ECF) denotes all body fluid outside the cells of any multicellular organism. Total body water in healthy adults is about 60% (range 45 to 75%) of total body weight; women and the obese typically have a lower percentage than lean men. Extracellular fluid makes up about one-third of body fluid, the remaining two-thirds is intracellular fluid within cells. The main component of the extracellular fluid is the interstitial fluid that surrounds cells.

Extracellular fluid is the internal environment of all multicellular animals, and in those animals with a blood circulatory system, a proportion of this fluid is blood plasma. Plasma and interstitial fluid are the two components that make up at least 97% of the ECF. Lymph makes up a small percentage of the interstitial fluid. The remaining small portion of the ECF includes the transcellular fluid (about 2.5%). The ECF can also be seen as having two components – plasma and lymph as a delivery system, and interstitial fluid for water and solute exchange with the cells.

The extracellular fluid, in particular the interstitial fluid, constitutes the body's internal environment that bathes all of the cells in the body. The ECF composition is therefore crucial for their normal functions, and is maintained by a number of homeostatic mechanisms involving negative feedback. Homeostasis regulates, among others, the pH, sodium, potassium, and calcium concentrations in the ECF. The volume of body fluid, blood glucose, oxygen, and carbon dioxide levels are also tightly homeostatically maintained.

The volume of extracellular fluid in a young adult male of 70 kg (154 lbs) is 20% of body weight – about fourteen litres. Eleven litres is interstitial fluid and the remaining three litres is plasma.

(W)

The distribution of the total body water in mammals between the intracellular compartment and the extracellular compartment, which is, in turn, subdivided into interstitial fluid and smaller components, such as the blood plasma, the cerebrospinal fluid and lymph.

Cell membrane details between extracellular and intracellular fluid. The cell membrane, also called the plasma membrane or plasmalemma, is a semipermeable lipid bilayer common to all living cells. It contains a variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes. It also serves as the attachment point for both the intracellular cytoskeleton and, if present, the cell wall.

Sodium-potassium pump and the diffusion between extracellular fluid and intracellular fluid.

Differences in the concentrations of ions giving the membrane potential..

Formation of interstitial fluid from blood.

Diagram showing the formation of lymph from interstitial fluid (labeled here as "Tissue fluid"). The tissue fluid is entering the blind ends of lymph capillaries (shown as deep green.

extremophile

An extremophile (from Latin extremus meaning "extreme" and Greek philiā (φιλία) meaning "love") is an organism with optimal growth in environmental conditions considered extreme in that it is challenging for a carbon-based life form with water as a solvent, such as all life on Earth, to survive.

This is not the same as a more anthropocentric and non-scientific view which considers an extremophile to be an organism that lives in environments uncomfortable to humans. In contrast, organisms that live in more moderate environmental conditions, according to an anthropocentric view, may be termed mesophiles or neutrophiles. (W)

The bright colors of Grand Prismatic Spring, Yellowstone National Park, are produced by Thermophiles, a type of extremophile.

extremotroph

An extremotroph (from Latin extremus meaning "extreme" and Greek troph (τροφ) meaning "food") is an organism that feeds on matter that is not typically considered to be food to most life on Earth. "These anthropocentric definitions that we make of extremophily and extremotrophy focus on a single environmental extreme but many extremophiles may fall into multiple categories, for example, organisms living inside hot rocks deep under the Earth's surface." (W)

fibroblast (cell)

A fibroblast is a type of biological cell that synthesizes the extracellular matrix and collagen, produces the structural framework (stroma) for animal tissues, and plays a critical role in wound healing. Fibroblasts are the most common cells of connective tissue in animals. (W)

Fibroblast. Image taken with Canon Powershot S3 on Nikon TS100 inverted microscope by the author using phase contrast microscopy. Location Connective tissue Function Extracellular matrix and collagen creation .

Microfilaments (blue and red), mitochondria (yellow), and nuclei (green) in fibroblast cells. Microfilaments, Mitochondria and Nuclei in Fibroblast Cells Mitochondria (shown in yellow) cellular energy-producing organelles, which will complete decomposition of glucose and synthesized ATP Cell nuclei (shown in green) organelles whose function is to control cellular function and the transfer of genetic information through DNA-based chromosomes Microfilaments (shown in blue and red) cells found in actin cytoskeleton composed of the finer filaments, which take part in cell movement and shape change All of these organelles in cells stained with specific fluorescent dyes. The 3D model is constructed by using special software.

filamentous bacteriophage

Filamentous bacteriophage is a family of viruses (Inoviridae) that infect bacteria. The phages are named for their filamentous shape, a worm-like chain (long, thin and flexible, reminiscent of a length of cooked spaghetti), about 6 nm in diameter and about 1000-2000 nm long. The coat of the virion comprises five types of viral protein, which are located during phage assembly in the inner membrane of the host bacteria, and are added to the nascent virion as it extrudes through the membrane. Filamentous bacteriophages are among the simplest living organisms known, with far fewer genes than the classical bacteriophages studied by the phage group. The simplicity of this family makes it an attractive model system to study fundamental aspects of molecular biology, and it has also proven useful as a tool in immunology and nanotechnology. (W)

Representation of the filamentous phage M13. Blue: Coat Protein pIII Brown: Coat Proteín pVI Red: Coat Protein pVII Limegreen: Coat Protein pVIII Fuchsia: Coat Proteín pIX Purple: Single Stranded DNA.

Assembled major coat protein subunits in Ff (fd, f1, M13) filamentous bacteriophage (Inovirus), exploded view. Assembled major coat protein subunits in Ff (fd, f1, M13) filamentous bacteriophage (Inovirus), exploded view. (This image was used on the cover of Journal of Molecular Biology 355(2), 13 January 2006). Virion axis is vertical. The display in the central portion depicts an axial slab, corresponding to about 1.4% of the total length of the virion. Each subunit is represented as a red space-filling coil following the protein backbone at 5 A radius. Three adjacent subunits are shown in atomic detail (yellow lines) within “semi-transparent” coils. A single isolated subunit is displayed at the right. The coordinates of the single subunit (and the symmetry operators required to generate the assembly of subunits) are deposited with the Protein Data Bank as PDB ID: 2C0X. An unpublished electron micrograph of a full-length phage is displayed at the left, showing a phage aligned by flow on an electron microscope grid as described by Marvin and Hoffmann-Berling 1963, Z. Naturforsch. B18, 884-893. (W)

fluid compartments

The human body and even its individual body fluids may be conceptually divided into various fluid compartments, which, although not literally anatomic compartments, do represent a real division in terms of how portions of the body's water, solutes, and suspended elements are segregated. The two main fluid compartments are the intracellular and extracellular compartments. The intracellular compartment is the space within the organism's cells; it is separated from the extracellular compartment by cell membranes.

About two-thirds of the total body water of humans is held in the cells, mostly in the cytosol, and the remainder is found in the extracellular compartment. The extracellular fluids may be divided into three types: interstitial fluid in the "interstitial compartment" (surrounding tissue cells and bathing them in a solution of nutrients and other chemicals), blood plasma and lymph in the "intravascular compartment" (inside the blood vessels and lymphatic vessels), and small amounts of transcellular fluid such as ocular and cerebrospinal fluids in the "transcellular compartment". The interstitial and intravascular compartments readily exchange water and solutes but the third extracellular compartment, the transcellular, is thought of as separate from the other two and not in dynamic equilibrium with them. (W)

A fossil (from Classical Latin: fossilis, literally "obtained by digging") is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved in amber, hair, petrified wood, oil, coal, and DNA remnants. The totality of fossils is known as the fossil record.

Paleontology is the study of fossils: their age, method of formation, and evolutionary significance. Specimens are usually considered to be fossils if they are over 10,000 years old. The oldest fossils are around 3.48 billion years old to 4.1 billion years old. The observation in the 19th century that certain fossils were associated with certain rock strata led to the recognition of a geological timescale and the relative ages of different fossils. The development of radiometric dating techniques in the early 20th century allowed scientists to quantitatively measure the absolute ages of rocks and the fossils they host.

There are many processes that lead to fossilization, including permineralization, casts and molds, authigenic mineralization, replacement and recrystallization, adpression, carbonization, and bioimmuration.

