% This file was created with JabRef 2.3.1.
% Encoding: Cp1252

@ARTICLE{agarraberes:01,
  author = {Agarraberes, F.A. and Dice, J.F.},
  title = {Protein translocation across membranes},
  journal = {Biochimica et Biophysica Acta},
  year = {2001},
  optnote = {intracellular proteins},
  optpages = {1-24},
  optvolume = {1513}
}

@ARTICLE{aizawa:00,
  author = {Aizawa, S. and Harwood, C. S. and Kadner, R. J.},
  title = {MINIREVIEW Signaling Components in Bacterial Locomotion and Sensory
	Reception},
  journal = {Journal of Bacteriology},
  year = {2000},
  volume = {182},
  pages = {1459-1471},
  number = {6},
  optnote = {general motors}
}

@BOOK{alberts,
  title = {Molecular Biology of the Cell},
  publisher = {Garland},
  year = {1989},
  author = {Alberts, Bruce and Bray, Dennis and Lewis, Julian and Raff, Martin
	and Roberts, Keith and Watson, James. D},
  optedition = {2},
  optkey = {0-8240-3696-4},
  optnote = {textbook}
}

@ARTICLE{allersma:98,
  author = {Allersma, M.W. and Gittes, F. and deCastro, M.J. and Stewart, R.J.
	and Schmidt, C.F.},
  title = {{Two-dimensional tracking of ncd motility by back focal plane interferometry}},
  journal = {Biophysical Journal},
  year = {1998},
  volume = {74},
  pages = {1074--1085},
  number = {2},
  publisher = {Biophysical Soc}
}

@ARTICLE{appleby1999acm,
  author = {Appleby, J.L. and Bourret, R.B.},
  title = {{Activation of CheY mutant D57N by phosphorylation at an alternative
	site, Ser-56}},
  journal = {Molecular Microbiolgy},
  year = {1999},
  volume = {34},
  pages = {915-925},
  number = {5},
  publisher = {Blackwell Science Ltd}
}

@ARTICLE{armitage03,
  author = {Armitage, JP.},
  title = {{Taxing questions in development}},
  journal = {Trends Microbiol},
  year = {2003},
  volume = {11},
  pages = {239-242},
  number = {6},
  month = {Jun},
  abstract = {{Bacteria use taxis-controlled movement to reach their optimum environment.
	Chemotaxis is probably the best understood behavioural system in
	biology, biasing the normal random movement of bacteria using a phospho-relay
	pathway from receptors to the motility organelles. The pathways are
	typified by signal recognition and receptor adaptation, enabling
	bacteria to sense and respond to changing environments. Models have
	been derived from the single chemosensory pathway of Escherichia
	coli but the sequencing of an increasing number of bacterial genomes
	is revealing genes that apparently encode multiple chemosensory pathways.
	Recently, data have accumulated suggesting that some of these pathways
	might not control motility, although the mechanisms by which this
	might happen remain unclear. Information from the soil bacterium
	Myxococcus xanthus could lead the way to an understanding of such
	mechanisms.}},
  pmid = {12823935},
  url = {http://www.hubmed.org/display.cgi?uids=12823935}
}

@ARTICLE{armitage99,
  author = {Armitage, JP.},
  title = {{Bacterial tactic responses}},
  journal = {Advances in Microbial Physiologyiol},
  year = {1999},
  volume = {41},
  pages = {229-289},
  abstract = {{Many, if not most, bacterial species swim. The synthesis and operation
	of the flagellum, the most complex organelle of a bacterium, takes
	a significant percentage of cellular energy, particularly in the
	nutrient limited environments in which many motile species are found.
	It is obvious that motility accords cells a survival advantage over
	non-motile mutants under normal, poorly mixed conditions and is an
	important determinant in the development of many associations between
	bacteria and other organisms, whether as pathogens or symbionts and
	in colonization of niches and the development of biofilms. This survival
	advantage is the result of sensory control of swimming behaviour.
	Although too small to sense a gradient along the length of the cell,
	and unable to swim great distances because of buffetting by Brownian
	motion and the curvature resulting from a rotating flagellum, bacteria
	can bias their random swimming direction towards a more favourable
	environment. The favourable environment will vary from species to
	species and there is now evidence that in many species this can change
	depending on the current physiological growth state of the cell.
	In general, bacteria sense changes in a range of nutrients and toxins,
	compounds altering electron transport, acceptors or donors into the
	electron transport chain, pH, temperature and even the magnetic field
	of the Earth. The sensory signals are balanced, and may be balanced
	with other sensory pathways such as quorum sensing, to identify the
	optimum current environment. The central sensory pathway in this
	process is common to most bacteria and most effectors. The environmental
	change is sensed by a sensory protein. In most species examined this
	is a transmembrane protein, sensing the external environment, but
	there is increasing evidence for additional cytoplasmic receptors
	in many species. All receptors, whether sensing sugars, amino acids
	or oxygen, share a cytoplasmic signalling domain that controls the
	activity of a histidine protein kinase, CheA, via a linker protein,
	CheW. A reduction in an attractant generally leads to the increased
	autophosphorylation of CheA. CheA passes its phosphate to a small,
	single domain response regulator, CheY. CheY-P can interact with
	the flagellar motor to cause it to change rotational direction or
	stop. Signal termination either via a protein, CheZ, which increases
	the dephosphorylation rate of CheY-P or via a second CheY which acts
	as a phosphate sink, allows the cell to swim off again, usually in
	a new direction. In addition to signal termination the receptor must
	be reset, and this occurs via methylation of the receptor to return
	it to a non-signalling conformation. The way in which bacteria use
	these systems to move to optimum environments and the interaction
	of the different sensory pathways to produce species-specific behavioural
	response will be the subject of this review.}},
  pmid = {10500847},
  url = {http://www.hubmed.org/display.cgi?uids=10500847}
}

@ARTICLE{armitage97a,
  author = {Armitage, JP.},
  title = {{Behavioural responses of bacteria to light and oxygen}},
  journal = {Arch Microbiol},
  year = {1997},
  volume = {168},
  pages = {249-261},
  number = {4},
  month = {Oct},
  abstract = {{Motile bacteria have long been known to swim towards or away from
	specific environmental stimuli such as nutrients, oxygen or light.
	Although there has been a detailed description of chemosensory responses
	in enteric species for several years, there has been little information
	on the mechanisms involved in responses to stimuli affecting electron
	transport as these usually also change the electrochemical proton
	gradient - at least transiently - and, thus, directly change flagellar
	rotation. There have, however, been major advances recently. Halobacterium
	salinarium uses a retinal-based sensory system to sense changes in
	specific wavelengths of light and to signal via a transmembrane sensory
	protein, which turns out to be homologous to the transmembrane chemoreceptors
	of Escherichia coli. A FAD-binding protein, also related to these
	receptors, signals changes in respiratory electron transport in E.
	coli. Rhodobacter sphaeroides cells do not respond to light or oxygen
	specifically, but sense a change in the rate of electron transfer,
	probably again using an electron-transport-chain-linked redox sensor,
	signalling through a common sensory pathway. These recent studies
	reveal that bacteria not only sense a range of environmental stimuli
	but also integrate the signals through common pathways to produce
	a balanced flagellar response.}},
  pmid = {9297461},
  url = {http://www.hubmed.org/display.cgi?uids=9297461}
}

@ARTICLE{armitage03a,
  author = {Armitage, JP. and Dorman, CJ. and Hellingwerf, K. and Schmitt, R.
	and Summers, D. and Holland, B.},
  title = {{Thinking and decision making, bacterial style: Bacterial Neural
	Networks, Obernai, France, 7th-12th June 2002}},
  journal = {Molecular Microbiology},
  year = {2003},
  volume = {47},
  pages = {583-593},
  number = {2},
  month = {Jan},
  pmid = {12519207},
  url = {http://www.hubmed.org/display.cgi?uids=12519207}
}

@ARTICLE{armitage80,
  author = {Armitage, JP. and Evans, MC.},
  title = {{Chemotactically induced increase in the membrane potential of spheroplasts
	of Rhodopseudomonas sphaeroides}},
  journal = {FEBS Lett},
  year = {1980},
  volume = {112},
  pages = {5-9},
  number = {1},
  month = {Mar},
  pmid = {6966230},
  url = {http://www.hubmed.org/display.cgi?uids=6966230}
}

@ARTICLE{armitage79,
  author = {Armitage, JP. and Evans, MC.},
  title = {{Membrane potential changes during chemotaxis of Rhodopseudomonas
	sphaeroides}},
  journal = {FEBS Lett},
  year = {1979},
  volume = {102},
  pages = {143-146},
  number = {1},
  month = {Jun},
  abstract = {{}},
  pmid = {313342},
  url = {http://www.hubmed.org/display.cgi?uids=313342}
}

@ARTICLE{armitage05,
  author = {Armitage, JP. and Holland, IB. and Jenal, U. and Kenny, B.},
  title = {{"Neural networks" in bacteria: making connections}},
  journal = {Journal of Bacteriology},
  year = {2005},
  volume = {187},
  pages = {26-36},
  number = {1},
  month = {Jan},
  abstract = {{}},
  pmid = {15601685},
  url = {http://www.hubmed.org/display.cgi?uids=15601685}
}

@ARTICLE{armitage87,
  author = {Armitage, J.P. and Macnab, R.M.},
  title = {{Unidirectional, intermittent rotation of the flagellum of \normalfont{Rhodobacter
	sphaeroides}}},
  journal = {Journal of Bacteriology},
  year = {1987},
  volume = {169},
  pages = {514-518},
  number = {2},
  month = {Feb},
  abstract = {{The single flagellum of the photosynthetic bacterium Rhodobacter
	sphaeroides was found to be medially located on the cell body. Observation
	of free-swimming bacteria, and bacteria tethered by their flagellar
	filaments, revealed that the flagellum could only rotate in the clockwise
	direction; switching of the direction of rotation was never observed.
	Flagellar rotation stopped periodically, typically several times
	a minute for up to several seconds each. Reorientation of swimming
	cells appeared to be the result of Brownian rotation during the stop
	periods. The flagellar filament displayed polymorphism; detached
	and nonrotating filaments were usually seen as large-amplitude helices
	of such short wavelength that they appeared as flat coils or circles,
	whereas the filaments on swimming cells showed a normal (small-amplitude,
	long-wavelength) helical form. With attached filaments, the transition
	from the normal to the coiled form occurred when the flagellar motor
	stopped rotating, proceeding from the distal end towards the cell
	body. It is possible that both the relaxation process and the smaller
	frictional resistance after relaxation may act to enhance the rate
	of reorientation of the cell. The transition from the coiled to the
	normal form occurred when the motor restarted, proceeding from the
	proximal end outwards, which might further contribute to the reorientation
	of the cell before it reaches a stable swimming geometry.}},
  pmid = {3492489},
  url = {http://www.hubmed.org/display.cgi?uids=3492489}
}

@ARTICLE{armitage99a,
  author = {Armitage, J.P. and Pitta, T.P. and Vigeant, M.A. and Packer, H.L.
	and Ford, R.M.},
  title = {{Transformations in flagellar structure of \normalfont{Rhodobacter
	sphaeroides} \textit{and possible relationship to changes in swimming
	speed}}},
  journal = {Journal of Bacteriology},
  year = {1999},
  volume = {181},
  pages = {4825-4833},
  number = {16},
  month = {Aug},
  abstract = {{Rhodobacter sphaeroides is a photosynthetic bacterium which swims
	by rotating a single flagellum in one direction, periodically stopping,
	and reorienting during these stops. Free-swimming R. sphaeroides
	was examined by both differential interference contrast (DIC) microscopy,
	which allows the flagella of swimming cells to be seen in vivo, and
	tracking microscopy, which tracks swimming patterns in three dimensions.
	DIC microscopy showed that when rotation stopped, the helical flagellum
	relaxed into a high-amplitude, short-wavelength coiled form, confirming
	previous observations. However, DIC microscopy also revealed that
	the coiled filament could rotate slowly, reorienting the cell before
	a transition back to the functional helix. The time taken to reform
	a functional helix depended on the rate of rotation of the helix
	and the length of the filament. In addition to these coiled and helical
	forms, a third conformation was observed: a rapidly rotating, apparently
	straight form. This form took shape from the cell body out and was
	seen to form directly from flagella that were initially in either
	the coiled or the helical conformation. This form was always significantly
	longer than the coiled or helical form from which it was derived.
	The resolution of DIC microscopy made it impossible to identify whether
	this form was genuinely in a straight conformation or was a low-amplitude,
	long-wavelength helix. Examination of the three-dimensional swimming
	pattern showed that R. sphaeroides changed speed while swimming,
	sometimes doubling the swimming speed between stops. The rate of
	acceleration out of stops was also variable. The transformations
	in waveform are assumed to be torsionally driven and may be related
	to the changes in speed measured in free-swimming cells. The roles
	of and mechanisms that may be involved in the transformations of
	filament conformations and changes in swimming speed are discussed.}},
  pmid = {10438751},
  url = {http://www.hubmed.org/display.cgi?uids=10438751}
}

@ARTICLE{armitage76,
  author = {Armitage, JP. and Rowbury, RJ. and Smith, DG.},
  title = {{The role of cyclic adenosine monophosphate in the swarming phenomenon
	of Proteus mirabilis}},
  journal = {Experientia},
  year = {1976},
  volume = {32},
  pages = {1266-1267},
  number = {10},
  month = {Oct},
  pmid = {185081},
  url = {http://www.hubmed.org/display.cgi?uids=185081}
}

@ARTICLE{armitage75,
  author = {Armitage, JP. and Rowbury, RJ. and Smith, DG.},
  title = {{Indirect evidence for cell wall and membrane differences between
	filamentous swarming cells and short non-swarming cells of Proteus
	mirabilis}},
  journal = {J Gen Microbiol},
  year = {1975},
  volume = {89},
  pages = {199-202},
  number = {1},
  month = {Jul},
  abstract = {{}},
  pmid = {1097593},
  url = {http://www.hubmed.org/display.cgi?uids=1097593}
}

@ARTICLE{armitage74,
  author = {Armitage, JP. and Rowbury, RJ. and Smith, DG.},
  title = {{The effects of chloramphenicol, nalidixic acid and penicillin on
	the growth and division of swarming cells of Proteus mirabilis}},
  journal = {J Med Microbiol},
  year = {1974},
  volume = {7},
  pages = {459-464},
  number = {4},
  month = {Nov},
  abstract = {{}},
  pmid = {4615151},
  url = {http://www.hubmed.org/display.cgi?uids=4615151}
}

@ARTICLE{armitage79a,
  author = {Armitage, JP. and Smith, DG. and Rowbury, RJ.},
  title = {{Alterations in the cell envelope composition of Proteus mirabilis
	during the development of swarmer cells}},
  journal = {Biochimica et Biophysica},
  year = {1979},
  volume = {584},
  pages = {389-397},
  number = {3},
  month = {May},
  abstract = {{Long, swarming cells of Proteus mirabilis had different proportions
	of some lipopolysaccharide components when compared to short cells,
	either agar grown or broth grown. Fluorescence spectrophotometry
	of antibody binding, and sodium dodecyl sulphate-polyacrylamide gel
	electrophoresis indicated that the change was in the proportion of
	lipopolysaccharide with long O-antigenic sidechains, swarmer lipopolysaccharide
	relative to short sidechain lipopolysaccharide than the non-swarming
	cells. The proteins and phospholipids of the envelop remained the
	same during swarmer development. The results are discussed in relation
	to the increase in flagella synthesis and permeability to some antibacterial
	agents during swarmer development.}},
  pmid = {378265},
  url = {http://www.hubmed.org/display.cgi?uids=378265}
}

@ARTICLE{asai:00,
  author = {Asai, Y. and Kawagishi, I. and Sockett, R.E. and Homma, M.},
  title = {{Coupling ion specificity of chimeras between H$^+$ and Na$^+$ driven
	motor proteins in \textnormal{Vibrio} polar flagella}},
  journal = {The EMBO Journal},
  year = {2000},
  volume = {19},
  pages = {3639-3648},
  number = {14},
  optnote = {vibrio}
}

@ARTICLE{asai:99,
  author = {Asai, Y. and Kawagishi, I. and Sockett, RE. and Homma, M.},
  title = {{Hybrid Motor with H+ - and Na+ -Driven Components can Rotate \textnormal{Vibrio}
	Polar Flagella by using Sodium Ions}},
  journal = {Journal of Bacteriology},
  year = {1999},
  volume = {181},
  pages = {6332-6338},
  number = {20},
  optnote = {vibrio}
}

