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153-478: Computational neuroscience employs computational simulations to validate and solve mathematical models, and so can be seen as a sub-field of theoretical neuroscience; however, the two fields are often synonymous. The term mathematical neuroscience is also used sometimes, to stress the quantitative nature of the field. Computational neuroscience focuses on the description of biologically plausible neurons (and neural systems ) and their physiology and dynamics, and it

306-485: A k ) {\displaystyle I_{l}=g_{leak}(V-V_{leak})} . The membrane potential depends upon the maintenance of ionic concentration gradients across it. The maintenance of these concentration gradients requires active transport of ionic species. The sodium-potassium and sodium-calcium exchangers are the best known of these. Some of the basic properties of the Na/Ca exchanger have already been well-established:

459-501: A Hopf bifurcation . As with most neuronal models, increasing the injected current will increase the firing rate of the neuron. One consequence of the Hopf bifurcation is that there is a minimum firing rate. This means that either the neuron is not firing at all (corresponding to zero frequency), or firing at the minimum firing rate. Because of the all-or-none principle , there is no smooth increase in action potential amplitude, but rather there

612-456: A cortical column on the Blue Gene supercomputer . Modeling the richness of biophysical properties on the single-neuron scale can supply mechanisms that serve as the building blocks for network dynamics. However, detailed neuron descriptions are computationally expensive and this computing cost can limit the pursuit of realistic network investigations, where many neurons need to be simulated. As

765-525: A last universal common ancestor that lived about 3.5 billion years ago . Geologists have developed a geologic time scale that divides the history of the Earth into major divisions, starting with four eons ( Hadean , Archean , Proterozoic , and Phanerozoic ), the first three of which are collectively known as the Precambrian , which lasted approximately 4 billion years. Each eon can be divided into eras, with

918-440: A lipid bilayer , including cholesterols that sit between phospholipids to maintain their fluidity at various temperatures. Cell membranes are semipermeable , allowing small molecules such as oxygen, carbon dioxide, and water to pass through while restricting the movement of larger molecules and charged particles such as ions . Cell membranes also contain membrane proteins , including integral membrane proteins that go across

1071-443: A nucleus , and prokaryotic cells, which do not. Prokaryotes are single-celled organisms such as bacteria , whereas eukaryotes can be single-celled or multicellular. In multicellular organisms , every cell in the organism's body is derived ultimately from a single cell in a fertilized egg . Every cell is enclosed within a cell membrane that separates its cytoplasm from the extracellular space . A cell membrane consists of

1224-504: A number of shapes , ranging from spheres to rods and spirals . Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats . Bacteria inhabit soil, water, acidic hot springs , radioactive waste , and the deep biosphere of the Earth's crust . Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of

1377-471: A cell's size, shape, membrane potential , metabolic activity , and responsiveness to signals, which are largely due to highly controlled modifications in gene expression and epigenetics . With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself. Thus, different cells can have very different physical characteristics despite having the same genome . Morphogenesis, or

1530-408: A chemical (e.g., nitrous acid , benzopyrene ) or radiation (e.g., x-ray , gamma ray , ultraviolet radiation , particles emitted by unstable isotopes). Mutations can lead to phenotypic effects such as loss-of-function, gain-of-function , and conditional mutations. Some mutations are beneficial, as they are a source of genetic variation for evolution. Others are harmful if they were to result in

1683-1227: A few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi . Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for 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 , including archaeols . 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 , but unlike plants and cyanobacteria , no known species of archaea does both. Archaea reproduce asexually by binary fission , fragmentation , or budding ; unlike bacteria, no known species of Archaea form endospores . The first observed archaea were extremophiles , living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to

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1836-403: A final electron acceptor, which is usually the oxidized form of NADP , which is reduced to NADPH, a process that takes place in a protein complex called photosystem I (PSI). The transport of electrons is coupled to the movement of protons (or hydrogen) from the stroma to the thylakoid membrane, which forms a pH gradient across the membrane as hydrogen becomes more concentrated in the lumen than in

1989-450: A fraction of visual input for further processing, guided by a bottom-up saliency map in the primary visual cortex. Current research in sensory processing is divided among a biophysical modeling of different subsystems and a more theoretical modeling of perception. Current models of perception have suggested that the brain performs some form of Bayesian inference and integration of different sensory information in generating our perception of

2142-459: A hollow sphere of cells , the blastula , during embryonic development . Over 1.5 million living animal species have been described —of which around 1 million are insects —but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs . Hodgkin%E2%80%93Huxley model The Hodgkin–Huxley model , or conductance-based model ,

2295-759: A loss of function of genes needed for survival. Gene expression is the molecular process by which a genotype encoded in DNA gives rise to an observable phenotype in the proteins of an organism's body. This process is summarized by the central dogma of molecular biology , which was formulated by Francis Crick in 1958. According to the Central Dogma, genetic information flows from DNA to RNA to protein. There are two gene expression processes: transcription (DNA to RNA) and translation (RNA to protein). The regulation of gene expression by environmental factors and during different stages of development can occur at each step of

2448-417: A more successful evolutionary theory based on natural selection ; similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions. The basis for modern genetics began with the work of Gregor Mendel in 1865. This outlined the principles of biological inheritance. However, the significance of his work was not realized until the early 20th century when evolution became

2601-457: A new cycle. In contrast to mitosis, meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions. Homologous chromosomes are separated in the first division ( meiosis I ), and sister chromatids are separated in the second division ( meiosis II ). Both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in

2754-409: A process known as allopatric speciation . A phylogeny is an evolutionary history of a specific group of organisms or their genes. It can be represented using a phylogenetic tree , a diagram showing lines of descent among organisms or their genes. Each line drawn on the time axis of a tree represents a lineage of descendants of a particular species or population. When a lineage divides into two, it

2907-408: A region of deoxyribonucleic acid (DNA) that carries genetic information that controls form or function of an organism. DNA is composed of two polynucleotide chains that coil around each other to form a double helix . It is found as linear chromosomes in eukaryotes , and circular chromosomes in prokaryotes . The set of chromosomes in a cell is collectively known as its genome . In eukaryotes, DNA

3060-515: A result, researchers that study large neural circuits typically represent each neuron and synapse with an artificially simple model, ignoring much of the biological detail. Hence there is a drive to produce simplified neuron models that can retain significant biological fidelity at a low computational overhead. Algorithms have been developed to produce faithful, faster running, simplified surrogate neuron models from computationally expensive, detailed neuron models. Glial cells participate significantly in