Fossils vary in size from one-micrometre (1 µm) bacteria to dinosaurs and trees, many meters long and weighing many tons. A fossil normally preserves only a portion of the deceased organism, usually that portion that was partially mineralized during life, such as the bones and teeth of vertebrates, or the chitinous or calcareous exoskeletons of invertebrates. Fossils may also consist of the marks left behind by the organism while it was alive, such as animal tracks or feces (coprolites). These types of fossil are called trace fossils or ichnofossils, as opposed to body fossils. Some fossils are biochemical and are called chemofossils or biosignatures. (W)

External mold of a bivalve from the Logan Formation, Lower Carboniferous, Ohio.

A fungus (plural: fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, which is separate from the other eukaryotic life kingdoms of plants and animals. (W)

Fungal hyphae cells Hyphal wall Septum Mitochondrion Vacuole Ergosterol crystal Ribosome Nucleus Endoplasmic reticulum Lipid body Plasma membrane Spitzenkörper Golgi apparatus. Fungal Hyphae Cells 1- Hyphal wall 2- Septum 3- Mitochondrion 4- Vacuole 5- Ergosterol crystal 6- Ribosome 7- Nucleus 8- Endoplasmic reticulum 9- Lipid body 10- Plasma membrane 11- Spitzenkörper/growth tip and vesicles 12- Golgi apparatus

Don't eat me.

The North American Mycological Association (NAMA) (Faculty participants at NAMA 2012, Scotts Valley, California)

fusion mechanism

A fusion mechanism is any mechanism by which cell fusion or virus–cell fusion takes place, as well as the machinery that facilitates these processes. Cell fusion is the formation of a hybrid cell from two separate cells. There are three major actions taken in both virus–cell fusion and cell–cell fusion: the dehydration of polar head groups, the promotion of a hemifusion stalk, and the opening and expansion of pores between fusing cells. Virus–cell fusions occur during infections of several viruses that are health concerns relevant today. Some of these include HIV, Ebola, and influenza. For example, HIV infects by fusing with the membranes of immune system cells. In order for HIV to fuse with a cell, it must be able to bind to the receptors CD4, CCR5, and CXCR4. Cell fusion also occurs in a multitude of mammalian cells including gametes and myoblasts. (W)

gamete

A gamete (from Ancient Greek γαμετή gamete from gamein "to marry") is a haploid cell that fuses with another haploid cell during fertilization in organisms that sexually reproduce. In species that produce two morphologically distinct types of gametes, and in which each individual produces only one type, a female is any individual that produces the larger type of gamete — called an ovum — and a male produces the smaller tadpole-like type — called a sperm. In short a gamete is an egg cell (female gamete) or a sperm (male gamete). This is an example of anisogamy or heterogamy, the condition in which females and males produce gametes of different sizes (this is the case in humans; the human ovum has approximately 100,000 times the volume of a single human sperm cell). In contrast, isogamy is the state of gametes from both sexes being the same size and shape, and given arbitrary designators for mating type. The name gamete was introduced by the German cytologist Eduard Strasburger. Gametes carry half the genetic information of an individual, one ploidy of each type, and are created through meiosis. (W)

X-chromosomes (red) and Y-chromosomes (green) in embryonic stem cells of male (X/Y) and female (X/X) mice.

gamma delta T cell

Gamma delta T cells (γδ T cells) are T cells that have a distinctive T-cell receptor (TCR) on their surface. Most T cells are αβ (alpha beta) T cells with TCR composed of two glycoprotein chains called α (alpha) and β (beta) TCR chains. In contrast, gamma delta (γδ) T cells have a TCR that is made up of one γ (gamma) chain and one δ (delta) chain. This group of T cells is usually less common than αβ T cells, but are at their highest abundance in the gut mucosa, within a population of lymphocytes known as intraepithelial lymphocytes (IELs).

The antigenic molecules that activate gamma delta T cells are still largely unknown. However, γδ T cells are peculiar in that they do not seem to require antigen processing and major-histocompatibility-complex (MHC) presentation of peptide epitopes, although some recognize MHC class Ib molecules. Furthermore, γδ T cells are believed to have a prominent role in recognition of lipid antigens. They are of an invariant nature and may be triggered by alarm signals, such as heat shock proteins (HSP).

There also exists a γδ-T-cell sub-population within the epidermal compartment of the skin of mice. Originally referred to as Thy-1+ dendritic epidermal cells (Thy1+DEC), these cells are more commonly known as dendritic epidermal T cells (DETC). DETCs arise during fetal development and express an invariant and canonical Vγ3 Vδ1 T-cell receptor (using Garman nomenclature).(W)

To-scale map of C57BL7 TCRVgamma locus. Mouse Vgamma locus for C57BL/6 genome; drawn to scale. Chromosome 13: 1.927 to 1.440 Megabp Heilig notation.

ganglion

A ganglion is a group of neuron cell bodies in the peripheral nervous system. In the somatic nervous system this includes dorsal root ganglia and trigeminal ganglia among a few others. In the autonomic nervous system there are both sympathetic and parasympathetic ganglia which contain the cell bodies of postganglionic sympathetic and parasympathetic neurons respectively.

A pseudoganglion looks like a ganglion, but only has nerve fibers and has no nerve cell bodies. (W)

High magnification micrograph of a ganglion. Prostatectomy specimen. H&E stain. Related images Intermed. mag. High mag. Very high mag..

A dorsal root ganglion (DRG) from a chicken embryo (around stage of day 7) after incubation overnight in NGF growth medium stained with anti-neurofilament antibody. Note the axons growing out of the ganglion.

gastrointestinal tract

The gastrointestinal tract, (GI tract, GIT, digestive tract, digestion tract, alimentary canal) is the tract from the mouth to the anus which includes all the organs of the digestive system in humans and other animals. Food taken in through the mouth is digested to extract nutrients and absorb energy, and the waste expelled as feces. The mouth, esophagus, stomach and intestines are all part of the gastrointestinal tract. Gastrointestinal is an adjective meaning of or pertaining to the stomach and intestines. A tract is a collection of related anatomic structures or a series of connected body organs. (W)

Schematic drawing of the digestive system.

gastrulation

In developmental biology, gastrulation is a phase early in the embryonic development of most animals, during which the blastula (a single-layered hollow sphere of cells) is reorganized into a multilayered structure known as the gastrula. Before gastrulation, the embryo is a continuous epithelial sheet of cells; by the end of gastrulation, the embryo has begun differentiation to establish distinct cell lineages, set up the basic axes of the body (e.g. dorsal-ventral, anterior-posterior), and internalized one or more cell types including the prospective gut. (W)

This image shows the process of gastrulation. Gastrulation occurs when a blastula, made up of one layer, folds inward and enlarges to create a gastrula. A gastrula has 3 germ layers--the ectoderm, the mesoderm, and the endoderm. Some of the ectoderm cells from the blastula collapse inward and form the endoderm. The blastospore is the hole created in this action. Whether this blastospore develops into a mouth or an anus determines whether the organism is a protostome or a dueterostome. This diagram is color coded. Ectoderm, blue. Endoderm, green. Blastocoel (the yolk sack), yellow. Archenteron (the gut), purple..

In biology, a gene is a sequence of nucleotides in DNA or RNA that encodes the synthesis of a gene product, either RNA or protein.

During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life. (W)

A gene is a region of DNA that encodes function. A chromosome consists of a long strand of DNA containing many genes. A human chromosome can have up to 500 million base pairs of DNA with thousands of genes.

Fluorescent microscopy image of a human female karyotype, showing 23 pairs of chromosomes . The DNA is stained red, with regions rich in housekeeping genes further stained in green. The largest chromosomes are around 10 times the size of the smallest.

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. Gene expression is summarized in the Central Dogma first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication.

The process of gene expression is used by all known life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life.

In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, i.e. observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the "interpretation" of that information. Such phenotypes are often expressed by the synthesis of proteins that control the organism's structure and development, or that act as enzymes catalyzing specific metabolic pathways.

