Living systems are all made of many molecular components that self- assemble, recognize as well as control each other and self- replicate ... How can it be that proteins, describable by the laws of physics, assemble themselves into cellular machines and structures, these into complete living cells, and the latter into whole organisms that require a whole new language for their description? Opportunities in Molecular Biomedicine in the Era of  Teraflop Computing, March 3 & 4, 1999, Rockville, MD  Molecular Biomedicine in the Era of Teraflop Computing - DDDAS.org

Biology term index   Related glossaries include Drugs Biologics  Technologies  Cell & tissue technologies   Microscopy   Molecular Imaging   Biology Chemistry  Functional genomics  Model & other organisms   Stem cells  

Adenosine Triphosphate ATP: Adenosine 5'- (tetrahydrogen triphosphate). An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter. MeSH

angiogenesis: Angiogenesis, the growth of new capillary blood vessels in the body, is an important natural process in the body used for healing and reproduction. The body controls angiogenesis by producing a precise balance of growth and inhibitory factors in healthy tissues. When this balance is disturbed, the result is either too much or too little angiogenesis. Abnormal blood vessel growth, either excessive or insufficient, is now recognized as a “common denominator” underlying many deadly and debilitating conditions, including cancer, skin diseases, age-related blindness, diabetic ulcers, cardiovascular disease, stroke, and many others. Angiogenesis Foundation " About Angiogenesis https://angio.org/about-angiogenesis/

apoptosis:  The molecular and morphological processes leading to controlled cellular self- destruction was first introduced in a publication by Kerr, Wyllie and Currie (Br. J. Cancer, 1972, 26: 239). 'Apoptosis' is of Greek origin, having the meaning "falling off or dropping off", in analogy to leaves falling from trees or petals from flowers. By choosing this term, the authors might have intended to stress that this form of cell death is a natural phenomenon, an active and defined process which plays an important role in the regulation of the cell population in tissues upon physiological and pathological conditions. Apoptotic cell death can be induced by a variety of stimuli, such as ligation of cell surface receptors, starvation, growth factor/ survival factor deprivation, heat shock, hypoxia, DNA damage, viral infection, and cytotoxic/ chemotherapeutical agents. The apoptotic process is of widespread biological significance, and it was reported to be involved in embryogenesis, differentiation, proliferation/ homoeostasis, removal of defect and therefore harmful cells, and especially in the regulation and function of the immune system. Thus, dysfunction or disregulation of the apoptotic program is implicated in a variety of pathological conditions, such as immunodeficiency, auto- immune diseases, neurodegenerative diseases, and cancer. Apoptopedia, Cell Death Encyclopedia, 2001 http://www.celldeath.de/encyclo/index.html Click on A, go to Apoptosis entry and click on more.

One of the two mechanisms by which CELL DEATH occurs (the other being the pathological process of NECROSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA (DNA FRAGMENTATION) at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth. MeSH, 1993  
Broader term: cell death   See also programmed cell death.
Apoptopedia, CellDeath.de, Germany   http://www.celldeath.de/encyclo/index.html

autosome:  A chromosome not involved in sex determination. The diploid human genome consists of 46 chromosomes, 22 pairs of autosomes, and 1 pair of  sex chromosomes (the X and Y chromosomes). DOE  Related terms: autosomal, somatic cells Molecular Medicine

cell, cells: The smallest structural unit of living matter capable of functioning autonomously. IUPAC Biotech

The basic unit of any living organism. It is a small, watery, compartment filled with chemicals and a complete copy of the organism's genome. NHGRI Narrower terms: clone, embryonic stem cells ES, gametes, germ cells, hematopoietic stem cells, Mesenchymal Stem Cells MSC, pluripotent stem cells, somatic cell, stem cells, CHO cells Chinese Hamster Ovary cells, T cells  Related terms: cell cycle, cell division, cell line, cell mapping, cellular component, cytogenetics, eukaryotes, FACS, flow sorting, host, hybridoma, Laser Capture Microdissection, multicellular, multipotent organelles, pluripotent, totipotent, cell culture, cell differentiation, cell fusion, cell patterning, cell strain, lysis, meiosis, mitosis, prokaryotes, subcellular fractionation

cell adhesion molecules:  Surface ligands, usually glycoproteins, that mediate cell- to- cell adhesion. Their functions include the assembly and interconnection of various vertebrate systems, as well as maintenance of tissue integration, wound healing, morphogenic movements, cellular migrations, and metastasis.  MeSH, 1990

Cell Atlas:  Chan Zuckerberg https://www.czbiohub.org/projects/cell-atlas/  Mapping every cell in the human body, using sequencing and CRISPR.

cell biology: The study of the structure, behavior, growth, reproduction, and pathology of cells; and the function and chemistry of cellular components. MeSH  2010 (1984)

cell cycle:  The growth cycle of a cell from one division to the next. In eukaryotic cells the growth cycle is divided into the following 4 phases: G1- phase: the period of the cycle beginning after mitosis and preceding the initiation of DNA synthesis. S-phase: discrete period of cell cycle when most DNA synthesis occurs. G2- phase: period of cell cycle when cells contain twice the G1 complement of DNA. M-phase: division of the cell into two (cf. mitosis), each with one complete genome. IUPAC Biotech

