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Specificity of Bionoise

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Glossary of Bio-noise Terms

  • 1/f noise Pink (1/f) noise is one of the most common noise encountered in biosystems. It is admitted that the stationary random stochastic processes under self-similar conditions (as we have in living systems) generate pink noise independently of the kind and number of variables. (Szendro, Vincze & Szasz)

  • Action potentials They are random electrical pulses (voltage spikes) that can travel down nerve fibers.They are generated by neurons to propagate signals rapidly over large distances.

  • Biochemical noise This terms refers to fluctuations in the rate of chemical reactions due to randomness in the contact between reactants molecules submitted to Brownian movement in the surrounding solvent, as well as random variations in their energy due to collisions with other molecules and local temperature fluctuations. As a result, within living cells the production of any kind of molecules is a slightly variable process. No two cells are alike in terms of their chemical composition.

  • Biosensor The general function of a biosensor is to transduce binding events between biological receptors and target agents into a quantifiable electrical signal (A. Gore, S. Chakrabartty, S. Pal, E. Alocilja)

  • Brownian motors They are nano-scale or molecular devices by which thermally activated processes (chemical reactions) are controlled and used to generate directed motion in space and to do mechanical or electrical work. They operate in an environment where viscosity dominates inertia. Many protein-based molecular motors in the cell are Brownian motors.

  • Chemical energy Is defined as the work of electric forces during re-arrangement of electric charges in the process of aggregation of atoms to form molecules.

  • Coupling Two systems are said to be coupled if they are interacting with each other.

  • Extrinsic noise It refers to:

    1. Variability in factors external to the system that usually result in fluctuation of the kinetic parameters of the system. (Jinzhi Lei) Note: as defined, extrinsic and intrinsic noise are correlated.

    2. Gene-extrinsic noise : Variability in cell populations arising from sources that are external to the biochemical process of gene expression.

  • Frozen noise A burst of white noise that has been recorded and is repeated over and over again. (Oxford Reference)

  • Genetic drift It is a random change in allele frequency within a population.

  • Information entropy Two definitions are available:

    1. It is a measure of the uncertainty associated with a random variable.

    2. It is the shortest average message length, in bits, that can be sent to communicate the true value of the random variable to a receiver.

  • Intrinsic noise The definition of intrinsic noise is problem-dependent. Usually it refers to thermal fluctuations inherent in the system. (Jinzhi Lei). However, other categories are proposed in the literature (M. Kaern, T.C. Elston, W.J. Blake, J.J. Collins. Stochasticity in Gene Expression: From Theory to Phenotypes):

    1. Gene-intrinsic noise refers to the variability generated by molecular-level noise in the reaction steps that are intrinsic to the process of gene expression.

    2. Network-intrinsic noise is generated by fluctuations and variability in signal transduction and includes gene-intrinsic noise in the expression of regulatory genes.

    3. Cell-intrinsic noise arises from gene-intrinsic noise and network-intrinsic noise, as well as fluctuations and variability in cell-specific factors, such as the activity of ribosomes and polymerases, metabolite concentrations, cell size, cell age and stage of the cell cycle.

  • Ion channel Ion channels facilitate diffusion of ions across cell membranes. They are pore-forming proteins that help establish and control the small voltage gradient across the membrane of cells by allowing the flow of ions down their electrochemical gradient. Channels are also ion selective.

  • Ion channel noise This term is related to the Hodgkin and Huxley model of a ion channel, whose gating variables are probabilistic. Basically, there are two states associated to any ion channel: the closed and open states. The free energies associated with closed and open states depend on membrane potential. Random switching between closed and open states appears, which is driven by thermal noise. This process is called ion channel noise. Under voltage clamp, the ratio of standard deviation to the mean value of the current passing through a population of independent and identically distributed stochastic channels is proportional to 1/√N , where N is the total number of channels.

  • Isogenic It refers to genetically identical. Individual cells within an isogenic population are usually the progeny of a single ancestor.

  • Life It is a condition that distinguishes organisms from inorganic objects, i.e. non-life or dead organisms, being manifested by growth through metabolism, reproduction, and the power of adaptation to environment through changes originating internally.

  • Mesoscopic It refers to a system or process where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy.

  • Metastability It is the ability of a non-equilibrium state to persist for some period of time.

  • Molecular machine (nanomachine) Is defined as a discrete number of molecular components which perform mechanical-like movements (output) in response to specific stimuli (input).