All steps in the gene expression process may be modulated (regulated), including the transcription, RNA splicing, translation, and post-translational modification of a protein. Regulation of gene expression gives control over the timing, location, and amount of a given gene product (protein or ncRNA) present in a cell and can have a profound effect on the cellular structure and function. Regulation of gene expression is the basis for cellular differentiation, development, morphogenesis and the versatility and adaptability of any organism. Gene regulation may therefore serve as a substrate for evolutionary change.(W)

genetic code

The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.

The code defines how codons specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in human mitochondria) exist.

While the "genetic code" is what determines a protein's amino acid sequence, other genomic regions determine when and where these proteins are produced according to various "gene regulatory codes". (W)

A series of codons in part of a messenger RNA (mRNA) molecule. Each codon consists of three nucleotides, usually corresponding to a single amino acid. The nucleotides are abbreviated with the letters A, U, G and C. This is mRNA, which uses U (uracil). DNA uses T (thymine) instead. This mRNA molecule will instruct a ribosome to synthesize a protein according to this code..

Reading frames in the DNA sequence of a region of the human mitochondrial genome coding for the genes MT-ATP8 and MT-ATP6 (in black: positions 8,525 to 8,580 in the sequence accession NC_012920). There are three possible reading frames in the 5' → 3' forward direction, starting on the first (+1), second (+2) and third position (+3). For each codon (square brackets), the amino acid is given by the vertebrate mitochondrial code, either in the +1 frame for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue). The MT-ATP8 genes terminates with the TAG stop codon (red dot) in the +1 frame. The MT-ATP6 gene starts with the ATG codon (blue circle for the M amino acid) in the +3 frame..

genetic drift

Genetic drift (also known as allelic drift or the Sewall Wright effect) is the change in the frequency of an existing gene variant (allele) in a population due to random sampling of organisms. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population's allele frequency is the fraction of the copies of one gene that share a particular form.

Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. It can also cause initially rare alleles to become much more frequent and even fixed.

When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. In the middle of the 20th century, vigorous debates occurred over the relative importance of natural selection versus neutral processes, including genetic drift. Ronald Fisher, who explained natural selection using Mendelian genetics, held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. In 1968, population geneticist Motoo Kimura rekindled the debate with his neutral theory of molecular evolution, which claims that most instances where a genetic change spreads across a population (although not necessarily changes in phenotypes) are caused by genetic drift acting on neutral mutations. (W)

In this simulation each black dot on a marble signifies that it has been chosen for copying (reproduction) one time. There is fixation in the blue "allele" within five generations. Simulation of a common example used describing the effect random sampling has in genetic drift. Dots indicate samples from each generation that are transferred to the next generation. In this population of 20, there is a shift from an allele frequency of 50% for the blue allele to 100% for the blue allele in just 5 generations.

Changes in a population's allele frequency following a population bottleneck: the rapid and radical decline in population size has reduced the population's genetic variation. Representation of a population bottleneck. Colored balls represent the alleles present in the population. The population numbers 500 initially, but within five years the size of the population has dwindled to 50, and within ten years to just ten. As a consequence of the population bottleneck, there has been a random drift in the allele frequency distribution, and a loss of two of the original five alleles.

In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses) . The genome includes both the genes (the coding regions) and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics. (w)

📂 A table of some significant or representative genomes A table of some significant or representative genomes (W) Organism type Organism Genome size (base pairs) Approx. no. of genes Note Virus Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating autonomously in eukaryotic cells. Virus Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome Virus SV40 5,224 5.2kb   Virus Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome Virus HIV 9,749 9.7kb   Virus Phage λ 48,502 48.5kb Often used as a vector for the cloning of recombinant DNA. Virus Megavirus 1,259,197 1.3Mb Until 2013 the largest known viral genome. Virus Pandoravirus salinus 2,470,000 2.47Mb Largest known viral genome. Bacterium Nasuia deltocephalinicola (strain NAS-ALF) 112,091 112kb Smallest non-viral genome. Bacterium Carsonella ruddii 159,662 160kb Bacterium Buchnera aphidicola 600,000 600kb   Bacterium Wigglesworthia glossinidia 700,000 700Kb Bacterium Haemophilus influenzae 1,830,000 1.8Mb First genome of a living organism sequenced, July 1995 Bacterium Escherichia coli 4,600,000 4.6Mb 4,288   Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000 10Mb   Bacterium – cyanobacterium Prochlorococcus spp. (1.7 Mb) 1,700,000 1.7Mb 1,884 Smallest known cyanobacterium genome Bacterium – cyanobacterium Nostoc punctiforme 9,000,000 9Mb 7,432 7432 open reading frames Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 670Gb Largest known genome. (Disputed) Eukaryotic organelle Human mitochondrion 16,569 16.6kb   Plant Genlisea tuberosa 61,000,000 61Mb Smallest recorded flowering plant genome, 2014. Plant Arabidopsis thaliana 135,000,000 135 Mb 27,655 First plant genome sequenced, December 2000. Plant Populus trichocarpa 480,000,000 480Mb 73,013 First tree genome sequenced, September 2006 Plant Fritillaria assyriaca 130,000,000,000 130Gb Plant Paris japonica (Japanese-native, pale-petal) 150,000,000,000 150Gb Largest plant genome known Plant – moss Physcomitrella patens 480,000,000 480Mb First genome of a bryophyte sequenced, January 2008. Fungus – yeast Saccharomyces cerevisiae 12,100,000 12.1Mb 6,294 First eukaryotic genome sequenced, 1996 Fungus Aspergillus nidulans 30,000,000 30Mb 9,541   Nematode Pratylenchus coffeae 20,000,000 20Mb Smallest animal genome known Nematode Caenorhabditis elegans 100,300,000 100Mb 19,000 First multicellular animal genome sequenced, December 1998 Insect Drosophila melanogaster (fruit fly) 175,000,000 175Mb 13,600 Size variation based on strain (175-180Mb; standard y w strain is 175Mb) Insect Apis mellifera (honey bee) 236,000,000 236Mb 10,157   Insect Bombyx mori (silk moth) 432,000,000 432Mb 14,623 14,623 predicted genes Insect Solenopsis invicta (fire ant) 480,000,000 480Mb 16,569   Mammal Mus musculus 2,700,000,000 2.7Gb 20,210   Mammal Homo sapiens 3,289,000,000 3.3Gb 20,000 Homo sapiens estimated genome size 3.2 billion bp Initial sequencing and analysis of the human genome Mammal Pan paniscus 3,286,640,000 3.3Gb 20,000 Bonobo - estimated genome size 3.29 billion bp Bird Gallus gallus 1,043,000,000 1.0Gb 20,000   Fish Tetraodon nigroviridis (type of puffer fish) 385,000,000 390Mb Smallest vertebrate genome known estimated to be 340 Mb – 385 Mb. Fish Protopterus aethiopicus (marbled lungfish) 130,000,000,000 130Gb Largest vertebrate genome known

An image of the 46 chromosomes making up the diploid genome of a human male. (The mitochondrial chromosome is not shown.)

Composition of the human genome.

genomic imprinting

Genomic imprinting is an epigenetic phenomenon that causes genes to be expressed in a parent-of-origin-specific manner. Genes however, can also be partially imprinted. Partial imprinting happens when alleles from both parents are differently expressed rather than complete expression and complete suppression of one parents allele. Forms of genomic imprinting have been demonstrated in fungi, plants and animals. As of 2014, there are about 150 imprinted genes known in the mouse and about half that in humans. In 2019, 260 imprinted genes have been reported in mice and 228 in humans.

Genomic imprinting is an inheritance process independent of the classical Mendelian inheritance. It is an epigenetic process that involves DNA methylation and histone methylation without altering the genetic sequence. These epigenetic marks are established ("imprinted") in the germline (sperm or egg cells) of the parents and are maintained through mitotic cell divisions in the somatic cells of an organism.

Appropriate imprinting of certain genes is important for normal development. Human diseases involving genomic imprinting include Angelman syndrome, Prader–Willi syndrome and male infertility. (W)

genotype

A genotype is an organism’s complete set of heritable genes, or genes that can be passed down from parents to offspring. These genes help encode the characteristics that are physically expressed (phenotype) in an organism, such as hair color, height, etc. The term was coined by the Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1903. An example of a characteristic determined by a genotype is the petal color in a pea plant. The collection of all genetic possibilities for a single trait are called alleles; two alleles for petal color are purple and white. (W)

Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal colour in a pea plant. The letters B and b represent alleles for colour and the pictures show the resultant flowers..

