Glossary of Bio-noise Terms
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
Vincze & Szasz)
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.
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.
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)
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
in the cell are Brownian motors.
defined as the work of electric forces during re-arrangement of
electric charges in the process of aggregation of atoms to form
Two systems are said to be coupled if they are interacting with each
It refers to:
Variability in factors external to the system that usually
result in fluctuation of the kinetic parameters of the system.
as defined, extrinsic and intrinsic noise are correlated.
: Variability in cell populations arising from sources that are
external to the biochemical process of gene expression.
A burst of white noise that has been recorded and is repeated over
and over again. (Oxford
It is a random change in allele frequency within a population.
Two definitions are available:
is a measure of the uncertainty associated with a random
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.
The definition of intrinsic noise is problem-dependent.
Usually it refers to thermal fluctuations inherent in the system.
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):
refers to the variability generated by molecular-level noise in
the reaction steps that are intrinsic to the process of gene
is generated by fluctuations and variability in signal
transduction and includes gene-intrinsic noise in the expression
of regulatory genes.
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 channels facilitate diffusion of ions across cell membranes.
They are pore-forming
that help establish and control the small
across the membrane of
the flow of
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
the closed and open states.
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.
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.
It refers to genetically identical. Individual cells within an
isogenic population are usually the progeny of a single ancestor.
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.
It refers to a system or process where the typical length scale is
of the order of nanometers and the energy scales comparable to
is the ability of a non-equilibrium state to persist for some period
Is defined as a discrete number of molecular components which
perform mechanical-like movements (output) in response to specific
They are biological
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
molecular motors harvest the chemical
released by the
in order to transport cargo inside the cell.
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
and these fluctuations are transmitted to dependent processes.
are a sub-class of molecular motors belonging to life systems. The
other sub-class concerns the man-made counterparts (synthetic
or equally called
self-propelled bionic machines).
Here are a few usual definitions:
motor protein is a protein that generates
intracellular movements in eukaryotic cells, by using energy
from ATP. (Bee
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.
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
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
have protein motors that bind two molecules, and using ATP as
energy, cause one molecule to shift in relationship to the other.
Virtual Library of Biochemistry, Molecular Biology and Cell
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
Note that some people
use the term “motor proteins” while others prefer “protein
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.
Can be defined as a very small hole. When a nanopore is present in
an electrically insulating
it can be used as a single-molecule
nanopores may be formed by pore-forming proteins, typically a hollow
core passing through a mushroom-shaped protein molecule.
a nanopore is created as a hole in synthetic materials such as
silicon, silicon nitride or graphene.
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
Noise in life systems
It refers to stochastic fluctuations affecting
translation rates in gene expression that induces random
fluctuations in protein levels.
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)
In system biology, it is a
perturbation-free, time-correlated, background gene expression
profile under normal physiological conditions.
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.
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
(S. Pyfrom & M. Campbell)
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).
This law applies to physical systems with a very limited number of
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.
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
since isolated systems
cannot decrease their entropy, only open systems can exhibit
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.
If a system is in steady-state then the lastly observed behaviour of
the system will continue into the future. In
the probabilities that various different states will be repeated
At neuron level, the synaptic bombardment consists in
excitatory and Ni
inhibitory pre-synaptic current pulses, where the pulse
strengths are Je
respectively. Each pulse train is a Poisson process, with firing
respectively. In the limit of large
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.
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.
There are several categories of conceptual systems
In thermodynamics, it is defined as a system
that can exchange energy and mechanical work with other systems,
but not matter.
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.
It has components and/or flows that change over time.
A physical system that does not interact with its surroundings.
It obeys a number of conservation laws (its total energy and
mass stay constant).
It is defined as a system
that continuously exchange matter and energy with its
surroundings. Life is possible in all organisms that are open
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
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.
thermal noise gives rise to a small current passing through
the short-circuited resistor, whose magnitude and direction randomly
thermal noise may affect the displacement of particles
submitted to a directed movement, imposing fluctuations on their
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
demonstrably caused by non-genetic differences. Variability in gene
expression may also contribute to resistance of sub-populations of
cancer cells to chemotherapy.
|Copyright 2010 © UNESCO
- All Rights Reserved.