  • Molecular motors They are biological molecular machines that are the essential agents of movement in living cells. A molecular motor consumes energy in one form and converts it into motion; for example, many protein-based molecular motors harvest the chemical free energy released by the hydrolysis of ATP in order to transport cargo inside the cell.

  • Molecular noise Usually, it is considered to be produced by random fluctuations in the levels of cellular components (molecules). These fluctuations arise spontaneously either due to random births and deaths of individual molecules or by random variation of environmental parameters (as temperature). Their intensity is perceived to be more pregnant whenever a small population of molecules is involved (Schrödinger's law), and these fluctuations are transmitted to dependent processes.

  • Motor proteins are a sub-class of molecular motors belonging to life systems. The other sub-class concerns the man-made counterparts (synthetic molecular motors or equally called self-propelled bionic machines). Here are a few usual definitions:

    1. A motor protein is a protein that generates intracellular movements in eukaryotic cells, by using energy from ATP. (Bee encyclopaedia)

    1. A motor protein is a protein (as dynein, kinesin, or myosin) that moves itself along a filament or polymeric molecule using energy generated by the hydrolysis of ATP. (Merriam-Webster OnLine dictionary)

    2. Motor protein is protein that walks or slides along microtubules or microfilaments using the energy provided by ATP or GTP hydrolysis, e.g. dyneins, myosins and kinesins. Or protein which mediates motility by other non enzymatic processes, e.g. prestin, a bidirectional voltage-to-force converter. (UniProt Knowledgebase)

    3. They are proteins that bind ATP and are able to move on a suitable substrate with concomitant ATP hydrolysis. Most eukaryotic motor proteins move by binding to a specific site on either actin filaments (myosin) or on microtubule (dynein, kinesin). They are normally elongated molecules with two active binding sites although some kinesin analogues have a single site. The distal end of the molecule normally binds adaptor proteins that enable them to make stable with membrane vesicles or with filamentous structures, which then constitute the cargo to be moved along the substrate filament. (Online Medical Dictionary)

    4. Cells have protein motors that bind two molecules, and using ATP as energy, cause one molecule to shift in relationship to the other. (The Virtual Library of Biochemistry, Molecular Biology and Cell Biology)

    5. According to, motor proteins are a class of molecular motors that are able to move along the surface of a suitable substrate. They are powered by the hydrolysis of ATP and convert chemical energy into mechanical work (Wikipedia).

    Note that some people use the term “motor proteins” while others prefer “protein motors”.

    When used at singular, both terms are appropriate. However, a problem appears when the plural is required. Since this term refers to molecular motors using a single protein, the plural form of the former is confusing and for this reason our preference goes to the later. Consequently, we propose the following definition: protein motors are proteins that use the energy stored in ATP, GTP, a.s.o. and sophisticated mechanisms to perform steady intracellular movement, along the surface of an appropriate substrate (cytoskeleton), with nanometric steps.

  • Nanopore Can be defined as a very small hole. When a nanopore is present in an electrically insulating membrane, it can be used as a single-molecule detector (Wikipedia). In vivo, nanopores may be formed by pore-forming proteins, typically a hollow core passing through a mushroom-shaped protein molecule. In vitro, a nanopore is created as a hole in synthetic materials such as silicon, silicon nitride or graphene.

  • Neuronal noise is a general term that designates random influences on the transmembrane voltage of single neurons and, by extension, the firing activity of neural networks. This noise can influence the transmission and integration of signals from other neurons as well as alter the firing activity of neurons in isolation (André Longtin).

  • Noise in life systems It refers to stochastic fluctuations affecting transcription and translation rates in gene expression that induces random fluctuations in protein levels.

  • Noise regulatory vector Represents a generalized framework for the analysis of any gene circuit by means of its noise autocorrelation function. It can be defined as the difference between the measured noise structure vector for the gene circuit of interest, and the theoretical noise structure vector for the a priori assumed circuit model. (Cox, McCollum, Allen, Dar & Simpson)

  • Noisome In system biology, it is a perturbation-free, time-correlated, background gene expression profile under normal physiological conditions. (Pawan K. Dhar)

  • Phenotypic noise

  1. It refers to random molecular processes during cell division allowing cellular components to be randomly distributed between the two daughter cells with each cell receiving a different amount. The difference between the two groups is a result of phenotypic noise. As a consequence, some cells may engage in a self-destructive act to generate a greater common good, thereby improving the situation of the surviving siblings. The two groups being clones of the same genotype, genetic differences do not play a role. (Martin Ackermann)

  2. In genetically identical populations, some cells produce different amounts of the same protein. The speed at which the variation in protein output occurs suggests that the changes are not due to mutation but rather to random fluctuation of the processes of transcription and translation within the cell. One explanation for this variation is promoters with variable protein output. (S. Pyfrom & M. Campbell)

Phenotypic noise has an important role in adaptation (the cell is able to respond quickly to environmental changes without having to mutate) and in genetic evolution.