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

A genus (plural genera) is a taxonomic rank used in the biological classification of living and fossil organisms, as well as viruses, in biology. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclature, the genus name forms the first part of the binomial species name for each species within the genus.

E.g. Panthera leo (lion) and Panthera onca (jaguar) are two species within the genus Panthera. Panthera is a genus within the family Felidae.

The composition of a genus is determined by a taxonomist. The standards for genus classification are not strictly codified, so different authorities often produce different classifications for genera. There are some general practices used, however, including the idea that a newly defined genus should fulfill these three criteria to be descriptively useful:

1. monophyly – all descendants of an ancestral taxon are grouped together (i.e. phylogenetic analysis should clearly demonstrate both monophyly and validity as a separate lineage).
2. reasonable compactness – a genus should not be expanded needlessly.
3. distinctness – with respect to evolutionarily relevant criteria, i.e. ecology, morphology, or biogeography; DNA sequences are a consequence rather than a condition of diverging evolutionary lineages except in cases where they directly inhibit gene flow (e.g. postzygotic barriers) .

Moreover, genera should be composed of phylogenetic units of the same kind as other (analogous) genera. (W)

germ cell

A germ cell is any biological cell that gives rise to the gametes of an organism that reproduces sexually. In many animals, the germ cells originate in the primitive streak and migrate via the gut of an embryo to the developing gonads. There, they undergo meiosis, followed by cellular differentiation into mature gametes, either eggs or sperm. Unlike animals, plants do not have germ cells designated in early development. Instead, germ cells can arise from somatic cells in the adult, such as the floral meristem of flowering plants.

Multicellular eukaryotes are made of two fundamental cell types. Germ cells produce gametes and are the only cells that can undergo meiosis as well as mitosis. These cells are sometimes said to be immortal because they are the link between generations. Somatic cells are all the other cells that form the building blocks of the body and they only divide by mitosis. The lineage of germ cells is called germ line. Germ cell specification begins during cleavage in many animals or in the epiblast during gastrulation in birds and mammals. After transport, involving passive movements and active migration, germ cells arrive at the developing gonads. In humans, sexual differentiation starts approximately 6 weeks after conception. The end-products of the germ cell cycle are the egg or sperm. (W)

X-chromosomes (red) and Y-chromosomes (green) in embryonic stem cells of male (X/Y) and female (X/X) mice.

germ layer

A germ layer is a primary layer of cells that forms during embryonic development. The three germ layers in vertebrates are particularly pronounced; however, all eumetazoans (animals more complex than the sponge) produce two or three primary germ layers. Some animals, like cnidarians, produce two germ layers (the ectoderm and endoderm) making them diploblastic. Other animals such as chordates produce a third layer (the mesoderm) between these two layers, making them triploblastic. Germ layers eventually give rise to all of an animal’s tissues and organs through the process of organogenesis (W)

📥 Germ layer (W)

giant virus

A giant virus, also known as a girus, is a very large virus, some of which are larger than typical bacteria. They have extremely large genomes compared to other viruses and contain many unique genes not found in life forms. All known giant viruses belong to the phylum Nucleocytoviricota. (W)

Mimivirus particle, electron microscopy.

Cryo-EM images of the giant viruses CroV and APMV. (A) Cryo-electron micrograph of four CroV particles. (B) Single CroV particle with concave core depression (white arrow). (C) Single APMV particle. Scale bars in (A–C) represent 2,000 Å..

The Golgi apparatus, also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles inside the cell before the vesicles are sent to their destination. It resides at the intersection of the secretory, lysosomal, and endocytic pathways. It is of particular importance in processing proteins for secretion, containing a set of glycosylation enzymes that attach various sugar monomers to proteins as the proteins move through the apparatus.

It was identified in 1897 by the Italian scientist Camillo Golgi and was named after him in 1898. (W)

Diagram of a typical animal cell. Organelles are labelled as follows: Nucleolus Nucleus Ribosomes (dots on rough reticulum walls) Vesicle Rough endoplasmic reticulum Golgi apparatus (or "Golgi body") Cytoskeleton Smooth endoplasmic reticulum Mitochondrion Vacuole Cytosol Lysosome Centriole Cell membrane.

growth factor

A growth factor is a naturally occurring substance capable of stimulating cell proliferation, wound healing, and occasionally cellular differentiation. Usually it is a secreted protein or a steroid hormone. Growth factors are important for regulating a variety of cellular processes.

Growth factors typically act as signaling molecules between cells. Examples are cytokines and hormones that bind to specific receptors on the surface of their target cells.

They often promote cell differentiation and maturation, which varies between growth factors. For example, epidermal growth factor (EGF) enhances osteogenic differentiation, while fibroblast growth factors and vascular endothelial growth factors stimulate blood vessel differentiation (angiogenesis). (W)

haematopoiesis

Haematopoiesis (from Greek αἷμα, 'blood' and ποιεῖν 'to make'; also hematopoiesis in American English; sometimes also h(a)emopoiesis) is the formation of blood cellular components. All cellular blood components are derived from haematopoietic stem cells. In a healthy adult person, approximately 1011–1012 new blood cells are produced daily in order to maintain steady state levels in the peripheral circulation. (W)

Diagram showing the development of different blood cells from haematopoietic stem cell to mature cells.

Sites of haematopoesis (human) in pre- and postnatal periods. (Illustration by : Michał Komorniczak.) (W)

More detailed and comprehensive diagram that shows the development of different blood cells in humans. 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. The polychromatic erythrocyte (reticulocyte) at the right shows its characteristic appearance when stained with methylene blue or Azure B. The erythrocyte at the right is a more accurate representation of its appearance in reality when viewed through a microscope. Other cells that arise from the monocyte: osteoclast, microglia (central nervous system), Langerhans cell (epidermis), Kupffer cell (liver). 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.

Diagram including some of the important cytokines that determine which type of blood cell will be created. SCF= Stem cell factor; Tpo= Thrombopoietin; IL= Interleukin; GM-CSF= Granulocyte Macrophage-colony stimulating factor; Epo= Erythropoietin; M-CSF= Macrophage-colony stimulating factor; G-CSF= Granulocyte-colony stimulating factor; SDF-1= Stromal cell-derived factor-1; FLT-3 ligand= FMS-like tyrosine kinase 3 ligand; TNF-a = Tumour necrosis factor-alpha; TGFβ = Transforming growth factor beta.. Hematopoiesis as it occurs in humans, with important hemopoietic growth factors affecting differentiation. Legend: SCF= Stem Cell Factor Tpo= Thrombopoietin IL= Interleukin GM-CSF= Granulocyte Macrophage-colony stimulating factor Epo= Erythropoietin M-CSF= Macrophage-colony stimulating factor G-CSF= Granulocyte-colony stimulating factor SDF-1= Stromal cell-derived factor-1 FLT-3 ligand= FMS-like tyrosine kinase 3 ligand TNF-a = Tumour necrosis factor-alpha TGF-β = Transforming growth factor beta References: For the growth factors also mentioned in previous version Hematopoiesis (human) cytokines.jpg: Molecular cell biology. Lodish, Harvey F. 5. ed. : - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3 The rest: Rod Flower; Humphrey P. Rang; Maureen M. Dale; Ritter, James M. (2007) Rang & Dale's pharmacology, Edinburgh: Churchill Livingstone ISBN: 0-443-06911-5.

haploid and monoploid

The term haploid is used with two distinct but related definitions. In the most generic sense, haploid refers to having the number of sets of chromosomes normally found in a gamete. Because two gametes necessarily combine during sexual reproduction to form a single zygote from which somatic cells are generated, healthy gametes always possess exactly half the number of sets of chromosomes found in the somatic cells, and therefore "haploid" in this sense refers to having exactly half the number of sets of chromosomes found in a somatic cell. By this definition, an organism whose gametic cells contain a single copy of each chromosome (one set of chromosomes) may be considered haploid while the somatic cells, containing two copies of each chromosome (two sets of chromosomes), are diploid. This scheme of diploid somatic cells and haploid gametes is widely used in the animal kingdom and is the simplest to illustrate in diagrams of genetics concepts. But this definition also allows for haploid gametes with more than one set of chromosomes. As given above, gametes are by definition haploid, regardless of the actual number of sets of chromosomes they contain. An organism whose somatic cells are tetraploid (four sets of chromosomes), for example, will produce gametes by meiosis that contain two sets of chromosomes. These gametes might still be called haploid even though they are numerically diploid.(W)

A comparison of sexual reproduction in predominantly haploid organisms and predominantly diploid organisms. (W)

heart development

Heart development (also known as cardiogenesis) refers to the prenatal development of the heart. This begins with the formation of two endocardial tubes which merge to form the tubular heart, also called the primitive heart tube. The heart is the first functional organ in vertebrate embryos, and in the human, beats spontaneously by week 4 of development.