@ARTICLE{asai:97,
  author = {Asai, Y. and Kojima, S. and Kato, H. and Nishioka, N. and Kawagishi,
	I. and Homma, M.},
  title = {Putative Channel Components for the Fast-Rotating Sodium-Driven Flagellar
	Motor of a Marine Bacterium},
  journal = {Journal of Bacteriology},
  year = {1997},
  volume = {179},
  pages = {5104-5110},
  number = {16},
  optnote = {structure}
}

@ARTICLE{asai03,
  author = {Asai, Y. and Yakushi, T. and Kawagishi, I. and Homma, M.},
  title = {{Ion-coupling determinants of Na$^+$-driven and H$^+$-driven flagellar
	motors}},
  journal = {Journal of Molecular Biology},
  year = {2003},
  volume = {327},
  pages = {453-463},
  number = {2},
  month = {Mar},
  abstract = {{The bacterial flagellar motor is a tiny molecular machine that uses
	a transmembrane flux of H(+) or Na(+) ions to drive flagellar rotation.
	In proton-driven motors, the membrane proteins MotA and MotB interact
	via their transmembrane regions to form a proton channel. The sodium-driven
	motors that power the polar flagellum of Vibrio species contain homologs
	of MotA and MotB, called PomA and PomB. They require the unique proteins
	MotX and MotY. In this study, we investigated how ion selectivity
	is determined in proton and sodium motors. We found that Escherichia
	coli MotA/B restore motility in DeltapomAB Vibrio alginolyticus.
	Most hypermotile segregants isolated from this weakly motile strain
	contain mutations in motB. We constructed proteins in which segments
	of MotB were fused to complementary portions of PomB. A chimera joining
	the N terminus of PomB to the periplasmic C terminus of MotB (PotB7(E))
	functioned with PomA as the stator of a sodium motor, with or without
	MotX/Y. This stator (PomA/PotB7(E)) supported sodium-driven motility
	in motA or motB E.coli cells, and the swimming speed was even higher
	than with the original stator of E.coli MotA/B. We conclude that
	the cytoplasmic and transmembrane domains of PomA/B are sufficient
	for sodium-driven motility. However, MotA expressed with a B subunit
	containing the N terminus of MotB fused to the periplasmic domain
	of PomB (MomB7(E)) supported sodium-driven motility in a MotX/Y-dependent
	fashion. Thus, although the periplasmic domain of PomB is not necessary
	for sodium-driven motility in a PomA/B motor, it can convert a MotA/B
	proton motor into a sodium motor.}},
  pmid = {12628250},
  url = {http://www.hubmed.org/display.cgi?uids=12628250}
}

@ARTICLE{ashkin:97,
  author = {Ashkin, A.},
  title = {Optical trapping and manipulation of neutral particles using lasers},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1997},
  optnote = {tweezers},
  optpages = {4853-4860},
  optvolume = {94}
}

@ARTICLE{ashkin:92,
  author = {Ashkin, A.},
  title = {Forces of a single-beam gradient laser trap on a dielectric sphere
	in the ray optics regime},
  journal = {Biophysical Journal},
  year = {1992},
  optnote = {tweezers},
  optpages = {569-582},
  optvolume = {61}
}

@ARTICLE{ashkin:87,
  author = {Ashkin, A. and Dziedzic, JM. and Yamane, T.},
  title = {Optical trapping and manipulation of single cells using infrared
	laser beams},
  journal = {Nature},
  year = {1987},
  volume = {330},
  pages = {769-771},
  optnote = {tweezers}
}

@ARTICLE{atsumi:01,
  author = {Atsumi, T.},
  title = {An ultrasonic motor model for bacterial flagellar motors},
  journal = {Journal of Theoretical Biology},
  year = {2001},
  optnote = {models},
  optpages = {31-51},
  optvolume = {213}
}

@ARTICLE{atsumi:96,
  author = {Atsumi, T. and Maekawa, Y. and Yamada, T. and Kawagishi, I. and Imae,
	Y. and Homma, M.},
  title = {Effect of Viscosity on Swimming by the Lateral and Polar Flagella
	of {\it Vibrio alginolyticus}},
  journal = {Journal of Bacteriology},
  year = {1996},
  volume = {178},
  pages = {5024-5026},
  number = {16},
  optnote = {vibrio}
}

@ARTICLE{atsumi:92,
  author = {Atsumi, T. and McCarter, L. and Imae, Y.},
  title = {Polar and lateral flagellar motors of marine vibrio are driven by
	different ion-motive forces},
  journal = {Nature},
  year = {1992},
  volume = {355},
  pages = {182-184},
  number = {6356},
  optnote = {vibrio}
}

@ARTICLE{attmannspacher2005csm,
  author = {Attmannspacher, U. and Scharf, B. and Schmitt, R.},
  title = {{Control of speed modulation (chemokinesis) in the unidirectional
	rotary motor of Sinorhizobium meliloti}},
  journal = {Molecular Microbiology},
  year = {2005},
  volume = {56},
  pages = {708--718},
  number = {3},
  publisher = {Blackwell Synergy}
}

@ARTICLE{baker04,
  author = {Baker, JE. and Krementsova, EB. and Kennedy, GG. and Armstrong, A.
	and Trybus, KM. and Warshaw, DM.},
  title = {{Myosin V processivity: multiple kinetic pathways for head-to-head
	coordination}},
  journal = {Proceedings of the National Academy of Science USA},
  year = {2004},
  volume = {101},
  pages = {5542-5546},
  number = {15},
  month = {Apr},
  abstract = {{Myosin V, a double-headed molecular motor, transports organelles
	within cells by walking processively along actin, a process that
	requires coordination between the heads. To understand the mechanism
	underlying this coordination, processive runs of single myosin V
	molecules were perturbed by varying nucleotide content. Contrary
	to current views, our results show that the two heads of a myosin
	V molecule communicate, not through any one mechanism but through
	an elaborate system of cooperative mechanisms involving multiple
	kinetic pathways. These mechanisms introduce redundancy and safeguards
	that ensure robust processivity under differing physiologic demands.}},
  pmid = {15056760},
  url = {http://www.hubmed.org/display.cgi?uids=15056760}
}

@ARTICLE{baker2006stb,
  author = {Baker, M.D. and Wolanin, P.M. and Stock, J.B.},
  title = {{Signal transduction in bacterial chemotaxis}},
  journal = {Bioessays},
  year = {2006},
  volume = {28},
  pages = {9--22},
  number = {1}
}

@ARTICLE{bath05,
  author = {Bath, J. and Green, SJ. and Turberfield, AJ.},
  title = {{A free-running DNA motor powered by a nicking enzyme}},
  journal = {Nature Structural and Molecular Biology},
  year = {2005},
  volume = {44},
  pages = {4358-4361},
  number = {28},
  month = {Jul},
  abstract = {{}},
  pmid = {15959864},
  url = {http://www.hubmed.org/display.cgi?uids=15959864}
}

@ARTICLE{berg2008bfm,
  author = {Berg, H.C.},
  title = {{Bacterial flagellar motor}},
  journal = {Current Biology},
  year = {2008},
  volume = {18},
  pages = {689--691},
  number = {16},
  publisher = {Elsevier}
}

@ARTICLE{berg03,
  author = {Berg, H.C.},
  title = {{The rotary motor of bacterial flagella}},
  journal = {Annual Review of Biochemistry},
  year = {2003},
  volume = {72},
  pages = {19-54},
  abstract = {{Flagellated bacteria, such as Escherichia coli, swim by rotating
	thin helical filaments, each driven at its base by a reversible rotary
	motor, powered by an ion flux. A motor is about 45 nm in diameter
	and is assembled from about 20 different kinds of parts. It develops
	maximum torque at stall but can spin several hundred Hz. Its direction
	of rotation is controlled by a sensory system that enables cells
	to accumulate in regions deemed more favorable. We know a great deal
	about motor structure, genetics, assembly, and function, but we do
	not really understand how it works. We need more crystal structures.
	All of this is reviewed, but the emphasis is on function.}},
  pmid = {12500982},
  url = {http://www.hubmed.org/display.cgi?uids=12500982}
}

@ARTICLE{berg2000mbb,
  author = {Berg, H.C.},
  title = {{Motile behavior of bacteria}},
  journal = {Physics Today},
  year = {2000},
  volume = {53},
  pages = {24-30},
  number = {1},
  publisher = {AMERICAN INSTITUTE OF PHYSICS}
}

@ARTICLE{berg:00,
  author = {Berg, H.C.},
  title = {Constraints on models for the flagellar rotary motor},
  journal = {Philosophical Transactions of the Royal Society of London B},
  year = {2000},
  volume = {355},
  pages = {491-501},
  optnote = {models}
}

@ARTICLE{berg:98,
  author = {Berg, HC.},
  title = {Keeping up with the F1-ATPase},
  journal = {Nature},
  year = {1998},
  volume = {394},
  pages = {324-325},
  optnote = {f1fo}
}

@BOOK{berg,
  title = {Random Walks in Biology},
  publisher = {Princeton University Press},
  year = {1993},
  author = {Berg, H.C.},
  optkey = {0-619-00064-6},
  optnote = {textbook}
}

@ARTICLE{berg:88,
  author = {Berg, HC.},
  title = {A physicist looks at bacterial chemotaxis},
  journal = {Cold Spring Harbor Symposia on Quantitative Biology},
  year = {1988},
  volume = {LIII},
  pages = {1-9},
  optnote = {taxis}
}

@ARTICLE{berg:74,
  author = {Berg, HC.},
  title = {Dynamic properties of bacterial flagellar motors},
  journal = {Nature},
  year = {1974},
  volume = {249},
  pages = {77-79},
  optnote = {general motors}
}

@ARTICLE{berg:73,
  author = {Berg, HC. and Anderson, RA.},
  title = {Bacteria swim by rotating their flagellar filaments},
  journal = {Nature},
  year = {1973},
  volume = {245},
  pages = {380-382},
  optnote = {general motors}
}

@ARTICLE{berg:93,
  author = {Berg, HC. and Turner, L.},
  title = {Torque generated by the flagellar motor of \textit{Escherichia coli}},
  journal = {Biophysical Journal},
  year = {1993},
  volume = {65},
  pages = {2201-2216},
  optnote = {ecoli}
}

@ARTICLE{berns1989uli,
  author = {Berns, M.W. and Wright, W.H. and Tromberg, B.J. and Profeta, G.A.
	and Andrews, J.J. and Walter, R.J.},
  title = {{Use of a Laser-Induced Optical Force Trap to Study Chromosome Movement
	on the Mitotic Spindle}},
  journal = {Proceedings of the National Academy of Sciences},
  year = {1989},
  volume = {86},
  pages = {4539--4543},
  number = {12},
  publisher = {National Acad Sciences}
}

@ARTICLE{berry:93,
  author = {Berry, RM.},
  title = {Torque and switching in the bacterial flagellar motor: an electrostatic
	model},
  journal = {Biophysical Journal},
  year = {1993},
  volume = {64},
  pages = {961-973},
  optnote = {models}
}

@ARTICLE{berry00,
  author = {Berry, R.M. and Armitage, J.P.},
  title = {{Response kinetics of tethered \normalfont{Rhodobacter sphaeroides}
	\textit{to changes in light intensity}}},
  journal = {Biophysical Journal},
  year = {2000},
  volume = {78},
  pages = {1207-1215},
  number = {3},
  month = {Mar},
  abstract = {{Rhodobacter sphaeroides can swim toward a wide range of attractants
	(a process known as taxis), propelled by a single rotating flagellum.
	The reversals of motor direction that cause tumbles in Eschericia
	coli taxis are replaced by brief motor stops, and taxis is controlled
	by a complex sensory system with multiple homologues of the E. coli
	sensory proteins. We tethered photosynthetically grown cells of R.
	sphaeroides by their flagella and measured the response of the flagellar
	motor to changes in light intensity. The unstimulated bias (probability
	of not being stopped) was significantly larger than the bias of tethered
	E. coli but similar to the probability of not tumbling in swimming
	E. coli. Otherwise, the step and impulse responses were the same
	as those of tethered E. coli to chemical attractants. This indicates
	that the single motor and multiple sensory signaling pathways in
	R. sphaeroides generate the same swimming response as several motors
	and a single pathway in E. coli, and that the response of the single
	motor is directly observable in the swimming pattern. Photo-responses
	were larger in the presence of cyanide or the uncoupler carbonyl
	cyanide 4-trifluoromethoxyphenylhydrazone (FCCP), consistent with
	the photo-response being detected via changes in the rate of electron
	transport.}},
  pmid = {10692310},
  url = {http://www.hubmed.org/display.cgi?uids=10692310}
}

@ARTICLE{berry99,
  author = {Berry, R.M. and Armitage, J.P.},
  title = {{The bacterial flagella motor}},
  journal = {Advances in Microbial Physiology},
  year = {1999},
  volume = {41},
  pages = {291-337},
  abstract = {{The bacterial flagellum is probably the most complex organelle found
	in bacteria. Although the ribosome may be made of slightly more subunits,
	the bacterial flagellum is a more organized and complex structure.
	The limited number of flagella must be targeted to the correct place
	on the cell membrane and a structure with cytoplasmic, cytoplasmic
	membrane, outer membrane and extracellular components must be assembled.
	The process of controlled transcription and assembly is still not
	fully understood. Once assembled, the motor complex in the cytoplasmic
	membrane rotates, driven by the transmembrane ion gradient, at speeds
	that can reach many 100 Hz, driving the bacterial cell at several
	body lengths a second. This coupling of an electrochemical gradient
	to mechanical rotational work is another fascinating feature of the
	bacterial motor. A significant percentage of a bacterium's energy
	may be used in synthesizing the complex structure of the flagellum
	and driving its rotation. Although patterns of swimming may be random
	in uniform environments, in the natural environment, where cells
	are confronted with gradients of metabolites and toxins, motility
	is used to move bacteria towards their optimum environment for growth
	and survival. A sensory system therefore controls the switching frequency
	of the rotating flagellum. This review deals primarily with the structure
	and operation of the bacterial flagellum. There has been a great
	deal of research in this area over the past 20 years and only some
	of this has been included. We apologize in advance if certain areas
	are covered rather thinly, but hope that interested readers will
	look at the excellent detailed reviews on those areas cited at those
	points.}},
  pmid = {10500848},
  url = {http://www.hubmed.org/display.cgi?uids=10500848}
}

@ARTICLE{berry:99,
  author = {Berry, RM. and Berg, HC.},
  title = {Torque Generated by the Flagellar Motor of \textnormal{Escherichia
	coli} while Driven Backward},
  journal = {Biophysical Journal},
  year = {1999},
  volume = {76},
  pages = {580-587},
  optnote = {ecoli}
}

@ARTICLE{berry:97,
  author = {Berry, RM. and Berg, HC.},
  title = {Absence of a barrier to backward rotation of the bacterial flagellar
	motor demonstrated with optical tweezers},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1997},
  volume = {94},
  pages = {14433-14437},
  optnote = {general motors}
}

@ARTICLE{berry:95,
  author = {Berry, RM. and Turner, L. and Berg, HC.},
  title = {Mechanical limits of bacterial flagellar motors probed by electrorotation},
  journal = {Biophysical Journal},
  year = {1995},
  volume = {69},
  pages = {280-286},
  optnote = {general motors}
}

@ARTICLE{bischoff1991sac,
  author = {Bischoff, D.S. and Ordal, G.W.},
  title = {{Sequence and characterization of \normalfont{Bacillus subtilis}
	\textit{CheB, a homolog of} \normalfont{Escherichia coli} \textit{CheY,
	and its role in a different mechanism of chemotaxis}}},
  journal = {Journal of Biological Chemistry},
  year = {1991},
  volume = {266},
  pages = {12301-12305},
  number = {19},
  publisher = {ASBMB}
}

@ARTICLE{blair2003fmd,
  author = {Blair, D.F.},
  title = {{Flagellar movement driven by proton translocation}},
  journal = {FEBS Letters},
  year = {2003},
  volume = {545},
  pages = {86--95},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{blair90,
  author = {Blair, DF. and Berg, HC.},
  title = {{The MotA protein of E. coli is a proton-conducting component of
	the flagellar motor}},
  journal = {Cell},
  year = {1990},
  volume = {60},
  pages = {439-449},
  number = {3},
  month = {Feb},
  abstract = {{A number of mutants of motA, a gene necessary for flagellar rotation
	in E. coli, were isolated and characterized. Many mutations were
	dominant, owing to competition between functional and nonfunctional
	MotA for a limited number of sites on the flagellar motor. A new
	class of mutant was discovered in which flagellar torque is normal
	at low speeds but reduced at high speeds. Hydrogen isotope effects
	on these mutants indicate that MotA catalyzes proton transfer. We
	confirmed an earlier observation that overproduction of MotA leads
	to accumulation of the protein in the cytoplasmic membrane and to
	significant decreases in growth rate. When nonfunctional mutant variants
	of MotA were overproduced instead, they accumulated in the cytoplasmic
	membrane, but growth was not impaired. These results also suggest
	that MotA conducts protons. This was confirmed by measuring the proton
	permeabilities of vesicles containing wild-type or mutant MotA proteins.}},
  pmid = {2154333},
  url = {http://www.hubmed.org/display.cgi?uids=2154333}
}