3213-541: A role in the synthesis and packaging of proteins, respectively. Biomolecules such as proteins can be engulfed by lysosomes , another specialized organelle. Plant cells have additional organelles that distinguish them from animal cells such as a cell wall that provides support for the plant cell, chloroplasts that harvest sunlight energy to produce sugar, and vacuoles that provide storage and structural support as well as being involved in reproduction and breakdown of plant seeds. Eukaryotic cells also have cytoskeleton that

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3366-436: A separate clade as some protists may be more closely related to plants, fungi, or animals than they are to other protists. Like groupings such as algae , invertebrates , or protozoans , the protist grouping is not a formal taxonomic group but is used for convenience. Most protists are unicellular; these are called microbial eukaryotes. Plants are mainly multicellular organisms , predominantly photosynthetic eukaryotes of

3519-511: A set of mechanisms that limit some processing to a subset of incoming stimuli. Attentional mechanisms shape what we see and what we can act upon. They allow for concurrent selection of some (preferably, relevant) information and inhibition of other information. In order to have a more concrete specification of the mechanism underlying visual attention and the binding of features, a number of computational models have been proposed aiming to explain psychophysical findings. In general, all models postulate

3672-423: A single carbon atom can form four single covalent bonds such as in methane , two double covalent bonds such as in carbon dioxide (CO 2 ), or a triple covalent bond such as in carbon monoxide (CO). Moreover, carbon can form very long chains of interconnecting carbon–carbon bonds such as octane or ring-like structures such as glucose . The simplest form of an organic molecule is the hydrocarbon , which

3825-440: A single neuron has complex biophysical characteristics and can perform computations (e.g.). Hodgkin and Huxley's original model only employed two voltage-sensitive currents (Voltage sensitive ion channels are glycoprotein molecules which extend through the lipid bilayer, allowing ions to traverse under certain conditions through the axolemma), the fast-acting sodium and the inward-rectifying potassium. Though successful in predicting

3978-446: A specific enzyme. 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 —they allow a reaction to proceed more rapidly without being consumed by it—by reducing the amount of activation energy needed to convert reactants into products . Enzymes also allow

4131-419: A theoretical framework are credited to Horace Barlow . Somewhat similar to the minimal wiring hypothesis described in the preceding section, Barlow understood the processing of the early sensory systems to be a form of efficient coding , where the neurons encoded information which minimized the number of spikes. Experimental and computational work have since supported this hypothesis in one form or another. For

4284-399: A unified theory as the modern synthesis reconciled Darwinian evolution with classical genetics . In the 1940s and early 1950s, a series of experiments by Alfred Hershey and Martha Chase pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes . A focus on new kinds of model organisms such as viruses and bacteria, along with

4437-421: A varied mix of traits, and reproduction is able to increase any population, Darwin argued that in the natural world, it was nature that played the role of humans in selecting for specific traits. Darwin inferred that individuals who possessed heritable traits better adapted to their environments are more likely to survive and produce more offspring than other individuals. He further inferred that this would lead to

4590-492: A water molecule again. In pure water , the number of hydrogen ions balances (or equals) the number of hydroxyl ions, resulting in a pH that is neutral. Organic compounds are molecules that contain carbon bonded to another element such as hydrogen. With the exception of water, nearly all the molecules that make up each organism contain carbon. Carbon can form covalent bonds with up to four other atoms, enabling it to form diverse, large, and complex molecules. For example,

4743-437: A wide array of questions, including: How do axons and dendrites form during development? How do axons know where to target and how to reach these targets? How do neurons migrate to the proper position in the central and peripheral systems? How do synapses form? We know from molecular biology that distinct parts of the nervous system release distinct chemical cues, from growth factors to hormones that modulate and influence

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4896-536: Is evolution , which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move , grow, and reproduce . Finally, all organisms are able to regulate their own internal environments . Biologists are able to study life at multiple levels of organization , from the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations. Hence, there are multiple subdisciplines within biology , each defined by

5049-429: Is a mathematical model that describes how action potentials in neurons are initiated and propagated. It is a set of nonlinear differential equations that approximates the electrical engineering characteristics of excitable cells such as neurons and muscle cells . It is a continuous-time dynamical system . Alan Hodgkin and Andrew Huxley described the model in 1952 to explain the ionic mechanisms underlying

5202-444: Is a central feature of sexual reproduction in eukaryotes, and the most fundamental function of meiosis appears to be conservation of the integrity of the genome that is passed on to progeny by parents. Two aspects of sexual reproduction , meiotic recombination and outcrossing , are likely maintained respectively by the adaptive advantages of recombinational repair of genomic DNA damage and genetic complementation which masks

5355-414: Is a large body of literature regarding how different currents interact with geometric properties of neurons. There are many software packages, such as GENESIS and NEURON , that allow rapid and systematic in silico modeling of realistic neurons. Blue Brain , a project founded by Henry Markram from the École Polytechnique Fédérale de Lausanne , aims to construct a biophysically detailed simulation of

5508-641: Is a large family of organic compounds that are composed of hydrogen atoms bonded to a chain of carbon atoms. A hydrocarbon backbone can be substituted by other elements such as oxygen (O), hydrogen (H), phosphorus (P), and sulfur (S), which can change the chemical behavior of that compound. Groups of atoms that contain these elements (O-, H-, P-, and S-) and are bonded to a central carbon atom or skeleton are called functional groups . There are six prominent functional groups that can be found in organisms: amino group , carboxyl group , carbonyl group , hydroxyl group , phosphate group , and sulfhydryl group . In 1953,

5661-616: Is a recent field that combines signal processing, neuroscience, clinical data and machine learning to predict the brain during coma or anesthesia. For example, it is possible to anticipate deep brain states using the EEG signal. These states can be used to anticipate hypnotic concentration to administrate to the patient. Computational psychiatry is a new emerging field that brings together experts in machine learning , neuroscience , neurology , psychiatry , psychology to provide an understanding of psychiatric disorders. A neuromorphic computer/chip

5814-480: Is a small polar molecule with a bent shape formed by the polar covalent bonds of two hydrogen (H) atoms to one oxygen (O) atom (H 2 O). Because the O–H bonds are polar, the oxygen atom has a slight negative charge and the two hydrogen atoms have a slight positive charge. This polar property of water allows it to attract other water molecules via hydrogen bonds, which makes water cohesive . Surface tension results from