The tubular heart quickly differentiates into the truncus arteriosus, bulbus cordis, primitive ventricle, primitive atrium, and the sinus venosus. The truncus arteriosus splits into the ascending aorta and the pulmonary trunk. The bulbus cordis forms part of the ventricles. The sinus venosus connects to the fetal circulation.

The heart tube elongates on the right side, looping and becoming the first visual sign of left-right asymmetry of the body. Septa form within the atria and ventricles to separate the left and right sides of the heart. (W)

Development of the human heart during the first eight weeks (top), and the formation of the heart chambers (bottom). In this figure, the blue and red colors represent blood inflow and outflow (not venous and arterial blood). Initially, all venous blood flows from the tail/atria to the ventricles/head, a very different pattern from that of an adult. Illustration from Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013..

hematopoietic stem cell

Hematopoietic stem cells (HSCs) are the stem cells that give rise to other blood cells. This process is called haematopoiesis. This process occurs in the red bone marrow, in the core of most bones. In embryonic development, the red bone marrow is derived from the layer of the embryo called the mesoderm.

Haematopoiesis is the process by which all mature blood cells are produced. It must balance enormous production needs (the average person produces more than 500 billion blood cells every day) with the need to regulate the number of each blood cell type in the circulation. In vertebrates, the vast majority of hematopoiesis occurs in the bone marrow and is derived from a limited number of hematopoietic stem cells that are multipotent and capable of extensive self-renewal.

Hematopoietic stem cells give rise to different types of blood cells, in lines called myeloid and lymphoid. Myeloid and lymphoid lineages both are involved in dendritic cell formation. Myeloid cells include monocytes, macrophages, neutrophils, basophils, eosinophils, erythrocytes, and megakaryocytes to platelets. Lymphoid cells include T cells, B cells, natural killer cells, and innate lymphoid cells. The definition of hematopoietic stem cell has evolved since they were first discovered in 1961. The hematopoietic tissue contains cells with long-term and short-term regeneration capacities and committed multipotent, oligopotent, and unipotent progenitors. Hematopoietic stem cells constitute 1:10,000 of cells in myeloid tissue.

HSC transplants are used in the treatment of cancers and other immune system disorders. (W)

Simplified hematopoiesis. Details System Hematopoietic system Location Bone marrow Function Stem cells that give rise to other blood cells

Diagram of cells that arise from Hematopoetic stem cells during the process of hematopoiesis. 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.

heterotroph (yanbeslek) (autotroph: kendibeslek)

A heterotroph (Ancient Greek ἕτερος héteros = "other" plus trophe = "nutrition") is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but not producers. Living organisms that are heterotrophic include all animals and fungi, some bacteria and protists, and many parasitic plants. The term heterotroph arose in microbiology in 1946 as part of a classification of microorganisms based on their type of nutrition. The term is now used in many fields, such as ecology in describing the food chain. (W)

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

histogenesis

Histogenesis is the formation of different tissues from undifferentiated cells. These cells are constituents of three primary germ layers, the endoderm, mesoderm, and ectoderm. The science of the microscopic structures of the tissues formed within histogenesis is termed histology. (W)

Gastrulation of a diploblast: The formation of germ layers from a (1) blastula to a (2) gastrula. Some of the ectoderm cells (orange) move inward forming the endoderm (red)..

The endoderm 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..

homeostasis

In biology, homeostasis is the state of steady internal, physical, and chemical conditions maintained by living systems. This is the condition of optimal functioning for the organism and includes many variables, such as body temperature and fluid balance, being kept within certain pre-set limits (homeostatic range). Other variables include the pH of extracellular fluid, the concentrations of sodium, potassium and calcium ions, as well as that of the blood sugar level, and these need to be regulated despite changes in the environment, diet, or level of activity. Each of these variables is controlled by one or more regulators or homeostatic mechanisms, which together maintain life. (W)

hormone

A hormone (from the Greek participle ὁρμῶν, "setting in motion") is any member of a class of signaling molecules, produced by glands in multicellular organisms, that are transported by the circulatory system to target distant organs to regulate physiology and behavior. Hormones have diverse chemical structures, mainly of three classes:

• eicosanoids
• steroids
• amino acid/protein derivatives (amines, peptides, and proteins)

The glands that secrete hormones comprise the endocrine signaling system. The term "hormone" is sometimes extended to include chemicals produced by cells that affect the same cell (autocrine or intracrine signaling) or nearby cells (paracrine signalling). (W)

Different types of hormones are secreted in the body, with different biological roles and functions.

The left diagram shows a steroid (lipid) hormone (1) entering a cell and (2) binding to a receptor protein in the nucleus, causing (3) mRNA synthesis which is the first step of protein synthesis. The right side shows protein hormones (1) binding with receptors which (2) begins a transduction pathway. The transduction pathway ends (3) with transcription factors being activated in the nucleus, and protein synthesis beginning. In both diagrams, a is the hormone, b is the cell membrane, c is the cytoplasm, and d is the nucleus.

human epigenome

Human epigenome is the complete set of structural modifications of chromatin and chemical modifications of histones and nucleotides (such as cytosine methylation). These modifications affect gene expression according to cellular type and development status. Various studies show that epigenome depends on exogenous factors. (W)

The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract. Types of human microbiota include bacteria, archaea, fungi, protists and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning. (W)

Graphic depicting the human skin microbiota, with relative prevalences of various classes of bacteria. Depiction of the human body and bacteria that predominate; there are both tremendous similarities and differences among the bacterial species found at different sites.

Flowchart illustrating how the human microbiome is studied on the DNA level.

Commensals vs pathogens mechanism. Mechanisms underlying the inflammation in COPD. Airway epithelium has complex structure: consists of at least seven diverse cell types interacting with each other by means of tight junctions. Moreover, epithelial calls can deliver the signals into the underlying tissues taking part in the mechanisms of innate and adaptive immune defence. The key transmitters of the signals are dendritic cells. Once pathogenic bacterium (e.g., S. pneumoniae, P. aeruginosa) has activated particular pattern recognition receptors on/in epithelial cells, the proinflammatory signaling pathways are activated. This results mainly in IL-1, IL-6 and IL-8 production. These cytokines induce the chemotaxis to the site of infection in its target cells (e.g., neutrophils, dendritic cells and macrophages). On the other hand, representatives of standard microbiota cause only weak signaling preventing the inflammation. The mechanism of distinguishing between harmless and harmful bacteria on the molecular as well as on physiological levels is not completely understood.

This diagram shows the biosynthesis of bioactive compounds (indole and certain other derivatives) from tryptophan by bacteria in the gut. Indole is produced from tryptophan by bacteria that express tryptophanase. Clostridium sporogenes metabolizes tryptophan into indole and subsequently 3-indolepropionic acid (IPA), a highly potent neuroprotective antioxidant that scavenges hydroxyl radicals. IPA binds to the pregnane X receptor (PXR) in intestinal cells, thereby facilitating mucosal homeostasis and barrier function. Following absorption from the intestine and distribution to the brain, IPA confers a neuroprotective effect against cerebral ischemia and Alzheimer's disease. Lactobacillus species metabolize tryptophan into indole-3-aldehyde (I3A) which acts on the aryl hydrocarbon receptor (AhR) in intestinal immune cells, in turn increasing interleukin-22 (IL-22) production. Indole itself triggers the secretion of glucagon-like peptide-1 (GLP-1) in intestinal L cells and acts as a ligand for AhR. Indole can also be metabolized by the liver into indoxyl sulfate, a compound that is toxic in high concentrations and associated with vascular disease and renal dysfunction. AST-120 (activated charcoal), an intestinal sorbent that is taken by mouth, adsorbs indole, in turn decreasing the concentration of indoxyl sulfate in blood plasma.

humoral immunity

Humoral immunity or humoural immunity is the aspect of immunity that is mediated by macromolecules found in extracellular fluids such as secreted antibodies, complement proteins, and certain antimicrobial peptides. Humoral immunity is so named because it involves substances found in the humors, or body fluids. It contrasts with cell-mediated immunity. Its aspects involving antibodies are often called antibody-mediated immunity.