@ARTICLE{blair88,
  author = {Blair, D.F. and Berg, H.C.},
  title = {{Restoration of torque in defective flagellar motors}},
  journal = {Science},
  year = {1988},
  volume = {242},
  pages = {1678-1681},
  number = {4886},
  month = {Dec},
  abstract = {{Paralyzed motors of motA and motB point and deletion mutants of Escherichia
	coli were repaired by synthesis of wild-type protein. As found earlier
	with a point mutant of motB, torque was restored in a series of equally
	spaced steps. The size of the steps was the same for both MotA and
	MotB. Motors with one torque generator spent more time spinning counterclockwise
	than did motors with two or more generators. In deletion mutants,
	stepwise decreases in torque, rare in point mutants, were common.
	Several cells stopped accelerating after eight steps, suggesting
	that the maximum complement of torque generators is eight. Each generator
	appears to contain both MotA and MotB.}},
  pmid = {2849208},
  url = {http://www.hubmed.org/display.cgi?uids=2849208}
}

@ARTICLE{Blair:2008:Science:18566286,
  author = {Blair, K.M. and Turner, L. and Winkelman, J.T. and Berg, H.C. and
	Kearns, D.B.},
  title = {{A molecular clutch disables flagella in the \normalfont{Bacillus
	subtilis} \textit{biofilm}}},
  journal = {Science},
  year = {2008},
  volume = {320},
  pages = {1636-1638},
  number = {5883},
  month = {Jun},
  abstract = {Biofilms are multicellular aggregates of sessile bacteria encased
	by an extracellular matrix and are important medically as a source
	of drug-resistant microbes. In Bacillus subtilis, we found that an
	operon required for biofilm matrix biosynthesis also encoded an inhibitor
	of motility, EpsE. EpsE arrested flagellar rotation in a manner similar
	to that of a clutch, by disengaging motor force-generating elements
	in cells embedded in the biofilm matrix. The clutch is a simple,
	rapid, and potentially reversible form of motility control.},
  doi = {10.1126/science.1157877},
  pmid = {18566286},
  url = {http://www.hubmed.org/display.cgi?uids=18566286}
}

@ARTICLE{block03,
  author = {Block, SM. and Asbury, CL. and Shaevitz, JW. and Lang, MJ.},
  title = {{Probing the kinesin reaction cycle with a 2D optical force clamp}},
  journal = {Proceedings of the National Academy of Science USA},
  year = {2003},
  volume = {100},
  pages = {2351-2356},
  number = {5},
  month = {Mar},
  abstract = {{With every step it takes, the kinesin motor undergoes a mechanochemical
	reaction cycle that includes the hydrolysis of one ATP molecule,
	ADPP(i) release, plus an unknown number of additional transitions.
	Kinesin velocity depends on both the magnitude and the direction
	of the applied load. Using specialized apparatus, we subjected single
	kinesin molecules to forces in differing directions. Sideways and
	forward loads up to 8 pN exert only a weak effect, whereas comparable
	forces applied in the backward direction lead to stall. This strong
	directional bias suggests that the primary working stroke is closely
	aligned with the microtubule axis. Sideways loads slow the motor
	asymmetrically, but only at higher ATP levels, revealing the presence
	of additional, load-dependent transitions late in the cycle. Fluctuation
	analysis shows that the cycle contains at least four transitions,
	and confirms that hydrolysis remains tightly coupled to stepping.
	Together, our findings pose challenges for models of kinesin motion.}},
  pmid = {12591957},
  url = {http://www.hubmed.org/display.cgi?uids=12591957}
}

@ARTICLE{block1984sif,
  author = {Block, S.M. and Berg, H.C.},
  title = {{Successive incorporation of force-generating units in the bacterial
	rotary motor}},
  journal = {Nature},
  year = {1984},
  volume = {309},
  pages = {470--472},
  number = {5967}
}

@ARTICLE{block:91,
  author = {Block, S.M. and Blair, D.F. and Berg, H.C.},
  title = {Compliance of bacterial polyhooks measured with optical tweezers},
  journal = {Cytometry},
  year = {1991},
  volume = {12},
  pages = {492-496},
  optnote = {structure}
}

@ARTICLE{block:89,
  author = {Block, SM. and Blair, DF. and Berg, HC.},
  title = {Compliance of bacterial flagella measured with optical tweezers},
  journal = {Nature},
  year = {1989},
  volume = {338},
  pages = {514-517},
  number = {6215},
  optnote = {structure}
}

@ARTICLE{block1990bms,
  author = {Block, S.M. and Goldstein, L.S.B. and Schnapp, B.J.},
  title = {{Bead movement by single kinesin molecules studied with optical tweezers}},
  journal = {Nature},
  year = {1990},
  volume = {348},
  pages = {348--352},
  number = {6299}
}

@ARTICLE{block1983akb,
  author = {Block, S.M. and Segall, J.E. and Berg, H.C.},
  title = {{Adaptation kinetics in bacterial chemotaxis}},
  journal = {Journal of Bacteriology},
  year = {1983},
  volume = {154},
  pages = {312-323},
  number = {1},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{bockelmann2002udo,
  author = {Bockelmann, U. and Thomen, P. and Essevaz-Roulet, B. and Viasnoff,
	V. and Heslot, F.},
  title = {{Unzipping DNA with Optical Tweezers: High Sequence Sensitivity and
	Force Flips}},
  journal = {Biophysical Journal},
  year = {2002},
  volume = {82},
  pages = {1537--1553},
  number = {3},
  publisher = {Biophysical Soc}
}

@ARTICLE{bourret1993app,
  author = {Bourret, R.B. and Drake, S.K. and Chervitz, S.A. and Simon, M.I.
	and Falke, J.J.},
  title = {{Activation of the phosphosignaling protein CheY. II. Analysis of
	activated mutants by 19F NMR and protein engineering}},
  journal = {Journal of Biological Chemistry},
  year = {1993},
  volume = {268},
  pages = {13089--13096},
  number = {18},
  publisher = {ASBMB}
}

@ARTICLE{bourret1990car,
  author = {Bourret, R.B. and Hess, J.F. and Simon, M.I.},
  title = {{Conserved aspartate residues and phosphorylation in signal transduction
	by the chemotaxis protein CheY}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {1990},
  volume = {87},
  pages = {41-45},
  number = {1},
  publisher = {National Acad Sciences}
}

@ARTICLE{braun:01,
  author = {Braun, TF. and Blair, DF.},
  title = {{Targeted disulfide cross-linking of the MotB protein of \textnormal{Escherichia
	coli}: evidence for two H+ channels in the stator complex}},
  journal = {Biochemistry},
  year = {2001},
  volume = {40},
  pages = {13051-13059},
  optnote = {structure}
}

@ARTICLE{braun:99,
  author = {Braun, TF. and Poulson, S. and Gully, JB. and Empey, C. and Van Way,
	S. and Putnam, A. and Blair, DF.},
  title = {{Function of proline residues of MotA in torque generation by the
	flagellar motor of \textnormal{Escherichia coli}}},
  journal = {Journal of Bacteriology},
  year = {1999},
  volume = {181},
  pages = {3542-3551},
  number = {11},
  optnote = {structure}
}

@ARTICLE{bray2006csp,
  author = {Bray, D. and Duke, T.A.J.},
  title = {{Conformational spread: the propagation of allosteric states in large
	multiprotein complexes}},
  journal = {Rendiconti Lincei},
  year = {2006},
  volume = {17},
  pages = {221-241},
  number = {1},
  publisher = {Springer}
}

@ARTICLE{bren1998ntf,
  author = {Bren, A. and Eisenbach, M.},
  title = {{The N terminus of the flagellar switch protein, FliM, is the binding
	domain for the chemotactic response regulator, CheY}},
  journal = {Journal of Molecular Biology},
  year = {1998},
  volume = {278},
  pages = {507--514},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{brokaw:01,
  author = {Brokaw, C.J.},
  title = {Protein-protein ratchets: stochastic simulation and application to
	processive enzymes},
  journal = {Biophysical Journal},
  year = {2001},
  optnote = {models},
  optpages = {1333-1344},
  optvolume = {81}
}

@ARTICLE{brown:02,
  author = {Brown, P.N. and Hill, C.P. and Blair, D.F.},
  title = {{Crystal structure of the middle and C-terminal domains of the flagellar
	rotor protein FliG}},
  journal = {The EMBO Journal},
  year = {2002},
  volume = {21},
  pages = {3225-3234},
  number = {13},
  optnote = {structure}
}

@ARTICLE{brown05,
  author = {Brown, PN. and Mathews, MA. and Joss, LA. and Hill, CP. and Blair,
	DF.},
  title = {{Crystal structure of the flagellar rotor protein FliN from Thermotoga
	maritima}},
  journal = {Journal of Bacteriology},
  year = {2005},
  volume = {187},
  pages = {2890-2902},
  number = {8},
  month = {Apr},
  abstract = {{FliN is a component of the bacterial flagellum that is present at
	levels of more than 100 copies and forms the bulk of the C ring,
	a drum-shaped structure at the inner end of the basal body. FliN
	interacts with FliG and FliM to form the rotor-mounted switch complex
	that controls clockwise-counterclockwise switching of the motor.
	In addition to its functions in motor rotation and switching, FliN
	is thought to have a role in the export of proteins that form the
	exterior structures of the flagellum (the rod, hook, and filament).
	Here, we describe the crystal structure of most of the FliN protein
	of Thermotoga maritima. FliN is a tightly intertwined dimer composed
	mostly of beta sheet. Several well-conserved hydrophobic residues
	form a nonpolar patch on the surface of the molecule. A mutation
	in the hydrophobic patch affected both flagellar assembly and switching,
	showing that this surface feature is important for FliN function.
	The association state of FliN in solution was studied by analytical
	ultracentrifugation, which provided clues to the higher-level organization
	of the protein. T. maritima FliN is primarily a dimer in solution,
	and T. maritima FliN and FliM together form a stable FliM(1)-FliN(4)
	complex. Escherichia coli FliN forms a stable tetramer in solution.
	The arrangement of FliN subunits in the tetramer was modeled by reference
	to the crystal structure of tetrameric HrcQB(C), a related protein
	that functions in virulence factor secretion in Pseudomonas syringae.
	The modeled tetramer is elongated, with approximate dimensions of
	110 by 40 by 35 Angstroms, and it has a large hydrophobic cleft formed
	from the hydrophobic patches on the dimers. On the basis of the present
	data and available electron microscopic images, we propose a model
	for the organization of FliN subunits in the C ring.}},
  pmid = {15805535},
  url = {http://www.hubmed.org/display.cgi?uids=15805535}
}

@ARTICLE{Brown:2007,
  author = {Brown, P.N. and Terrazas, M. and Paul, K. and Blair, D.F.},
  title = {{Mutational analysis of the flagellar protein FliG: sites of interaction
	with FliM and implications for organization of the switch complex}},
  journal = {Journal of Bacteriology},
  year = {2007},
  volume = {189},
  pages = {305-312},
  number = {2},
  month = {Jan},
  abstract = {The switch complex at the base of the bacterial flagellum is essential
	for flagellar assembly, rotation, and switching. In Escherichia coli
	and Salmonella, the complex contains about 26 copies of FliG, 34
	copies of FliM, and more then 100 copies of FliN, together forming
	the basal body C ring. FliG is involved most directly in motor rotation
	and is located in the upper (membrane-proximal) part of the C ring.
	A crystal structure of the middle and C-terminal parts of FliG shows
	two globular domains connected by an alpha-helix and a short extended
	segment. The middle domain of FliG has a conserved surface patch
	formed by the residues EHPQ(125-128) and R(160) (the EHPQR motif),
	and the C-terminal domain has a conserved surface hydrophobic patch.
	To examine the functional importance of these and other surface features
	of FliG, we made mutations in residues distributed over the protein
	surface and measured the effects on flagellar assembly and function.
	Mutations preventing flagellar assembly occurred mainly in the vicinity
	of the EHPQR motif and the hydrophobic patch. Mutations causing aberrant
	clockwise or counterclockwise motor bias occurred in these same regions
	and in the waist between the upper and lower parts of the C-terminal
	domain. Pull-down assays with glutathione S-transferase-FliM showed
	that FliG interacts with FliM through both the EHPQR motif and the
	hydrophobic patch. We propose a model for the organization of FliG
	and FliM subunits that accounts for the FliG-FliM interactions identified
	here and for the different copy numbers of FliG and FliM in the flagellum.},
  doi = {10.1128/JB.01281-06},
  pmid = {17085573},
  url = {http://www.hubmed.org/display.cgi?uids=17085573}
}

@ARTICLE{brown1993crs,
  author = {Brown, S. and Poole, P.S. and Jeziorska, W. and Armitage, J.P.},
  title = {{Chemokinesis in \normalfont{Rhodobacter sphaeroides} \textit{is
	the result of a long term increase in the rate of flagellar rotation}}},
  journal = {Biochimica et biophysica acta. Bioenergetics},
  year = {1993},
  volume = {1141},
  pages = {309-312},
  number = {2-3},
  publisher = {Elsevier Science}
}

@ARTICLE{bustamante:01,
  author = {Bustamante, C. and Keller, D. and Oster, G.},
  title = {The physics of molecular motors},
  journal = {Accounts of Chemical Research},
  year = {2001},
  optnote = {models},
  optpages = {412-420},
  optvolume = {34}
}

@ARTICLE{bustamante:00,
  author = {Bustamante, C. and Macosko, J.C. and Wuite, G.J.L.},
  title = {Grabbing the cat by the tail: manipulating molecules one by one},
  journal = {Nature Reviews},
  year = {2000},
  optnote = {tweezers},
  optpages = {130-136},
  optvolume = {1}
}

@ARTICLE{delcampo2007cct,
  author = {del Campo, A.M. and Ballado, T. and de la Mora, J. and Poggio, S.
	and Camarena, L. and Dreyfus, G.},
  title = {{Chemotactic control of the two flagellar systems of \normalfont{Rhodobacter
	sphaeroides} \textit{is mediated by different sets of CheY and FliM
	Proteins}}},
  journal = {Journal of Bacteriology},
  year = {2007},
  volume = {189},
  pages = {8397-8401},
  number = {22},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{carter05,
  author = {Carter, NJ. and Cross, RA.},
  title = {{Mechanics of the kinesin step}},
  journal = {Nature},
  year = {2005},
  volume = {435},
  pages = {308-312},
  number = {7040},
  month = {May},
  abstract = {{Kinesin is a molecular walking machine that organizes cells by hauling
	packets of components directionally along microtubules. The physical
	mechanism that impels directional stepping is uncertain. We show
	here that, under very high backward loads, the intrinsic directional
	bias in kinesin stepping can be reversed such that the motor walks
	sustainedly backwards in a previously undescribed mode of ATP-dependent
	backward processivity. We find that both forward and backward 8-nm
	steps occur on the microsecond timescale and that both occur without
	mechanical substeps on this timescale. The data suggest an underlying
	mechanism in which, once ATP has bound to the microtubule-attached
	head, the other head undergoes a diffusional search for its next
	site, the outcome of which can be biased by an applied load.}},
  pmid = {15902249},
  url = {http://www.hubmed.org/display.cgi?uids=15902249}
}