5967-918: Is a term of convenience as not all algae are closely related. Algae comprise several distinct clades such as glaucophytes , which are microscopic freshwater algae that may have resembled in form to the early unicellular ancestor of Plantae. Unlike glaucophytes, the other algal clades such as red and green algae are multicellular. Green algae comprise three major clades: chlorophytes , coleochaetophytes , and stoneworts . Fungi are eukaryotes that digest foods outside their bodies, secreting digestive enzymes that break down large food molecules before absorbing them through their cell membranes. Many fungi are also saprobes , feeding on dead organic matter, making them important decomposers in ecological systems. Animals are multicellular eukaryotes. With few exceptions, animals consume organic material , breathe oxygen , are able to move , can reproduce sexually , and grow from

6120-563: Is any device that uses physical artificial neurons (made from silicon) to do computations (See: neuromorphic computing , physical neural network ). One of the advantages of using a physical model computer such as this is that it takes the computational load of the processor (in the sense that the structural and some of the functional elements don't have to be programmed since they are in hardware). In recent times, neuromorphic technology has been used to build supercomputers which are used in international neuroscience collaborations. Examples include

6273-403: Is catalyzed by lactate dehydrogenase in a reversible reaction. Lactate can also be used as an indirect precursor for liver glycogen. During recovery, when oxygen becomes available, NAD attaches to hydrogen from lactate to form ATP. In yeast, the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation . The ATP generated in this process

Computational neuroscience - Misplaced Pages Continue

6426-897: Is created in the primary visual cortex to guide attention exogenously. Computational neuroscience provides a mathematical framework for studying the mechanisms involved in brain function and allows complete simulation and prediction of neuropsychological syndromes. Computational modeling of higher cognitive functions has only recently begun. Experimental data comes primarily from single-unit recording in primates . The frontal lobe and parietal lobe function as integrators of information from multiple sensory modalities. There are some tentative ideas regarding how simple mutually inhibitory functional circuits in these areas may carry out biologically relevant computation. The brain seems to be able to discriminate and adapt particularly well in certain contexts. For instance, human beings seem to have an enormous capacity for memorizing and recognizing faces . One of

6579-420: Is denoted by V m . Mathematically, the current flowing through the lipid bilayer is written as and the current through a given ion channel is the product of that channel's conductance and the driving potential for the specific ion where V i {\displaystyle V_{i}} is the reversal potential of the specific ion channel. Thus, for a cell with sodium and potassium channels,

6732-523: Is difficult to study because it is a nonlinear system , cannot be solved analytically, and therefore has no closed-form solution. However, there are many numerical methods available to analyze the system. Certain properties and general behaviors, such as limit cycles , can be proven to exist. Because there are four state variables, visualizing the path in phase space can be difficult. Usually two variables are chosen, voltage V m ( t ) {\displaystyle V_{m}(t)} and

6885-441: Is made by substrate-level phosphorylation , which does not require oxygen. Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organism's metabolic activities via cellular respiration. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water. In most cases, oxygen

7038-535: Is made up of microtubules , intermediate filaments , and microfilaments , all of which provide support for the cell and are involved in the movement of the cell and its organelles. In terms of their structural composition, the microtubules are made up of tubulin (e.g., α-tubulin and β-tubulin ) whereas intermediate filaments are made up of fibrous proteins. Microfilaments are made up of actin molecules that interact with other strands of proteins. All cells require energy to sustain cellular processes. Metabolism

7191-526: Is mainly in the cell nucleus . In prokaryotes, the DNA is held within the nucleoid . The genetic information is held within genes, and the complete assemblage in an organism is called its genotype . DNA replication is a semiconservative process whereby each strand serves as a template for a new strand of DNA. Mutations are heritable changes in DNA. They can arise spontaneously as a result of replication errors that were not corrected by proofreading or can be induced by an environmental mutagen such as

7344-429: Is not known, however, whether such descriptive dynamics impart any important computational function. With the emergence of two-photon microscopy and calcium imaging , we now have powerful experimental methods with which to test the new theories regarding neuronal networks. In some cases the complex interactions between inhibitory and excitatory neurons can be simplified using mean-field theory , which gives rise to

7497-399: Is one of the key ways a cell releases chemical energy to fuel cellular activity. The overall reaction occurs in a series of biochemical steps, some of which are redox reactions. Although cellular respiration is technically a combustion reaction , it clearly does not resemble one when it occurs in a cell because of the slow, controlled release of energy from the series of reactions. Sugar in

7650-407: Is pulled to the separate poles of the bacterium as it increases the size to prepare for splitting. Growth of a new cell wall begins to separate the bacterium (triggered by FtsZ polymerization and "Z-ring" formation). The new cell wall ( septum ) fully develops, resulting in the complete split of the bacterium. The new daughter cells have tightly coiled DNA rods, ribosomes , and plasmids . Meiosis

7803-399: Is released as a waste product. Most plants, algae , and cyanobacteria perform photosynthesis, which is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. Photosynthesis has four stages: Light absorption , electron transport, ATP synthesis, and carbon fixation . Light absorption is

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7956-412: Is represented as a fork or split on the phylogenetic tree. Phylogenetic trees are the basis for comparing and grouping different species. Different species that share a feature inherited from a common ancestor are described as having homologous features (or synapomorphy ). Phylogeny provides the basis of biological classification. This classification system is rank-based, with the highest rank being

8109-418: Is the maximal value of the conductance. n , m , and h are dimensionless probabilities between 0 and 1 that are associated with potassium channel subunit activation, sodium channel subunit activation, and sodium channel subunit inactivation, respectively. For instance, given that potassium channels in squid giant axon are made up of four subunits which all need to be in the open state for the channel to allow

8262-468: Is the process by which genes and traits are passed on from parents to offspring. It has several principles. The first is that genetic characteristics, alleles , are discrete and have alternate forms (e.g., purple vs. white or tall vs. dwarf), each inherited from one of two parents. Based on the law of dominance and uniformity , which states that some alleles are dominant while others are recessive ; an organism with at least one dominant allele will display

8415-485: Is the set of chemical reactions in an organism. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to monomer building blocks; and the elimination of metabolic wastes . These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolic reactions may be categorized as catabolic —the breaking down of compounds (for example,

8568-466: Is the specific ion channel) that depend on both voltage and time. Leak channels are represented by linear conductances ( g L ). The electrochemical gradients driving the flow of ions are represented by voltage sources ( E n ) whose voltages are determined by the ratio of the intra- and extracellular concentrations of the ionic species of interest. Finally, ion pumps are represented by current sources ( I p ). The membrane potential

8721-410: Is the study of chemical processes within and relating to living organisms . Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including molecular synthesis, modification, mechanisms, and interactions. Life arose from the Earth's first ocean, which formed some 3.8 billion years ago. Since then, water continues to be

