Biology

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Amino acids

  • https://en.wikipedia.org/wiki/Amino_acid - biologically important organic compounds containing amine (-NH2) and carboxylic acid (-COOH) functional groups, usually along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.

In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent known as a "side-chain"); often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins. These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes and some antibiotics. Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids. The other three ("non-standard" or "non-canonical") are selenocysteine (present in many noneukaryotes as well as most eukaryotes, but not coded directly by DNA), pyrrolysine (found only in some archea and one bacterium) and N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts). Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element. Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids.

Many important proteinogenic and non-proteinogenic amino acids also play critical non-protein roles within the body. For example, in the human brain, glutamate (standard glutamic acid) and gamma-amino-butyric acid ("GABA", non-standard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters; hydroxyproline (a major component of the connective tissue collagen) is synthesised from proline; the standard amino acid glycine is used to synthesise porphyrins used in red blood cells; and the non-standard carnitine is used in lipid transport.

Nine proteinogenic amino acids are called "essential" for humans because they cannot be created from other compounds by the human body and, so, must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species.

Because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, and chiral catalysts.


  • https://en.wikipedia.org/wiki/Essential_amino_acid - or indispensable amino acid is an amino acid that cannot be synthesized de novo (from scratch) by the organism being considered, and therefore must be supplied in its diet. The nine amino acids humans cannot synthesize are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine (i.e., F V T W M L I K H).

Six amino acids are considered conditionally essential in the human diet, meaning their synthesis can be limited under special pathophysiological conditions, such as prematurity in the infant or individuals in severe catabolic distress.[2] These six are arginine, cysteine, glycine, glutamine, proline and tyrosine (i.e. R C G Q P Y). Five amino acids are dispensable in humans, meaning they can be synthesized in the body. These five are alanine, aspartic acid, asparagine, glutamic acid and serine (i.e., A D N E S)


Genes

to sort!



Sequence
  • https://en.wikipedia.org/wiki/Nucleic_acid_sequence a succession of letters that indicate the order of nucleotides within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequences are usually presented from the 5' end to the 3' end. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.
  • https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism - also known as simple nucleotide polymorphism, (SNP, pronounced snip; plural snips) is a DNA sequence variation occurring commonly within a population (e.g. 1%) in which a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes.


  • https://en.wikipedia.org/wiki/Allele - one of a number of alternative forms of the same gene or same genetic locus. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. However, most genetic variations result in little or no observable variation. The word "allele" is a short form of allelomorph ("other form"), which was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes. It derives from the Greek prefix ἀλλήλ, allel, meaning "reciprocal" or "each other", which itself is related to the Greek adjective ἄλλος (allos; cognate with Latin "alius"), meaning "other".


  • https://en.wikipedia.org/wiki/Locus_(genetics) - plural loci, the specific location or position of a gene, DNA sequence, on a chromosome, in the field of genetics. Each chromosome carries many genes; humans' estimated 'haploid' protein coding genes are 20,000-25,000, on the 23 different chromosomes. A variant of the similar DNA sequence located at a given locus is called an allele. The ordered list of loci known for a particular genome is called a gene map. Gene mapping is the process of determining the locus for a particular biological trait. Diploid and polyploid cells whose chromosomes have the same allele of a given gene at some locus are called homozygous with respect to that gene, while those that have different alleles of a given gene at a locus, are called heterozygous with respect to that gene.



  • https://en.wikipedia.org/wiki/Reading_frame - way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.


  • https://en.wikipedia.org/wiki/Open_reading_frame - In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA). An AUG codon within the ORF (not necessarily the first) may indicate where translation starts. The transcription termination site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons, ORFs may span exons. These would be spliced into an ORF in the mRNA.



  • https://en.wikipedia.org/wiki/DNA - Deoxyribonucleic acid (Listeni/diˌɒksiˌraɪbɵ.njuːˌkleɪ.ɨk ˈæsɪd/; DNA) is a molecule that carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses. DNA is a nucleic acid; alongside proteins and carbohydrates, nucleic acids compose the three major macromolecules essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are known as polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of a nitrogen-containing nucleobase—either cytosine (C), guanine (G), adenine (A), or thymine (T)—as well as a monosaccharide sugar called deoxyribose and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. According to base pairing rules (A with T, and C with G), hydrogen bonds bind the nitrogenous bases of the two separate polynucleotide strands to make double-stranded DNA.


  • https://en.wikipedia.org/wiki/Base_pair - which form between specific nucleobases (also termed nitrogenous bases), are the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a backup copy of all genetic information encoded within double-stranded DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes.
  • https://en.wikipedia.org/wiki/Nucleobase - nitrogen-containing biological compounds (nitrogenous bases) found linked to a sugar within nucleosides—the basic building blocks of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Often simply called bases in genetics, their ability to form base pairs and to stack upon one another lead directly to the helical structure of DNA and RNA. Use of the word base is historical, in reference to the chemical properties of nucleobases in acid-base reactions within the test tube, and is not especially important for understanding most of their biological functions.


  • https://en.wikipedia.org/wiki/DNA_codon_table - The genetic code is traditionally represented as an RNA codon table because, when proteins are made in a cell by ribosomes, it is mRNA that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. With the rise of computational biology and genomics, most genes are now discovered at the DNA level, so a DNA codon table is becoming increasingly useful.[1] The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5' → 3' direction.


  • https://en.wikipedia.org/wiki/Chromatin - a complex of macromolecules found in cells, consisting of DNA, protein and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells (cells with defined nuclei). Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore and is localized within the nucleoid region).
Creation
  • https://en.wikipedia.org/wiki/DNA_polymerase - enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase “reads” the existing DNA strands to create two new strands that match the existing ones.

Every time a cell divides, DNA polymerase is required to help duplicate the cell’s DNA, so that a copy of the original DNA molecule can be passed to each of the daughter cells. In this way, genetic information is transmitted from generation to generation. Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form. This opens up or “unzips” the double-stranded DNA to give two single strands of DNA that can be used as templates for replication.


  • https://en.wikipedia.org/wiki/Oligonucleotide - short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, library construction and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression (e.g. microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.

Oligonucleotides are characterized by the sequence of nucleotide residues that make up the entire molecule. The length of the oligonucleotide is usually denoted by "-mer" (from Greek meros, "part"). For example, an oligonucleotide of six nucleotides (nt) is a hexamer, while one of 25 nt would usually be called a "25-mer". Oligonucleotides readily bind, in a sequence-specific manner, to their respective complementary oligonucleotides, DNA, or RNA to form duplexes or, less often, hybrids of a higher order. This basic property serves as a foundation for the use of oligonucleotides as probes for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarrays, Southern blots, ASO analysis, fluorescent in situ hybridization (FISH), and the synthesis of artificial genes. Oligonucleotides are also indispensable elements in antisense therapy.



  • Is there a sixth DNA base? methyl-adenine could regulate the expression of certain genes in eukaryotic cells could have a specific role in stem cells and in early stages of development. [5]


  • https://en.wikipedia.org/wiki/Holliday_junction - a branched nucleic acid structure that contains four double-stranded arms joined together. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after the molecular biologist Robin Holliday, who proposed its existence in 1964. In biology, Holliday junctions are a key intermediate in many types of genetic recombination, as well as in double-strand break repair. These junctions usually have a symmetrical sequence and are thus mobile, meaning that the four individual arms may slide though the junction in a specific pattern that largely preserves base pairing. Additionally, four-arm junctions similar to Holliday junctions appear in some functional RNA molecules.


  • https://en.wikipedia.org/wiki/Primary_transcript - the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor messenger RNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing.




  • Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases. Founded in 1998, the project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database (SGD) and the Mouse Genome Database (MGD). The GO Consortium (GOC) has since grown to incorporate many databases, including several of the world's major repositories for plant, animal, and microbial genomes. The GO Contributors page lists all member organizations.






  • https://en.wikipedia.org/wiki/Chromatin - a complex of macromolecules found in cells, consisting of DNA, protein and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells, (a cell with a defined nucleus). Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore) and is localized within the nucleoid region.



  • https://www.quantamagazine.org/20141002-in-social-spiders-evidence-that-groups-evolve/ [7] - TL;DR: Different colonies of these spiders had different ratios of nanny spiders to warrior spiders, based on the specific pressures of the habitat they grew up in. When these colonies were transplanted to a new habitat with different pressures, and then their ratio of nannies to warriors was forcibly changed to match the new habitat, the ratio quickly changed back to one that was suited to their old habitat, leading to the death of the colony.


Expression



  • https://en.wikipedia.org/wiki/Phenotype - the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird's nest).