@ARTICLE{chan00,
  author = {Chan, KL. and Morgan, H. and Morgan, E. and Cameron, IT. and Thomas,
	MR.},
  title = {{Measurements of the dielectric properties of peripheral blood mononuclear
	cells and trophoblast cells using AC electrokinetic techniques}},
  journal = {Biochimica et Biophysica},
  year = {2000},
  volume = {1500},
  pages = {313-322},
  number = {3},
  month = {Mar},
  abstract = {{The separation of trophoblast cells from the maternal circulation
	could provide a valuable diagnostic tool for prenatal diagnosis of
	genetic abnormalities. This has been attempted using antibody methods,
	but due to non-specificity of the antibodies, maternal cell contamination
	remains a problem. We have investigated the potential of dielectrophoretic
	separation methods as a means of isolating trophoblast cells from
	mixed peripheral blood mononuclear cells. To determine the potential
	of this method the dielectric properties of trophoblast cells and
	mixed peripheral blood mononuclear cells were measured using dielectrophoretic
	crossover and single cell electrorotation methods. Both dielectrophoretic
	crossover data and electrorotation data gave an average specific
	membrane capacitance of the peripheral blood mononuclear cells of
	11.5 mF m(-2). Trophoblast cells prepared using three different methods
	had a higher average specific membrane capacitance in the range 13-18
	mF m(-2). The differences in capacitance between the cell types could
	be exploited as the basis of an AC electrokinetic-based system for
	the separation of trophoblast cells from peripheral blood mononuclear
	cells.}},
  pmid = {10699373},
  url = {http://www.hubmed.org/display.cgi?uids=10699373}
}

@ARTICLE{chemla:99,
  author = {Chemla, Y. and Grossman, H. and Lee, T. and Clarke, J. and Adamkiewicz,
	M. and Buchanan, B.},
  title = {A new study of bacterial motion: superconducting quantum interference
	device microscopy of magnetotactic bacteria},
  journal = {Biophysical Journal},
  year = {1999},
  optnote = {taxis},
  optpages = {3323-3330},
  optvolume = {76}
}

@ARTICLE{chen:00f,
  author = {Chen, X. and Berg, H.C.},
  title = {{Torque-speed relationship of the flagellar rotary motor of \normalfont{Escherichia
	coli}}},
  journal = {Biophysical Journal},
  year = {2000},
  volume = {78},
  pages = {1036-1041},
  optnote = {ecoli}
}

@ARTICLE{chen:00m,
  author = {Chen, X. and Berg, HC.},
  title = {Solvent-Isotope and pH Effects on Flagellar Rotation in {\it Escherichia
	coli}},
  journal = {Biophysical Journal},
  year = {2000},
  volume = {78},
  pages = {2280-2284},
  optnote = {ecoli}
}

@ARTICLE{cheney93,
  author = {Cheney, RE. and O'Shea, MK. and Heuser, JE. and Coelho, MV. and Wolenski,
	JS. and Espreafico, EM. and Forscher, P. and Larson, RE. and Mooseker,
	MS.},
  title = {{Brain myosin-V is a two-headed unconventional myosin with motor
	activity}},
  journal = {Cell},
  year = {1993},
  volume = {75},
  pages = {13-23},
  number = {1},
  month = {Oct},
  abstract = {{Chicken myosin-V is a member of a recently recognized class of myosins
	distinct from both the myosins-I and the myosins-II. We report here
	the purification, electron microscopic visualization, and motor properties
	of a protein of this class. Myosin-V molecules consist of two heads
	attached to an approximately 30 nm stalk that ends in a globular
	region of unknown function. Myosin-V binds to and decorates F-actin,
	has actin-activated magnesium-ATPase activity, and is a barbed-end-directed
	motor capable of moving actin filaments at rates of up to 400 nm/s.
	Myosin-V does not form filaments. Each myosin-V heavy chain is associated
	with approximately four calmodulin light chains as well as two less
	abundant proteins of 23 and 17 kd.}},
  pmid = {8402892},
  url = {http://www.hubmed.org/display.cgi?uids=8402892}
}

@ARTICLE{chung91,
  author = {Chung, SH. and Kennedy, RA.},
  title = {{Forward-backward non-linear filtering technique for extracting small
	biological signals from noise}},
  journal = {Journal of Neuroscience Methods},
  year = {1991},
  volume = {40},
  pages = {71-86},
  number = {1},
  month = {Nov},
  abstract = {{A novel and computationally efficient, non-linear signal processing
	technique for reducing background noise to reveal small biological
	signals is described. The signal estimate is formed by weighting
	the outputs of a set of causal (forward) and anti-causal (backward)
	predictors. The weights used to combine the predictors are adaptively
	determined at each data point to reflect the performance of the respective
	predictor within a short analysis window. The method is specifically
	designed for revealing fast transient signals dominated by noise,
	such as single-channel or post-synaptic currents. Markovian and exponentially
	decaying signals embedded in the amplifier noise were extracted using
	this method and compared with the original signals. The results of
	such simulations demonstrate the advantage of this non-linear method
	over low-pass filtering. Brief pulses imbedded in a broad-band amplifier
	noise can be reliably recovered using our non-linear filtering technique.
	Moreover, the kinetics of a single channel and the time constant
	of exponentially decaying signals can be measured with acceptable
	accuracy even when the signals are dominated by noise.}},
  pmid = {1795554},
  url = {http://www.hubmed.org/display.cgi?uids=1795554}
}

@ARTICLE{cluzel2000ubm,
  author = {Cluzel, P. and Surette, M. and Leibler, S.},
  title = {{An ultrasensitive bacterial motor revealed by monitoring signaling
	proteins in single cells}},
  journal = {Science},
  year = {2000},
  volume = {287},
  pages = {1652-1655},
  number = {5458},
  publisher = {AAAS}
}

@ARTICLE{coppin:96,
  author = {Coppin, C.M. and Finer, J.T. and Spudich, J.A. and Vale, R.D.},
  title = {Detection of sub-8-nm movements of kinesin by high resolution optical-trap
	microscopy},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1996},
  volume = {93},
  pages = {1913-1917},
  month = {March}
}

@ARTICLE{cross04,
  author = {Cross, RA.},
  title = {{Molecular motors: Dynein's gearbox}},
  journal = {Curr Biol},
  year = {2004},
  volume = {14},
  pages = {355-356},
  number = {9},
  month = {May},
  pmid = {15120091},
  url = {http://www.hubmed.org/display.cgi?uids=15120091}
}

@ARTICLE{cross04a,
  author = {Cross, RA.},
  title = {{Molecular motors: kinesin's interesting limp}},
  journal = {Curr Biol},
  year = {2004},
  volume = {14},
  pages = {158-159},
  number = {4},
  month = {Feb},
  abstract = {{An ingenious new experiment used a form of kinesin with one slow
	head and one fast head to demonstrate definitively that this motor
	protein moves along a microtubule using alternating left and right
	steps.}},
  pmid = {15027469},
  url = {http://www.hubmed.org/display.cgi?uids=15027469}
}

@ARTICLE{cross04b,
  author = {Cross, RA.},
  title = {{The kinetic mechanism of kinesin}},
  journal = {Trends Biochem Sci},
  year = {2004},
  volume = {29},
  pages = {301-309},
  number = {6},
  month = {Jun},
  abstract = {{The chemical kinetic mechanism of kinesin (K) is considered by using
	a consensus scheme incorporating biochemically defined open, closed
	and trapped states. In the absence of microtubules, the dominant
	species is a trapped K*ADP state, which is defined by its ultra-slow
	release of ADP (off rate, k(off) approximately 0.002 s(-1)) and weak
	microtubule binding (dissociation constant, K(d) approximately 10-20
	microM). Once bound, this trapped state equilibrates with a strongly
	binding open state that rapidly releases ADP (k(off) approximately
	300 s(-1)). After ADP release, Mg*ATP binds (on rate, k(on) approximately
	2 microM(-1)s(-1)) driving formation of a closed state that is defined
	by hydrolysis competence and by strong binding to microtubules. Hydrolysis
	(k(hyd) approximately 100-300 s(-1)) and phosphate release (k(off)>100
	s(-1)) both occur in this microtubule-bound closed state. Phosphate
	release acts as a gate that controls reversion to the trapped K*ADP
	state, which detaches from the microtubule, completing the cycle.}},
  pmid = {15276184},
  url = {http://www.hubmed.org/display.cgi?uids=15276184}
}

@ARTICLE{darnton2007tat,
  author = {Darnton, N.C. and Turner, L. and Rojevsky, S. and Berg, H.C.},
  title = {{On torque and tumbling in swimming \normalfont{Escherichia coli}}},
  journal = {Journal of Bacteriology},
  year = {2007},
  volume = {189},
  pages = {1756-1764},
  number = {5},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{datsenko00,
  author = {Datsenko, KA. and Wanner, BL.},
  title = {{One-step inactivation of chromosomal genes in \textnormal{Escherichia
	coli} K-12 using PCR products}},
  journal = {Proceedings of the National Academy of Science USA},
  year = {2000},
  volume = {97},
  pages = {6640-6645},
  number = {12},
  month = {Jun},
  abstract = {{We have developed a simple and highly efficient method to disrupt
	chromosomal genes in Escherichia coli in which PCR primers provide
	the homology to the targeted gene(s). In this procedure, recombination
	requires the phage lambda Red recombinase, which is synthesized under
	the control of an inducible promoter on an easily curable, low copy
	number plasmid. To demonstrate the utility of this approach, we generated
	PCR products by using primers with 36- to 50-nt extensions that are
	homologous to regions adjacent to the gene to be inactivated and
	template plasmids carrying antibiotic resistance genes that are flanked
	by FRT (FLP recognition target) sites. By using the respective PCR
	products, we made 13 different disruptions of chromosomal genes.
	Mutants of the arcB, cyaA, lacZYA, ompR-envZ, phnR, pstB, pstCA,
	pstS, pstSCAB-phoU, recA, and torSTRCAD genes or operons were isolated
	as antibiotic-resistant colonies after the introduction into bacteria
	carrying a Red expression plasmid of synthetic (PCR-generated) DNA.
	The resistance genes were then eliminated by using a helper plasmid
	encoding the FLP recombinase which is also easily curable. This procedure
	should be widely useful, especially in genome analysis of E. coli
	and other bacteria because the procedure can be done in wild-type
	cells.}},
  pmid = {10829079},
  url = {http://www.hubmed.org/display.cgi?uids=10829079}
}

@ARTICLE{cruz:99,
  author = {De La Cruz, E.M. and Wells, A.L. and Rosenfeld, S.S. and Ostap, E.M.
	and Sweeney, H.L.},
  title = {The kinetic mechanism of Myosin-V},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1999},
  optnote = {myosin},
  optnumber = {24},
  optpages = {13726-13731},
  optvolume = {96}
}

@ARTICLE{decoursey:99,
  author = {DeCoursey, Thomas E. and Cherney, V.V.},
  title = {Common Themes and Problems of Bioenergetics and Voltage-Gated Proton
	Channels},
  journal = {Biochimica et Biophysica Acta},
  year = {2000},
  optnote = {energetics},
  optnumber = {1458},
  optpages = {104-119}
}

@ARTICLE{deng:00,
  author = {Deng, T. and Wu, H. and Brittain, S.T. and Whitesides, G.M.},
  title = {Prototyping of masks, masters and stamps/molds for soft lithography
	using an office printer and photographic reduction},
  journal = {Analytical Chemistry},
  year = {2000},
  optnote = {nano fab},
  optnumber = {14},
  optpages = {3176-3180},
  optvolume = {72}
}

@ARTICLE{derosier98,
  author = {DeRosier, DJ.},
  title = {{The turn of the screw: the bacterial flagellar motor}},
  journal = {Cell},
  year = {1998},
  volume = {93},
  pages = {17-20},
  number = {1},
  month = {Apr},
  pmid = {9546387},
  url = {http://www.hubmed.org/display.cgi?uids=9546387}
}

@ARTICLE{diez04,
  author = {Diez, M. and Zimmermann, B. and B{\"o}rsch, M. and K{\"o}nig, M.
	and Schweinberger, E. and Steigmiller, S. and Reuter, R. and Felekyan,
	S. and Kudryavtsev, V. and Seidel, CA. and Gr{\"a}ber, P.},
  title = {{Proton-powered subunit rotation in single membrane-bound F0F1-ATP
	synthase}},
  journal = {Nature Structural and Molecular Biology},
  year = {2004},
  volume = {11},
  pages = {135-141},
  number = {2},
  month = {Feb},
  abstract = {{Synthesis of ATP from ADP and phosphate, catalyzed by F(0)F(1)-ATP
	synthases, is the most abundant physiological reaction in almost
	any cell. F(0)F(1)-ATP synthases are membrane-bound enzymes that
	use the energy derived from an electrochemical proton gradient for
	ATP formation. We incorporated double-labeled F(0)F(1)-ATP synthases
	from Escherichia coli into liposomes and measured single-molecule
	fluorescence resonance energy transfer (FRET) during ATP synthesis
	and hydrolysis. The gamma subunit rotates stepwise during proton
	transport-powered ATP synthesis, showing three distinct distances
	to the b subunits in repeating sequences. The average durations of
	these steps correspond to catalytic turnover times upon ATP synthesis
	as well as ATP hydrolysis. The direction of rotation during ATP synthesis
	is opposite to that of ATP hydrolysis.}},
  pmid = {14730350},
  url = {http://www.hubmed.org/display.cgi?uids=14730350}
}

@ARTICLE{dimroth:99,
  author = {Dimroth, P. and Kaim, G. and Matthey, U.},
  title = {Crucial role of the membrane potential for ATP synthesis by F1Fo
	ATP synthases},
  journal = {Journal of Experimental Biology},
  year = {1999},
  optnote = {f1fo},
  optnumber = {203},
  optpages = {51-59}
}

@ARTICLE{duffy:98,
  author = {Duffy, DC. and McDonald, JC. and Schueller, OJA. and Whitesides,
	GM.},
  title = {Rapid prototyping of microfluidic systems in poly(dimethylsiloxane)},
  journal = {Analytical Chemistry},
  year = {1998},
  volume = {70},
  pages = {4974-4984},
  number = {23},
  optnote = {nano fab}
}

@ARTICLE{duke:02,
  author = {Duke, T.},
  title = {Push or Pull? Teams of motor proteins have it both ways},
  journal = {Proceedings of the National Academy of Science USA},
  year = {2002},
  optnote = {models},
  optnumber = {10},
  optpages = {6521-6523},
  optvolume = {99}
}

@ARTICLE{duke2001csr,
  author = {Duke, T.A.J. and Le Novere, N. and Bray, D.},
  title = {{Conformational spread in a ring of proteins: a stochastic approach
	to allostery}},
  journal = {Journal of Molecular Biology},
  year = {2001},
  volume = {308},
  pages = {541-553},
  number = {3},
  publisher = {Elsevier Ltd}
}

@ARTICLE{dyer2006son,
  author = {Dyer, C.M. and Dahlquist, F.W.},
  title = {{Switched or not?: the structure of unphosphorylated CheY bound to
	the N terminus of FliM}},
  journal = {Journal of Bacteriology},
  year = {2006},
  volume = {188},
  pages = {7354--7363},
  number = {21},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{dyer2004sca,
  author = {Dyer, C.M. and Quillin, M.L. and Campos, A. and Lu, J. and McEvoy,
	M.M. and Hausrath, A.C. and Westbrook, E.M. and Matsumura, P. and
	Matthews, B.W. and Dahlquist, F.W.},
  title = {{Structure of the constitutively active double mutant CheYD13K Y106W
	alone and in complex with a FliM peptide}},
  journal = {Journal of Molecular Biology},
  year = {2004},
  volume = {342},
  pages = {1325--1335},
  number = {4},
  publisher = {Elsevier}
}

@ARTICLE{economou:00,
  author = {Economou, A.},
  title = {Bacterial protein translocase: a unique molecular machine with an
	army of substrates},
  journal = {FEBS Letters},
  year = {2000},
  optkey = {23786},
  optnote = {intracellular proteins},
  optpages = {1-4}
}

@ARTICLE{felgner1998vmi,
  author = {Felgner, H. and Grolig, F. and Muller, O. and Schliwa, M.},
  title = {{In vivo manipulation of internal cell organelles.}},
  journal = {Methods Cell Biol},
  year = {1998},
  volume = {55},
  pages = {195--203}
}

@ARTICLE{ferre2004bsm,
  author = {Ferre, A. and de la Mora, J. and Ballado, T. and Camarena, L. and
	Dreyfus, G.},
  title = {{Biochemical study of multiple CheY response regulators of the chemotactic
	pathway of \normalfont{Rhodobacter sphaeroides}}},
  journal = {Journal of Bacteriology},
  year = {2004},
  volume = {186},
  pages = {5172-5177},
  number = {15},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{friedrich:00,
  author = {Friedrich, T and Scheide, D.},
  title = {The respiratory complex I of bacteria, archaea and eukarya and its
	module common with membrane-bound multisubunit hydrogenases},
  journal = {FEBS Letters},
  year = {2000},
  optnote = {energetics},
  optnumber = {479},
  optpages = {1-5}
}