8874-445: Is therefore not directly concerned with biologically unrealistic models used in connectionism , control theory , cybernetics , quantitative psychology , machine learning , artificial neural networks , artificial intelligence and computational learning theory ; although mutual inspiration exists and sometimes there is no strict limit between fields, with model abstraction in computational neuroscience depending on research scope and

9027-493: Is to store, transmit, and express hereditary information. Cell theory states that cells are the fundamental units of life, that all living things are composed of one or more cells, and that all cells arise from preexisting cells through cell division . Most cells are very small, with diameters ranging from 1 to 100  micrometers and are therefore only visible under a light or electron microscope . There are generally two types of cells: eukaryotic cells, which contain

9180-629: The Cambrian explosion . During the Permian period, synapsids , including the ancestors of mammals , dominated the land, but most of this group became extinct in the Permian–Triassic extinction event 252 million years ago. During the recovery from this catastrophe, archosaurs became the most abundant land vertebrates; one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods. After

9333-495: The Cretaceous–Paleogene extinction event 66 million years ago killed off the non-avian dinosaurs, mammals increased rapidly in size and diversity . Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify. Bacteria are a type of cell that constitute a large domain of prokaryotic microorganisms . Typically a few micrometers in length, bacteria have

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9486-598: The Human Brain Project SpiNNaker supercomputer and the BrainScaleS computer. Biology Biology is the scientific study of life . It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of at least one cell that processes hereditary information encoded in genes , which can be transmitted to future generations. Another major theme

9639-535: The Miller–Urey experiment showed that organic compounds could be synthesized abiotically within a closed system mimicking the conditions of early Earth , thus suggesting that complex organic molecules could have arisen spontaneously in early Earth (see abiogenesis ). Macromolecules are large molecules made up of smaller subunits or monomers . Monomers include sugars, amino acids, and nucleotides. Carbohydrates include monomers and polymers of sugars. Lipids are

9792-492: The Precambrian about 1.5 billion years ago and can be classified into eight major clades : alveolates , excavates , stramenopiles , plants, rhizarians , amoebozoans , fungi , and animals. Five of these clades are collectively known as protists , which are mostly microscopic eukaryotic organisms that are not plants, fungi, or animals. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor ), protists by themselves do not constitute

9945-727: The activator is the transcription factor that stimulates transcription when it binds to the sequence near or at the promoter. Negative regulation occurs when another transcription factor called a repressor binds to a DNA sequence called an operator , which is part of an operon, to prevent transcription. Repressors can be inhibited by compounds called inducers (e.g., allolactose ), thereby allowing transcription to occur. Specific genes that can be activated by inducers are called inducible genes , in contrast to constitutive genes that are almost constantly active. In contrast to both, structural genes encode proteins that are not involved in gene regulation. In addition to regulatory events involving

10098-585: The bacterial phyla have species that can be grown in the laboratory. Archaea constitute the other domain of prokaryotic cells and were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom ), a term that has fallen out of use. Archaeal cells have unique properties separating them from the other two domains , Bacteria and Eukaryota . Archaea are further divided into multiple recognized phyla . Archaea and bacteria are generally similar in size and shape, although

10251-404: The cell . In 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells, continuing to support spontaneous generation . However, Robert Remak and Rudolf Virchow were able to reify

10404-403: The cell membrane of another cell or located deep inside a cell. There are generally four types of chemical signals: autocrine , paracrine , juxtacrine , and hormones . In autocrine signaling, the ligand affects the same cell that releases it. Tumor cells, for example, can reproduce uncontrollably because they release signals that initiate their own self-division. In paracrine signaling,

10557-416: The circulatory systems of animals or vascular systems of plants to reach their target cells. Once a ligand binds with a receptor, it can influence the behavior of another cell, depending on the type of receptor. For instance, neurotransmitters that bind with an inotropic receptor can alter the excitability of a target cell. Other types of receptors include protein kinase receptors (e.g., receptor for

10710-528: The domain followed by kingdom , phylum , class , order , family , genus , and species . All organisms can be classified as belonging to one of three domains : Archaea (originally Archaebacteria), bacteria (originally eubacteria), or eukarya (includes the fungi, plant, and animal kingdoms). The history of life on Earth traces how organisms have evolved from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago and all life on Earth, both living and extinct, descended from

10863-481: The duplication of its DNA and some of its organelles , and the subsequent partitioning of its cytoplasm into two daughter cells in a process called cell division . In eukaryotes (i.e., animal, plant, fungal , and protist cells), there are two distinct types of cell division: mitosis and meiosis . Mitosis is part of the cell cycle, in which replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which

11016-533: The equilibrium point . Specifically, the eigenvalues of the Jacobian are indicative of the center manifold 's existence. Likewise, the eigenvectors of the Jacobian reveal the center manifold's orientation . The Hodgkin–Huxley model has two negative eigenvalues and two complex eigenvalues with slightly positive real parts. The eigenvectors associated with the two negative eigenvalues will reduce to zero as time t increases. The remaining two complex eigenvectors define

11169-456: The hippocampus . One of the major problems in neurophysiological memory is how it is maintained and changed through multiple time scales. Unstable synapses are easy to train but also prone to stochastic disruption. Stable synapses forget less easily, but they are also harder to consolidate. It is likely that computational tools will contribute greatly to our understanding of how synapses function and change in relation to external stimulus in

11322-403: The kingdom Plantae, which would exclude fungi and some algae . Plant cells were derived by endosymbiosis of a cyanobacterium into an early eukaryote about one billion years ago, which gave rise to chloroplasts. The first several clades that emerged following primary endosymbiosis were aquatic and most of the aquatic photosynthetic eukaryotic organisms are collectively described as algae, which

11475-423: The microscope . It was then that scholars discovered spermatozoa , bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop techniques of microscopic dissection and staining . Advances in microscopy had a profound impact on biological thinking. In the early 19th century, biologists pointed to the central importance of

11628-412: The mitochondrial cristae . Oxidative phosphorylation comprises the electron transport chain, which is a series of four protein complexes that transfer electrons from one complex to another, thereby releasing energy from NADH and FADH 2 that is coupled to the pumping of protons (hydrogen ions) across the inner mitochondrial membrane ( chemiosmosis ), which generates a proton motive force . Energy from

11781-546: The phenotype of that dominant allele. During gamete formation, the alleles for each gene segregate, so that each gamete carries only one allele for each gene. Heterozygotic individuals produce gametes with an equal frequency of two alleles. Finally, the law of independent assortment , states that genes of different traits can segregate independently during the formation of gametes, i.e., genes are unlinked. An exception to this rule would include traits that are sex-linked . Test crosses can be performed to experimentally determine