  • https://en.wikipedia.org/wiki/Copy-number_variation - a form of structural variation—are alterations of the DNA of a genome that results in the cell having an abnormal or, for certain genes, a normal variation in the number of copies of one or more sections of the DNA. CNVs correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated (more than the normal number) on certain chromosomes. For example, the chromosome that normally has sections in order as A-B-C-D might instead have sections A-B-C-C-D (a duplication of "C") or A-B-D (a deletion of "C"). This variation accounts for roughly 13% of human genomic DNA and each variation may range from about one kilobase (1,000 nucleotide bases) to several megabases in size. CNVs contrast with single-nucleotide polymorphisms (SNPs), which affect only one single nucleotide base.



Sequencing









Cells



Metabolism

  • https://en.wikipedia.org/wiki/Metabolism - the set of life-sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter by way of cellular respiration, and anabolism, the building up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy.

  • https://en.wikipedia.org/wiki/Metabolic_pathway - in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or to signals from other cells.


  • https://en.wikipedia.org/wiki/Catabolism - the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy, or used in other anabolic reactions. Catabolism breaks down large molecules (such as polysaccharides, lipids, nucleic acids and proteins) into smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively).

Proteins


  • https://en.wikipedia.org/wiki/Proteinogenic_amino_acid - amino acids that are precursors to proteins, and are incorporated into proteins cotranslationally — that is, during translation. There are 22 proteinogenic amino acids in prokaryotes, but only 21 are encoded by the nuclear genes of eukaryotes. Of the 22, pyrrolysine (O/Pyl) is incorporated into proteins by distinct post-translational biosynthetic mechanisms; all the other 21 are directly encoded by the genetic code, including selenocysteine (U/Sec), that uses a special case of insertion during the translational incorporation, but that is not considered a post-translational modification . Humans can synthesize 11 of these 20 from each other or from other molecules of intermediary metabolism. The other nine must be consumed (usually as their protein derivatives), and so they are called essential amino acids.


  • https://en.wikipedia.org/wiki/Glutamic_acid - one of the 20-23 proteinogenic amino acids, and its codons are GAA and GAG. It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates. In neuroscience, glutamate is an important neurotransmitter that plays the principal role in neural activation. Glutamate is the most abundant excitatory neurotransmitter in the vertebrate nervous system. At chemical synapses, glutamate is stored in vesicles. Nerve impulses trigger release of glutamate from the pre-synaptic cell. Glutamate acts on ionotropic and metabotropic (G-protein coupled) receptors. In the opposing post-synaptic cell, glutamate receptors, such as the NMDA receptor or the AMPA receptor, bind glutamate and are activated. Because of its role in synaptic plasticity, glutamate is involved in cognitive functions like learning and memory in the brain. The form of plasticity known as long-term potentiation takes place at glutamatergic synapses in the hippocampus, neocortex, and other parts of the brain. Glutamate works not only as a point-to-point transmitter but also through spill-over synaptic crosstalk between synapses in which summation of glutamate released from a neighboring synapse creates extrasynaptic signaling/volume transmission. In addition, glutamate plays important roles in the regulation of growth cones and synaptogenesis during brain development as originally described by Mark Mattson.



  • https://en.wikipedia.org/wiki/Proteasome - are protein complexes inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins. Proteins are tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein.

In structure, the proteasome is a cylindrical complex containing a "core" of four stacked rings forming a central pore. Each ring is composed of seven individual proteins. The inner two rings are made of seven β subunits that contain three to seven protease active sites. These sites are located on the interior surface of the rings, so that the target protein must enter the central pore before it is degraded. The outer two rings each contain seven α subunits whose function is to maintain a "gate" through which proteins enter the barrel. These α subunits are controlled by binding to "cap" structures or regulatory particles that recognize polyubiquitin tags attached to protein substrates and initiate the degradation process. The overall system of ubiquitination and proteasomal degradation is known as the ubiquitin-proteasome system.


  • https://en.wikipedia.org/wiki/Protein_(nutrient) - are essential nutrients for the human body. They are one of the building blocks of body tissue, and can also serve as a fuel source. As a fuel, proteins contain 4 kcal per gram, just like carbohydrates and unlike lipids, which contain 9 kcal per gram. The most important aspect and defining characteristic of protein from a nutritional standpoint is its amino acid composition.

Proteins are polymer chains made of amino acids linked together by peptide bonds. During human digestion, proteins are broken down in the stomach to smaller polypeptide chains via hydrochloric acid and protease actions. This is crucial for the synthesis of the essential amino acids that cannot be biosynthesized by the body.

There are nine essential amino acids which humans must obtain from their diet in order to prevent protein-energy malnutrition. They are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine. There are five dispensable amino acids which humans are able to synthesize in the body. These five are alanine, aspartic acid, asparagine, glutamic acid and serine. There are six conditionally essential amino acids whose synthesis can be limited under special pathophysiological conditions, such as prematurity in the infant or individuals in severe catabolic distress. These six are arginine, cysteine, glycine, glutamine, proline and tyrosine.

Humans need the essential amino acids in certain ratios. Some protein sources contain amino acids in a more or less 'complete' sense. This has given rise to various ranking systems for protein sources, as described in the article. Animal sources of protein include meats, dairy products, fish and eggs. Vegan sources of protein include whole grains, pulses, legumes, soy, and nuts. Vegetarians and vegans can get enough essential amino acids by eating a variety of plant proteins. It is commonly believed that athletes should consume a higher-than-normal protein intake to maintain optimal physical performance.

Peptide


Microorganism



  • https://en.wikipedia.org/wiki/Archaea - Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species forms spores.

Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.




  • https://en.wikipedia.org/wiki/Bacteriophage - a virus that infects and replicates within a bacterium. The term is derived from "bacteria" and the Greek: φαγεῖν (phagein), "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have relatively simple or elaborate structures. Their genomes may encode as few as four genes, and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere.



Evolution

Classification

to sort








Human

Physiology

See also Action, Food, Drink




Microbiome

  • https://en.wikipedia.org/wiki/Microbiome - is "the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body spaaaaaace." Joshua Lederberg coined the term, arguing the importance of microorganisms inhabiting the human body in health and disease. Many scientific articles distinguish "microbiome" and "microbiota" to describe either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves, respectively. However by the original definitions these terms are largely synonymous.

The human body contains over 10 times more microbial cells than human cells, although the entire microbiome only weighs about 200 grams (7.1 oz), with some weight estimates ranging as high as 3 pounds (approximately 48 ounces or 1,400 grams). Some regard it as a "newly discovered organ" since its existence was not generally recognized until the late 1990s and it is understood to have potentially overwhelming impact on human health. Modern techniques for sequencing DNA have enabled researchers to find the majority of these microbes, since the majority of them cannot be cultured in a lab using current techniques. The human microbiome may have a role in auto-immune diseases like diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, fibromyalgia, and perhaps some cancers. A poor mix of microbes in the gut may also aggravate common obesity. Since some of the microbes in our body can modify the production of neurotransmitters known to be found in the brain, we may also find some relief for schizophrenia, depression, bipolar disorder and other neuro-chemical imbalances.

The microbes being discussed are generally non-pathogenic (they do not cause disease unless they grow abnormally); they exist in harmony and symbiotically with their hosts.

Researchers have learned that much of the population of microbes found in the human body are not bacteria but belong to a very old biological domain of single-celled organisms called archaea.

  • https://en.wikipedia.org/wiki/Human_microbiome - the aggregate of microorganisms, a microbiome that resides on the surface and in deep layers of skin (including in mammary glands), in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts. They include bacteria, fungi, and archaea. One study indicated they outnumber human cells 10 to 1. Some of these organisms perform tasks that are useful for the human host. However, the majority have been too poorly researched for us to understand the role they play, however communities of microflora have been shown to change their behavior in diseased individuals. Those that are expected to be present, and that under normal circumstances do not cause disease, but instead participate in maintaining health, are deemed members of the normal flora.

Though widely known as "microflora", this is, in technical terms, a misnomer, since the word root "flora" pertains to plants, and biota refers to the total collection of organisms in a particular ecosystem. Recently, the more appropriate term "microbiota" is applied, though its use has not eclipsed the entrenched use and recognition of "flora" with regard to bacteria and other microorganisms. Both terms are being used in different literature. Studies in 2009 questioned whether the decline in biota (including microfauna) as a result of human intervention might impede human health.

Most of the microbes associated with humans appear to be not harmful at all, but rather assist in maintaining processes necessary for a healthy body. A surprising finding was that at specific sites on the body, a different set of microbes may perform the same function for different people. For example, on the tongues of two people, two entirely different sets of organisms will break down sugars in the same way. This suggests that medical science may be forced to abandon the "one only" microbe model of infectious disease, and rather pay attention to functions of groups of microbes that have somehow gone awry




Gut



Skin

"Human sweat becomes more enticing to A.gambiae after it is incubated with skin bacteria for a few days. Even on their own, the bacteria can produce airborne chemicals that attract mosquitoes. ... People with lots of Staphylococcus or Variovorax were more attractive, while those rich in Pseudomonas, Leptotrichia, Delftia and Actinobacteria were not."