The complex series of phenomena, occurring between the end of one cell division and the end of the next, by which cellular material is divided between daughter cells. MeSH, 1978    Related terms: meiosis, mitosis; Proteins  checkpoint control proteins; Functional genomics

cell cycle proteins: Proteins that control the cell division cycle. This family of proteins includes a wide variety of classes, including CYCLIN- DEPENDENT KINASES, mitogen- activated kinases, CYCLINS, and phosphoprotein phosphatases (PHOSPHOPROTEIN PHOSPHATASE) as well as their putative substrates such as chromatin- associated proteins, cytoskeletal proteins, and transcription factors. MeSH, 1995   Related terms: cell cycle; Expression: transcription factors

cell death: The termination of the cell's ability to carry out vital functions such as metabolism, growth, reproduction, responsiveness, and adaptability.  MeSH 1992   See also programmed cell death. Narrower term: apoptosis

cell differentiation: Progressive restriction of the developmental potential and increasing specialization of function which takes place during the development of the embryo and leads to the formation of specialized cells, tissues, and organs. MeSH, 1966  Related terms: Stem cells multipotent, pluripotent, , totipotent

cell division: Milestones, from Nature Publishing http://www.nature.com/celldivision/index.html

cell function: The level at which we wish to understand the function of the cell determines to a large extent the degree of experimental reductionism required. The smallest building block required to understand the function of the cell appears to be the protein. While the genetic sequence provides the basic informational foundation of the cell, it is the network of protein- gene, protein- protein, and protein- metabolite interactions - the fluxes and flows of material and information -  which result in cell function. Studies of whole cell dynamics currently employ optical imaging of diffusion, generally through the use of steady state or dynamic photobleaching recovery methods. Associated with such studies is the need to label specific intracellular entities. Expansion of these approaches to include the wealth of protein species in the cell will involve development of new labeling methods, new dyes and means of introducing them; widely scaling imaging techniques permitting examination of the whole cell or of intracellular compartments; NMR micro- imaging techniques, particularly those sensitive to chemical species; environmental EM techniques, which may provide the capability of rapid single cell microprobe analysis; creative evanescent wave approaches to characterizing the cell membrane; and new tools capable of mechanical assessment of global (and local) mechanical properties of the cell. ... Ultimately, the systematic characterization of cell biology will be the result of the efforts of a great many laboratories integrated over many years. Archiving and interpreting (understanding) these results will require coordination at all levels. Whether or not the paradigm of the Human Genome Project is appropriate for integrating such cell- level studies was discussed at length with the full realization that overriding clinical, pharmaceutical, and cell biology questions may ultimately focus the effort more effectively than a central coordinating agency. Whatever organizational paradigm is employed, there are fundamental and overriding infrastructural issues which must be addressed at the outset, the most urgent of which are the development of enabling technologies and the creation of highly defined panels of cell types for the use of the research community National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999 

cell genotype: Genetic makeup of cells. Related term: cell phenotypes

cell migration:  the process by which cells move from one location to another by adopting different motility modes, such as mesenchymal, amoeboid or collective migration. Cell motility is observed in unicellular organisms, is essential for the development and maintenance of multicellular organisms, and is also involved in immune responses and pathological conditions.  Nature: Cell migration latest research https://www.nature.com/subjects/cell-migration 
Wikipedia http://en.wikipedia.org/wiki/Cell_migration 

cell ontology: http://obofoundry.org/ontology/cl.html  A structured controlled vocabulary for cell types in animals.

cell patterning: Cell-cell signaling is an important component of the stem cell microenvironment, affecting both differentiation and self-renewal. However, traditional cell-culture techniques do not provide precise control over cell-cell interactions, while existing cell patterning technologies are limited when used with proliferating or motile cells. To address these limitations, we created the Bio Flip Chip (BFC), a microfabricated polymer chip containing thousands of microwells, each sized to trap down to a single stem cell.  Cell Patterning Chip for Controlling the Stem Cell Microenvironment Adam Rosenthal,^1,2 Alice Macdonald,³ and Joel Voldman² Biomaterials. Author manuscript; available in PMC 2008 July 1. Published in final edited form as: Biomaterials. 2007 July; 28(21): 3208–3216. Published online 2007 March 27. doi:   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929166/ 

cell phenotype: Examples of cell phenotypes found in the literature include life and death cell phenotypes, and gene expression studies of cancer cells.  Related term: biomarkers, cell genotype 

cell physiology: While it [prediction of  the three- dimensional structure and function of proteins from their linear sequence information] would be a remarkable accomplishment, the future achievement of a satisfactory protein structure/ function predictive capability will simply provide a second important substratum upon which to begin the exploration of the intricacies of the operation of the living cell, since it is the interactions among cell proteins which, in large part, define cell physiology. Biologists understand a great deal about the protein constituents of cells, their roles in metabolism, the signaling roles of small molecules and selective modifications of intracellular proteins, and how cellular structures assemble themselves and transduce energy, but it is unlikely that a useful understanding of the cell will be possible until a quantitative appreciation of both rates and equilibria of molecular processes in the living cell is achieved. National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999