11934-490: The population model of neural networks. While many neurotheorists prefer such models with reduced complexity, others argue that uncovering structural-functional relations depends on including as much neuronal and network structure as possible. Models of this type are typically built in large simulation platforms like GENESIS or NEURON. There have been some attempts to provide unified methods that bridge and integrate these levels of complexity. Visual attention can be described as

12087-497: The regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells. Cellular respiration is a set of metabolic reactions and processes that take place in cells to convert chemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. The reactions involved in respiration are catabolic reactions , which break large molecules into smaller ones, releasing energy. Respiration

12240-606: The stoichiometry of exchange is 3 Na : 1 Ca and the exchanger is electrogenic and voltage-sensitive. The Na/K exchanger has also been described in detail, with a 3 Na : 2 K stoichiometry. The Hodgkin–Huxley model can be thought of as a differential equation system with four state variables , V m ( t ) , n ( t ) , m ( t ) {\displaystyle V_{m}(t),n(t),m(t)} , and h ( t ) {\displaystyle h(t)} , that change with respect to time t {\displaystyle t} . The system

12393-399: The voltage clamp and created the first biophysical model of the action potential . Hubel and Wiesel discovered that neurons in the primary visual cortex , the first cortical area to process information coming from the retina , have oriented receptive fields and are organized in columns. David Marr's work focused on the interactions between neurons, suggesting computational approaches to

12546-475: The Phanerozoic eon that began 539 million years ago being subdivided into Paleozoic , Mesozoic , and Cenozoic eras. These three eras together comprise eleven periods ( Cambrian , Ordovician , Silurian , Devonian , Carboniferous , Permian , Triassic , Jurassic , Cretaceous , Tertiary , and Quaternary ). The similarities among all known present-day species indicate that they have diverged through

12699-696: The accumulation of favorable traits over successive generations, thereby increasing the match between the organisms and their environment. A species is a group of organisms that mate with one another and speciation is the process by which one lineage splits into two lineages as a result of having evolved independently from each other. For speciation to occur, there has to be reproductive isolation . Reproductive isolation can result from incompatibilities between genes as described by Bateson–Dobzhansky–Muller model . Reproductive isolation also tends to increase with genetic divergence . Speciation can occur when there are physical barriers that divide an ancestral species,

12852-413: The bases for some quantitative modeling of large-scale brain activity. The Computational Representational Understanding of Mind ( CRUM ) is another attempt at modeling human cognition through simulated processes like acquired rule-based systems in decision making and the manipulation of visual representations in decision making. One of the ultimate goals of psychology/neuroscience is to be able to explain

13005-586: The body plan and the number, identity, and pattern of body parts. Among the most important toolkit genes are the Hox genes . Hox genes determine where repeating parts, such as the many vertebrae of snakes, will grow in a developing embryo or larva. Evolution is a central organizing concept in biology. It is the change in heritable characteristics of populations over successive generations . In artificial selection , animals were selectively bred for specific traits. Given that traits are inherited, populations contain

13158-614: The book Computational Neuroscience . The first of the annual open international meetings focused on Computational Neuroscience was organized by James M. Bower and John Miller in San Francisco, California in 1989. The first graduate educational program in computational neuroscience was organized as the Computational and Neural Systems Ph.D. program at the California Institute of Technology in 1985. The early historical roots of

13311-450: The breaking down of glucose to pyruvate by cellular respiration ); or anabolic —the building up ( synthesis ) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy. The chemical reactions of metabolism are organized into metabolic pathways , in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by

13464-462: The center manifold. In other words, the 4-dimensional system collapses onto a 2-dimensional plane. Any solution starting off the center manifold will decay towards the center manifold. Furthermore, the limit cycle is contained on the center manifold. If the injected current I {\displaystyle I} were used as a bifurcation parameter , then the Hodgkin–Huxley model undergoes

13617-410: The cohesive force due to the attraction between molecules at the surface of the liquid. Water is also adhesive as it is able to adhere to the surface of any polar or charged non-water molecules. Water is denser as a liquid than it is as a solid (or ice). This unique property of water allows ice to float above liquid water such as ponds, lakes, and oceans, thereby insulating the liquid below from

13770-433: The cold air above. Water has the capacity to absorb energy, giving it a higher specific heat capacity than other solvents such as ethanol . Thus, a large amount of energy is needed to break the hydrogen bonds between water molecules to convert liquid water into water vapor . As a molecule, water is not completely stable as each water molecule continuously dissociates into hydrogen and hydroxyl ions before reforming into

13923-407: The coming decades. Biological neurons are connected to each other in a complex, recurrent fashion. These connections are, unlike most artificial neural networks , sparse and usually specific. It is not known how information is transmitted through such sparsely connected networks, although specific areas of the brain, such as the visual cortex , are understood in some detail. It is also unknown what

14076-449: The computational functions of these specific connectivity patterns are, if any. The interactions of neurons in a small network can be often reduced to simple models such as the Ising model . The statistical mechanics of such simple systems are well-characterized theoretically. Some recent evidence suggests that dynamics of arbitrary neuronal networks can be reduced to pairwise interactions. It

14229-429: The current term I on the left-hand side of the first differential equation in terms of V , so that the equation becomes an equation for voltage alone. The relation between I and V can be derived from cable theory and is given by where a is the radius of the axon , R is the specific resistance of the axoplasm , and x is the position along the nerve fiber. Substitution of this expression for I transforms

14382-501: The cytoplasm of a cell, there are many biomolecules such as proteins and nucleic acids . In addition to biomolecules, eukaryotic cells have specialized structures called organelles that have their own lipid bilayers or are spatially units. These organelles include the cell nucleus , which contains most of the cell's DNA, or mitochondria , which generate adenosine triphosphate (ATP) to power cellular processes. Other organelles such as endoplasmic reticulum and Golgi apparatus play

14535-455: The cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the electron carriers so that they can perform glycolysis again and removing the excess pyruvate. Fermentation oxidizes NADH to NAD so it can be re-used in glycolysis. In the absence of oxygen, fermentation prevents the buildup of NADH in the cytoplasm and provides NAD for glycolysis. This waste product varies depending on

14688-673: The development of biological knowledge. He explored biological causation and the diversity of life. His successor, Theophrastus , began the scientific study of plants. Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dīnawarī (828–896), who wrote on botany, and Rhazes (865–925) who wrote on anatomy and physiology . Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought. Biology began to quickly develop with Anton van Leeuwenhoek 's dramatic improvement of