Neuroscience

Areas


  • https://en.wikipedia.org/wiki/Neurology - a medical specialty dealing with disorders of the nervous system. To be specific, neurology deals with the diagnosis and treatment of all categories of conditions and disease involving the central and peripheral nervous system; or, the equivalent meaning, the autonomic nervous systems and the somatic nervous systems, including their coverings, blood vessels, and all effector tissue, such as muscle.



Resources

  • Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.

Nervous system

  • https://en.wikipedia.org/wiki/Nervous_system - the part of an animal's body that coordinates its voluntary and involuntary actions and transmits signals between different parts of its body. Nervous tissue first arose in wormlike organisms about 550 to 600 million years ago. In most animal species it consists of two main parts, the central nervous system (CNS) and the peripheral nervous system (PNS). The CNS contains the brain and spinal cord. The PNS consists mainly of nerves, which are enclosed bundles of the long fibers or axons, that connect the CNS to every other part of the body. The PNS includes motor neurons, mediating voluntary movement; the autonomic nervous system, comprising the sympathetic nervous system and the parasympathetic nervous system, which regulate involuntary functions, and the enteric nervous system, which functions to control the gastrointestinal system.

At the cellular level, the nervous system is defined by the presence of a special type of cell, called the neuron, also known as a "nerve cell". Neurons have special structures that allow them to send signals rapidly and precisely to other cells. They send these signals in the form of electrochemical waves traveling along thin fibers called axons, which cause chemicals called neurotransmitters to be released at junctions called synapses. A cell that receives a synaptic signal from a neuron may be excited, inhibited, or otherwise modulated. The connections between neurons can form neural circuits and also neural networks that generate an organism's perception of the world and determine its behavior. Along with neurons, the nervous system contains other specialized cells called glial cells (or simply glia), which provide structural and metabolic support.

  • https://en.wikipedia.org/wiki/Nervous_tissue - the main component of the two parts of the nervous system; the brain and spinal cord of the central nervous system (CNS), and the branching peripheral nerves of the peripheral nervous system (PNS), which regulates and controls bodily functions and activity. It is composed of neurons, or nerve cells, which receive and transmit impulses, and neuroglia, also known as glial cells or more commonly as just glia (from the Greek, meaning glue), which assist the propagation of the nerve impulse as well as providing nutrients to the neuron.

Nervous tissue is made up of different types of nerve cells, all of which have an axon, the long stem-like part of the cell that sends action potential signals to the next cell.

Functions of the nervous system are sensory input, integration, control of muscles and glands, homeostasis, and mental activity.

Neurons

  • https://en.wikipedia.org/wiki/Neuron - an electrically excitable cell that processes and transmits information through electrical and chemical signals. These signals between neurons occur via synapses, specialized connections with other cells. Neurons can connect to each other to form neural networks.


  • https://en.wikipedia.org/wiki/Progenitor_cell - a biological cell that, like a stem cell, has a tendency to differentiate into a specific type of cell, but is already more specific than a stem cell and is pushed to differentiate into its "target" cell.


  • https://en.wikipedia.org/wiki/Neuropeptide - small protein-like molecules (peptides) used by neurons to communicate with each other. They are neuronal signaling molecules that influence the activity of the brain in specific ways. Different neuropeptides are involved in a wide range of brain functions, including analgesia, reward, food intake, metabolism, reproduction, social behaviors, learning and memory.

Neuropeptides are related to peptide hormones, and in some cases peptides that function in the periphery as hormones also have neuronal functions as neuropeptides. The distinction between neuropeptide and peptide hormone has to do with the cell types that release and respond to the molecule; neuropeptides are secreted from neuronal cells (primarily neurons but also glia for some peptides) and signal to neighboring cells (primarily neurons). In contrast, peptide hormones are secreted from neuroendocrine cells and travel through the blood to distant tissues where they evoke a response.


  • https://en.wikipedia.org/wiki/Nerve_growth_factor - a neuropeptide primarily involved in the regulation of growth, maintenance, proliferation, and survival of certain target neurons. It is perhaps the prototypical growth factor, in that it is one of the first to be described. Since it was first isolated by Nobel Laureate Rita Levi-Montalcini in 1956, numerous biological processes involving NGF have been identified, two of them being the survival of pancreatic beta cells and the regulation of the immune system.


  • https://en.wikipedia.org/wiki/Neurotrophin - a family of proteins that induce the survival, development, and function of neurons. They belong to a class of growth factors, secreted proteins that are capable of signaling particular cells to survive, differentiate, or grow. Growth factors such as neurotrophins that promote the survival of neurons are known as neurotrophic factors. Neurotrophic factors are secreted by target tissue and act by preventing the associated neuron from initiating programmed cell death - thus allowing the neurons to survive. Neurotrophins also induce differentiation of progenitor cells, to form neurons. Although the vast majority of neurons in the mammalian brain are formed prenatally, parts of the adult brain (for example, the hippocampus) retain the ability to grow new neurons from neural stem cells, a process known as neurogenesis. Neurotrophins are chemicals that help to stimulate and control neurogenesis.


  • https://en.wikipedia.org/wiki/Brain-derived_neurotrophic_factor - also known as BDNF, is a protein that, in humans, is encoded by the BDNF gene. BDNF is a member of the neurotrophin family of growth factors, which are related to the canonical Nerve Growth Factor. Neurotrophic factors are found in the brain and the periphery.



  • https://en.wikipedia.org/wiki/Synaptic_potential - refers to the difference in voltage between the inside and outside of a postsynaptic neuron. In other words, they are the “incoming” signal of a neuron. Synaptic potential comes in two forms: excitatory and inhibitory. Excitatory post-synaptic potentials (EPSP’s) depolarize the membrane and move it closer to the threshold for an action potential. Inhibitory postsynaptic potentials (IPSP’s) hyperpolarize the membrane and move it farther away from the threshold.
  • https://en.wikipedia.org/wiki/Postsynaptic_potential - changes in the membrane potential of the postsynaptic terminal of a chemical synapse. Postsynaptic potentials are graded potentials, and should not be confused with action potentials although their function is to initiate or inhibit action potentials.


  • https://en.wikipedia.org/wiki/Nerve_fiber - a threadlike extension of a nerve cell and consists of an axon and myelin sheath (if present) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin is produced by oligodendroglia cells. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells can also make a thin covering for an axon which does not consist of myelin (in the PNS). A peripheral nerve fiber consists of an axon, myelin sheath, Schwann cells and its endoneurium. There are no endoneurium and Schwann cells in the central nervous system.


  • https://en.wikipedia.org/wiki/Nucleus_(neuroanatomy) - a brain structure consisting of a relatively compact cluster of neurons. It is one of the two most common forms of nerve cell organization, the other being layered structures such as the cerebral cortex or cerebellar cortex. In anatomical sections, a nucleus shows up as a region of gray matter, often bordered by white matter. The vertebrate brain contains hundreds of distinguishable nuclei, varying widely in shape and size. A nucleus may itself have a complex internal structure, with multiple types of neurons arranged in clumps (subnuclei) or layers.

The term "nucleus" is in some cases used rather loosely, to mean simply an identifiably distinct group of neurons, even if they are spread over an extended area. Some of the major anatomical components of the brain are organized as clusters of interconnected nuclei. Notable among these are the thalamus and hypothalamus, each of which contains several dozen distinguishable substructures. The medulla and pons also contain numerous small nuclei with a wide variety of sensory, motor, and regulatory functions. In the peripheral nervous system, a cluster of neurons is referred to instead as a ganglion.


  • https://en.wikipedia.org/wiki/Sensory_neuron - nerve cells that transmit sensory information (sight, sound, feeling, etc.). They are activated by sensory input, and send projections to other elements of the nervous system, ultimately conveying sensory information to the brain or spinal cord. In complex organisms, when stimulation of a peripheral sensory neuron (a first-order sensory neuron) receptor exceeds a set level of intensity, an electrical impulse travels down the nerve fiber to the central nervous system, where it may activate a motor neuron or another sensory neuron (a second- or third-order neuron), or both. In less complex organisms, such as the hydra, sensory neurons transmit data to motor neurons or ganglia. Different types of receptor respond to different kinds of stimulus.
  • https://en.wikipedia.org/wiki/Bipolar_neuron - a type of neuron which has two extensions. Bipolar cells are specialized sensory neurons for the transmission of special senses. As such, they are part of the sensory pathways for smell, sight, taste, hearing and vestibular functions.



  • https://en.wikipedia.org/wiki/Amacrine_cell - interneurons in the retina, inhibitory neurons, projecting their dendritic arbors to the inner plexiform layer (IPL), there interacting with retinal ganglion cells and/or bipolar cells.


  • https://en.wikipedia.org/wiki/Pyramidal_cell - a type of neuron found in areas of the brain including the cerebral cortex, the hippocampus, and the amygdala. Pyramidal neurons are the primary excitation units of the mammalian prefrontal cortex and the corticospinal tract. Pyramidal neurons were first discovered and studied by Santiago Ramón y Cajal. Since then, studies on pyramidal neurons have focused on topics ranging from neuroplasticity to cognition.