cellular component: The place in the cell where a gene product is active. Gene Ontology Consortium "Gene Ontology: tool for the unification of biology Nature Genetics 25: 25-29 May 2000
Related terms: Functional genomics biological function gene function,  Gene Ontology^TM Consortium; Proteins protein localization

cellular metabolism:  New genomic tools, particularly DNA microarrays, provide a previously unattainable global view of how gene expression patterns respond to various physiological stimuli, to mutations, and in disease states. Such knowledge provides a basis for insights into cellular metabolism that were not possible by studies of a few selected genes at a time. However, a DNA microarray, or any nucleic acid- based [DNA or RNA] methodology, is blind to many events that occur at the protein level. Therefore, they provide an indirect and incomplete picture of cellular function and hence additional information is needed for advancing human medicine and health care. The field of proteomics seeks to supply this knowledge by revealing the levels, activities, regulation, and interactions of every protein in the cell and how these quantities respond to a particular stimulus (e.g. drug, food, infection) or disease state or DNA alteration. In essence, proteomics builds on and complements the knowledge gained from  genomics .This significant effort in proteomics will provide discoveries about the cells' protein machinery that will likely yield important clinical applications. National Heart, Lung & Blood Institute, Proteomics Initiative, NIH, US,  2001 http://grants1.nih.gov/grants/guide/notice-files/NOT-HL-02-004.html

Cellular Reprogramming: coverage includes: Somatic cell nuclear transfer and reprogramming in early embryos, Embryonic stem cells, Nuclear transfer stem cells (stem cells derived from nuclear transfer embryos), Generation of induced pluripotent stem (iPS) cells and/or potential for cell-based therapies, Epigenetics, Adult stem cells and pluripotency. Cellular Reprogramming Aims and Scope, Mary Ann Liebert  http://home.liebertpub.com/publications/cellular-reprogramming/9/overview#aims  
Wikipedia http://en.wikipedia.org/wiki/Reprogramming   Related terms: epigenetics, stem cells

centromere: The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division. MeSH, 1991

chromatin: The material of CHROMOSOMES. It is a complex of DNA, HISTONES, and nonhistone proteins (CHROMOSOMAL PROTEINS, NON- HISTONE) found within the nucleus of a cell. MeSH, 1972

chromosome: A self-replicating structure consisting of DNA complexed with various proteins and involved in the storage and transmission of genetic information; the physical structure that contains genes (cf., plasmid). Eukaryotic cells have a characteristic number of chromosomes per cell (cf. ploidy [haploid or diploid]) and contain DNA as linear duplexes ... The chromosomes of bacteria consist of double- stranded, circular DNA molecules. MeSH

One of the threadlike "packages" of genes and other DNA in the nucleus of a cell. Different kinds of organisms have different numbers of chromosomes. Humans have 23 pairs of  chromosomes, 46 in all: 44 autosomes and two sex chromosomes. Each parent contributes one chromosome to each pair, so children get half of  their chromosomes from their mothers and half  from their fathers. NHGRI  Narrower terms: autosome, centromere, chromatin, euchromatin, heterochromatin, homologous chromosomes, telomere Related terms chromosome maps, cytogenetics, diploid, euchromatic, haploid, karyotype, ploidies, ploidy, somatic cell hybridization

cytogenetics: Branch of genetics which correlates the structure and number of chromosomes as seen in isolated cells with variation in genotype and phenotype. MeSH, 1967  Related terms: Genomics: genotype, phenotype

cytotoxic T cell: (also known as T_C, cytotoxic T lymphocyte, CTL, T-killer cell, cytolytic T cell, CD8+ T-cell or killer T cell) is a T lymphocyte (a type of white blood cell) that kills cancer cells, cells that are infected (particularly with viruses), or cells that are damaged in other ways. Not to be confused with Natural killer T cell. Wikipedia accessed 2018 April 5 https://en.wikipedia.org/wiki/Cytotoxic_T_cell

dendritic cells. A set of antigen- presenting cells present in lymph nodes, spleen and at low levels in blood, which are particularly active in stimulating T cells.  
Wikipedia http://en.wikipedia.org/wiki/Dendritic_cell 

developmental biology:  The field of biology which deals with the process of the growth and differentiation of an organism.  MeSH, 1990

differentiation cellular: The process by which cells become structurally and functionally specialized during embryonic development. In cancer, refers to how mature (developed) the cancer cells are in a tumor. Differentiated tumor cells resemble normal cells and tend to grow and spread at a slower rate than undifferentiated or poorly- differentiated tumor cells, which lack the structure and function of normal cells and grow uncontrollably.  CancerNet 
Related terms: DNA methylation, epigenetics,  Stem cells multipotent, pluripotent, totipotent  Narrower term: cell differentiation- or is this equivalent? Broader term: developmental biology