The study of the molecular and cellular components that form the immune system, including their function and interaction, is the central science of immunology. The immune system is divided into a more primitive innate immune system, and acquired or adaptive immune system of vertebrates, each of which contains humoral and cellular components.

Humoral immunity refers to antibody production and the accessory processes that accompany it, including: Th2 activation and cytokine production, germinal center formation and isotype switching, affinity maturation and memory cell generation. It also refers to the effector functions of antibodies, which include pathogen and toxin neutralization, classical complement activation, and opsonin promotion of phagocytosis and pathogen elimination.(W)

B cell activation is a large part of the humoral immune response.

immune system

The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease. To function properly, an immune system must detect a wide variety of agents, known as pathogens, from viruses to parasitic worms, and distinguish them from the organism's own healthy tissue. In many species, there are two major subsystems of the immune system: the innate immune system and the adaptive immune system. Both subsystems use humoral immunity and cell-mediated immunity to perform their functions. In humans, the blood–brain barrier, blood–cerebrospinal fluid barrier, and similar fluid–brain barriers separate the peripheral immune system from the neuroimmune system, which protects the brain (W)

A scanning electron microscope image of a single neutrophil (yellow), engulfing anthrax bacteria (orange).

induced stem cells

Induced stem cells (iSC) are stem cells derived from somatic, reproductive, pluripotent or other cell types by deliberate epigenetic reprogramming. They are classified as either totipotent (iTC), pluripotent (iPSC) or progenitor (multipotent – iMSC, also called an induced multipotent progenitor cell – iMPC) or unipotent – (iUSC) according to their developmental potential and degree of dedifferentiation. Progenitors are obtained by so-called direct reprogramming or directed differentiation and are also called induced somatic stem cells.

Three techniques are widely recognized:

• Transplantation of nuclei taken from somatic cells into an oocyte (egg cell) lacking its own nucleus (removed in lab)
• Fusion of somatic cells with pluripotent stem cells and
• Transformation of somatic cells into stem cells, using the genetic material encoding reprogramming protein factors, recombinant proteins; microRNA, a synthetic, self-replicating polycistronic RNA and low-molecular weight biologically active substances. (W)
  
  

Induced totipotent cells usually can be obtained by reprogramming somatic cells by somatic-cell nuclear transfer (SCNT).

ingression (biology)

Ingression is one of the many changes in the location or relative position of cells that takes place during the gastrulation stage of animal development. It produces an animal's mesenchyme cells at the onset of gastrulation. During the epithelial–mesenchymal transition (EMT), the primary mesenchyme cells (PMCs) detach from the epithelium and become internalized mesenchyme cells that can migrate freely (Figure 1). Each animal system utilizes an EMT to produce mesenchyme cells. (W)

innate immune system

The innate immune system is one of the two main immunity strategies found in vertebrates (the other being the adaptive immune system). The innate immune system is an older evolutionary defense strategy, relatively speaking, and is the dominant immune system response found in plants, fungi, insects, and primitive multicellular organisms.

The major functions of the vertebrate innate immune system include:

• Recruiting immune cells to sites of infection through the production of chemical factors, including specialized chemical mediators called cytokines
• Activation of the complement cascade to identify bacteria, activate cells, and promote clearance of antibody complexes or dead cells
• Identification and removal of foreign substances present in organs, tissues, blood and lymph, by specialized white blood cells
• Activation of the adaptive immune system through a process known as antigen presentation
• Acting as a physical and chemical barrier to infectious agents; via physical measures like skin or tree bark and chemical measures like clotting factors in blood or sap from a tree, which are released following a contusion or other injury that breaks through the first-line physical barrier (not to be confused with a second-line physical or chemical barrier, such as the blood-brain barrier, which protects the extremely vital and highly sensitive nervous system from pathogens that have already gained access to the host's body). (W)

Innate immune system.

A scanning electron microscope 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-shape 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

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

A neutrophil. Neutrophile segmented Granulocyte .

An eosinophil. Eosinophile Granulocyte .

innate lymphoid cell

Innate lymphoid cells (ILCs) are the most recently discovered family of innate immune cells, derived from common lymphoid progenitors (CLPs). In response to pathogenic tissue damage, ILCs contribute to immunity via the secretion of signalling molecules, and the regulation of both innate and adaptive immune cells. ILCs are primarily tissue resident cells, found in both lymphoid (immune associated), and non- lymphoid tissues, and rarely in the peripheral blood. They are particularly abundant at mucosal surfaces, playing a key role in mucosal immunity and homeostasis. Characteristics allowing their differentiation from other immune cells include the absence of regular lymphoid morphology, rearranged antigen receptors found on T cells and B cells (due to the lack of the RAG gene), and phenotypic markers usually present on myeloid or dendritic cells. (W)

The different phenotypic markers present on LTi cells present in an embryo and an adult.

Schematic diagram of the development of ILCs, mainly based on mouse differentiation pathways..

The different ILC subtypes and how they are implicated in tissue repair and regeneration after infection with oversized organs such as helminths.

ILCs in the intestinal mucosa. ILCs and some of their key roles in the intestinal mucosa, allowing maintenance of intestinal homeostasis, via their associated cytokines and effector cells.

The different ILC subtypes and how they are implicated in metabolism.

ILC3s and ILC2s are recruited to the wounded dermis in both mice and humans in order to aid in the healing process, by recruiting effector cells to the damaged epidermis.

The ILCs present in the lungs of patients with asthma, and the effector cytokines and cells involved in contributing to the pathophysiology of the disorder, by promoting a Th2 immune response.

The ILCs present in the nasal polyps of patients with allergic rhinitis, forming a positive feedback loop, promoting inflammation, therefore contributing to the pathophysiology of the disease.

The ILCs present in the intestine of patients with IBD, and the effector cytokines and cells contributing to the pathophysiology of the disease.

The ILCs present in the epidermis of patients with atopic dermatitis, and the effector cells and cytokines involved in causing the pathophysiology of the disease.

The ILCs present in the epidermis of patients with psoriasis, and the effector cytokines and cells involved in causing inflammation/ epidermal thickening.

he ILCs present in the lungs of patients with COPD, which have the ability to convert into different ILC phenotypes, depending on the microenvironment, which can increase inflammation, contributing to the pathophysiology of the disease.

intermediate filament

Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma.

Intermediate filaments are composed of a family of related proteins sharing common structural and sequence features. Initially designated 'intermediate' because their average diameter (10 nm) is between those of narrower microfilaments (actin) and wider myosin filaments found in muscle cells, the diameter of intermediate filaments is now commonly compared to actin microfilaments (7 nm) and microtubules (25 nm). Animal intermediate filaments are subcategorized into six types based on similarities in amino acid sequence and protein structure. Most types are cytoplasmic, but one type, Type V is a nuclear lamin. Unlike microtubules, IF distribution in cells show no good correlation with the distribution of either mitochondria or endoplasmic reticulum. (W)

Structure of lamin a/c globular domain.

Cartoon representation of the molecular structure of protein registered with 1gk4 code.