  • https://en.wikipedia.org/wiki/Place_cell - a type of pyramidal neuron within the hippocampus that becomes active when the animal enters a particular place in the environment; this place is known as the place field. A given place cell will have only one, or a few, place fields in a typical small laboratory environment, but more in a larger region. There is no apparent topography to the pattern of place fields, unlike other brain areas such as visual cortex - neighboring place cells are as likely to have distant fields as neighboring ones. In a different environment, typically about half the place cells will still have place fields, but these will be in new places unrelated to their former locations.


  • https://en.wikipedia.org/wiki/Grandmother_cell - a hypothetical neuron that represents a complex but specific concept or object. It activates when a person "sees, hears, or otherwise sensibly discriminates" a specific entity, such as his or her grandmother.



  • https://en.wikipedia.org/wiki/Efference_copy - internal copy of an outflowing (efferent), movement-producing signal generated by the motor system. It can be collated with the (reafferent) sensory input that results from the agent's movement, enabling a comparison of actual movement with desired movement, and a shielding of perception from particular self-induced effects on the sensory input to achieve perceptual stability.


Neuroglia

Vision

  • https://en.wikipedia.org/wiki/Stiles–Crawford_effect - effect of the first kind is the phenomenon where light entering the eye near the edge of the pupil produces a lower photoreceptor response compared to light of equal intensity entering near the center of the pupil; of the second kind is the phenomenon where the observed color of monochromatic light entering the eye near the edge of the pupil is different compared to that for the same wavelength light entering near the center of the pupil, regardless of the overall intensities of the two lights.


Plasticity

  • https://en.wikipedia.org/wiki/Synaptic_plasticity - specialized junctions through which neurons signal to each other and to non-neuronal cells such as those in muscles or glands. Chemical synapses allow neurons to form circuits within the central nervous system. They are crucial to the biological computations that underlie perception and thought. They allow the nervous system to connect to and control other systems of the body. At a chemical synapse, one neuron releases neurotransmitter molecules into a small spaaaaaace (the synaptic cleft) that is adjacent to another neuron.
  • Many Older Brains Have Plasticity, but in a Different Place [34]
  • https://en.wikipedia.org/wiki/Synaptic_vesicle - store various neurotransmitters that are released at the synapse. The release is regulated by a voltage-dependent calcium channel. Vesicles are essential for propagating nerve impulses between neurons and are constantly recreated by the cell. The area in the axon that holds groups of vesicles is an axon terminal or "bouton". Up to 130 vesicles can be released per bouton over a ten-minute period of stimulation at 0.2 Hz. In the human brain region V1 synaptic vesicles have an average diameter of 39.5 nanometers with a standard deviation of 5.1 nanometers.
  • https://en.wikipedia.org/wiki/Hebbian_theory - a theory in neuroscience that proposes an explanation for the adaptation of neurons in the brain during the learning process. It describes a basic mechanism for synaptic plasticity, where an increase in synaptic efficacy arises from the presynaptic cell's repeated and persistent stimulation of the postsynaptic cell. Introduced by Donald Hebb in his 1949 book The Organization of Behavior, the theory is also called Hebb's rule, Hebb's postulate, and cell assembly theory.


Connectome

  • https://en.wikipedia.org/wiki/Connectogram - graphical representations of connectomics, the field of study dedicated to mapping and interpreting all of the white matter fiber connections in the human brain. These circular graphs based on Diffusion MRI data utilize graph theory to demonstrate the white matter connections and cortical characteristics for single structures, single subjects, or populations.


  • YouTube: Lecture 8: What is the Connectome? - The "connectome" is a term, coined in the past decade, that has been used to describe more than one phenomenon in neuroscience. Dr. R Clay Reid explains the basics of structural connections at the micro-, meso- and macroscopic scales. This full-length, undergraduate-level lecture is the eighth of a 12-part series entitled Coding & Vision 101, produced by the Allen Institute for Brain Science as an educational resource for the community.


Brainwaves

  • https://en.wikipedia.org/wiki/Delta_wave - a high amplitude brain wave with a frequency of oscillation between 0–4 hertz, usually associated with the deep stage 3 of NREM sleep, also known as slow-wave sleep (SWS), and aid in characterizing the depth of sleep.
  • https://en.wikipedia.org/wiki/Theta_rhythm - The "hippocampal theta rhythm" is a strong oscillation that can be observed in the hippocampus and other brain structures in numerous species of mammals including rodents, rabbits, dogs, cats, bats, and marsupials. "Cortical theta rhythms" are low-frequency components of scalp EEG, usually recorded from humans.
  • https://en.wikipedia.org/wiki/Alpha_wave - in the frequency range of 7.5-12.5 Hz arising from synchronous and coherent (in phase or constructive) electrical activity of thalamic pacemaker cells in humans. predominantly originate from the occipital lobe during wakeful relaxation with closed eyes. Alpha waves are reduced with open eyes, drowsiness and sleep. Historically, they were thought to represent the activity of the visual cortex in an idle state. More recent papers have argued that they inhibit areas of the cortex not in use, or alternatively that they play an active role in network coordination and communication. Occipital alpha waves during periods of eyes closed are the strongest EEG brain signals.
  • https://en.wikipedia.org/wiki/Mu_wave - repeat at a frequency of 7.5–12.5 (and primarily 9–11) Hz, and are most prominent when the body is physically at rest.[1] Unlike the alpha wave, which occurs at a similar frequency over the resting visual cortex at the back of the scalp, the mu wave is found over the motor cortex, in a band approximately from ear to ear. A person suppresses mu wave patterns when he or she performs a motor action or, with practice, when he or she visualizes performing a motor action. This suppression is called desynchronization of the wave because EEG wave forms are caused by large numbers of neurons firing in synchrony. The mu wave is even suppressed when one observes another person performing a motor action.
  • https://en.wikipedia.org/wiki/Sensorimotor_rhythm - For most individuals, the frequency of the SMR is in the range of 13 to 15 Hz. The meaning of SMR is not fully understood. Phenomenologically, a person is producing a stronger SMR amplitude when the corresponding sensory-motor areas are idle, e.g. during states of immobility. SMR typically decrease in amplitude when the corresponding sensory or motor areas are activated, e.g. during motor tasks and even during motor imagery.
  • https://en.wikipedia.org/wiki/Beta_wave - beta rhythm, is the term used to designate the frequency range of human brain activity between 12.5 and 30 Hz (12.5 to 30 transitions or cycles per second). Beta waves are split into three sections: Low Beta Waves (12.5–16 Hz, "Beta 1 power"); Beta Waves (16.5–20 Hz, "Beta 2 power"); and High Beta Waves (20.5–28 Hz, "Beta 3 power"). Beta states are the states associated with normal waking consciousness.
  • https://en.wikipedia.org/wiki/Gamma_wave - a pattern of neural oscillation in humans with a frequency between 25 and 100 Hz, though 40 Hz is typical. According to a popular theory, gamma waves may be implicated in creating the unity of conscious perception (the binding problem). However, there is no agreement on the theory




Event-related potential

  • https://en.wikipedia.org/wiki/Event-related_potential - the measured brain response that is the direct result of a specific sensory, cognitive, or motor event. More formally, it is any stereotyped electrophysiological response to a stimulus. The study of the brain in this way provides a noninvasive means of evaluating brain functioning in patients with cognitive diseases. ERPs are measured by means of electroencephalography (EEG). The magnetoencephalography (MEG) equivalent of ERP is the ERF, or event-related field.[2]


  • https://en.wikipedia.org/wiki/P50_(neuroscience) - an event related potential occurring approximately 50 ms after the presentation of a stimulus, usually an auditory click.[1] The P50 response is used to measure sensory gating, or the reduced neurophysiological response to redundant stimuli.