@ARTICLE{friedrich:95,
  author = {Friedrich, T. and Steinmuller, K. and Weiss, H.},
  title = {The proton-pumping respiratory complex I of bacteria and mitochondria
	and its homologue in chloroplasts},
  journal = {FEBS Letters},
  year = {1995},
  volume = {2},
  pages = {107-11},
  number = {367},
  month = {June}
}

@ARTICLE{fuhrer1991bsc,
  author = {Fuhrer, D.K. and Ordal, G.W.},
  title = {{\normalfont{Bacillus subtilis} \textit{CheN, a homolog of CheA,
	the central regulator of chemotaxis in} \normalfont{Escherichia coli}}},
  journal = {Journal of Bacteriology},
  year = {1991},
  volume = {173},
  pages = {7443-7448},
  number = {23},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{fujii2008ppa,
  author = {Fujii, M. and Shibata, S. and Aizawa, S.I.},
  title = {{Polar, peritrichous, and lateral flagella belong to three distinguishable
	flagellar families}},
  journal = {Journal of Molecular Biology},
  year = {2008},
  volume = {379},
  pages = {273-283},
  number = {2},
  publisher = {Elsevier}
}

@ARTICLE{Fukuoka08,
  author = {Fukuoka, H. and Wada, T. and Kojima, S. and Ishijima, A. and Homma,
	M.},
  title = {{Sodium-dependent dynamic assembly of membrane complexes in sodium-driven
	flagellar motors}},
  journal = {Molecular Microbiology},
  year = {2009},
  volume = {71},
  pages = {825-835}
}

@ARTICLE{fung95,
  author = {Fung, DC. and Berg, HC.},
  title = {{Powering the flagellar motor of Escherichia coli with an external
	voltage source}},
  journal = {Nature},
  year = {1995},
  volume = {375},
  pages = {809-812},
  number = {6534},
  month = {Jun},
  abstract = {{Rotary motors of bacterial flagella are driven by ions that move
	across the cytoplasmic membrane down an electrochemical gradient.
	For Escherichia coli, the ions are protons, and the maximum work
	per unit charge that they can do is the protonmotive force. To test
	whether motor efficiency is limited by proton leakage or mechanical
	nonlinearities, we measured torque as a function of protonmotive
	force. Filamentous cells were drawn into micropipettes and energized
	with an external voltage source. Torque was proportional to protonmotive
	force up to -150 mV, twice the span accessible by earlier techniques.
	This is consistent with a mechanism in which a fixed number of protons,
	working at unit efficiency, carry the motor through each revolution.
	We also found that individual torque-generating elements inactivate
	at low potentials or potentials of reverse sign. When normal potentials
	are restored, they reactivate sequentially.}},
  pmid = {7541114},
  url = {http://www.hubmed.org/display.cgi?uids=7541114}
}

@ARTICLE{furuno:97,
  author = {Furuno, M. and Atsumi, T. and Yamada, T. and Kojima, S. and Nishioka,
	N. and Kawagishi, I. and Homma, M.},
  title = {Characterisation of polar-flagellar-length mutants in \textit{Vibrio
	alginolyticus}},
  journal = {Microbiology},
  year = {1997},
  optnote = {vibrio},
  optnumber = {143},
  optpages = {1615-1621}
}

@ARTICLE{furuno:99,
  author = {Furuno, M. and Nishioka, N. and Kawagishi, I. and Homma, M.},
  title = {Suppression by the DNA fragment of the \textit{motX} promoter region
	on long flagellar mutants of \textit{Vibrio alginolyticus}},
  journal = {Microbiology and Immunology},
  year = {1999},
  optnote = {vibrio},
  optnumber = {1},
  optpages = {39-43},
  optvolume = {43}
}

@ARTICLE{gabel03,
  author = {Gabel, C.V. and Berg, H.C.},
  title = {{The speed of the flagellar rotary motor of \textnormal{Escherichia
	coli} \textit{varies linearly with protonmotive force}}},
  journal = {Proceedings of the National Academy of Science USA},
  year = {2003},
  volume = {100},
  pages = {8748-8751},
  number = {15},
  month = {Jul},
  abstract = {{A protonmotive force (pmf) across the cell's inner membrane powers
	the flagellar rotary motor of Escherichia coli. Speed is known to
	be proportional to pmf when viscous loads are heavy. Here we show
	that speed also is proportional to pmf when viscous loads are light.
	Two motors on the same bacterium were monitored as the cell was slowly
	deenergized. The first motor rotated the entire cell body (a heavy
	load), while the second motor rotated a small latex bead (a light
	load). The first motor rotated slowly and provided a measure of the
	cell's pmf. The second motor rotated rapidly and was compared with
	the first, to give the speed-pmf relation for light loads. Experiments
	were done at 24.0 degrees C and 16.2 degrees C, with initial speeds
	indicating operation well into the high-speed, low-torque regime.
	Speed was found to be proportional to pmf over the entire (accessible)
	dynamic range (0-270 Hz). If the passage of a fixed number of protons
	carries the motor through each revolution, i.e., if the motor is
	tightly coupled, a linear speed-pmf relation is expected close to
	stall, where the work done against the viscous load matches the energy
	dissipated in proton flow. A linear relation is expected at high
	speeds if proton translocation is rate-limiting and involves multiple
	steps, a model that also applies to simple proton channels. The present
	work shows that a linear relation is true more generally, providing
	an additional constraint on possible motor mechanisms.}},
  pmid = {12857945},
  url = {http://www.hubmed.org/display.cgi?uids=12857945}
}

@ARTICLE{garcia1998fsg,
  author = {Garcia, N. and Campos, A. and Osorio, A. and Poggio, S. and Gonzalez-Pedrajo,
	B. and Camarena, L. and Dreyfus, G.},
  title = {{The flagellar switch genes fliM and fliN of \normalfont{Rhodobacter
	sphaeroides} \textit{are contained in a large flagellar gene cluster}}},
  journal = {Journal of Bacteriology},
  year = {1998},
  volume = {180},
  pages = {3978-3982},
  number = {15},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{gardel1996avc,
  author = {Gardel, C.L. and Mekalanos, J.J.},
  title = {{Alterations in \normalfont{Vibrio cholerae} \textit{motility phenotypes
	correlate with changes in virulence factor expression}}},
  journal = {Infection and Immunity},
  year = {1996},
  volume = {64},
  pages = {2246-2255},
  number = {6},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{garrity1997ack,
  author = {Garrity, L.F. and Ordal, G.W.},
  title = {{Activation of the CheA kinase by asparagine in \normalfont{Bacillus
	subtilis} \textit{chemotaxis}}},
  journal = {Microbiology},
  year = {1997},
  volume = {143},
  pages = {2945-2951},
  number = {9},
  publisher = {Soc General Microbiol}
}

@PHDTHESIS{gauden_thesis,
  author = {Gauden, D.E.},
  title = {{Electron transport dependent taxis in \textit{Rhodobacter sphaeroides}}},
  school = {University of Oxford},
  year = {1996},
  owner = {mostyn},
  timestamp = {2008.08.24}
}

@ARTICLE{gauden95,
  author = {Gauden, DE. and Armitage, JP.},
  title = {{Electron transport-dependent taxis in Rhodobacter sphaeroides}},
  journal = {Journal of Bacteriology},
  year = {1995},
  volume = {177},
  pages = {5853-5859},
  number = {20},
  month = {Oct},
  abstract = {{Rhodobacter sphaeroides showed chemotaxis to the terminal electron
	acceptors oxygen and dimethyl sulfoxide, and the responses to these
	effectors were shown to be influenced by the relative activities
	of the different electron transport pathways. R. sphaeroides cells
	tethered by their flagella showed a step-down response to a decrease
	in the oxygen or dimethyl sulfoxide concentration when using them
	as terminal acceptors. Bacteria using photosynthetic electron transport,
	however, showed a step-down response to oxygen addition. Addition
	of the proton ionophore carbonyl cyanide 4-trifluoromethoxyphenylhydrazone
	did not cause a transient behavioral response, although it decreased
	the electrochemical proton gradient (delta p) and increased the rate
	of electron transport. However, removal of the ionophore, which caused
	an increase in delta p and a decrease in the electron transport rate,
	resulted in a step-down response. Together, these data suggest that
	behavioral responses of R. sphaeroides to electron transport effectors
	are caused by changes in the rate of electron transport rather than
	changes in delta p.}},
  pmid = {7592334},
  url = {http://www.hubmed.org/display.cgi?uids=7592334}
}

@ARTICLE{gimsa94,
  author = {Gimsa, J. and Schnelle, T. and Zechel, G. and Glaser, R.},
  title = {{Dielectric spectroscopy of human erythrocytes: investigations under
	the influence of nystatin}},
  journal = {Biophysical Journal},
  year = {1994},
  volume = {66},
  pages = {1244-1253},
  number = {4},
  month = {Apr},
  abstract = {{When placed in rotating electric fields red blood cells show a typical
	electrorotation spectrum with antifield rotation in the lower and
	cofield rotation in the higher frequency range. Assuming a spherical
	cell geometry, however, dielectrical parameters were obtained that
	differ from those measured by independent methods. Dielectrophoresis
	and, in particular, electrorotation yielded lower membrane capacitance
	values than expected. Introduction of an ellipsoidal model with an
	axis ratio of 1:2 allowed a description that proved to be consistent
	with dielectrophoresis and electrorotation data. For control cells
	an internal conductivity of 0.535 S/m, a specific membrane capacitance
	of 0.82 x 10(-2) F/m2, and a specific conductance of 480 S/m2 were
	obtained. The first characteristic frequency (frequency of fastest
	antifield rotation) and the related rotation speed can be measured
	quite quickly by means of a compensation method. Thus it was possible
	to follow changes of dielectric properties on individual cells after
	nystatin application. Ionophore-membrane interaction caused cell
	shrinkage in parallel to a decrease of the first characteristic frequency
	and rotation speed. Analysis of data revealed a decrease of the internal
	conductivity that is not only caused by ion loss but also, to a large
	extent, by a strong increase of hindrance because of shrinkage. Ionophore-induced
	membrane permeabilities can be calculated from volume decrease as
	well as from electrorotational data. In no case can these permeabilities
	count for the high membrane-AC conductivity that is attributed to
	the band-3 anion exchanging protein. The membrane-AC conductance
	was found not to be decreased for cells in Donnan equilibrium, which
	had leaked out almost completely.}},
  pmid = {8038395},
  url = {http://www.hubmed.org/display.cgi?uids=8038395}
}

@BOOK{glaser,
  title = {Biophysics},
  publisher = {Springer},
  year = {1996},
  author = {Glaser, Roland},
  optedition = {4},
  optkey = {3-540-67088-2}
}

@ARTICLE{gosink:00,
  author = {Gosink, KK. and Hase, CC.},
  title = {{Requirements for conversion of the Na+ driven flagellar motor of
	\textnormal{Vibrio cholerae} to the H+ driven motor of \textnormal{Escherichia
	coli}}},
  journal = {Journal of Bacteriology},
  year = {2000},
  volume = {182},
  pages = {4234-4240},
  number = {15},
  optnote = {structure}
}

@PHDTHESIS{gould_thesis,
  author = {Gould, M.},
  title = {{Chemotaxis gene expression in \textit{Rhodobacter sphaeroides} WS8N}},
  school = {University of Oxford},
  year = {2006},
  owner = {mostyn},
  timestamp = {2008.08.24}
}

@ARTICLE{gray1999me,
  author = {Gray, M.W. and Burger, G. and Lang, B.F.},
  title = {{Mitochondrial Evolution}},
  journal = {Science},
  year = {1999},
  volume = {283},
  pages = {1476},
  number = {5407},
  publisher = {AAAS}
}

@BOOK{gutfreund,
  title = {Kinetics for the Life Sciences: receptors, transmitters and catalysts},
  publisher = {Cambridge},
  year = {1995},
  author = {Gutfreund, H.},
  optkey = {0-521-48586-X},
  optnote = {textbook}
}

@ARTICLE{hamaide83,
  author = {Hamaide, F. and Kushner, DJ. and Sprott, GD.},
  title = {{Proton motive force and Na+/H+ antiport in a moderate halophile}},
  journal = {Journal of Bacteriology},
  year = {1983},
  volume = {156},
  pages = {537-544},
  number = {2},
  month = {Nov},
  abstract = {{The influence of pH on the proton motive force of Vibrio costicola
	was determined by measuring the distributions of triphenylmethylphosphonium
	cation (membrane potential, delta psi) and either dimethyloxazolidinedione
	or methylamine (osmotic component, delta pH). As the pH of the medium
	was adjusted from 5.7 to 9.0, the proton motive force steadily decreased
	from about 170 to 100 mV. This decline occurred, despite a large
	increase in the membrane potential to its maximum value at pH 9.0,
	because of the loss of the pH gradient (inside alkaline). The cytoplasm
	and medium were of equal pH at 7.5; membrane permeability properties
	were lost at the pH extremes of 5.0 and 9.5. Protonophores and monensin
	prevented the net efflux of protons normally found when an oxygen
	pulse was given to an anaerobic cell suspension. A Na+/H+ antiport
	activity was measured for both Na+ influx and efflux and was shown
	to be dissipated by protonophores and monensin. These results strongly
	favor the concept that respiratory energy is used for proton efflux
	and that the resulting proton motive force may be converted to a
	sodium motive force through Na+/H+ antiport (driven by delta psi).
	A role for antiport activity in pH regulation of the cytosol can
	also explain the broad pH range for optimal growth, extending to
	the alkaline extreme of pH 9.0.}},
  pmid = {6313606},
  url = {http://www.hubmed.org/display.cgi?uids=6313606}
}

@ARTICLE{hamblin1997ccp,
  author = {Hamblin, P.A. and Bourne, N.A. and Armitage, J.P.},
  title = {{Characterization of the chemotaxis protein CheW from Rhodobacter
	sphaeroides and its effect on the behaviour of Escherichia coli}},
  journal = {Molecular Microbiology},
  year = {1997},
  volume = {24},
  pages = {41--51},
  number = {1},
  publisher = {Blackwell Synergy}
}

@BOOK{happel,
  title = {Low Reynolds number hydrodynamics},
  publisher = {Martinus Nijhoff Publishers (Kluwer Group)},
  year = {1983},
  author = {Happel, J. and Brenner, H.}
}

@ARTICLE{harold:01,
  author = {Harold, F.M.},
  title = {Gleanings of a Chemiosmotic Eye},
  journal = {BioEssays},
  year = {2001},
  optnote = {energetics},
  optnumber = {23},
  optpages = {848-855}
}

@ARTICLE{Harrison:1994:FEBS-Lett:8026580,
  author = {Harrison, D M and Packer, H L and Armitage, J P},
  title = {Swimming speed and chemokinetic response of Rhodobacter sphaeroides
	investigated by natural manipulation of the membrane potential},
  journal = {FEBS Lett},
  year = {1994},
  volume = {348},
  pages = {37-40},
  number = {1},
  month = {Jul},
  abstract = {The delta psi of R. sphaeroides, grown under high light to reduce
	the levels of light-harvesting bacteriochlorophyll, was naturally
	manipulated using light intensity. The relationship between delta
	psi and the swimming speed of free swimming populations of cells
	was investigated. After de-energisation by incubation in the dark
	there was an apparent threshold of about -13 mV which had to be overcome
	before functional motor rotation could resume and at -45 mV the motor
	saturated. Further increases in delta psi over -45 mV did not increase
	the free swimming velocity. However, when a chemokinetic effector
	was added there was an increase in swimming speed, even though the
	delta psi was well above saturation, indicating that the chemokinetic
	response is independent of normal relationship between motor rotation
	and delta psi.},
  pmid = {8026580},
  url = {http://www.hubmed.org/display.cgi?uids=8026580}
}

@ARTICLE{hase:01,
  author = {Hase, C.C. and Barquera, B.},
  title = {Role of sodium bioenergetics in \textit{Vibrio cholerae}},
  journal = {Biochimica et Biophysica Acta},
  year = {2001},
  optnote = {vibrio},
  optpages = {169-178},
  optvolume = {1505}
}

@ARTICLE{hashimoto2007frh,
  author = {Hashimoto, M. and Mashimo, T. and Hirano, T. and Yamaguchi, S. and
	Aizawa, S.I.},
  title = {{Functional roles of the hook in a rotating tethered cell}},
  journal = {Journal of Molecular Biology},
  year = {2007},
  volume = {375},
  pages = {367-375},
  publisher = {Elsevier}
}