Structure of intermediate filament.

internal elastic lamina

The internal elastic lamina or internal elastic lamella is a layer of elastic tissue that forms the outermost part of the tunica intima of blood vessels. It separates tunica intima from tunica media. (W)

Micrograph showing the internal elastic lamina (thin pink wavy line - image edge mid-left to image edge bottom-centre-left). H&E stain. Very high magnification micrograph of a cholesterol embolus in a medium sized artery of the kidney. This is also known as atheroembolic renal disease and atheroembolism. Kidney biopsy. H&E stain. The image shows numerous intra-arterial cholesterol clefts with an associated giant cell reaction. Related images Intermed. mag. High mag. Very high mag. References ↑ (Aug 2001). "Atheroembolic renal disease.". J Am Soc Nephrol 12 (8): 1781-7.

invagination

In developmental biology, invagination is a mechanism that takes place during gastrulation. This mechanism or cell movement happens mostly in the vegetal pole. Invagination consists of the folding of an area of the exterior sheet of cells towards the inside of the blastula. In each organism, the complexity will be different depending on the number of cells. Invagination can be referenced as one of the steps of the establishment of the body plan. The term, originally used in embryology, has been adopted in other disciplines as well. There is more than one type of movement for invagination. Two common types are axial and orthogonal. The difference between the production of the tube formed in the cytoskeleton and extracellular matrix. Axial can be formed at a single point along the axis of a surface. Orthogonal is linear and trough.(W)

Mechanism of Invagination.

Invagination process in Amphioxus.

invertebrate

Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snail, bivalves, squids, and octopuses), annelid (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).

The majority of animal species are invertebrates; one estimate puts the figure at 97%. Many invertebrate taxa have a greater number and variety of species than the entire subphylum of Vertebrata. Invertebrates vary widely in size, from 50 μm (0.002 in) rotifers to the 9–10 m (30–33 ft) colossal squid.

Some so-called invertebrates, such as the Tunicata and Cephalochordata, are more closely related to vertebrates than to other invertebrates. This makes the invertebrates paraphyletic, so the term has little meaning in taxonomy. (W)

involution (medicine)

Involution is the shrinking or return of an organ to a former size. At a cellular level, involution is characterized by the process of proteolysis of the basement membrane (basal lamina), leading to epithelial regression and apoptosis, with accompanying stromal fibrosis. The consequent reduction in cell number and reorganization of stromal tissue leads to the reduction in the size of the organ. (W)

Karyotyping is the process by which photographs of chromosomes are taken in order to determine the chromosome complement of an individual, including the number of chromosomes and any abnormalities. The term is also used for the complete set of chromosomes in a species or in an individual organism and for a test that detects this complement or measures the number.

Karyogram of human male using Giemsa staining.

Karyotypes describe the chromosome count of an organism and what these chromosomes look like under a light microscope. Attention is paid to their length, the position of the centromeres, banding pattern, any differences between the sex chromosomes, and any other physical characteristics. The preparation and study of karyotypes is part of cytogenetics.

The study of whole sets of chromosomes is sometimes known as karyology. The chromosomes are depicted (by rearranging a photomicrograph) in a standard format known as a karyogram or idiogram: in pairs, ordered by size and position of centromere for chromosomes of the same size.

The basic number of chromosomes in the somatic cells of an individual or a species is called the somatic number and is designated 2n. In the germ-line (the sex cells) the chromosome number is n (humans: n = 23). Thus, in humans 2n = 46.

So, in normal diploid organisms, autosomal chromosomes are present in two copies. There may, or may not, be sex chromosomes. Polyploid cells have multiple copies of chromosomes and haploid cells have single copies.

Karyotypes can be used for many purposes; such as to study chromosomal aberrations, cellular function, taxonomic relationships, medicine and to gather information about past evolutionary events.(karyosystematics). (W)

Lamarckism, or Lamarckian inheritance, also known as "Neo-Lamarckism", is the notion that an organism can pass on to its offspring physical characteristics that the parent organism acquired through use or disuse during its lifetime. This idea is also called the inheritance of acquired characteristics or soft inheritance. It is inaccurately named after the French biologist Jean-Baptiste Lamarck (1744-1829), who incorporated the action of soft inheritance into his evolutionary theories as a supplement to his concept of orthogenesis, a drive towards complexity. The theory is cited in textbooks to contrast with Darwinism. This paints a false picture of the history of biology, as Lamarck did not originate the idea of soft inheritance, which was known from the classical era onwards, and it was not the primary focus of Lamarck's theory of evolution. Further, in On the Origin of Species (1859), Charles Darwin supported the idea of "use and disuse inheritance", though rejecting other aspects of Lamarck's theory. Darwin's own concept of pangenesis implied soft inheritance. (W)

Lamarck's two-factor theory involves 1) a complexifying force that drives animal body plans towards higher levels (orthogenesis) creating a ladder of phyla, and 2) an adaptive force that causes animals with a given body plan to adapt to circumstances (use and disuse, inheritance of acquired characteristics) , creating a diversity of species and genera. Popular views of Lamarckism only consider an aspect of the adaptive force.

lentivirus

Lentivirus is a genus of retroviruses that cause chronic and deadly diseases characterized by long incubation periods, in the human and other mammalian species. The best known lentivirus is the human immunodeficiency virus (HIV), which causes AIDS. Lentiviruses are also hosted in apes, cows, goats, horses, cats, and sheep. Recently, lentiviruses have been found in monkeys, lemurs, Malayan flying lemur (neither a true lemur nor a primate), rabbits, and ferrets. Lentiviruses and their hosts have worldwide distribution. Lentiviruses can integrate a significant amount of viral cDNA into the DNA of the host cell and can efficiently infect nondividing cells, so they are one of the most efficient methods of gene delivery. Lentiviruses can become endogenous (ERV), integrating their genome into the host germline genome, so that the virus is henceforth inherited by the host's descendants. (W)

Lentiviral delivery of designed shRNA's and the mechanism of RNA interference in mammalian cells.. Lentiviral delivery of shRNA expression construct for stable integration and expresion of shRNA. ShRNA processing and inhibitory mechanisms.

leukocyte extravasation

Leukocyte extravasation (also commonly known as leukocyte adhesion cascade or diapedesis – the passage of cells through the intact vessel wall) is the movement of leukocytes out of the circulatory system and towards the site of tissue damage or infection. This process forms part of the innate immune response, involving the recruitment of non-specific leukocytes. Monocytes also use this process in the absence of infection or tissue damage during their development into macrophages. (W)

Neutrophils extravasate from blood vessels to the site of tissue injury or infection during the innate immune response. 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.

Micrograph showing leukocyte migration, H&E stain.

Leukocyte extravasation.

The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and other membranes surrounding sub-cellular structures. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. Lipid bilayers are ideally suited to this role, even though they are only a few nanometers in width, because they are impermeable to most water-soluble (hydrophilic) molecules. Bilayers are particularly impermeable to ions, which allows cells to regulate salt concentrations and pH by transporting ions across their membranes using proteins called ion pumps. (W)

The three main structures phospholipids form in solution; the liposome (a closed bilayer), the micelle and the bilayer.

Diagram showing the effect of unsaturated lipids on a bilayer. The lipids with an unsaturated tail (blue) disrupt the packing of those with only saturated tails (black). The resulting bilayer has more free space and is, as a consequence, more permeable to water and other small molecules.

lipid bilayer fusion

In membrane biology, fusion is the process by which two initially distinct lipid bilayers merge their hydrophobic cores, resulting in one interconnected structure. If this fusion proceeds completely through both leaflets of both bilayers, an aqueous bridge is formed and the internal contents of the two structures can mix. Alternatively, if only one leaflet from each bilayer is involved in the fusion process, the bilayers are said to be hemifused. In hemifusion, the lipid constituents of the outer leaflet of the two bilayers can mix, but the inner leaflets remain distinct. The aqueous contents enclosed by each bilayer also remain separated.

Fusion is involved in many cellular processes, particularly in eukaryotes since the eukaryotic cell is extensively sub-divided by lipid bilayer membranes. Exocytosis, fertilization of an egg by sperm and transport of waste products to the lysosome are a few of the many eukaryotic processes that rely on some form of fusion. Fusion is also an important mechanism for transport of lipids from their site of synthesis to the membrane where they are needed. Even the entry of pathogens can be governed by fusion, as many bilayer-coated viruses have dedicated fusion proteins to gain entry into the host cell. (W)

Illustration of lipid vesicles fusing showing two possible outcomes: hemifusion and full fusion. In hemifusion only the outer bilayer leaflets mix. In full fusion both leaflets as well as the internal contents mix. Schematic illustration of two lipid vesicles fusing. Both the fully fused and the hemifused states are shown. In the hemifused state only the outer leaflet of the lipid bilayers fuse. In full fusion both leaflets fuse and internal aqueous contents mix.