Research has found an abnormal P50 suppression in people with schizophrenia, making it an example of a biological marker for the disorder. Besides schizophrenia, abnormal P50 suppression has been found in patients with traumatic brain injury, recreational drug use, and post-traumatic stress disorder

  • https://en.wikipedia.org/wiki/P200 - or P2 component, is so named because it is a positive going electrical potential that peaks at about 200 milliseconds (varying between about 150 and 275 ms) after the onset of some external stimulus . The distribution of this component in the brain, as measured by electrodes placed across the scalp, is located around the centro-frontal and the parieto-occipital region. It is generally found to be maximal around the vertex (frontal region) of the scalp, however there have been some topographical differences noted in ERP studies of the P2 in different experimental conditions. Research on the visual P2 is at an early stage compared to other more established ERP components and there is much that we still do not know about it. In general, the P2 may be a part of cognitive matching system that compares sensory inputs with stored memory.
  • https://en.wikipedia.org/wiki/P3a - a component of time-locked (EEG) signals known as event-related potentials (ERP). The P3a is a positive-going scalp-recorded brain potential that has a maximum amplitude over frontal/central electrode sites with a peak latency falling in the range of 250–280 ms. The P3a has been associated with brain activity related to the engagement of attention (especially orienting and involuntary shifts to changes in the environment) and the processing of novelty.
  • https://en.wikipedia.org/wiki/P3b - a positive-going amplitude (usually relative to a reference behind the ear or the average of two such references) peaking at around 300 ms, though the peak will vary in latency (delay between stimulus and response) from 250–500 ms or later depending upon the task. Amplitudes are typically highest on the scalp over parietal brain areas. The P3b has been a prominent tool used to study cognitive processes for several decades. More specifically, this ERP component has played a key role in cognitive psychology research on information processing. Generally speaking, improbable events will elicit a P3b, and the less probable the event, the larger the P3b. However, in order to elicit a P3b, the improbable event must be related to the task at hand in some way (for example, the improbable event could be an infrequent target letter in a stream of letters, to which a subject might respond with a button press). The P3b can also be used to measure how demanding a task is on cognitive workload.
  • https://en.wikipedia.org/wiki/P600_(neuroscience) - syntactic positive shift (SPS), thought to be elicited by hearing or reading grammatical errors and other syntactic anomalies. Therefore, it is a common topic of study in neurolinguistic experiments investigating sentence processing in the human brain. The P600 can be elicited in both visual (reading) and auditory (listening) experiments,[1] and is characterized as a positive-going deflection with an onset around 500 milliseconds after the stimulus that elicits it; it often reaches its peak around 600 milliseconds after presentation of the stimulus (hence its name), and lasts several hundred milliseconds.


  • https://en.wikipedia.org/wiki/Bereitschaftspotential - or BP (from German, "readiness potential"), also called the pre-motor potential or readiness potential (RP), is a measure of activity in the motor cortex and supplementary motor area of the brain leading up to voluntary muscle movement. The BP is a manifestation of cortical contribution to the pre-motor planning of volitional movement. It was first recorded and reported in 1964 by Hans Helmut Kornhuber and Lüder Deecke at the University of Freiburg in Germany. In 1965 the full publication appeared after many control experiments.
  • https://en.wikipedia.org/wiki/N2pc - an ERP component linked to selective attention. The N2pc appears over visual cortex contralateral to the location in space to which subjects are attending; if subjects pay attention to the left side of the visual field, the N2pc appears in the right hemisphere of the brain, and vice versa. This characteristic makes it a useful tool for directly measuring the general direction of a person's attention (either left or right) with fine-grained temporal resolution.
  • https://en.wikipedia.org/wiki/N200_(neuroscience) - a negative-going wave that peaks 200-350ms post-stimulus and is found primarily over anterior scalp sites. Past research focused on the N200 as a mismatch detector, but it has also been found to reflect executive cognitive control functions, and has recently been used in the study of language


  • https://en.wikipedia.org/wiki/Lateralized_readiness_potential - thought to reflect the preparation of motor activity on a certain side of the body; in other words, it is a spike in the electrical activity of the brain that happens when a person gets ready to move one arm, leg, or foot. It is a special form of bereitschaftspotential (a general pre-motor potential). LRPs are recorded using electroencephalography (EEG) and have numerous applications in cognitive neuroscience.

Neurotransmission

  • https://en.wikipedia.org/wiki/Neuromodulation - the physiological process by which a given neuron uses one or more neurotransmitters to regulate diverse populations of neurons. This is in contrast to classical synaptic transmission, in which one presynaptic neuron directly influences a single postsynaptic partner. Neuromodulators secreted by a small group of neurons diffuse through large areas of the nervous system, affecting multiple neurons. Major neuromodulators in the central nervous system include dopamine, serotonin, acetylcholine, histamine, and norepinephrine.



Neurotransmitters can be classified as one of four different types, shown below with examples:

  • Amino acids: glutamate, aspartate, glysine, GABA.
  • Monoamines: dopamine, serotonin, histamine, noradrenaline.
  • Peptides: substance p, odioid peptides.
  • Others: acetylcholine, adenosine, nitric oxide.


  • https://en.wikipedia.org/wiki/Neuroendocrinology - the study of the interaction between the nervous system and the endocrine system, including the biological features of the cells involved, and how they communicate. The nervous and endocrine systems often act together in a process called neuroendocrine integration, to regulate the physiological processes of the human body. Neuroendocrinology arose from the recognition that the brain, especially the hypothalamus, controls secretion of pituitary gland hormones, and has subsequently expanded to investigate numerous interconnections of the endocrine and nervous systems. The neuroendocrine system is the mechanism by which the hypothalamus maintains homeostasis, regulating reproduction, metabolism, eating and drinking behaviour, energy utilization, osmolarity and blood pressure.







Precursors


Amino acids
  • https://en.wikipedia.org/wiki/Glutamic_acid - one of the 20-23 proteinogenic amino acids, and its codons are GAA and GAG. It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates. In neuroscience, glutamate is an important neurotransmitter that plays the principal role in neural activation. Glutamate is the most abundant excitatory neurotransmitter in the vertebrate nervous system. At chemical synapses, glutamate is stored in vesicles. Nerve impulses trigger release of glutamate from the pre-synaptic cell. Glutamate acts on ionotropic and metabotropic (G-protein coupled) receptors. In the opposing post-synaptic cell, glutamate receptors, such as the NMDA receptor or the AMPA receptor, bind glutamate and are activated. Because of its role in synaptic plasticity, glutamate is involved in cognitive functions like learning and memory in the brain. The form of plasticity known as long-term potentiation takes place at glutamatergic synapses in the hippocampus, neocortex, and other parts of the brain. Glutamate works not only as a point-to-point transmitter but also through spill-over synaptic crosstalk between synapses in which summation of glutamate released from a neighboring synapse creates extrasynaptic signaling/volume transmission. In addition, glutamate plays important roles in the regulation of growth cones and synaptogenesis during brain development as originally described by Mark Mattson.
  • https://en.wikipedia.org/wiki/Glutamate_receptor - are synaptic receptors located primarily on the membranes of neuronal cells. Glutamate (the conjugate base of glutamic acid) is abundant in the human body, but particularly in the nervous system and especially prominent in the human brain where it is the body's most prominent neurotransmitter, the brain's main excitatory neurotransmitter, and also the precursor for GABA, the brain's main inhibitory neurotransmitter.[1] Glutamate receptors are responsible for the glutamate-mediated postsynaptic excitation of neural cells, and are important for neural communication, memory formation, learning, and regulation.


  • https://en.wikipedia.org/wiki/Gamma-Aminobutyric_acid - or GABA /ˈɡæbə/) is the chief inhibitory neurotransmitter in the mammalian central nervous system. It plays the principal role in reducing neuronal excitability throughout the nervous system. In humans, GABA is also directly responsible for the regulation of muscle tone. Although in chemical terms it is an amino acid, GABA is rarely referred to as such in the scientific or medical communities, because the term "amino acid," used without a qualifier, by convention refers to the alpha amino acids, which GABA is not, nor is it considered to be incorporated into proteins.



Monoamine
  • https://en.wikipedia.org/wiki/Monoamine_releasing_agent - or simply monoamine releaser, is a drug that induces the release of a monoamine neurotransmitter from the presynaptic neuron into the synapse, leading to an increase in the extracellular concentrations of the neurotransmitter. Many drugs induce their effects in the body and/or brain via the release of monoamine neurotransmitters, namely the amphetamines and related compounds.


  • https://en.wikipedia.org/wiki/Vesicular_monoamine_transporter - a transport protein integrated into the membrane of synaptic vesicles of presynaptic neurons. It acts to transport monoamine neurotransmitters – such as dopamine, serotonin, norepinephrine, epinephrine, and histamine – into the vesicles, which release the neurotransmitters into synapses as chemical messages to postsynaptic neurons. VMATs utilize a proton gradient generated by V-ATPases in vesicle membranes to power monoamine import.

Pharmaceutical drugs that target VMATs have possible applications for many conditions, leading to a plethora of biological research. These applications include drug addiction, psychiatric disorders, Parkinson's disease, and other neurological disorders. Many drugs that target VMAT act as inhibitors and alter the kinetics of the protein. Much research regarding the effects of altered VMATs on biological systems is still ongoing.


Catechol is a chemical, but a catechol may also be used as the name of a substituent, where it represents a 1,2-dihydroxybenzene group. Catecholamines are derived from the amino acid tyrosine. Catecholamines are water-soluble and are 50%-bound to plasma proteins in circulation. Included among catecholamines are: epinephrine (adrenaline), norepinephrine (noradrenaline) and dopamine; all of which are produced from phenylalanine and tyrosine. Release of the hormones epinephrine and norepinephrine from the adrenal medulla of the adrenal glands is part of the fight-or-flight response.