@ARTICLE{hatt2008cng,
  author = {Hatt, J.K. and Rather, P.N.},
  title = {{Characterization of a novel gene, \normalfont{wosA}, \textit{regulating
	FlhDC expression in} \normalfont{Proteus mirabilis}}},
  journal = {Journal of Bacteriology},
  year = {2008},
  volume = {190},
  pages = {1946-1955},
  number = {6},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{henrichsen1972bst,
  author = {Henrichsen, J.},
  title = {{Bacterial surface translocation: a survey and a classification.}},
  journal = {Microbiology and Molecular Biology Reviews},
  year = {1972},
  volume = {36},
  pages = {478--503},
  number = {4},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{vandenheuvel2007mpw,
  author = {van den Heuvel, M.G.L. and Dekker, C.},
  title = {{Motor proteins at work for nanotechnology}},
  journal = {Science},
  year = {2007},
  volume = {317},
  pages = {333-336},
  number = {5836},
  publisher = {AAAS}
}

@ARTICLE{hirose99,
  author = {Hirose, K. and L{\"o}we, J. and Alonso, M. and Cross, RA. and Amos,
	LA.},
  title = {{3D electron microscopy of the interaction of kinesin with tubulin}},
  journal = {Cell Struct Funct},
  year = {1999},
  volume = {24},
  pages = {277-284},
  number = {5},
  month = {Oct},
  abstract = {{We have studied the structure of microtubules decorated with kinesin
	motor domains in different nucleotide states by 3D electron microscopy.
	Having docked the atomic coordinates of both dimeric ADP.kinesin
	and tubulin heterodimer into a map of kinesin dimers bound to microtubules
	in the presence of ADP, we try to predict which regions of the proteins
	interact in the weakly binding state. When either the presence of
	5'-adenylyimidodiphosphate (AMP-PNP) or an absence of nucleotides
	puts motor domains into a strongly-bound state, the 3D maps show
	changes in the motor domains which modify their interaction with
	beta-tubulin. The maps also show differences in beta-tubulin conformation
	compared with undecorated microtubules or those decorated with weakly-bound
	motors. Strongly-bound ncd appears to produce an identical change.}},
  pmid = {15216883},
  url = {http://www.hubmed.org/display.cgi?uids=15216883}
}

@ARTICLE{hirota:83,
  author = {Hirota, N and Imae, Y.},
  title = {Na+ driven Flagellar Motors of an Alkalophilic {\it Bacillus} Strain
	YN-1},
  journal = {Journal of Biological Chemistry},
  year = {1983},
  optnote = {na+mf},
  optnumber = {17},
  optpages = {10577-10581},
  optvolume = {258}
}

@ARTICLE{hodgson:98,
  author = {Hodgson, C.E. and Pethig, R.},
  title = {Determination of the viability of \textit{Escherichia coli} at the
	single organism level by electrorotation},
  journal = {Clinical Chemistry},
  year = {1998},
  optnote = {electrorotation},
  optnumber = {9},
  optpages = {2049-2051},
  optvolume = {44}
}

@ARTICLE{homma:01,
  author = {Homma, K. and Yoshimura, M. and Saito, J. and Ikebe, R. and Ikebe,
	M.},
  title = {The core of the motor domain determines the direction of myosin movement},
  journal = {Nature},
  year = {2001},
  optnote = {myosin},
  optpages = {831-834},
  optvolume = {412}
}

@ARTICLE{homma:96,
  author = {Homma, M. and Oota, H. and Kojima, S. and Kawagishi, I. and Imae,
	Y.},
  title = {Chemotactic responses to an attractant and a repellent by the polar
	and lateral flagellar systems of {\it Vibrio alginolyticus}},
  journal = {Microbiology},
  year = {1996},
  volume = {142},
  pages = {2777-2783},
  optnote = {taxis}
}

@ARTICLE{hormeno2006emp,
  author = {Hormeno, S. and Arias-Gonzalez, J.R.},
  title = {{Exploring mechanochemical processes in the cell with optical tweezers}},
  journal = {Biology of the Cell},
  year = {2006},
  volume = {98},
  pages = {679--95},
  number = {12}
}

@ARTICLE{hosking2006ecm,
  author = {Hosking, E.R. and Vogt, C. and Bakker, E.P. and Manson, M.D.},
  title = {{The \normalfont{Escherichia coli} \textit{MotAB proton channel unplugged}}},
  journal = {Journal of Molecular Biology},
  year = {2006},
  volume = {364},
  pages = {921-937},
  number = {5},
  publisher = {Elsevier}
}

@ARTICLE{hyakutake2005oof,
  author = {Hyakutake, A. and Homma, M. and Austin, M.J. and Boin, M.A. and H{\"a}se,
	C.C. and Kawagishi, I.},
  title = {{Only one of the five CheY homologs in \normalfont{Vibrio cholerae}
	\textit{directly switches flagellar rotation}}},
  journal = {Journal of Bacteriology},
  year = {2005},
  volume = {187},
  pages = {8403-8410},
  number = {24},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{imada05,
  author = {Imada, K. and Samatey, FA. and Matsunami, H. and Nagashima, S. and
	Kitao, A. and Yonekura, K. and Maki-Yonekuraz, S. and Namba, K.},
  title = {{[Structure, function and self-assembly of the bacterial flagellum]}},
  journal = {Tanpakushitsu Kakusan Koso},
  year = {2005},
  volume = {50},
  pages = {1328-1334},
  number = {10 Suppl},
  month = {Aug},
  abstract = {{}},
  pmid = {16104602},
  url = {http://www.hubmed.org/display.cgi?uids=16104602}
}

@ARTICLE{imae:89,
  author = {Imae, Y. and Atsumi, T.},
  title = {Na+ driven bacterial flagellar motors},
  journal = {Journal of Bioenergetics and Biomembranes},
  year = {1989},
  volume = {21},
  pages = {705-716},
  number = {6},
  optnote = {general motors}
}

@ARTICLE{ind2009,
  author = {Ind, A.C. and Porter, S.L. and Byles, E.D. and Godfrey, S.A.C. and
	Brown, M.T. and Armitage, J.P.},
  title = {{An inducible expression plasmid for \normalfont{Rhodobacter sphaeroides}
	\textit{and its use to investigate chemotaxis}}},
  year = {In preparation}
}

@ARTICLE{inoue2007tsr,
  author = {Inoue, Y. and Lo, C.J. and Fukuoka, H. and Takahashi, H. and Sowa,
	Y. and Pilizota, T. and Wadhams, G.H. and Homma, M. and Berry, R.M.
	and Ishijima, A.},
  title = {{Torque--speed relationships of Na$^+$-driven chimeric flagellar
	motors in \normalfont{Escherichia coli}}},
  journal = {Journal of Molecular Biology},
  year = {2007},
  volume = {376},
  pages = {1251-1259},
  publisher = {Elsevier}
}

@ARTICLE{itoh04,
  author = {Itoh, H. and Takahashi, A. and Adachi, K. and Noji, H. and Yasuda,
	R. and Yoshida, M. and Kinosita, K.},
  title = {{Mechanically driven ATP synthesis by F1-ATPase}},
  journal = {Nature},
  year = {2004},
  volume = {427},
  pages = {465-468},
  number = {6973},
  month = {Jan},
  abstract = {{ATP, the main biological energy currency, is synthesized from ADP
	and inorganic phosphate by ATP synthase in an energy-requiring reaction.
	The F1 portion of ATP synthase, also known as F1-ATPase, functions
	as a rotary molecular motor: in vitro its gamma-subunit rotates against
	the surrounding alpha3beta3 subunits, hydrolysing ATP in three separate
	catalytic sites on the beta-subunits. It is widely believed that
	reverse rotation of the gamma-subunit, driven by proton flow through
	the associated F(o) portion of ATP synthase, leads to ATP synthesis
	in biological systems. Here we present direct evidence for the chemical
	synthesis of ATP driven by mechanical energy. We attached a magnetic
	bead to the gamma-subunit of isolated F1 on a glass surface, and
	rotated the bead using electrical magnets. Rotation in the appropriate
	direction resulted in the appearance of ATP in the medium as detected
	by the luciferase-luciferin reaction. This shows that a vectorial
	force (torque) working at one particular point on a protein machine
	can influence a chemical reaction occurring in physically remote
	catalytic sites, driving the reaction far from equilibrium.}},
  pmid = {14749837},
  url = {http://www.hubmed.org/display.cgi?uids=14749837}
}

@ARTICLE{kakinuma85,
  author = {Kakinuma, Y. and Unemoto, T.},
  title = {{Sucrose uptake is driven by the Na+ electrochemical potential in
	the marine bacterium Vibrio alginolyticus}},
  journal = {Journal of Bacteriology},
  year = {1985},
  volume = {163},
  pages = {1293-1295},
  number = {3},
  month = {Sep},
  abstract = {{Na+ was found to be essential for the accumulation of sucrose by
	Vibrio alginolyticus. Sucrose uptake was completely inhibited by
	the addition of proton conductor at neutral pH, but not at alkaline
	pH, where the primary electrogenic Na+ pump generates the Na+ electrochemical
	gradient. We therefore conclude that sucrose transport is driven
	by the electrochemical potential of Na+ in this organism.}},
  pmid = {4030698},
  url = {http://www.hubmed.org/display.cgi?uids=4030698}
}

@ARTICLE{kawagishi:95,
  author = {Kawagishi, I. and Maekawa, Y. and Atsumi, T. and Homma, M. and Imae,
	Y.},
  title = {Isolation of the Polar and Lateral Flagellum-Defective Mutants in
	{\it Vibrio alginolyticus} and Identification of Their Flagellar
	Driving Energy Sources},
  journal = {Journal of Bacteriology},
  year = {1995},
  volume = {177},
  pages = {5158-5160},
  number = {17},
  optnote = {vibrio}
}

@ARTICLE{kerssemakers2006adm,
  author = {Kerssemakers, J.W.J. and Munteanu, E.L. and Laan, L. and Noetzel,
	T.L. and Janson, M.E. and Dogterom, M.},
  title = {{Assembly dynamics of microtubules at molecular resolution}},
  journal = {Nature},
  year = {2006},
  volume = {442},
  pages = {709-712},
  number = {7103},
  publisher = {Nature Publishing Group}
}

@ARTICLE{khan88,
  author = {Khan, S. and Dapice, M. and Reese, TS.},
  title = {{Effects of mot gene expression on the structure of the flagellar
	motor}},
  journal = {Journal of Molecular Biology},
  year = {1988},
  volume = {202},
  pages = {575-584},
  number = {3},
  month = {Aug},
  abstract = {{Direct freezing procedures have enabled us to visualize distinctive
	intramembrane particle ring structures in the cytoplasmic membranes
	of peritrichously flagellated bacteria by means of freeze-fracture
	electron microscopy. These structures were identified as flagellar
	motor components because their distribution matched that of flagella,
	and because they were absent in non-flagellated mutants of Escherichia
	coli. Particle rings were present in both the Gram-positive Streptococcus
	and the Gram-negative E. coli. In E. coli, a non-functional mocha
	operon produced flagellated but immotile cells lacking the particle
	rings. Simultaneous introduction of the motA and motB genes, led
	to recovery of both motility and the ring structures but neither
	gene alone was sufficient. The concomitant loss of the rings and
	motility is consistent with the ring particles having a central role
	in the flagellar motor.}},
  pmid = {3050128},
  url = {http://www.hubmed.org/display.cgi?uids=3050128}
}

@ARTICLE{Kimura2006,
  author = {Kimura, K. and Bianco, PR.},
  title = {Single molecule studies of DNA binding proteins using optical tweezers.},
  journal = {Analyst},
  year = {2006},
  volume = {131},
  pages = {868--874},
  number = {8},
  month = {Aug},
  abstract = {Optical tweezers have become a versatile tool in the biological sciences.
	Combined with various types of optical microscopy, they are being
	successfully used to discover the fundamental mechanism of biological
	processes. Recently, the study of proteins acting on DNA was aggressively
	undertaken at the single-molecule level. Here, we review the most
	recent studies which have revealed the dynamic behavior of individual
	protein molecules at work on DNA, providing detailed mechanistic
	insight that could not be revealed, at least not easily, using bulk-phase
	or ensemble approaches.},
  doi = {10.1039/b600157m},
  institution = {Center for Single Molecule Biophysics, University at Buffalo, Buffalo,
	NY 14214, USA.},
  keywords = {Animals; DNA-Binding Proteins; Humans; Micromanipulation; Molecular
	Motor Proteins; Nanotechnology; Optical Tweezers},
  owner = {mostyn},
  pmid = {17028717},
  timestamp = {2008.08.23},
  url = {http://dx.doi.org/10.1039/b600157m}
}

@ARTICLE{kobayashi2003pac,
  author = {Kobayashi, K. and Saitoh, T. and Shah, D.S.H. and Ohnishi, K. and
	Goodfellows, I.G. and Sockett, R.E. and Aizawa, S.I.},
  title = {{Purification and characterization of the flagellar basal body of
	\normalfont{Rhodobacter sphaeroides}}},
  journal = {Journal of Bacteriology},
  year = {2003},
  volume = {185},
  pages = {5295-5300},
  number = {17},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{kogure:98,
  author = {Kogure, K.},
  title = {Bioenergetics of Marine Bacteria},
  journal = {Current Opinion in Biotechnology},
  year = {1998},
  optnote = {energetics},
  optnumber = {9},
  optpages = {278-282}
}

@ARTICLE{kojima2007bpa,
  author = {Kojima, M. and Kubo, R. and Yakushi, T. and Homma, M. and Kawagishi,
	I.},
  title = {{The bidirectional polar and unidirectional lateral flagellar motors
	of \normalfont{Vibrio alginolyticus} \textit{are controlled by a
	single CheY species}}},
  journal = {Molecular Microbiology},
  year = {2007},
  volume = {64},
  pages = {57-67},
  number = {1},
  publisher = {Blackwell Synergy}
}

@ARTICLE{kojima:99jmb,
  author = {Kojima, S. and Asai, Y. and Atsumi, T. and Kawagishi, I. and Homma,
	M.},
  title = {Na+ driven flagellar motor resistant to phenamil, an amiloride analog,
	caused by mutations in putative channel components},
  journal = {Journal of Molecular Biology},
  year = {1999},
  volume = {285},
  pages = {1537-1547},
  optnote = {vibrio}
}

@ARTICLE{kojima:97,
  author = {Kojima, S. and Atsumi, T. and Muramoto, K. and Kudo, S. and Kawagishi,
	I. and Homma, M.},
  title = {\textnormal{Vibrio alginolyticus} mutants resistant to phenamil,
	a specific inhibitor of the sodium-driven flagellar motor},
  journal = {Journal of Molecular Biology},
  year = {1997},
  volume = {265},
  pages = {310-318},
  optnote = {vibrio}
}

@ARTICLE{kojima2004sap,
  author = {Kojima, S. and Blair, D.F.},
  title = {{Solubilization and purification of the MotA/MotB complex of \textnormal{Escherichia
	coli}}},
  journal = {Biochemistry},
  year = {2004},
  volume = {43},
  pages = {26--34},
  number = {1}
}

@ARTICLE{kojima:01,
  author = {Kojima, S. and Blair, DF.},
  title = {Conformational change in the stator of the bacterial flagellar motor},
  journal = {Biochemistry},
  year = {2001},
  volume = {40},
  pages = {13041-13050},
  optnote = {structure}
}

@ARTICLE{kojima2008cpd,
  author = {Kojima, S. and Furukawa, Y. and Matsunami, H. and Minamino, T. and
	Namba, K.},
  title = {{Characterization of the periplasmic domain of MotB and implications
	for its role in the stator assembly of the bacterial flagellar motor}},
  journal = {Journal of Bacteriology},
  year = {2008},
  volume = {190},
  pages = {3314--3322},
  number = {9},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{kojima:99mb,
  author = {Kojima, S. and Kuroda, M. and Kawagishi, I. and Homma, M.},
  title = {Random mutagenesis of the \textit{pomA} gene encoding a putative
	channel component of the Na+ driven polar flagellar motor of \textit{Vibrio
	alginolyticus}},
  journal = {Microbiology},
  year = {1999},
  volume = {145},
  pages = {1759-1767},
  optnote = {vibrio}
}

@ARTICLE{kojima:00,
  author = {Kojima, S. and Shoji, T. and Asai, Y. and Kawagishi, I. and Homma,
	M.},
  title = {A Slow-Motility Phenotype caused by Substitutions at Residue Asp31
	in the PomA Channel Component of a Sodium-Driven Flagellar Motor},
  journal = {Journal of Bacteriology},
  year = {2000},
  volume = {182},
  pages = {3314-3318},
  number = {11},
  optnote = {vibrio}
}