14841-418: The development of body form, is the result of spatial differences in gene expression. A small fraction of the genes in an organism's genome called the developmental-genetic toolkit control the development of that organism. These toolkit genes are highly conserved among phyla , meaning that they are ancient and very similar in widely separated groups of animals. Differences in deployment of toolkit genes affect

14994-440: The developmental fate of a cell, which becomes more restrictive during development. Differentiation is the process by which specialized cells arise from less specialized cells such as stem cells . Stem cells are undifferentiated or partially differentiated cells that can differentiate into various types of cells and proliferate indefinitely to produce more of the same stem cell. Cellular differentiation dramatically changes

15147-411: The discovery of archaea in almost every habitat , including soil, oceans, and marshlands . 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 . They are part of the microbiota of all organisms. In the human microbiome , they are important in the gut , mouth, and on

15300-420: The discovery of the double-helical structure of DNA by James Watson and Francis Crick in 1953, marked the transition to the era of molecular genetics . From the 1950s onwards, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana , Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons . The Human Genome Project

15453-616: The earliest terrestrial ecosystems , at least 2.7 billion years ago. Microorganisms are thought to have paved the way for the inception of land plants in the Ordovician period. Land plants were so successful that they are thought to have contributed to the Late Devonian extinction event . Ediacara biota appear during the Ediacaran period, while vertebrates , along with most other modern phyla originated about 525 million years ago during

15606-438: The equation for the total current mentioned above, these are: where I is the current per unit area and α i {\displaystyle \alpha _{i}} and β i {\displaystyle \beta _{i}} are rate constants for the i -th ion channel, which depend on voltage but not time. g ¯ n {\displaystyle {\bar {g}}_{n}}

15759-677: The everyday experience of conscious life. Francis Crick , Giulio Tononi and Christof Koch made some attempts to formulate consistent frameworks for future work in neural correlates of consciousness (NCC), though much of the work in this field remains speculative. Computational clinical neuroscience is a field that brings together experts in neuroscience, neurology , psychiatry , decision sciences and computational modeling to quantitatively define and investigate problems in neurological and psychiatric diseases , and to train scientists and clinicians that wish to apply these models to diagnosis and treatment. Predictive computational neuroscience

15912-474: The example of visual processing, efficient coding is manifested in the forms of efficient spatial coding, color coding, temporal/motion coding, stereo coding, and combinations of them. Further along the visual pathway, even the efficiently coded visual information is too much for the capacity of the information bottleneck, the visual attentional bottleneck. A subsequent theory, V1 Saliency Hypothesis (V1SH) , has been developed on exogenous attentional selection of

16065-477: The existence of a saliency or priority map for registering the potentially interesting areas of the retinal input, and a gating mechanism for reducing the amount of incoming visual information, so that the limited computational resources of the brain can handle it. An example theory that is being extensively tested behaviorally and physiologically is the V1 Saliency Hypothesis that a bottom-up saliency map

16218-473: The expression of deleterious recessive mutations . The beneficial effect of genetic complementation, derived from outcrossing (cross-fertilization) is also referred to as hybrid vigor or heterosis. Charles Darwin in his 1878 book The Effects of Cross and Self-Fertilization in the Vegetable Kingdom at the start of chapter XII noted “The first and most important of the conclusions which may be drawn from

16371-413: The field can be traced to the work of people including Louis Lapicque , Hodgkin & Huxley , Hubel and Wiesel , and David Marr . Lapicque introduced the integrate and fire model of the neuron in a seminal article published in 1907, a model still popular for artificial neural networks studies because of its simplicity (see a recent review). About 40 years later, Hodgkin and Huxley developed

16524-453: The figure). The current generated by ion pumps is dependent on the ionic species specific to that pump. The following sections will describe these formulations in more detail. Using a series of voltage clamp experiments and by varying extracellular sodium and potassium concentrations, Hodgkin and Huxley developed a model in which the properties of an excitable cell are described by a set of four ordinary differential equations . Together with

16677-455: The form of glucose is the main nutrient used by animal and plant cells in respiration. Cellular respiration involving oxygen is called aerobic respiration, which has four stages: glycolysis , citric acid cycle (or Krebs cycle), electron transport chain , and oxidative phosphorylation . Glycolysis is a metabolic process that occurs in the cytoplasm whereby glucose is converted into two pyruvates , with two net molecules of ATP being produced at

16830-558: The granularity at which biological entities are analyzed. Models in theoretical neuroscience are aimed at capturing the essential features of the biological system at multiple spatial-temporal scales, from membrane currents, and chemical coupling via network oscillations , columnar and topographic architecture, nuclei, all the way up to psychological faculties like memory, learning and behavior. These computational models frame hypotheses that can be directly tested by biological or psychological experiments. The term 'computational neuroscience'

16983-485: The growth and development of functional connections between neurons. Theoretical investigations into the formation and patterning of synaptic connection and morphology are still nascent. One hypothesis that has recently garnered some attention is the minimal wiring hypothesis , which postulates that the formation of axons and dendrites effectively minimizes resource allocation while maintaining maximal information storage. Early models on sensory processing understood within

17136-426: The hormone insulin ) and G protein-coupled receptors . Activation of G protein-coupled receptors can initiate second messenger cascades. The process by which a chemical or physical signal is transmitted through a cell as a series of molecular events is called signal transduction . The cell cycle is a series of events that take place in a cell that cause it to divide into two daughter cells. These events include

17289-452: The idea that the brain efficiently solves its problems. Earlier models of memory are primarily based on the postulates of Hebbian learning . Biologically relevant models such as Hopfield net have been developed to address the properties of associative (also known as "content-addressable") style of memory that occur in biological systems. These attempts are primarily focusing on the formation of medium- and long-term memory , localizing in

17442-414: The initial step of photosynthesis whereby light energy is absorbed by chlorophyll pigments attached to proteins in the thylakoid membranes . The absorbed light energy is used to remove electrons from a donor (water) to a primary electron acceptor, a quinone designated as Q. In the second stage, electrons move from the quinone primary electron acceptor through a series of electron carriers until they reach

17595-500: The initiation and propagation of action potentials in the squid giant axon . They received the 1963 Nobel Prize in Physiology or Medicine for this work. The typical Hodgkin–Huxley model treats each component of an excitable cell as an electrical element (as shown in the figure). The lipid bilayer is represented as a capacitance (C m ). Voltage-gated ion channels are represented by electrical conductances ( g n , where n

17748-511: The key goals of computational neuroscience is to dissect how biological systems carry out these complex computations efficiently and potentially replicate these processes in building intelligent machines. The brain's large-scale organizational principles are illuminated by many fields, including biology, psychology, and clinical practice. Integrative neuroscience attempts to consolidate these observations through unified descriptive models and databases of behavioral measures and recordings. These are