diploid: The number of chromosomes in most cells except the gametes. In humans, the diploid number is 46. NHGRI  Broader term: ploidies, ploidy Related terms haploid; Sequencing haplotype

effector: Effector cells are the superset of all the various T cell types that actively respond immediately to a stimulus, such as co-stimulation. This includes helper, killer, regulatory, and potentially other T cell types. Memory cells are their opposite counterpart that are longer lived to target future infections as necessary. Wikipedia accessed 2018 April 5 https://en.wikipedia.org/wiki/T_cell  Broader term: T cell

endothelium: refers to cells that line the interior surface of blood vessels and lymphatic vessels,[1] forming an interface between circulating blood or lymph in the lumen and the rest of the vessel wall. It is a thin layer of simple, or single-layered, squamous cells called endothelial cells. Endothelial cells in direct contact with blood are called vascular endothelial cells, whereas those in direct contact with lymph are known as lymphatic endothelial cells. Vascular endothelial cells line the entire circulatory system, from the heart to the smallest capillaries.  Wikipedia accessed 2018 Dec 11 https://en.wikipedia.org/wiki/Endothelium

euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.  MeSH, 2001

In humans are particularly rich in genes.

eukaryotes: Organisms whose cells have their genetic material packed in a membrane- surrounded, structurally discrete nucleus and with well- developed cell organelles.  Eukaryotes include all organisms except archaebacteria and eubacteria (cg. prokaryotes). IUPAC Biotech

eukaryotic cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane MeSH, 1991

exosomes: Vesicles secreted from MULTIVESICULAR BODIES into the extracellular environment when the multivesicular bodies fuse with the PLASMA MEMBRANE. Multivesicular bodies are formed from ENDOSOMES when they accumulate vesicles (sometimes referred to as "intraluminal vesicles") from inward budding of the endosome membrane. MeSH 2009

cell-derived vesicles that are present in many and perhaps all eukaryotic fluids, including blood, urine, and cultured medium of cell cultures.^[1][2] A sub-type of exosomes, defined as matrix-bound nanovesicles (MBVs), was reported to be present in extracellular matrix (ECM) bioscaffolds (non-fluid).^[3] The reported diameter of exosomes is between 30 and 100 nm, which is larger than low-density lipoproteins (LDL) but much smaller than, for example, red blood cells. Exosomes are either released from the cell when multivesicular bodies fuse with the plasma membrane or released directly from the plasma membrane.^[4] Evidence is accumulating that exosomes have specialized functions and play a key role in processes such as coagulation, intercellular signaling, and waste management.^[1] Consequently, there is a growing interest in the clinical applications of exosomes. Exosomes can potentially be used for prognosis, for therapy, and as biomarkers for health and disease. … Increasingly, exosomes are being recognized as potential therapeutics as they have the ability to elicit potent cellular responses in vitro and in vivo.^[48][49][50]  Exosomes offer distinct advantages that uniquely position them as highly effective drug carriers. Wikipedia accessed 2018 Feb 5 https://en.wikipedia.org/wiki/Exosome_(vesicle)

Exosomes, which originate from late endosomes, are naturally occurring nanoparticles, secreted endogenously by cells. They are 30–100 nm cup-shaped vesicles with a lipid bilayer morphology ^[11,12,20].  https://www.sciencedirect.com/science/article/pii/S0169409X1200213X  Broader term: vesicles 
American Society for Exosomes and Microvesicles http://www.asemv.org/

extracellular matrix: A meshwork- like substance found within the extracellular space and in association with the basement membrane of the cell surface. It promotes cellular proliferation and provides a supporting structure to which cells or cell lysates in culture dishes adhere. MeSH, 1984  Related term: Protein Structures basement membranes

extracellular vesicles: membrane surrounded structures released by cells in an evolutionally conserved manner. Their diagnostic and therapeutic exploitation is under intense investigation.  Extracellular Vesicles Research Group at Semmelveis University, Budapest, Hungary http://extracellularvesicles.org/

Cells have been known for a long time to release vesicles to the extracellular environment during apoptosis. However, the fact that healthy cells also release vesicles to the extracellular environment has only being recently realized. Many diverse names have been used to refer to these vesicles released by healthy cells including ectosomes, microparticles, and shedding microvesicles, just to name a few. In order to bring harmonization to the field, researchers are now encouraged to use the term extracellular vesicles (EVs) as a generic term for all secreted vesicles. Although confusion on the nomenclature of EVs has spread throughout the literature, EVs may be broadly classified into exosomes, microvesicles (MVs) and apoptotic bodies according to their cellular origin  Abcam, Extracellular Vesicles An Introduction http://www.abcam.com/primary-antibodies/extracellular-vesicles-an-introduction

International Society for Extracellular Vesicles http://www.isev.org/
Journal of Extracellular Vesicles https://www.isev.org/page/JEV

fibroblasts Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules. MeSH, 1965  Related terms: stem cells

fusion: The amalgamation of two distinct cells or macromolecules into a single integrated unit. IUPAC Biotech  Narrower term: cell fusion.