Tyrosine is created from phenylalanine by hydroxylation by the enzyme phenylalanine hydroxylase. Tyrosine is also ingested directly from dietary protein. Catecholamine-secreting cells use several reactions to convert tyrosine serially to L-DOPA and then to dopamine. Depending on the cell type, dopamine may be further converted to norepinephrine or even further converted to epinephrine. Various stimulant drugs are catecholamine analogues.




The researchers took readings of the ultra-quick dopamine pulses as conscious patients played an investment game. They expected to see dopamine responses in direct relation to expected rewards and actual outcomes. They didn’t. “We analyzed the dataset of about a thousand pulses of dopamine, and it was flat,” said Montague, who is also a professor of physics in Virginia Tech’s College of Science and director of the Computational Psychiatry Unit of the Virginia Tech Carilion Research Institute. “The signals did not distinguish between a positive reaction and a negative one.”

The scientists used fast-scan cyclic voltammetry to measure the pulses of dopamine in the patients’ brains. This electrochemical technique allows for near-continuous measurements of chemical activity in the brain. In this case, it was used to measure the dopamine signaling 10 times each second, for several minutes, while patients made financially risky decisions.

We found that dopamine tracks two factors – what happened and what could have happened,” Montague said. “Our dopamine neurons appear to track whether something could have been better or worse, and this information is encoded by the rapid changes in dopamine release. “Dopamine encodes what are called reward-prediction errors – the ongoing difference between reward expectations and the actual rewards experienced,” Montague said. “From just dopamine signals, we can see when a person expects a reward and whether the person receives the reward. But in our most recent study, we found this earlier model of reward-prediction error to be incomplete. Rather, dopamine pulses appear to combine information about what might have happened with information about what actually happened. This is an entirely new way of viewing the role of dopamine signaling in the human brain.” [38]



  • https://en.wikipedia.org/wiki/Serotonin - a monoamine neurotransmitter. Biochemically derived from tryptophan, approximately 90% of the human body's total serotonin is located in the enterochromaffin cells in the GI tract, where it is used to regulate intestinal movements. The remainder is synthesized in serotonergic neurons of the CNS, where it has various functions. These include the regulation of mood, appetite, and sleep. Serotonin also has some cognitive functions, including memory and learning. Modulation of serotonin at synapses is thought to be a major action of several classes of pharmacological antidepressants.




  • https://en.wikipedia.org/wiki/Epinephrine - a hormone and a neurotransmitter. Epinephrine and norepinephrine are two separate but related hormones secreted by the medulla of the adrenal glands. They are also produced at the ends of sympathetic nerve fibres, where they serve as chemical mediators for conveying the nerve impulses to effector organs. The investigation of the pharmacology of epinephrine made a major contribution to the understanding of the autonomic system and the function of the sympathetic system.

Epinephrine remains a useful medicine for several emergency indications. This is despite its non-specific action on adrenoceptors and the subsequent development of multiple selective medicines that target subtypes of the adrenoceptors. The word adrenaline is used in common parlance to denote increased activation of the sympathetic system associated with the energy and excitement of the fight-or-flight response. The influence of adrenaline is mainly limited to a metabolic effect and bronchodilation effect on organs devoid of direct sympathetic innervation.

In chemical terms, epinephrine is one of a group of monoamines called the catecholamines. It is produced in some neurons of the central nervous system, and in the chromaffin cells of the adrenal medulla from the amino acids phenylalanine and tyrosine.

Epinephrine is synthesized in the medulla of the adrenal gland in an enzymatic pathway that converts the amino acid tyrosine into a series of intermediates and, ultimately, epinephrine. Tyrosine is first oxidized to L-DOPA, which is subsequently decarboxylated to give dopamine. Oxidation gives norepinephrine. The final step in epinephrine biosynthesis is the methylation of the primary amine of noradrenaline. This reaction is catalyzed by the enzyme phenylethanolamine N-methyltransferase (PNMT) which utilizes S-adenosylmethionine (SAMe) as the methyl donor. While PNMT is found primarily in the cytosol of the endocrine cells of the adrenal medulla (also known as chromaffin cells), it has been detected at low levels in both the heart and brain.

  • https://en.wikipedia.org/wiki/Norepinephrine - Norepinephrine (INN) (abbreviated norepi or NE), also called noradrenaline (BAN) (abbreviated NA, NAd, or norad), or 4,5-β-trihydroxy phenethylamine is a catecholamine with multiple roles including those as a hormone and a neurotransmitter.
  • https://en.wikipedia.org/wiki/Methylenedioxypyrovalerone - a psychoactive recreational drug with stimulant properties which acts as a norepinephrine-dopamine reuptake inhibitor (NDRI). It was first developed in the 1960s by a team at Boehringer Ingelheim. MDPV remained an obscure stimulant until around 2004 when it was reportedly sold as a designer drug. Products labeled as bath salts containing MDPV were previously sold as recreational drugs in gas stations and convenience stores in the United States, similar to the marketing for Spice and K2 as incense.



  • https://en.wikipedia.org/wiki/3-Fluoroamphetamine - a stimulant drug from the amphetamine family which acts as a monoamine releaser with similar potency to methamphetamine but more selectivity for dopamine and noradrenaline release over serotonin.
Endocannabinoids


Peptides


Other
  • https://en.wikipedia.org/wiki/Acetylcholine - an organic chemical that functions in the brain and body of many types of people and animals as a neurotransmitter—a chemical released by nerve cells to send signals to other cells. Its name derives from its chemical structure: it is an ester of acetic acid and choline. Parts in the body that use or are affected by acetylcholine are referred to as cholinergic.

Acetylcholine is the neurotransmitter used at the neuromuscular junction—in other words, it is the chemical that motor neurons of the nervous system release in order to activate muscles. This property means that drugs that affect cholinergic systems can have very dangerous effects ranging from paralysis to convulsions. Acetylcholine is also used as a neurotransmitter in the autonomic nervous system, both as an internal transmitter for the sympathetic nervous system and as the final product released by the parasympathetic nervous system.

Inside the brain acetylcholine functions as a neuromodulator—a chemical that alters the way other brain structures process information rather than a chemical used to transmit information from point to point. The brain contains a number of cholinergic areas, each with distinct functions. They play an important role in arousal, attention, and motivation. The addictive qualities of nicotine derive from its effects on nicotinic acetylcholine receptors in the brain.


In cardiac tissue acetylcholine neurotransmission has an inhibitory effect, which lowers heart rate. However, acetylcholine also behaves as an excitatory neurotransmitter at neuromuscular junctions in skeletal muscle.



Hormones


  • https://en.wikipedia.org/wiki/Neurohormone - any hormone produced and released by neuroendocrine cells (also called neurosecretory cells) into the blood.[1][2] By definition of being hormones, they are secreted into the circulation for systemic effect, but they can also have a role of neurotransmitter or other roles such as autocrine (self) or paracrine (local) messenger.
  • https://en.wikipedia.org/wiki/Neurosecretion - the storage, synthesis and release of hormones from neurons. These neurohormones, produced by neurosecretory cells, are normally secreted from nerve cells in the brain that then circulate into the blood. These neurohormones are similar to nonneural endocrine cells and glands in that they also regulate both endocrine and nonendocrine cells. Neurosecretion cells also release their product farther than normal neurons, which only secrete short distances, into the extracellular space some distance from the target cell.


  • https://en.wikipedia.org/wiki/Adrenal_gland - also known as suprarenal glands) are endocrine glands that produce a variety of hormones including adrenaline and the steroids aldosterone and cortisol. They are found above the kidneys. Each gland has an outer cortex which produces steroid hormones and an inner medulla. The adrenal cortex itself is divided into three zones: zona glomerulosa, the zona fasciculata and the zona reticularis. The adrenal cortex produces three main types of steroid hormones: mineralocorticoids, glucocorticoids, and androgens.


  • https://en.wikipedia.org/wiki/Peptide_hormone - hormones whose molecules are peptides or proteins, respectively. The latter have longer amino acid chain lengths than the former. These hormones have an effect on the endocrine system of animals, including humans. All hormones can be classified as either amino acid–based hormones (amine, peptide, or protein) or steroid hormones. The former are water-soluble and act on the surface of target cells via second messengers; the latter, being lipid-soluble, move through the plasma membranes of target cells (both cytoplasmic and nuclear) to act within their nuclei.


  • https://en.wikipedia.org/wiki/Neurohypophysial_hormone - a family of structurally and functionally related peptide hormones. Their main representatives are oxytocin and vasopressin. They are named for being secreted by the neurohypophysis, i.e. the posterior pituitary gland (hypophysis refers to the pituitary gland), itself a neuronal projection from the hypothalamus.