Schematic illustration of the process of fusion through stalk formation.

Diagram of the action of SNARE proteins docking a vesicle for exocytosis. Complementary versions of the protein on the vesicle and the target membrane bind and wrap around each other, drawing the two bilayers close together in the process.

(1.) Illustration of lipid mixing assay based on Förster resonance energy transfer.

(3.) Illustration of lipid mixing assay based on Fluorescence self-quenching.

liposome

Liposomes were first described by British haematologist Alec D Bangham in 1961 (published 1964)

A liposome is a spherical vesicle having at least one lipid bilayer.The liposome can be used as a vehicle for administration of nutrients and pharmaceutical drugs. Liposomes can be prepared by disrupting biological membranes (such as by sonication).

Liposomes are most often composed of phospholipids,especially phosphatidylcholine, but may also include other lipids, such as egg phosphatidylethanolamine, so long as they are compatible with lipid bilayer structure. A liposome design may employ surface ligands for attaching to unhealthy tissue.

The major types of liposomes are the multilamellar vesicle (MLV, with several lamellar phase lipid bilayers), the small unilamellar liposome vesicle (SUV, with one lipid bilayer), the large unilamellar vesicle (LUV), and the cochleate vesicle. A less desirable form are multivesicular liposomes in which one vesicle contains one or more smaller vesicles.

Liposomes should not be confused with lysosomes, or with micelles and reverse micelles composed of monolayers. (W)

Scheme of a liposome formed by phospholipids in an aqueous solution. Schema of a liposome showing phospholipid bilayer surrounding an aqueous interior and excluding an aqueous exterior environment.

Liposomes are composite structures made of phospholipids and may contain small amounts of other molecules. Though liposomes can vary in size from low micrometer range to tens of micrometers, unilamellar liposomes, as pictured here, are typically in the lower size range with various targeting ligands attached to their surface allowing for their surface-attachment and accumulation in pathological areas for treatment of disease.

List of human cell types derived from the germ layers

This is a list of cells in humans derived from the three embryonic germ layers – ectoderm, mesoderm, and endoderm (W)

📥 List of human cell types derived from the germ layers (W)

List of unsolved problems in neuroscience

There are yet unsolved problems in neuroscience, although some of these problems have evidence supporting a hypothesized solution, and the field is rapidly evolving. (W)

📥 List of unsolved problems in neuroscience (W)

lumen (anatomy)

In biology, a lumen (plural lumina) is the inside space of a tubular structure, such as an artery or intestine. It comes from Latin lumen 'an opening'.

It can refer to:

• The interior of a vessel, such as the central space in an artery, vein or capillary through which blood flows.
• The interior of the gastrointestinal tract
• The pathways of the bronchi in the lungs
• The interior of renal tubules and urinary collecting ducts
• The pathways of the female genital tract, starting with a single pathway of the vagina, splitting up in two lumina in the uterus, both of which continue through the fallopian tubes

In cell biology, a lumen is a membrane-defined space that is found inside several organelles, cellular components, or structures:

• thylakoid, endoplasmic reticulum, Golgi apparatus, lysosome, mitochondrion, or microtubule. (W)
  
  

Cross section of the gut. The lumen is the space in the middle also known as the volume.

lymphatic system

The lymphatic system, or lymphoid system, is an organ system in vertebrates that is part of the circulatory system and the immune system. It is made up of a large network of lymphatic vessels, lymphatic or lymphoid organs, and lymphoid tissues. The vessels carry a clear fluid called lymph (the Latin word lympha refers to the deity of fresh water, "Lympha") towards the heart.

Unlike the cardiovascular system, the lymphatic system is not a closed system. The human circulatory system processes an average of 20 litres of blood per day through capillary filtration, which removes plasma from the blood. Roughly 17 litres of the filtered plasma is reabsorbed directly into the blood vessels, while the remaining three litres remain in the interstitial fluid. One of the main functions of the lymphatic system is to provide an accessory return route to the blood for the surplus three litres.

The other main function is that of immune defense. Lymph is very similar to blood plasma, in that it contains waste products and cellular debris, together with bacteria and proteins. The cells of the lymph are mostly lymphocytes. Associated lymphoid organs are composed of lymphoid tissue, and are the sites either of lymphocyte production or of lymphocyte activation. These include the lymph nodes (where the highest lymphocyte concentration is found), the spleen, the thymus, and the tonsils. Lymphocytes are initially generated in the bone marrow. The lymphoid organs also contain other types of cells such as stromal cells for support. Lymphoid tissue is also associated with mucosas such as mucosa-associated lymphoid tissue (MALT).

Fluid from circulating blood leaks into the tissues of the body by capillary action, carrying nutrients to the cells. The fluid bathes the tissues as interstitial fluid, collecting waste products, bacteria, and damaged cells, and then drains as lymph into the lymphatic capillaries and lymphatic vessels. These vessels carry the lymph throughout the body, passing through numerous lymph nodes which filter out unwanted materials such as bacteria and damaged cells. Lymph then passes into much larger lymph vessels known as lymph ducts. The right lymphatic duct drains the right side of the region and the much larger left lymphatic duct, known as the thoracic duct, drains the left side of the body. The ducts empty into the subclavian veins to return to the blood circulation. Lymph is moved through the system by muscle contractions. In some vertebrates, a lymph heart is present that pumps the lymph to the veins.

The lymphatic system was first described in the 17th century independently by Olaus Rudbeck and Thomas Bartholin. .(W)

Lymphatic System.

lymphocyte

A lymphocyte is one type of white blood cell in the vertebrate immune system. Lymphocytes include natural killer cells (which function in cell-mediated, cytotoxic innate immunity), T cells (for cell-mediated, cytotoxic adaptive immunity), and B cells (for humoral, antibody-driven adaptive immunity). They are the main type of cell found in lymph, which prompted the name "lymphocyte".

Lymphocyte makes up between 18% and 42% of circulating leukocytes. (W)

Electron microscopic image of a single human lymphocyte.

lymphopoiesis

Lymphopoiesis (lĭm'fō-poi-ē'sĭs) (or lymphocytopoiesis) is the generation of lymphocytes, one of the five types of white blood cell (WBC). It is more formally known as lymphoid hematopoiesis.

Disruption in lymphopoiesis can lead to a number of lymphoproliferative disorders, such as the lymphomas and lymphoid leukemias. (W)

Early B cell development: from stem cell to immature B cell.

Transitional B cell development: from immature B cell to MZ B cell or mature FO B cell.

Side by side. Comparing the new and old lineage models.

Revised Lineage Myelo-lymphoid flowchart. Products of MLP cell showing mixed myeloid and lymphoid output, preserving TCR ongoing rearrangements evidence of the transitions in cell type.

A lysosome is a membrane-bound organelle found in many animal cells. They are spherical vesicles that contain hydrolytic enzymes that can break down many kinds of biomolecules. A lysosome has a specific composition, of both its membrane proteins, and its lumenal proteins. The lumen's pH (~4.5–5.0) is optimal for the enzymes involved in hydrolysis, analogous to the activity of the stomach. Besides degradation of polymers, the lysosome is involved in various cell processes, including secretion, plasma membrane repair, apoptosis, cell signaling, and energy metabolism. (W)

Diagram of a typical animal cell. Organelles are labelled as follows: Nucleolus Nucleus Ribosomes (dots on rough reticulum walls) Vesicle Rough endoplasmic reticulum Golgi apparatus (or "Golgi body") Cytoskeleton Smooth endoplasmic reticulum Mitochondrion Vacuole Cytosol Lysosome Centriole Cell membrane.

Lysosomes digest materials taken into the cell and recycle intracellular materials. Step one shows material entering a food vacuole through the plasma membrane, a process known as endocytosis. In step two a lysosome with an active hydrolytic enzyme comes into the picture as the food vacuole moves away from the plasma membrane. Step three consists of the lysosome fusing with the food vacuole and hydrolytic enzymes entering the food vacuole. In the final step, step four, hydrolytic enzymes digest the food particles.