gamete: Mature male or female reproductive cell (sperm or ovum) with a haploid set of chromosomes (23 for  humans). DOE  Related term: germ cells

gene fusion: Fusion of structural genes to analyze protein behavior or fusion of regulatory sequences with structural genes to determine mechanisms of regulation. MeSH, 1998

germ cells: The reproductive cells in multicellular organisms. Includes Ovum (Oocytes, Oogonia,   Zona Pellucida , Zygote) and Spermatozoa (Sperm Head + , Sperm Tail, Spermatids, Spermatocytes, Spermatogonia MeSH  Related terms: gamete, germline mutations

An organelle composed of membranous sacs that packages proteins into vesicles and sends them to the cell's surface or to lysosomes.  NIGMS

haploid: The number of chromosomes in a sperm or egg cell, half the diploid number. NHGRI

A single set of chromosomes (half the full set of genetic material), present in the egg and sperm cells  of animals and in the egg and pollen cells of plants. Human beings have 23 chromosomes in their reproductive cells. Compare diploid.  DOE   Broader terms: ploidies, ploidy Related terms: diploid; Sequencing haplotype

heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE. MeSH, 1972

Highly repetitive lengths of DNA with little genetic information.

homologous chromosomes: A pair of chromosomes containing the same linear gene sequences, each derived from one parent. DOE

Human Cell Atlas The cell is the core unit of the human body—the key to understanding the biology of health and the ways in which molecular dysfunction leads to disease. Yet our characterization of the hundreds of types and subtypes of cells in the human body is limited, based partly on techniques that have limited resolution and classifications that do not always map neatly to each other. Genomics has offered a systematic approach, but it has largely been applied in bulk to many cell types at once—masking critical differences between cells—and in isolation from other valuable sources of data. Recent advances in single-cell genomic analysis of cells and tissues have put systematic, high-resolution and comprehensive reference maps of all human cells within reach. In other words, we can now realistically envision a human cell atlas to serve as a basis for both understanding human health and diagnosing, monitoring,  https://www.humancellatlas.org/    https://www.humancellatlas.org/learn-more

human cloning: Human cloning and human dignity: an ethical report, Presidents Council on Bioethics, 2002 http://bioethics.georgetown.edu/pcbe/reports/cloningreport/ 

image analysis/image processing:  Assays [in context of high -content screening

karyotype: A photomicrograph of an individuals chromosomes arranged in a standard format showing the number, size, and shape of each chromosome type; used in low- resolution physical mapping to correlate gross chromosomal abnormalities with the characteristics of specific diseases. DOE

The full set of CHROMOSOMES presented as a systematized array of METAPHASE chromosomes from a photomicrograph of a single CELL NUCLEUS arranged in pairs in descending order of size and according to the position of the CENTROMERE. (From Stedman, 25th ed)  MeSH 2012

library: Combinatorial libraries & synthesis  How does this relate to combinatorial library and related terms in Drug discovery & development (or more general meanings of  "library").  
Narrower terms: gene library, genomic library;  Microarrays  arrayed library; Sequencing DNA library 

lymphokines: Soluble protein factors generated by activated lymphocytes that affect other cells, primarily those involved in cellular immunity. MeSH 1974  Broader term: Protein categories: cytokines

lysis: Cell rupture caused by physical or chemical means, or by phage infection and propagation leading to the release of the cell content; also the death of microorganisms after the stationary phase of a batch fermentation. IUPAC Biotech

meiosis: The reductive cell division which results in daughter cells containing one copy of each of the chromosomes of the parent. The entire meiotic process involves two separate divisions (meiosis I and meiosis II). The first division is a true reductive division with the chromosome number being halved, whereas the second division resembles mitosis in many ways. Thus, a diploid parental cell will give rise to haploid daughter cells (cf. ploidy). IUPAC Biotech

A special method of cell division, occurring in maturation of the germ cells, by means of which each daughter nucleus receives half the number of chromosomes characteristic of the somatic cells of the species. MeSH, 1968 
Related term: cell cycle

mesenchymal: Refers to cells that develop into connective tissue, blood vessels, and lymphatic tissue. [Cancernet] Part of the embryonic mesoderm.
Related terms: Stem cells mesenchymal, mesenchymal stem cells, mesoderm, hematopoietic stem cells

mesoderm:  The middle germ layer of the embryo derived from three paired mesenchymal aggregates along the neural tube. . MeSH

microvesicles: sometimes called, circulating microvesicles, or microparticles) …are a type of extracellular vesicle (EV), between 50 and 1,000 nanometers (nm) in diameter, found in many types of body fluids as well as the interstitial space between cellscircular fragments of plasma membrane ranging from 100 nm to 1000 nm shed from almost all cell types. Not to be confused with smaller intracellularly generated extracellular vesicles known as exosomes. … Though initially dismissed as cellular debris, microvesicles have a role in cell signaling and the process of molecular communication between cells, and are released by a number of cell types.^[2] Although a consistent and precise definition is lacking, microvesicles are generally considered to be a heterogeneous population of exosomes (<100 nm) and shed microvesicles (100-1000 nm), which are similar but have distinct mechanisms of formation. Through these mechanisms, microvesicles are released into the extracellular space and interact with specific target cells, delivering bioactive molecules. Changes in microvesicle levels are implicated in a variety of diseases, including cancer. These changes can be used as biomarkers in a variety of diagnostic assays.  Wikipedia accessed 2018 Feb 5 https://en.wikipedia.org/wiki/Microvesicles    See also exosomes. 