17901-406: The last eukaryotic common ancestor. Prokaryotes (i.e., archaea and bacteria) can also undergo cell division (or binary fission ). Unlike the processes of mitosis and meiosis in eukaryotes, binary fission in prokaryotes takes place without the formation of a spindle apparatus on the cell. Before binary fission, DNA in the bacterium is tightly coiled. After it has uncoiled and duplicated, it

18054-467: The last two conductances depend explicitly on the membrane voltage ( V m ) as well. In voltage-gated ion channels, the channel conductance is a function of both time and voltage ( g n ( t , V ) {\displaystyle g_{n}(t,V)} in the figure), while in leak channels, g l {\displaystyle g_{l}} , it is a constant ( g L {\displaystyle g_{L}} in

18207-405: The ligand diffuses to nearby cells and affects them. For example, brain cells called neurons release ligands called neurotransmitters that diffuse across a synaptic cleft to bind with a receptor on an adjacent cell such as another neuron or muscle cell . In juxtacrine signaling, there is direct contact between the signaling and responding cells. Finally, hormones are ligands that travel through

18360-444: The membrane potential is held at a constant value (i.e., with a voltage clamp), for each value of the membrane potential the nonlinear gating equations reduce to equations of the form: Thus, for every value of membrane potential V m {\displaystyle V_{m}} the sodium and potassium currents can be described by In order to arrive at the complete solution for a propagated action potential, one must write

18513-444: The membrane serving as membrane transporters , and peripheral proteins that loosely attach to the outer side of the cell membrane, acting as enzymes shaping the cell. Cell membranes are involved in various cellular processes such as cell adhesion , storing electrical energy , and cell signalling and serve as the attachment surface for several extracellular structures such as a cell wall , glycocalyx , and cytoskeleton . Within

18666-403: The mitotic phase of an animal cell cycle—the division of the mother cell into two genetically identical daughter cells. The cell cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells , and some internal organs are renewed. After cell division, each of the daughter cells begin the interphase of

18819-437: The most abundant molecule in every organism. Water is important to life because it is an effective solvent , capable of dissolving solutes such as sodium and chloride ions or other small molecules to form an aqueous solution . Once dissolved in water, these solutes are more likely to come in contact with one another and therefore take part in chemical reactions that sustain life. In terms of its molecular structure , water

18972-482: The natural permeability of the membrane to ions and take the form of the equation for voltage-gated channels, where the conductance g l e a k {\displaystyle g_{leak}} is a constant. Thus, the leak current due to passive leak ion channels in the Hodgkin-Huxley formalism is I l = g l e a k ( V − V l e

19125-403: The nature of their research questions and the tools that they use. Like other scientists, biologists use the scientific method to make observations , pose questions, generate hypotheses , perform experiments, and form conclusions about the world around them. Life on Earth, which emerged more than 3.7 billion years ago, is immensely diverse. Biologists have sought to study and classify

19278-428: The negative depolarization in mV. In many current software programs Hodgkin–Huxley type models generalize α {\displaystyle \alpha } and β {\displaystyle \beta } to In order to characterize voltage-gated channels, the equations can be fitted to voltage clamp data. For a derivation of the Hodgkin–Huxley equations under voltage-clamp, see. Briefly, when

19431-441: The observations given in this volume, is that generally cross-fertilisation is beneficial and self-fertilisation often injurious, at least with the plants on which I experimented.” Genetic variation , often produced as a byproduct of sexual reproduction, may provide long-term advantages to those sexual lineages that engage in outcrossing . Genetics is the scientific study of inheritance. Mendelian inheritance , specifically,

19584-517: The only class of macromolecules that are not made up of polymers. They include steroids , phospholipids , and fats, largely nonpolar and hydrophobic (water-repelling) substances. Proteins are the most diverse of the macromolecules. They include enzymes , transport proteins , large signaling molecules, antibodies , and structural proteins . The basic unit (or monomer) of a protein is an amino acid . Twenty amino acids are used in proteins. Nucleic acids are polymers of nucleotides . Their function

19737-404: The organism. In skeletal muscles, the waste product is lactic acid . This type of fermentation is called lactic acid fermentation . In strenuous exercise, when energy demands exceed energy supply, the respiratory chain cannot process all of the hydrogen atoms joined by NADH. During anaerobic glycolysis, NAD regenerates when pairs of hydrogen combine with pyruvate to form lactate. Lactate formation

19890-436: The original set of equations into a set of partial differential equations , because the voltage becomes a function of both x and t . The Levenberg–Marquardt algorithm is often used to fit these equations to voltage-clamp data. While the original experiments involved only sodium and potassium channels, the Hodgkin–Huxley model can also be extended to account for other species of ion channels . Leak channels account for

20043-544: The passage of potassium ions, the n needs to be raised to the fourth power. For p = ( n , m , h ) {\displaystyle p=(n,m,h)} , α p {\displaystyle \alpha _{p}} and β p {\displaystyle \beta _{p}} take the form p ∞ {\displaystyle p_{\infty }} and ( 1 − p ∞ ) {\displaystyle (1-p_{\infty })} are

20196-463: The physical world. Many models of the way the brain controls movement have been developed. This includes models of processing in the brain such as the cerebellum's role for error correction, skill learning in motor cortex and the basal ganglia, or the control of the vestibulo ocular reflex. This also includes many normative models, such as those of the Bayesian or optimal control flavor which are built on

20349-428: The possibility of common descent . Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck , who presented a coherent theory of evolution. The British naturalist Charles Darwin , combining the biogeographical approach of Humboldt , the uniformitarian geology of Lyell , Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, forged

20502-459: The potassium gating variable n ( t ) {\displaystyle n(t)} , allowing one to visualize the limit cycle . However, one must be careful because this is an ad-hoc method of visualizing the 4-dimensional system. This does not prove the existence of the limit cycle. A better projection can be constructed from a careful analysis of the Jacobian of the system, evaluated at

20655-907: The process of evolution from their common ancestor. Biologists regard the ubiquity of the genetic code as evidence of universal common descent for all bacteria , archaea , and eukaryotes . Microbial mats of coexisting bacteria and archaea were the dominant form of life in the early Archean eon and many of the major steps in early evolution are thought to have taken place in this environment. The earliest evidence of eukaryotes dates from 1.85 billion years ago, and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism . Later, around 1.7 billion years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions. Algae-like multicellular land plants are dated back to about 1 billion years ago, although evidence suggests that microorganisms formed