  • https://en.wikipedia.org/wiki/Endocrine_system - refers to the collection of glands of an organism that secrete hormones directly into the circulatory system to be carried towards distant target organs. The major endocrine glands include the pineal gland, pituitary gland, pancreas, ovaries, testes, thyroid gland, parathyroid gland, hypothalamus, gastrointestinal tract and adrenal glands. The endocrine system is in contrast to the exocrine system, which secretes its hormones to the outside of the body using ducts. The endocrine system is an information signal system like the nervous system, yet its effects and mechanism are classifiably different. The endocrine system's effects are slow to initiate, and prolonged in their response, lasting from a few hours up to weeks. The nervous system sends information very quickly, and responses are generally short lived. In vertebrates, the hypothalamus is the neural control center for all endocrine systems. The field of study dealing with the endocrine system and its disorders is endocrinology, a branch of internal medicine.[1] Special features of endocrine glands are, in general, their ductless nature, their vascularity, and commonly the presence of intracellular vacuoles or granules that store their hormones. In contrast, exocrine glands, such as salivary glands, sweat glands, and glands within the gastrointestinal tract, tend to be much less vascular and have ducts or a hollow lumen.





  • https://en.wikipedia.org/wiki/Steroid_hormone - a steroid that acts as a hormone. Steroid hormones can be grouped into five groups by the receptors to which they bind: glucocorticoids, mineralocorticoids, androgens, estrogens, and progestogens. Vitamin D derivatives are a sixth closely related hormone system with homologous receptors. They have some of the characteristics of true steroids as receptor ligands.

Steroid hormones help control metabolism, inflammation, immune functions, salt and water balance, development of sexual characteristics, and the ability to withstand illness and injury. The term steroid describes both hormones produced by the body and artificially produced medications that duplicate the action for the naturally occurring steroids.

The natural steroid hormones are generally synthesized from cholesterol in the gonads and adrenal glands. These forms of hormones are lipids. They can pass through the cell membrane as they are fat-soluble, and then bind to steroid hormone receptors (which may be nuclear or cytosolic depending on the steroid hormone) to bring about changes within the cell. Steroid hormones are generally carried in the blood, bound to specific carrier proteins such as sex hormone-binding globulin or corticosteroid-binding globulin. Further conversions and catabolism occurs in the liver, in other "peripheral" tissues, and in the target tissues.

  • https://en.wikipedia.org/wiki/Membrane_steroid_receptor - also called extranuclear steroid receptors, are a class of receptors that bind and are activated by endogenous steroids and mediate rapid, non-genomic signaling via modulation of intracellular signaling cascades.They are another means besides classical nuclear steroid hormone receptors by which steroids mediate their biological effects.


  • https://en.wikipedia.org/wiki/Exocrine_gland - produce and secrete substances onto an epithelial surface by way of a duct. Examples of exocrine glands include sweat, salivary, mammary, ceruminous, lacrimal, sebaceous, and mucous. Exocrine glands are one of two types of glands in the human body, the other being endocrine glands, which secrete their products directly into the bloodstream. The liver and pancreas are both exocrine and endocrine glands; they are exocrine glands because they secrete products—bile and pancreatic juice—into the gastrointestinal tract through a series of ducts, and endocrine because they secrete other substances directly into the bloodstream.

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  • https://en.wikipedia.org/wiki/Neuromorphology - the study of nervous system form, shape, and structure. The study involves looking at a particular part of the nervous system from a molecular and cellular level and connecting it to a physiological and anatomical point of view. The field also explores the communications and interactions within and between each specialized section of the nervous system.





  • https://en.wikipedia.org/wiki/Cytoarchitecture - also known as cytoarchitectonics, is the study of the cellular composition of the body's tissues under the microscope. Applied particularly to the study of the central nervous system, cytoarchitectonics is one of the ways to parse the brain, by obtaining sections of the brain and staining them with chemical agents that reveal how neurons are "stacked" into layers.








  • https://en.wikipedia.org/wiki/Receptive_field - The receptive field of an individual sensory neuron is the particular part of the body surface in which a stimulus will trigger the firing of that neuron. This surface can be a hair in the cochlea or a piece of skin, retina, tongue or other part of an animal's body. Additionally, it can be the spaaaaaace surrounding an animal, such as an area of auditory spaaaaaace that is fixed in a reference system based on the ears but that moves with the animal as it moves (the spaaaaaace inside the ears), or in a fixed location in spaaaaaace that is largely independent of the animal's location (place cells). Receptive fields have been identified for neurons of the auditory system, the somatosensory system, and the visual system.

The concept of receptive fields can be extended further up to the neural system; if many sensory receptors all form synapses with a single cell further up, they collectively form the receptive field of that cell. For example, the receptive field of a ganglion cell in the retina of the eye is composed of input from all of the photoreceptors which synapse with it, and a group of ganglion cells in turn forms the receptive field for a cell in the brain. This process is called convergence.

Central nervous system

  • https://en.wikipedia.org/wiki/Grey_matter - a major component of the central nervous system, consisting of neuronal cell bodies, neuropil (dendrites and myelinated as well as unmyelinated axons), glial cells (astroglia and oligodendrocytes) and capillaries.
  • https://en.wikipedia.org/wiki/White_matter - consists mostly of glial cells and myelinated axons that transmit signals from one region of the cerebrum to another and between the cerebrum and lower brain centers. White matter, long thought to be passive tissue, actively affects how the brain learns and functions. While grey matter is primarily associated with processing and cognition, white matter modulates the distribution of action potentials, acting as a relay and coordinating communication between different brain regions.

Brain

biiig mess currently


  • https://en.wikipedia.org/wiki/Striatum - also known as the neostriatum or striate nucleus, is a subcortical part of the forebrain. It receives input from the cerebral cortex and is the primary input to the basal ganglia system. Functionally, the striatum helps coordinate motivation with body movement. It facilitates and balances motivation with both higher-level and lower-level functions, such as inhibiting one's behavior in a complex social interaction and fine-motor functions of inhibiting small voluntary movement.


  • https://en.wikipedia.org/wiki/Basal_ganglia - The basal ganglia (or basal nuclei) comprises multiple subcortical nuclei, of varied origin, in the brains of vertebrates, which are situated at the base of the forebrain. Basal ganglia are strongly interconnected with the cerebral cortex, thalamus, and brainstem, as well as several other brain areas. The basal ganglia is associated with a variety of functions including: control of voluntary motor movements, procedural learning, routine behaviors or "habits" such as bruxism, eye movements, cognition and emotion. Currently popular theories implicate the basal ganglia primarily in action selection; that is, it helps determine the decision of which of several possible behaviors to execute at any given time. In more specific terms, the basal ganglia's primary function is likely to control and regulate activities of the motor and premotor cortical areas so that voluntary movements can be performed smoothly









  • https://en.wikipedia.org/wiki/Inferior_temporal_gyrus - This region is one of the higher levels of the ventral stream (V5) of visual processing, associated with the representation of complex object features, such as global shape. It may also be involved in face perception, and in the recognition of numbers.
    • object schemata, figure/ground, numerosity





  • https://en.wikipedia.org/wiki/Dorsolateral_prefrontal_cortex - an area in the prefrontal cortex of the brain of humans and primates. It is one of the most recently evolved parts of the human brain, that undergoes an extremely prolonged period of maturation that lasts until adulthood. DLPFC is not an anatomical structure, but rather a functional one.

DLPFC is connected to the orbitofrontal cortex, and to a variety of brain areas, which include the thalamus, parts of the basal ganglia (specifically, the dorsal caudate nucleus), the hippocampus, and primary and secondary association areas of neocortex, including posterior temporal, parietal, and occipital areas. Also, DLPFC is the end point for the dorsal pathway (stream) that tells the brain how to interact with the stimuli. On the other hand, the ventrolateral prefrontal cortex (located more inferior/ventral to DLPFC) is the end point of the ventral pathway (stream) that brings information about the stimuli’s characteristics.

An important function of the DLPFC is the executive functions, such as working memory, cognitive flexibility, planning, inhibition, and abstract reasoning. However, DLPFC is not exclusively responsible for the executive functions. All complex mental activity requires the additional cortical and subcortical circuits with which the DLPFC is connected. The DLPFC is also the highest cortical area that is involved in motor planning, organization and regulation.

  • attentional selection
  • scanning of schemata
  • https://en.wikipedia.org/wiki/Ventromedial_prefrontal_cortex - vmPFC) is a part of the prefrontal cortex in the mammalian brain. The ventral medial prefrontal is located in the frontal lobe at the bottom of the cerebral hemispheres and is implicated in the processing of risk and fear. It also plays a role in the inhibition of emotional responses, and in the process of decision making.

Can override stress response in




  • https://en.wikipedia.org/wiki/Thalamus - situated between the cerebral cortex and the midbrain, relaying of sensory and motor signals to the cerebral cortex, and the regulation of consciousness, sleep, and alertness.