mitochondria: Organelles appearing in all eukaryotic cells which produce ATP as useful energy for the cell by oxidative phosphorylation. The proteins for the adenoseine  5’- triphosphate (ATP)- generating electron transport of the respiration chain are located in the inner mitochondrial membrane. Mitochondria contain many enzymes of the citric acid cycle and for fatty acid [beta]- oxidation. Many of them are coded for by nuclear DNA. IUPAC Biotech  Related terms: ATP,  mitochondrion; mitochondrial genes Gene definitions

mitosis: The process whereby a cell nucleus divides into two daughter nuclei, each having the same genetic component as the parent cell. IUPAC Biotech

A method of indirect cell division by means of which the two daughter nuclei normally receive identical complements of the number of chromosomes of the somatic cells of the species MeSH Related term: cell cycle

morphometry: Measurement of shape, structure and form.  Used in a variety of disciplines, including environmental studies, geology, imaging and cell biology.

multicellular: Practically speaking, few processes peculiar to multicellular organisms have meaning when abstracted from anatomy, a particularly good example being developmental processes. The general consensus is that 'when it gets multicellular, it gets complicated'. Minutes of Gene Ontology Consortium Meeting 4- 6 November 2000 Lawrence Berkeley Labs Meeting)  http://www.geneontology.org/meeting/minutes/20001106_Berkeley.txt

Natural killer cells or NK cells are a type of cytotoxic lymphocyte critical to the innate immune system. The role NK cells play is analogous to that of cytotoxic T cells in the vertebrate adaptive immune response. NK cells provide rapid responses to viral-infected cells, acting at around 3 days after infection, and respond to tumor formation. Wikipedia accessed 2018 April 5 https://en.wikipedia.org/wiki/Natural_killer_cell

Natural killer T (NKT) cells are a heterogeneous group of T cells that share properties of both T cells and natural killer cells. Many of these cells recognize the non-polymorphic CD1d molecule, an antigen-presenting molecule that binds self and foreign lipids and glycolipids. They constitute only approximately 0.1% of all peripheral blood T cells.^[1] Natural killer T cells should not be confused with natural killer cells. Wikipedia accessed 2018 April 5 https://en.wikipedia.org/wiki/Natural_killer_T_cell

nucleus: The central cell structure that houses the chromosomes. NHGRI Related terms: chromosomes, enucleated, mitochondria, organelles.

organelles: Separated components within a cell with specialized functions, e.g. nuclei (containing most of the genetic material), mitochondria (respiratory energy supply for the cell), chloroplasts (location of photosynthesis) etc. IUPAC Biotechnology

Specific, usually subcellular, particles of membrane- bound organized living substances present in  practically all eukaryotic cells, including mitochondria, the Golgi complex, endoplasmic reticulum, lysosomes, centrioles and the cell center, as well as the plastids of plant cells. Includes also the minute organs of protozoa concerned with such functions as locomotion and metabolism. MeSH, 1989

ploidies:  The degree of replication of the chromosome set in the karyotype. MeSH, 1976 

ploidy: Indicates the number of sets of chromosomes present in an organism, e.g. haploid (one) or diploid (two). IUPAC Biotech

programmed cell death:  Frequently, the terms 'apoptosis' and 'programmed cell death' are used as synonyms. Programmed cell death was originally used in order to describe the locally and temporally defined cell death during embryogenesis. It was already in the middle of our century that cell death was recognized as a natural process in the development of organisms (Gluecksmann, 1951, Biol. Rev., 26: 59).  Apoptopedia, Cell Death Encyclopedia, 2001 http://www.celldeath.de/encyclo/index.html Click on A, go to Apoptosis entry and click on more.  Narrower term: apoptosis

prokaryote: A unicellular organism characterized by the absence of a membrane- bound nucleus.. Includes bacteria, blue- green algae (Cyanobacteria) and mycoplasmas. IUPAC Biotech

ribosomes:  Subcellular unit composed of specific rRNA molecules and a large number of proteins that are responsible for protein synthesis. IUPAC Compendium

Cellular organelle that is the site of protein synthesis. NHGRI

Early in 1958, a three-day symposium on microsomal particles in protein synthesis met at MIT, sponsored by the Biophysical Society, organized by Richard Roberts, who was head of a group at the Carnegie Institution in Washington... The most important development at the meeting was semantic. Roberts suggested that for clear and handy distinction between the particles and the amorphous cellular fraction of protein and fat in which they were found, the particles themselves should be called "ribosomes" - short for "ribonucleoprotein particles of the microsome fraction." The new term quickly spread into general use. HJ Freeman, Eighth Day of Creation Cold Spring Harbor Laboratory Press, 1996, p. 338