@ARTICLE{kojima:99jb,
  author = {Kojima, S. and Yamamoto, K. and Kawagishi, I. and Homma, M.},
  title = {The Polar Flagellar Motor of {\it Vibrio cholerae} is Driven by an
	Na+ Motive Force},
  journal = {Journal of Bacteriology},
  year = {1999},
  volume = {181},
  pages = {1927-1930},
  number = {6},
  optnote = {vibrio}
}

@ARTICLE{GrzegorzKudla04102009,
  author = {Kudla, G. and Murray, A.W. and Tollervey, D. and Plotkin, J.B.},
  title = {{Coding-sequence determinants of gene expression in \normalfont{Escherichia
	coli}}},
  journal = {Science},
  year = {2009},
  volume = {324},
  pages = {255-258},
  number = {5924},
  abstract = {Synonymous mutations do not alter the encoded protein, but they can
	influence gene expression. To investigate how, we engineered a synthetic
	library of 154 genes that varied randomly at synonymous sites, but
	all encoded the same green fluorescent protein (GFP). When expressed
	in Escherichia coli, GFP protein levels varied 250-fold across the
	library. GFP messenger RNA (mRNA) levels, mRNA degradation patterns,
	and bacterial growth rates also varied, but codon bias did not correlate
	with gene expression. Rather, the stability of mRNA folding near
	the ribosomal binding site explained more than half the variation
	in protein levels. In our analysis, mRNA folding and associated rates
	of translation initiation play a predominant role in shaping expression
	levels of individual genes, whereas codon bias influences global
	translation efficiency and cellular fitness.},
  doi = {10.1126/science.1170160},
  eprint = {http://www.sciencemag.org/cgi/reprint/324/5924/255.pdf},
  url = {http://www.sciencemag.org/cgi/content/abstract/324/5924/255}
}

@ARTICLE{kudo:90,
  author = {Kudo, S. and Magariyama, Y. and Aizawa, S.},
  title = {Abrupt changes in flagellar rotation observed by laser darkfield
	microscopy},
  journal = {Nature},
  year = {1990},
  optnote = {general motors},
  optpages = {677-680},
  optvolume = {346}
}

@ARTICLE{kural05,
  author = {Kural, C. and Kim, H. and Syed, S. and Goshima, G. and Gelfand, VI.
	and Selvin, PR.},
  title = {{Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated
	movement?}},
  journal = {Science},
  year = {2005},
  volume = {308},
  pages = {1469-1472},
  number = {5727},
  month = {Jun},
  abstract = {{We used fluorescence imaging with one nanometer accuracy (FIONA)
	to analyze organelle movement by conventional kinesin and cytoplasmic
	dynein in a cell. We located a green fluorescence protein (GFP)-tagged
	peroxisome in cultured Drosophila S2 cells to within 1.5 nanometers
	in 1.1 milliseconds, a 400-fold improvement in temporal resolution,
	sufficient to determine the average step size to be approximately
	8 nanometers for both dynein and kinesin. Furthermore, we found that
	dynein and kinesin do not work against each other in vivo during
	peroxisome transport. Rather, multiple kinesins or multiple dyneins
	work together, producing up to 10 times the in vitro speed.}},
  pmid = {15817813},
  url = {http://www.hubmed.org/display.cgi?uids=15817813}
}

@ARTICLE{kuwajima88,
  author = {Kuwajima, G.},
  title = {{Construction of a minimum-size functional flagellin of \textnormal{Escherichia
	coli}}},
  journal = {Journal of Bacteriology},
  year = {1988},
  volume = {170},
  pages = {3305-3309},
  number = {7},
  month = {Jul},
  abstract = {{Various deletions were introduced into the central region of Escherichia
	coli flagellin (497 residues) without destroying its ability to form
	flagellar filaments. The smallest flagellin retained only the N-terminal
	193 residues and the C-terminal 117 residues, which are suggested
	to be the domains essential for filament formation.}},
  pmid = {3290204},
  url = {http://www.hubmed.org/display.cgi?uids=3290204}
}

@BOOK{landau,
  title = {Statistical Physics},
  publisher = {Pergamon NY},
  year = {1980},
  author = {Landau, LD. and Lifshitz, EM. and Pitaevskii, LP.}
}

@ARTICLE{lang:02,
  author = {Lang, MJ. and Asbury, CL. and Shavitz, JW. and Block, SM.},
  title = {An automated two-dimensional force clamp for single molecule studies},
  journal = {Biophysical Journal},
  year = {2002},
  volume = {83},
  pages = {491-501},
  optnote = {tweezers}
}

@ARTICLE{lang:02a,
  author = {Lang, MJ. and Block, SM.},
  title = {Laser-based optical tweezers},
  journal = {American Journal of Physics},
  year = {2002},
  volume = {71},
  pages = {201-215},
  number = {3},
  month = {August}
}

@ARTICLE{larsen:74,
  author = {Larsen, SH. and Reader, RW. and Kort, EN. and Tso, WW. and Adler,
	J.},
  title = {Change in direction of flagellar rotation is the basis of the chemotactic
	response in \textit{Escherichia coli}},
  journal = {Nature},
  year = {1974},
  volume = {249},
  pages = {74-77},
  optnote = {general motors}
}

@PHDTHESIS{leake,
  author = {Leake, MC.},
  title = {The Elasticity of the Giant Muscle Protein Titin Investigated Using
	a Laser-Tweezers Technique},
  school = {King's College London},
  year = {2001}
}

@ARTICLE{leake2006sat,
  author = {Leake, M.C. and Chandler, J.H. and Wadhams, G.H. and Bai, F. and
	Berry, R.M. and Armitage, J.P.},
  title = {{Stoichiometry and turnover in single, functioning membrane protein
	complexes}},
  journal = {Nature},
  year = {2006},
  volume = {443},
  pages = {355-358},
  number = {7109},
  publisher = {Nature Publishing Group}
}

@ARTICLE{leake04,
  author = {Leake, MC. and Wilson, D. and Gautel, M. and Simmons, RM.},
  title = {{The elasticity of single titin molecules using a two-bead optical
	tweezers assay}},
  journal = {Biophysical Journal},
  year = {2004},
  volume = {87},
  pages = {1112-1135},
  number = {2},
  month = {Aug},
  abstract = {{Titin is responsible for the passive elasticity of the muscle sarcomere.
	The mechanical properties of skeletal and cardiac muscle titin were
	characterized in single molecules using a novel dual optical tweezers
	assay. Antibody pairs were attached to beads and used to select the
	whole molecule, I-band, A-band, a tandem-immunoglobulin (Ig) segment,
	and the PEVK region. A construct from the PEVK region expressing
	>25% of the full-length skeletal muscle isoform was chemically conjugated
	to beads and similarly characterized. By elucidating the elasticity
	of the different regions, we showed directly for the first time,
	to our knowledge, that two entropic components act in series in the
	skeletal muscle titin I-band (confirming previous speculations),
	one associated with tandem-immunoglobulin domains and the other with
	the PEVK region, with persistence lengths of 2.9 nm and 0.76 nm,
	respectively (150 mM ionic strength, 22 degrees C). Novel findings
	were: the persistence length of the PEVK component rose (0.4-2.7
	nm) with an increase in ionic strength (15-300 mM) and fell (3.0-0.3
	nm) with a temperature increase (10-60 degrees C); stress-relaxation
	in 10-12-nm steps was observed in the PEVK construct and hysteresis
	in the native PEVK region. The region may not be a pure random coil,
	as previously thought, but contains structured elements, possibly
	with hydrophobic interactions.}},
  pmid = {15298915},
  url = {http://www.hubmed.org/display.cgi?uids=15298915}
}

@ARTICLE{li2006lfm,
  author = {Li, G. and Tang, J.X.},
  title = {{Low Flagellar Motor Torque and High Swimming Efficiency of Caulobacter
	crescentus Swarmer Cells}},
  journal = {Biophysical Journal},
  year = {2006},
  volume = {91},
  pages = {2726},
  number = {7},
  publisher = {Biophysical Soc}
}

@ARTICLE{li2004csc,
  author = {Li, M. and Hazelbauer, G.L.},
  title = {{Cellular stoichiometry of the components of the chemotaxis signaling
	complex}},
  journal = {Journal of Bacteriology},
  year = {2004},
  volume = {186},
  pages = {3687-3694},
  number = {12},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{liu:90,
  author = {Liu, JZ. and Dapice, M. and Khan, S.},
  title = {Ion Selectivity of the \textnormal{Vibrio alginolyticus} Flagellar
	Motor},
  journal = {Journal of Bacteriology},
  year = {1990},
  volume = {172},
  pages = {5236-5244},
  number = {9},
  optnote = {vibrio}
}

@ARTICLE{lloyd:99,
  author = {Lloyd, SA. and Whitby, FG. and Blair, DF. and Hill, CP.},
  title = {Structure of the C-terminal domain of FliG, a component of the rotor
	in the bacterial flagellar motor},
  journal = {Nature},
  year = {1999},
  volume = {400},
  pages = {472-475},
  optnote = {structure}
}

@ARTICLE{lo05,
  author = {Lo, CJ. and Leake, MC. and Berry, RM.},
  title = {{Fluorescence Measurement of Intracellular Sodium Concentration in
	single \textnormal{Escherichia coli} cells}},
  journal = {Biophysical Journal - IN PRESS},
  year = {2005}
}

@ARTICLE{lo2007nmv,
  author = {Lo, C.J. and Leake, M.C. and Pilizota, T. and Berry, R.M.},
  title = {{Nonequivalence of membrane voltage and ion-gradient as driving forces
	for the bacterial flagellar motor at low load}},
  journal = {Biophysical Journal},
  year = {2007},
  volume = {93},
  pages = {294-302},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{lock04i,
  author = {Lock, JA.},
  title = {{Calculation of the radiation trapping force for laser tweezers by
	use of generalized Lorenz-Mie theory. I. Localized model description
	of an on-axis tightly focused laser beam with spherical aberration}},
  journal = {Applied Optics},
  year = {2004},
  volume = {43},
  pages = {2532-2544},
  number = {12},
  month = {Apr},
  pmid = {15119623},
  url = {http://www.hubmed.org/display.cgi?uids=15119623}
}

@ARTICLE{lowe:87,
  author = {Lowe, G. and Meister, M. and Berg, HC.},
  title = {Rapid rotation of flagellar bundles in swimming bacteria},
  journal = {Nature},
  year = {1987},
  volume = {325},
  pages = {637-640},
  optnote = {general motors}
}

@ARTICLE{lukat1993rrb,
  author = {Lukat, G.S. and Stock, J.B.},
  title = {{Response regulation in bacterial chemotaxis}},
  journal = {Journal of Cellular Biochemistry},
  year = {1993},
  volume = {51},
  pages = {41-46},
  number = {1}
}

@ARTICLE{mackenzie07,
  author = {Mackenzie, C. and Eraso, J.M. and Choudhary, M. and Roh, J.H. and
	Zeng, X. and Bruscella, P. and Pusk{\'a}s, {\'A}. and Kaplan, S.},
  title = {Postgenomic Adventures with Rhodobacter sphaeroides},
  journal = {Annual Review of Microbiology},
  year = {2007},
  volume = {61},
  pages = {283-307},
  publisher = {Annual Reviews}
}

@ARTICLE{macnab03,
  author = {Macnab, R.M.},
  title = {{How bacteria assemble flagella}},
  journal = {Annual Review of Microbiology},
  year = {2003},
  volume = {57},
  pages = {77-100},
  abstract = {{The bacterial flagellum is both a motor organelle and a protein export/assembly
	apparatus. It extends from the cytoplasm to the cell exterior. All
	the protein subunits of the external elements have to be exported.
	Export employs a type III pathway, also utilized for secretion of
	virulence factors. Six of the components of the export apparatus
	are integral membrane proteins and are believed to be located within
	the flagellar basal body. Three others are soluble: the ATPase that
	drives export, a regulator of the ATPase, and a general chaperone.
	Exported substrates diffuse down a narrow channel in the growing
	structure and assemble at the distal end, often with the help of
	a capping structure.}},
  pmid = {12730325},
  url = {http://www.hubmed.org/display.cgi?uids=12730325}
}

@ARTICLE{macnab:96,
  author = {Macnab, RM.},
  title = {{Flagella and motility in \textnormal{Escherichia coli} and \textnormal{S.
	typhimurium}}},
  journal = {Cellular and Molecular Biology},
  year = {1996},
  pages = {123-145},
  optnote = {general motors}
}

@ARTICLE{magariyama05,
  author = {Magariyama, Y. and Ichiba, M. and Nakata, K. and Baba, K. and Ohtani,
	T. and Kudo, S. and Goto, T.},
  title = {{Difference in bacterial motion between forward and backward swimming
	caused by the wall effect}},
  journal = {Biophysical Journal},
  year = {2005},
  volume = {88},
  pages = {3648-3658},
  number = {5},
  month = {May},
  abstract = {{A bacterial cell that has a single polar flagellum alternately repeats
	forward swimming, in which the flagellum pushes the cell body, and
	backward swimming, in which the flagellum pulls the cell body. We
	have reported that the backward swimming speeds of Vibrio alginolyticus
	are on average greater than the forward swimming speeds. In this
	study, we quantitatively measured the shape of the trajectory as
	well as the swimming speed. The trajectory shape in the forward mode
	was almost straight, whereas that in the backward mode was curved.
	The same parameters were measured at different distances from a surface.
	The difference in the motion characteristics between swimming modes
	was significant when a cell swam near a surface. In contrast, the
	difference was indistinguishable when a cell swam >60 microm away
	from any surfaces. In addition, a cell in backward mode tended to
	stay near the surface longer than a cell in forward mode. This wall
	effect on the bacterial motion was independent of chemical modification
	of the glass surface. The macroscopic behavior is numerically simulated
	on the basis of experimental results and the significance of the
	phenomenon reported here is discussed.}},
  pmid = {15695638},
  url = {http://www.hubmed.org/display.cgi?uids=15695638}
}

@ARTICLE{magariyama:01,
  author = {Magariyama, Y. and Masuda, S. and Takano, Y. and Ohtani, T. and Kudo,
	S.},
  title = {Difference between forward and backward swimming speeds of the single
	polar-flagellated bacterium, \textit{Vibrio alginolyticus}},
  journal = {FEMS Microbiology Letters},
  year = {2001},
  optnote = {vibrio},
  optpages = {343-347},
  optvolume = {205}
}

@ARTICLE{magariyama:00,
  author = {Magariyama, Y. and Sugiyama, S. and Kudo, S.},
  title = {Bacterial swimming speed and rotation rate of bundled flagella},
  journal = {FEMS Microbiology Letters},
  year = {2000},
  optnote = {general motors},
  optpages = {125-129},
  optvolume = {199}
}

@ARTICLE{magariyama:95,
  author = {Magariyama, Y. and Sugiyama, S. and Muramoto, K. and Kawagishi, I.
	and Imae, Y. and Kudo, S.},
  title = {Simultaneous measurement of bacterial flagellar rotation rate and
	swimming speed},
  journal = {Biophysical Journal},
  year = {1995},
  volume = {69},
  pages = {2154-2162},
  optnote = {general motors}
}

@ARTICLE{magariyama:94,
  author = {Magariyama, Y. and Sugiyama, S. and Muramoto, K. and Maekawa, Y.
	and Kawagishi, I. and Imae, Y. and Kudo, S.},
  title = {Very fast flagellar rotation},
  journal = {Nature},
  year = {1994},
  optnote = {general motors},
  optpages = {752},
  optvolume = {371}
}

@ARTICLE{mallik04,
  author = {Mallik, R. and Carter, BC. and Lex, SA. and King, SJ. and Gross,
	SP.},
  title = {{Cytoplasmic dynein functions as a gear in response to load}},
  journal = {Nature},
  year = {2004},
  volume = {427},
  pages = {649-652},
  number = {6975},
  month = {Feb},
  abstract = {{Cytoskeletal molecular motors belonging to the kinesin and dynein
	families transport cargos (for example, messenger RNA, endosomes,
	virus) on polymerized linear structures called microtubules in the
	cell. These 'nanomachines' use energy obtained from ATP hydrolysis
	to generate force, and move in a step-like manner on microtubules.
	Dynein has a complex and fundamentally different structure from other
	motor families. Thus, understanding dynein's force generation can
	yield new insight into the architecture and function of nanomachines.
	Here, we use an optical trap to quantify motion of polystyrene beads
	driven along microtubules by single cytoplasmic dynein motors. Under
	no load, dynein moves predominantly with a mixture of 24-nm and 32-nm
	steps. When moving against load applied by an optical trap, dynein
	can decrease step size to 8 nm and produce force up to 1.1 pN. This
	correlation between step size and force production is consistent
	with a molecular gear mechanism. The ability to take smaller but
	more powerful strokes under load--that is, to shift gears--depends
	on the availability of ATP. We propose a model whereby the gear is
	downshifted through load-induced binding of ATP at secondary sites
	in the dynein head.}},
  pmid = {14961123},
  url = {http://www.hubmed.org/display.cgi?uids=14961123}
}