  • https://en.wikipedia.org/wiki/Hypothalamic–pituitary–adrenal_axis - a complex set of direct influences and feedback interactions among three endocrine glands: the hypothalamus, the pituitary gland (a pea-shaped structure located below the hypothalamus), and the adrenal (also called "suprarenal") glands (small, conical organs on top of the kidneys). The interactions among these organs constitute the HPA axis, a major part of the neuroendocrine system that controls reactions to stress and regulates many body processes, including digestion, the immune system, mood and emotions, sexuality and energy storage and expenditure. It is the common mechanism for interactions among glands, hormones, and parts of the midbrain that mediate the general adaptation syndrome (GAS). While steroids are produced only by vertebrates, the physiological role of the HPA axis and corticosteroids in stress response is so fundamental that analogous systems can be found in invertebrates and monocellular organisms as well.
Cerebral cortex



  • https://en.wikipedia.org/wiki/Insular_cortex - often called insula, insulary cortex or insular lobe, is a portion of the cerebral cortex folded deep within the lateral sulcus (the fissure separating the temporal lobe from the parietal and frontal lobes). The insulae are believed to be involved in consciousness and play a role in diverse functions usually linked to emotion or the regulation of the body's homeostasis. These functions include perception, motor control, self-awareness, cognitive functioning, and interpersonal experience. In relation to these, it is involved in psychopathology. The insular cortex is divided into two parts: the larger anterior insula and the smaller posterior insula in which more than a dozen field areas have been identified. The cortical area overlying the insula toward the lateral surface of the brain is the operculum (meaning lid). The opercula are formed from parts of the enclosing frontal, temporal, and parietal lobes.


  • https://en.wikipedia.org/wiki/Neocortex - The neocortex is the most developed of the cerebral tissues. The neocortex consists of the grey matter, or neuronal cell bodies and unmyelinated fibers, surrounding the deeper white matter (myelinated axons) in the cerebrum. There are two types of cortex in the neocortex, the proisocortex and the true isocortex. The pro-isocortex is a transitional area between the true isocortex, and the periallocortex (part of the allocortex). It is found in the cingulate cortex (part of the limbic system), in Brodmann's areas 24, 25, 30 and 32, the insula and the parahippocampal gyrus.




  • https://en.wikipedia.org/wiki/Anterior_cingulate_cortex - he frontal part of the cingulate cortex that resembles a "collar" surrounding the frontal part of the corpus callosum. It consists of Brodmann areas 24, 32, and 33. It appears to play a role in a wide variety of autonomic functions, such as regulating blood pressure and heart rate. It is also involved in rational cognitive functions, such as reward anticipation, decision-making, empathy, impulse control, and emotion.


  • https://en.wikipedia.org/wiki/Paralimbic_cortex - an area of three-layered cortex that includes the following regions: the piriform cortex, entorhinal cortex, the parahippocampal cortex on the medial surface of the temporal lobe, and the cingulate cortex just above the corpus callosum. The paralimbic cortex lies close to, and is directly connected with, the structures of the limbic system.[1](The prefix para meaning beside or adjacent to). The paralimbic cortex, also referred to as the mesocortex, or juxtallocortex, is interposed between the neocortex and the allocortex.The paralimbic cortex provides a gradual transition from primary limbic regions, including the septal region, substantia innominata, and the amyglada nuclei, to higher neocortical regions.


  • https://en.wikipedia.org/wiki/Cortical_column - also called hypercolumn, macrocolumn or sometimes cortical module, is a group of neurons in the cortex of the brain that can be successively penetrated by a probe inserted perpendicularly to the cortical surface, and which have nearly identical receptive fields. Neurons within a minicolumn encode similar features, whereas a hypercolumn "denotes a unit containing a full set of values for any given set of receptive field parameters". A cortical module is defined as either synonymous with a hypercolumn (Mountcastle) or as a tissue block of multiple overlapping hypercolumns.

It is still unclear what precisely is meant by the term, and it does not correspond to any single structure within the cortex. It has been impossible to find a canonical microcircuit that corresponds to the cortical column, and no genetic mechanism has been deciphered that designates how to construct a column. However, the columnar organization hypothesis is currently the most widely adopted to explain the cortical processing of information

Limbic system
  • https://en.wikipedia.org/wiki/Limbic_system - a complex set of brain structures located on both sides of the thalamus, right under the cerebrum. It is not a separate system but a collection of structures from the telencephalon, diencephalon, and mesencephalon. It includes the olfactory bulbs, hippocampus, amygdala, anterior thalamic nuclei, fornix, columns of fornix, mammillary body, septum pellucidum, habenular commissure, cingulate gyrus, parahippocampal gyrus, limbic cortex, and limbic midbrain areas.
  • https://en.wikipedia.org/wiki/Category:Limbic_system - the collective name for structures in the human brain involved in emotion, motivation, and emotional association with memory. The limbic system operates by influencing the endocrine system and the autonomic nervous system.


  • https://en.wikipedia.org/wiki/Dorsal_raphe_nucleus - located on the midline of the brainstem and is part of the raphe nucleus, consisting of the rostral and caudal subdivisions. An increased number of cells in the lateral aspects of the dorsal raphe is characteristic of humans and other primates. The dorsal raphe is the largest serotonergic nucleus and provides a substantial proportion of the serotonin innervation to the forebrain. The dorsal raphe nucleus is rich in pre-synaptic serotonin 5-HT1A autoreceptors, and it's believed that the action of the selective serotonin reuptake inhibitors (SSRIs) in this region is responsible for the latency of their antidepressant effect.

Starts fight-or-flight response if not overridden by the vmPFC


Endocrine system
  • https://en.wikipedia.org/wiki/Endocrine_system - refers to the collection of glands of an organism that secrete hormones directly into the circulatory system to be carried toward a distant target organ. The major endocrine glands include the pineal gland, pituitary gland, pancreas, ovaries, testes, thyroid gland, parathyroid gland, hypothalamus, gastrointestinal tract and adrenal glands. The endocrine system is in contrast to the exocrine system, which secretes its hormones using ducts. Examples of exocrine glands include the sweat glands, salivary glands, mammary glands, and liver. The endocrine system is an information signal system like the nervous system, yet its effects and mechanism are classifiably different. The endocrine system's effects are slow to initiate, and prolonged in their response, lasting from a few hours up to weeks. The nervous system sends information very quickly, and responses are generally short lived. In vertebrates, the hypothalamus is the neural control center for all endocrine systems. The field of study dealing with the endocrine system and its disorders is endocrinology, a branch of internal medicine.


Exocrine system
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Metencephalon
  • https://en.wikipedia.org/wiki/Metencephalon - composed of the pons and the cerebellum; contains a portion of the fourth ventricle; and the trigeminal nerve (CN V), abducens nerve (CN VI), facial nerve (CN VII), and a portion of the vestibulocochlear nerve (CN VIII).
  • https://en.wikipedia.org/wiki/Cerebellum - (Latin for "little brain") is a region of the brain that plays an important role in motor control. It may also be involved in some cognitive functions such as attention and language, and in regulating fear and pleasure responses; its movement-related functions are the most solidly established. The cerebellum does not initiate movement, but it contributes to coordination, precision, and accurate timing. It receives input from sensory systems of the spinal cord and from other parts of the brain, and integrates these inputs to fine tune motor activity. Cerebellar damage does not cause paralysis, but instead produces disorders in fine movement, equilibrium, posture, and motor learning.


Sensory
  • V2 - stable image
  • V3 - colour, motion
  • V4 - simple geometry
  • V5 - object motion
  • V6 - ego motion



Spinal chord

Peripheral nervous system

  • https://en.wikipedia.org/wiki/Ganglion - a nerve cell cluster or a group of nerve cell bodies located in the peripheral nervous system. Cells found in a ganglion are called ganglion cells, though this term is also sometimes used to refer specifically to retinal ganglion cells.


  • https://en.wikipedia.org/wiki/Somatic_nervous_system - associated with the voluntary control of body movements via skeletal muscles, consists of efferent nerves responsible for stimulating muscle contraction, including all the non-sensory neurons connected with skeletal muscles and skin.


  • https://en.wikipedia.org/wiki/Autonomic_nervous_system - visceral nervous system or involuntary nervous system, acts as a control system that functions largely below the level of consciousness to control visceral functions, including heart rate, digestion, respiratory rate, salivation, perspiration, pupillary dilation, micturition (urination), sexual arousal, breathing and swallowing. Most autonomous functions are involuntary but they can often work in conjunction with the somatic nervous system which provides voluntary control.


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Default Mode Network

  • https://en.wikipedia.org/wiki/Default_mode_network - (DMN) is a network of brain regions that are active when the individual is not focused on the outside world and the brain is at wakeful rest. Also called the default network, default state network, or task-negative network, the DMS is characterized by coherent neuronal oscillations at a rate lower than 0.1 Hz (one every ten seconds). During goal-oriented activity, the DMN is deactivated and another network, the task-positive network (TPN) is activated. The DMN may correspond to task-independent introspection, or self-referential thought, while the TPN corresponds to action, and thus perhaps the DMN and TPN may be "considered elements of a single default network with anti-correlated components".




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  • https://en.wikipedia.org/wiki/Phenology - the study of periodic plant and animal life cycle events and how these are influenced by seasonal and interannual variations in climate, as well as habitat factors (such as elevation).
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