From the Greek soma body

second messenger: An intracellular metabolite or ion increasing or decreasing as a response to the stimulation of receptors by agonists, considered as the "first messenger". This generic term usually does not prejudge the rank order of intracellular biochemical events. IUPAC Medicinal Chemistry

second messenger systems: Systems in which an intracellular signal is generated in response to an intercellular primary messenger such as a hormone or neurotransmitter. They are intermediate signals in cellular processes such as metabolism, secretion, contraction, phototransduction, and cell growth. Examples of second messenger systems are the adenyl cyclase- cyclic AMP system, the phosphatidylinositol diphosphate- inositol triphosphate system, and the cyclic GMP system. MeSH, 1989

A multi-step signal amplification process used by the cell to transmit, for example, signals from many hormones that cannot enter the cell directly. NIGMS

somatic cell:  Any cell in the body except gametes and their precursors. [DOE] Are the precursors stem cells?

All body cells, except the reproductive cells. NHGRI 

spliceosomes: Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear RNA molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message. MeSH, 1993  Related term: splicing Sequences DNA & beyond

subcellular fractionation: Concentrating a sample by separating out certain compartments of the cell. Allows study of cellular compartments and can provide greater resolution and sensitivity. 

T Cell:  A T cell, or T lymphocyte, is a type of lymphocyte (a subtype of white blood cell) that plays a central role in cell-mediated immunity. T cells can be distinguished from other lymphocytes, such as B cells and natural killer cells, by the presence of a T-cell receptor on the cell surface. They are called T cells because they mature in the thymus from thymocytes^[1] (although some also mature in the tonsils^[2]). The several subsets of T cells each have a distinct function...All T cells originate from haematopoietic stem cells in the bone marrow  Wikipedia accessed 2018 April 5 https://en.wikipedia.org/wiki/T_cell   Narrower terms:  cytotoxic T cell receptor, T Cells,  effector, T helper, Natural Killer T cells, T helper Memory

T-cell receptor, or TCR, is a molecule found on the surface of T cells, or T lymphocytes,^[1] that is responsible for recognizing fragments of antigen as peptides bound to major histocompatibility complex (MHC) molecules. The binding between TCR and antigen peptides is of relatively low affinity and is degenerate: that is, many TCRs recognize the same antigen peptide and many antigen peptides are recognized by the same TCR. Wikipedia accessed 2018 April 5 https://en.wikipedia.org/wiki/T-cell_receptor

T Helper: The T helper cells (T_h cells) are a type of T cell that play an important role in the immune system, particularly in the adaptive immune system. They help the activity of other immune cells by releasing T cell cytokines. These cells help suppress or regulate immune responses. Wikipedia accessed 2018 April 5 https://en.wikipedia.org/wiki/T_helper_cell

T-Lymphocytes T Cells: Lymphocytes responsible for cell- mediated immunity. Two types have been identified - cytotoxic (T-LYMPHOCYTES, CYTOTOXIC) and helper T-lymphocytes (T-LYMPHOCYTES, HELPER- INDUCER). They are formed when lymphocytes circulate through the thymus gland and differentiate to thymocytes. When exposed to an antigen, they divide rapidly and produce large numbers of new T cells sensitized to that antigen.  MeSH, 1990 

telomere: A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs. MeSH, 1992    Involved in aging and senescence.

tissue: In biology, tissue is a cellular organizational level between cells and a complete organ. A tissue is an ensemble of similar cells and their extracellular matrix from the same origin that together carry out a specific function. Organs are then formed by the functional grouping together of multiple tissues. The English word is derived from the French tissu, meaning something that is woven, from the verb tisser, "to weave". The study of human and animal tissues is known as histology or, in connection with disease, histopathology. For plants, the discipline is called plant anatomy. The classical tools for studying tissues are the paraffin block in which tissue is embedded and then sectioned, the histological stain, and the optical microscope. In the last couple of decades,[clarification needed] developments in electron microscopy, immunofluorescence, and the use of frozen tissue sections have enhanced the detail that can be observed in tissues.  Wikipedia accessed 2018 Nov 9 https://en.wikipedia.org/wiki/Tissue_(biology)  

An aggregate of cells with different specialized characteristics that are organized anatomically, usually in the fixed framework of an organic matrix. The architectural organization that is maintained contributes to the performance of the specific collective function. Tissues are parts of organs. The term tissue is most often referred to in the context of solid tissue, as originating from a solid organ; however, tissue also can be defined broadly to include collections of cells and the extracellular matrix and/or intercellular substances from bodily fluids such as blood (NCI Best Practices working definition). BioLINC Glossary, NHLBI https://biolincc.nhlbi.nih.go