20808-539: The process such as transcription , RNA splicing , translation , and post-translational modification of a protein. Gene expression can be influenced by positive or negative regulation, depending on which of the two types of regulatory proteins called transcription factors bind to the DNA sequence close to or at a promoter. A cluster of genes that share the same promoter is called an operon , found mainly in prokaryotes and some lower eukaryotes (e.g., Caenorhabditis elegans ). In positive regulation of gene expression,

20961-517: The promoter, gene expression can also be regulated by epigenetic changes to chromatin , which is a complex of DNA and protein found in eukaryotic cells. Development is the process by which a multicellular organism (plant or animal) goes through a series of changes, starting from a single cell, and taking on various forms that are characteristic of its life cycle. There are four key processes that underlie development: Determination , differentiation , morphogenesis , and growth. Determination sets

21114-406: The proton motive force drives the enzyme ATP synthase to synthesize more ATPs by phosphorylating ADPs . The transfer of electrons terminates with molecular oxygen being the final electron acceptor . If oxygen were not present, pyruvate would not be metabolized by cellular respiration but undergoes a process of fermentation . The pyruvate is not transported into the mitochondrion but remains in

21267-452: The regulation of neuronal activity at both the cellular and the network level. Modeling this interaction allows to clarify the potassium cycle , so important for maintaining homeostasis and to prevent epileptic seizures. Modeling reveals the role of glial protrusions that can penetrate in some cases the synaptic cleft to interfere with the synaptic transmission and thus control synaptic communication. Computational neuroscience aims to address

21420-449: The same time. Each pyruvate is then oxidized into acetyl-CoA by the pyruvate dehydrogenase complex , which also generates NADH and carbon dioxide. Acetyl-CoA enters the citric acid cycle, which takes places inside the mitochondrial matrix. At the end of the cycle, the total yield from 1 glucose (or 2 pyruvates) is 6 NADH, 2 FADH 2 , and 2 ATP molecules. Finally, the next stage is oxidative phosphorylation, which in eukaryotes, occurs in

21573-676: The second and third stages, respectively, provide the energy and electrons to drive the synthesis of glucose by fixing atmospheric carbon dioxide into existing organic carbon compounds, such as ribulose bisphosphate (RuBP) in a sequence of light-independent (or dark) reactions called the Calvin cycle . Cell signaling (or communication) is the ability of cells to receive, process, and transmit signals with its environment and with itself. Signals can be non-chemical such as light, electrical impulses , and heat, or chemical signals (or ligands ) that interact with receptors , which can be found embedded in

21726-553: The skin. Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example. Eukaryotes are hypothesized to have split from archaea, which was followed by their endosymbioses with bacteria (or symbiogenesis ) that gave rise to mitochondria and chloroplasts, both of which are now part of modern-day eukaryotic cells. The major lineages of eukaryotes diversified in

21879-545: The steady state values for activation and inactivation, respectively, and are usually represented by Boltzmann equations as functions of V m {\displaystyle V_{m}} . In the original paper by Hodgkin and Huxley, the functions α {\displaystyle \alpha } and β {\displaystyle \beta } are given by where V = V r e s t − V m {\displaystyle V=V_{rest}-V_{m}} denotes

22032-476: The stroma. This is analogous to the proton-motive force generated across the inner mitochondrial membrane in aerobic respiration. During the third stage of photosynthesis, the movement of protons down their concentration gradients from the thylakoid lumen to the stroma through the ATP synthase is coupled to the synthesis of ATP by that same ATP synthase. The NADPH and ATPs generated by the light-dependent reactions in

22185-571: The study of how functional groups of neurons within the hippocampus and neocortex interact, store, process, and transmit information. Computational modeling of biophysically realistic neurons and dendrites began with the work of Wilfrid Rall , with the first multicompartmental model using cable theory . Research in computational neuroscience can be roughly categorized into several lines of inquiry. Most computational neuroscientists collaborate closely with experimentalists in analyzing novel data and synthesizing new models of biological phenomena. Even

22338-471: The third tenet, and by the 1860s most biologists accepted all three tenets which consolidated into cell theory . Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735, and in the 1750s introduced scientific names for all his species. Georges-Louis Leclerc, Comte de Buffon , treated species as artificial categories and living forms as malleable—even suggesting

22491-489: The timing and qualitative features of the action potential, it nevertheless failed to predict a number of important features such as adaptation and shunting . Scientists now believe that there are a wide variety of voltage-sensitive currents, and the implications of the differing dynamics, modulations, and sensitivity of these currents is an important topic of computational neuroscience. The computational functions of complex dendrites are also under intense investigation. There

22644-564: The total current through the membrane is given by: where I is the total membrane current per unit area, C m is the membrane capacitance per unit area, g K and g Na are the potassium and sodium conductances per unit area, respectively, V K and V Na are the potassium and sodium reversal potentials, respectively, and g l and V l are the leak conductance per unit area and leak reversal potential, respectively. The time dependent elements of this equation are V m , g Na , and g K , where

22797-439: The total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA is replicated) and is often followed by telophase and cytokinesis ; which divides the cytoplasm , organelles and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of mitosis all together define

22950-431: The underlying genotype of an organism with a dominant phenotype. A Punnett square can be used to predict the results of a test cross. The chromosome theory of inheritance , which states that genes are found on chromosomes, was supported by Thomas Morgans 's experiments with fruit flies , which established the sex linkage between eye color and sex in these insects. A gene is a unit of heredity that corresponds to

23103-656: The various forms of life, from prokaryotic organisms such as archaea and bacteria to eukaryotic organisms such as protists , fungi, plants, and animals. These various organisms contribute to the biodiversity of an ecosystem , where they play specialized roles in the cycling of nutrients and energy through their biophysical environment . The earliest of roots of science, which included medicine, can be traced to ancient Egypt and Mesopotamia in around 3000 to 1200 BCE . Their contributions shaped ancient Greek natural philosophy . Ancient Greek philosophers such as Aristotle (384–322 BCE) contributed extensively to

23256-523: Was introduced by Eric L. Schwartz , who organized a conference, held in 1985 in Carmel, California , at the request of the Systems Development Foundation to provide a summary of the current status of a field which until that point was referred to by a variety of names, such as neural modeling, brain theory and neural networks. The proceedings of this definitional meeting were published in 1990 as

23409-434: Was launched in 1990 to map the human genome . All organisms are made up of chemical elements ; oxygen , carbon , hydrogen , and nitrogen account for most (96%) of the mass of all organisms, with calcium , phosphorus , sulfur , sodium , chlorine , and magnesium constituting essentially all the remainder. Different elements can combine to form compounds such as water, which is fundamental to life. Biochemistry

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