  • Ratchet Is a device used to restrict motion in one direction (in mechanical engineering: ratchet and pawl).

  • Schrödinger's law This law applies to physical systems with a very limited number of particles. It states that in any statistical experiment involving n identical particles, the degree of inaccuracy to be expected in any physical law is inversely proportional to square root of the number of particles. By extension, any fluctuation can be viewed as an “inaccuracy” with respect to its mean value and therefore the intensity of the generated noise is inversely proportional to square root of the number of particles. Hence, at mesoscopic scale, due to a reduced population of particles, even small fluctuations in one parameter give rise to a noise much more intense as expected.

  • Secondary (Second) messenger system It is a procedure of cellular signalling where the signalling molecule does not enter the cell, but rather utilizes a cascade of events that transduces the signal into a cellular change.

  • Self-organization It is a process in which the internal organization of a system, normally an open system, increases in complexity without being guided or managed by an outside source.

    It is admitted that self-organization can only occur far away from thermodynamic equilibrium (Ilya Prigogine). Note: since isolated systems cannot decrease their entropy, only open systems can exhibit self-organization.

  • Signal transduction It refers to any process by which a cell converts one kind of signal (or stimulus) into another, usually involving ordered sequences of biochemical reactions inside the cell.

  • Steady-state If a system is in steady-state then the lastly observed behaviour of the system will continue into the future. In stochastic systems, the probabilities that various different states will be repeated remain constant.

  • Synaptic noise There are two main components of this kind of noise (Scholarpedia):

  1. Synaptic bombardment At neuron level, the synaptic bombardment consists in Ne excitatory and Ni inhibitory pre-synaptic current pulses, where the pulse strengths are Je and Ji respectively. Each pulse train is a Poisson process, with firing rate νe and νi respectively. In the limit of large Neνe and Niνi, the overall process can be identified to white noise. Finally, every spike arriving at this synapse contributes a small amount of charge to the cell.

  2. Synaptic release noise It is due to the random molecular events that follow the synaptic bombardment. Chemical synapses imply transfer of information via molecules of transmitters. Transmitters are packed in vesicles and consequently are released in quanta-packets that contain roughly 7000 molecules of transmitters. The release probability depends on the history of firing of both the pre- and the postsynaptic neuron. For instance, the probability of releasing a quanta increases when the action potential arrives at synaptic terminal.

  •  Systems (classification) There are several categories of conceptual systems (Wikipedia):

    1. Closed system In thermodynamics, it is defined as a system that can exchange energy and mechanical work with other systems, but not matter.

    2. Dissipative system It refers to a system that is thermodynamically open and is operating far from thermodynamic equilibrium, in an environment with which it exchanges energy, matter and/or entropy.

    3. Dynamical system It has components and/or flows that change over time.

    4. Isolated system A physical system that does not interact with its surroundings. It obeys a number of conservation laws (its total energy and mass stay constant).

    5. Open system It is defined as a system that continuously exchange matter and energy with its surroundings. Life is possible in all organisms that are open systems.

  • Thermal bath It is a reservoir of particles at finite temperature that is in thermal contact and is undergoing Brownian motion. Because of its nonzero temperature, this system contains thermal energy.

  •  Thermal noise In biology, it refers to the random forces impelling upon a Brownian particle. Analogous to the disordered movement of electrons in a metallic volume causing temporal agglomerations and hence fluctuations in the electrical potential at the ends, the Brownian particle has a random movement resulting in fluctuations in particles density in a given elementary volume.

    The electrical thermal noise gives rise to a small current passing through the short-circuited resistor, whose magnitude and direction randomly changes.

    The biological thermal noise may affect the displacement of particles submitted to a directed movement, imposing fluctuations on their vector speed.

  • Transcriptional noise It refers to the variability in gene activity between cells in genetically identical populations. Noise in gene activity has tremendous consequences on cell behavior, and must be mitigated or integrated. Noise impacts upon the effectiveness of clinical treatment, with resistance of bacteria to antibiotics demonstrably caused by non-genetic differences. Variability in gene expression may also contribute to resistance of sub-populations of cancer cells to chemotherapy.

 

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