Toll Like Receptors TLRs: A family of pattern recognition receptors characterized by an extracellular leucine-rich domain and a cytoplasmic domain that share homology with the INTERLEUKIN 1 RECEPTOR and the DROSOPHILA toll protein. Following pathogen recognition, toll-like receptors recruit and activate a variety of SIGNAL TRANSDUCING ADAPTOR PROTEINS. MeSH 2006 (1998)   Wikipedia   http://en.wikipedia.org/wiki/Toll-like_receptor 

Tumor Necrosis Factor TNF: tumor necrosis factor alpha, TNFα, cachexin, or cachectin) is a cell signaling protein (cytokine) involved in systemic inflammation and is one of the cytokines that make up the acute phase reaction. It is produced chiefly by activated macrophages, although it can be produced by many other cell types such asCD4+ lymphocytes, NK cells, neutrophils, mast cells, eosinophils, and neurons.[5]  The primary role of TNF is in the regulation of immune cells. …   Anti-TNF therapy has shown only modest effects in cancer therapy. Wikipedia accessed 2018 Nov 18 https://en.wikipedia.org/wiki/Tumor_necrosis_factor_alpha

A family of proteins that were originally identified by their ability to cause NECROSIS of NEOPLASMS. Their necrotic effect on cells is mediated through TUMOR NECROSIS FACTOR RECEPTORS which induce APOPTOSIS. MeSH 2005

vesicles: In cell biology, a vesicle is a small structure within a cell, or extracellular, consisting of fluid enclosed by a lipid bilayer. Vesicles form naturally during the processes of secretion (exocytosis), uptake (endocytosis) and transport of materials within the cytoplasm. Alternatively, they may be prepared artificially, in which case they are called liposomes (not to be confused with lysosomes). If there is only one phospholipid bilayer, they are called unilamellar liposome vesicles; otherwise they are called multilamellar. … Vesicles perform a variety of functions. Because it is separated from the cytosol, the inside of the vesicle can be made to be different from the cytosolic environment. For this reason, vesicles are a basic tool used by the cell for organizing cellular substances. Vesicles are involved in metabolism, transport, buoyancy control,^[1] and temporary storage of food and enzymes . They can also act as chemical reaction chambers. … Extracellular vesicles (EVs) are produced by all domains of life including complex eukaryotes, both Gram-negative and Gram-positive bacteria, mycobacteria and fungi.

Types  ·  Exosomes: membraneous vesicles of endocytic origin (50-100 nm diameter)^{[6]:Table 1} enriched in CD63 and CD81.^[6] ·         microvesicle (also referred to as shedding microvesicles, SMVs^{[citation needed]}), that are shed directly from the plasma membrane (20–1000 nm ^{[6]:Table 1}). ·  membrane particles (50–80 nm), or large membranous vesicles (~600 nm) CD133⁺, CD63^−[6] ·  Apoptotic blebs or vesicles (1000–5000 nm diameter): released by dying cells.^{[6]:Table 1}  Ectosomes were named in 2008, but in 2012 are not considered a separate type.^[6] In humans, endogenous extracellular vesicles likely play a role in coagulation, intercellular signaling and waste management.^[6] The extracellular vesicles of  (mesenchymal) stem cells, also known as the secretome of stem cells, are being researched and applied for therapeutic purposes, predominantly degenerative, auto-immune  and/or  inflammatory  diseases.^[7]  Wikipedia accessed 2018 Feb 5  https://en.wikipedia.org/wiki/Vesicle_(biology_and_chemistry)   Narrower terms:  exosomes, extracellular vesicles, microvesicles

virtual cell:  The Virtual Cell is a unique computational environment for modeling and simulation of cell biology . It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The creation of biological or mathematical models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. Such models can be based on both experimental data and purely theoretical assumptions. http://www.nrcam.uchc.edu/ 

Cell biology resources
BioLINC Glossary, NHLBI https://biolincc.nhlbi.nih.gov/glossary/ 
Cells Alive!, James. A. Sullivan, 2001 http://www.cellsalive.com/  Video and computer enhanced images of living cells and organisms.
ECACC European Collection of Cell Cultures and Sigma Aldrich, Fundamental Techniques in Cell Culture Laboratory Handbook 2nd ed. http://www.sigmaaldrich.com/life-science/cell-culture/learning-center/ecacc-handbook-2nd-edition.html
International Union of Pure & Applied Chemistry, IUPAC Biotechnology
Lackie JM and JAT Dow, Dictionary of Cell & Molecular Biology, Academic Press, 3^rd ed., 1999. 7,000+ definitions. 
Matveev, Vladimir, History of Cell Biology, http://actomyosin.narod.ru/history/history.htm
NHGRI (National Human Genome Research Institute), Talking Glossary of Genetic Terms, 250+ definitions Includes extended audio definitions.  https://www.genome.gov/genetics-glossary
WWW Virtual Library of Biochemistry and Cell Biology http://biochemweb.net/ 
WWW Virtual Library Developmental Biology, Society for Developmental Biology, 2004 http://www.sdbonline.org/archive/Other/VL_DB.html  

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.