9,121 research outputs found
'Extremotaxis': Computing with a bacterial-inspired algorithm
We present a general-purpose optimization algorithm inspired by “run-and-tumble”, the biased random walk chemotactic swimming strategy used by the bacterium Escherichia coli to locate regions of high nutrient concentration The method uses particles (corresponding to bacteria) that swim through the variable space (corresponding to the attractant concentration profile). By constantly performing temporal comparisons, the particles drift towards the minimum or maximum of the function of interest. We illustrate the use of our method with four examples. We also present a discrete version of the algorithm. The new algorithm is expected to be useful in combinatorial optimization problems involving many variables, where the functional landscape is apparently stochastic and has local minima, but preserves some derivative structure at intermediate scales
Protein connectivity in chemotaxis receptor complexes
The chemotaxis sensory system allows bacteria such as Escherichia coli to swim towards nutrients and away from repellents. The underlying pathway is remarkably sensitive in detecting chemical gradients over a wide range of ambient concentrations. Interactions among receptors, which are predominantly clustered at the cell poles, are crucial to this sensitivity. Although it has been suggested that the kinase CheA and the adapter protein CheW are integral for receptor connectivity, the exact coupling mechanism remains unclear. Here, we present a statistical-mechanics approach to model the receptor linkage mechanism itself, building on nanodisc and electron cryotomography experiments. Specifically, we investigate how the sensing behavior of mixed receptor clusters is affected by variations in the expression levels of CheA and CheW at a constant receptor density in the membrane. Our model compares favorably with dose-response curves from in vivo Förster resonance energy transfer (FRET) measurements, demonstrating that the receptor-methylation level has only minor effects on receptor cooperativity. Importantly, our model provides an explanation for the non-intuitive conclusion that the receptor cooperativity decreases with increasing levels of CheA, a core signaling protein associated with the receptors, whereas the receptor cooperativity increases with increasing levels of CheW, a key adapter protein. Finally, we propose an evolutionary advantage as explanation for the recently suggested CheW-only linker structures
Predicting chemical environments of bacteria from receptor signaling
Sensory systems have evolved to respond to input stimuli of certain
statistical properties, and to reliably transmit this information through
biochemical pathways. Hence, for an experimentally well-characterized sensory
system, one ought to be able to extract valuable information about the
statistics of the stimuli. Based on dose-response curves from in vivo
fluorescence resonance energy transfer (FRET) experiments of the bacterial
chemotaxis sensory system, we predict the chemical gradients chemotactic
Escherichia coli cells typically encounter in their natural environment. To
predict average gradients cells experience, we revaluate the phenomenological
Weber's law and its generalizations to the Weber-Fechner law and fold-change
detection. To obtain full distributions of gradients we use information theory
and simulations, considering limitations of information transmission from both
cell-external and internal noise. We identify broad distributions of
exponential gradients, which lead to log-normal stimuli and maximal drift
velocity. Our results thus provide a first step towards deciphering the
chemical nature of complex, experimentally inaccessible cellular
microenvironments, such as the human intestine.Comment: DG and GM contributed equally to this wor
Implications of 3-step swimming patterns in bacterial chemotaxis
We recently found that marine bacteria Vibrio alginolyticus execute a cyclic
3-step (run- reverse-flick) motility pattern that is distinctively different
from the 2-step (run-tumble) pattern of Escherichia coli. How this novel
swimming pattern is regulated by cells of V. alginolyticus is not currently
known, but its significance for bacterial chemotaxis is self- evident and will
be delineated herein. Using an approach introduced by de Gennes, we calculated
the migration speed of a cell executing the 3-step pattern in a linear chemical
gradient, and found that a biphasic chemotactic response arises naturally. The
implication of such a response for the cells to adapt to ocean environments and
its possible connection to E. coli 's response are also discussed.Comment: 18 pages, 4 figures, submitted to biophysical journa
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