@ARTICLE{manson2007pfi,
  author = {Manson, M.D.},
  title = {{How 34 pegs fit into 26 + 8 holes in the flagellar motor?}},
  journal = {Journal of Bacteriology},
  year = {2007},
  volume = {189},
  pages = {291-293},
  number = {2},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{manson98,
  author = {Manson, MD. and Armitage, JP. and Hoch, JA. and Macnab, RM.},
  title = {{Bacterial locomotion and signal transduction}},
  journal = {Journal of Bacteriology},
  year = {1998},
  volume = {180},
  pages = {1009-1022},
  number = {5},
  month = {Mar},
  abstract = {{}},
  pmid = {9495737},
  url = {http://www.hubmed.org/display.cgi?uids=9495737}
}

@ARTICLE{manson:80,
  author = {Manson, M.D. and Tedesco, P.M. and Berg, H.C.},
  title = {Energetics of Flagellar Rotation in Bacteria},
  journal = {Journal of Molecular Biology},
  year = {1980},
  optnote = {energetics},
  optnumber = {138},
  optpages = {541-561}
}

@PHDTHESIS{mantotta,
  author = {Mantotta, J.},
  title = {{Analysis of chemosensory proteins in \textit{Rhodobacter sphaeroides}}},
  school = {University of Oxford},
  year = {2002},
  owner = {mostyn},
  timestamp = {2008.08.24}
}

@ARTICLE{mathews:98,
  author = {Matherws, M.A. and Tang, H.L. and Blair, D.F.},
  title = {Domain analysis of the FliM protein of \textit{Escerichia coli}},
  journal = {Journal of Bacteriology},
  year = {1998},
  optnote = {structure},
  optnumber = {21},
  optpages = {5580-5590},
  optvolume = {180}
}

@ARTICLE{mccarter:01,
  author = {McCarter, LL.},
  title = {Polar flagellar motility of the \textnormal{Vibrionaceae}},
  journal = {Microbiology and Molecular Biology Reviews},
  year = {2001},
  volume = {65},
  pages = {445-462},
  number = {3},
  optnote = {vibrio}
}

@ARTICLE{mccarter:99,
  author = {McCarter, LL.},
  title = {The multiple identities of \textit{Vibrio parahaemolyticus}},
  journal = {Journal of Molecular Microbiology and Biotechnology},
  year = {1999},
  optnote = {vibrio},
  optnumber = {1},
  optpages = {51-57},
  optvolume = {1}
}

@ARTICLE{mccarter:94jul,
  author = {McCarter, LL.},
  title = {{MotY, a Component of the Sodium-Type Flagellar Motor}},
  journal = {Journal of Bacteriology},
  year = {1994},
  volume = {176},
  pages = {4219-4225},
  number = {14},
  optnote = {vibrio}
}

@ARTICLE{mccarter:94oct,
  author = {McCarter, LL.},
  title = {{MotX, the Channel Component of the Sodium-Type Flagellar Motor}},
  journal = {Journal of Bacteriology},
  year = {1994},
  volume = {176},
  pages = {5988-5998},
  number = {119},
  optnote = {vibrio}
}

@ARTICLE{mcevoy1998tbm,
  author = {McEvoy, M.M. and Hausrath, A.C. and Randolph, G.B. and Remington,
	S.J. and Dahlquist, F.W.},
  title = {{Two binding modes reveal flexibility in kinase/response regulator
	interactions in the bacterial chemotaxis pathway}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {1998},
  volume = {95},
  pages = {7333-7338},
  number = {13},
  publisher = {National Academy of Sciences}
}

@INBOOK{mclaughlin,
  pages = {71-144},
  title = {Electrostatic potentials at membrane-solution interfaces},
  author = {McLaughlin, S},
  optnote = {membranes}
}

@ARTICLE{mehta:99,
  author = {Mehta, AD. and Rock, RS. and Rief, M. and Spudich, JA. and Mooseker,
	MS. and Cheney, RE.},
  title = {{Myosin-V is a processive actin-based motor}},
  journal = {Nature},
  year = {1999},
  volume = {400},
  pages = {590-593},
  optnote = {myosin}
}

@ARTICLE{meister:89,
  author = {Meister, M. and Caplan, SR. and Berg, HC.},
  title = {Dynamics of a tightly coupled mechanism for flagellar rotation},
  journal = {Biophysical Journal},
  year = {1989},
  volume = {55},
  pages = {905-914},
  optnote = {models}
}

@ARTICLE{meister:87,
  author = {Meister, M. and Lowe, G. and Berg, HC.},
  title = {The proton flux through the bacterial flagellar motor},
  journal = {Cell},
  year = {1987},
  volume = {49},
  pages = {643-650},
  optnote = {general motors}
}

@ARTICLE{mimori1995srt,
  author = {Mimori, Y. and Yamashita, I. and Murata, K. and Fujiyoshi, Y. and
	Yonekura, K. and Toyoshima, C. and Namba, K.},
  title = {{The structure of the R-type straight flagellar filament of \normalfont{Salmonella}
	\textit{at 9 \AA{} resolution by electron cryomicroscopy}}},
  journal = {Journal of Molecular Biology},
  year = {1995},
  volume = {249},
  pages = {69-87},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{minamino2008mmb,
  author = {Minamino, T. and Imada, K. and Namba, K.},
  title = {{Molecular motors of the bacterial flagella}},
  journal = {Current Opinion in Structural Biology},
  year = {2008},
  volume = {18},
  pages = {693-701},
  publisher = {Elsevier}
}

@ARTICLE{minamino04,
  author = {Minamino, T. and Saijo-Hamano, Y. and Furukawa, Y. and Gonz{\'a}lez-Pedrajo,
	B. and Macnab, RM. and Namba, K.},
  title = {{Domain organization and function of Salmonella FliK, a flagellar
	hook-length control protein}},
  journal = {Journal of Molecular Biology},
  year = {2004},
  volume = {341},
  pages = {491-502},
  number = {2},
  month = {Aug},
  abstract = {{Salmonella hook-length control protein FliK, which consists of 405
	amino acid residues, switches substrate specificity of the type III
	flagellar protein export apparatus from rod/ hook-type to filament-type
	by causing a conformational change in the cytoplasmic domain of FlhB
	(FlhB(C)) upon completion of the hook assembly. An N-terminal region
	of FliK contains an export signal, and a highly conserved C-terminal
	region consisting of amino acid residues 265-405 (FliK((265-405)))
	is directly involved in the switching of FlhB(C). Here, we have investigated
	the structural properties of FliK. Gel filtration chromatography,
	multi-angle light scattering and analytical ultracentrifugation showed
	that FliK is monomeric in solution and has an elongated shape. Limited
	proteolysis showed that FliK consists of two domains, the N-terminal
	(FliK(N)) and C-terminal domains (FliK(C)), and that the first 203
	and the last 35 amino acid residues are partially unfolded and subjected
	to proteolysis. Both FliK(N) and FliK(C) are more globular than full-length
	FliK, suggesting that these domains are connected in tandem. Overproduced
	His-FliK((199-405)) failed to switch export specificity of the export
	apparatus. Affinity blotting revealed that FlhB(C) binds to FliK
	and FliK((1-147)), but not to FliK((265-405)). Based on these results,
	we propose that FliK(N) within the central channel of the hook-basal
	body during the export of FliK is the sensor and transmitter of hook
	completion information and that the binding interaction of FliK(C)
	to FlhB(C) is structurally regulated by FliK(N) so as to occur only
	when the hook has reached a preset length. The conformational flexibility
	of FliK(C) may play a role in interfering with switching at an inappropriate
	point of flagellar assembly.}},
  pmid = {15276839},
  url = {http://www.hubmed.org/display.cgi?uids=15276839}
}

@ARTICLE{molloy2002lao,
  author = {Molloy, J.E. and Padgett, M.J.},
  title = {{Lights, action: optical tweezers}},
  journal = {Contemporary Physics},
  year = {2002},
  volume = {43},
  pages = {241--258},
  number = {4},
  publisher = {Taylor and Francis Ltd}
}

@ARTICLE{morehouse05,
  author = {Morehouse, K.A. and Goodfellow, I.G. and Sockett, R.E.},
  title = {{A chimeric N-terminal \normalfont{Escherichia coli}-\textit{C-terminal}
	\normalfont{Rhodobacter sphaeroides} \textit{FliG rotor protein supports
	bidirectional} \normalfont{E. coli} \textit{flagellar rotation and
	chemotaxis}}},
  journal = {Journal of Bacteriology},
  year = {2005},
  volume = {187},
  pages = {1695-1701},
  number = {5},
  month = {Mar},
  abstract = {{Flagellate bacteria such as Escherichia coli and Salmonella enterica
	serovar Typhimurium typically express 5 to 12 flagellar filaments
	over their cell surface that rotate in clockwise (CW) and counterclockwise
	directions. These bacteria modulate their swimming direction towards
	favorable environments by biasing the direction of flagellar rotation
	in response to various stimuli. In contrast, Rhodobacter sphaeroides
	expresses a single subpolar flagellum that rotates only CW and responds
	tactically by a series of biased stops and starts. Rotor protein
	FliG transiently links the MotAB stators to the rotor, to power rotation
	and also has an essential function in flagellar export. In this study,
	we sought to determine whether the FliG protein confers directionality
	on flagellar motors by testing the functional properties of R. sphaeroides
	FliG and a chimeric FliG protein, EcRsFliG (N-terminal and central
	domains of E. coli FliG fused to an R. sphaeroides FliG C terminus),
	in an E. coli FliG null background. The EcRsFliG chimera supported
	flagellar synthesis and bidirectional rotation; bacteria swam and
	tumbled in a manner qualitatively similar to that of the wild type
	and showed chemotaxis to amino acids. Thus, the FliG C terminus alone
	does not confer the unidirectional stop-start character of the R.
	sphaeroides flagellar motor, and its conformation continues to support
	tactic, switch-protein interactions in a bidirectional motor, despite
	its evolutionary history in a bacterium with a unidirectional motor.}},
  pmid = {15716440},
  url = {http://www.hubmed.org/display.cgi?uids=15716440}
}

@ARTICLE{morgan:01,
  author = {Morgan, D.G. and Khan, S.},
  title = {Bacterial flagella},
  journal = {Encyclopedia of Life Sciences},
  year = {2001},
  optnote = {structure}
}

@ARTICLE{muramoto:95,
  author = {Muramoto, K. and Kawagishi, I. and Kudo, S. and Magariyama, Y. and
	Imae, Y. and Homma, M.},
  title = {High-speed Rotation and Speed Stability of the Sodium-driven Flagellar
	Motor in {\it Vibrio alginolyticus}},
  journal = {Journal of Molecular Biology},
  year = {1995},
  volume = {251},
  pages = {50-58},
  optnote = {vibrio}
}

@ARTICLE{muramoto:96,
  author = {Muramoto, K. and Magariyama, Y. and Homma, M. and Kawagishi, I. and
	Sugiyama, S. and Imae, Y. and Kudo, S.},
  title = {Rotational Fluctuation of the Sodium-Driven Flagellar Motor of {\it
	Vibrio alginolyticus} Induced by Binding of Inhibitors},
  journal = {Journal of Molecular Biology},
  year = {1996},
  volume = {259},
  pages = {687-695},
  optnote = {vibrio}
}

@ARTICLE{murphy2006ssc,
  author = {Murphy, G.E. and Leadbetter, J.R. and Jensen, G.J.},
  title = {{\normalfont{In situ} \textit{structure of the complete} \normalfont{Treponema
	primitia} \textit{flagellar motor}}},
  journal = {Nature},
  year = {2006},
  volume = {442},
  pages = {1062-1064},
  number = {7106},
  publisher = {Nature Publishing}
}

@ARTICLE{nakamura84,
  author = {Nakamura, T. and Tokuda, H. and Unemoto, T.},
  title = {{K+/H+ antiporter functions as a regulator of cytoplasmic pH in a
	marine bacterium, Vibrio alginolyticus}},
  journal = {Biochimica et Biophysica},
  year = {1984},
  volume = {776},
  pages = {330-336},
  number = {2},
  month = {Oct},
  abstract = {{The marine bacterium, Vibrio alginolyticus, regulates the cytoplasmic
	pH at about 7.8 over the pH range 6.0-9.0. By the addition of diethanolamine
	(a membrane-permeable amine) at pH 9.0, the internal pH was alkalized
	and simultaneously the cellular K+ was released. Following the K+
	exit, the internal pH was acidified until 7.8, where the K+ exit
	leveled off. The K+ exit was mediated by a K+/H+ antiporter that
	is driven by the outwardly directed K+ gradient and ceases to function
	at the internal pH of 7.8 and below. The Na+-loaded cells assayed
	in the absence of KCl generated inside acidic delta pH at alkaline
	pH due to the function of an Na+/H+ antiporter, but the internal
	pH was not maintained at a constant value. At acidic pH range, the
	addition of KCl to the external medium was necessary for the alkalization
	of cell interior. These results suggested that in cooperation with
	the K+ uptake system and H+ pumps, the K+/H+ antiporter functions
	as a regulator of cytoplasmic pH to maintain a constant value of
	7.8 over the pH range 6.0-9.0.}},
  pmid = {6477914},
  url = {http://www.hubmed.org/display.cgi?uids=6477914}
}

@BOOK{neidhardt1,
  title = {Escherichia coli and Salmonella typhimurium Cellular and Molecular
	Biology},
  publisher = {American Society for Microbiology},
  year = {1987},
  author = {Neidhardt, FC. and Ingraham, JL. and Low, KB. and Magasanik, B. and
	Schaechter, M. and Umbarger, HE.},
  volume = {1}
}

@BOOK{neidhardt2,
  title = {Escherichia coli and Salmonella Typhimurium Cellular and Molecular
	Biology},
  publisher = {American Society for Microbiology},
  year = {1987},
  author = {Neidhardt, FC. and Ingraham, JL. and Low, KB. and Magasanik, B. and
	Schaechter, M. and Umbarger, HE.},
  volume = {2}
}

@ARTICLE{nelson:94,
  author = {Nelson, N.},
  title = {Energizing porters b6y proton-motive force},
  journal = {Journal of Experimental Biology},
  year = {1994},
  optnote = {pmf},
  optpages = {7-13},
  optvolume = {196}
}

@ARTICLE{neuman2004ot,
  author = {Neuman, K.C. and Block, S.M.},
  title = {{Optical trapping}},
  journal = {Review of Scientific Instruments},
  year = {2004},
  volume = {75},
  pages = {2787-2809},
  publisher = {AIP}
}

@ARTICLE{neuman:99,
  author = {Neuman, K.C. and Chadd, E.H. and Liu, G.F. and Bergman, K. and Block,
	S.M.},
  title = {Characterisation of photodamage to \textnormal{Escherichia coli}
	in optical traps},
  journal = {Biophysical Journal},
  year = {1999},
  volume = {77},
  pages = {2856-2863},
  optnote = {tweezers}
}

@ARTICLE{newton1997dmp,
  author = {Newton, S.M.C. and Allen, J.S. and Cao, Z. and Qi, Z. and Jiang,
	X. and Sprencel, C. and Igo, J.D. and Foster, S.B. and Payne, M.A.
	and Klebba, P.E.},
  title = {{Double mutagenesis of a positive charge cluster in the ligand-binding
	site of the ferric enterobactin receptor, FepA}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {1997},
  volume = {94},
  pages = {4560-4565},
  number = {9},
  publisher = {National Acad Sciences}
}

@ARTICLE{nishioka:98,
  author = {Nishioka, N. and Furuno, M. and Kawagishi, I. and Homma, M.},
  title = {Flagelling-containing vesicles excreted from \textit{Vibrio alginolyticus}
	mutants lacking a polar flagellar filament},
  journal = {Journal of Biochemistry},
  year = {1998},
  optnote = {vibrio},
  optpages = {1169-1173},
  optvolume = {123}
}

@ARTICLE{nishizaka04,
  author = {Nishizaka, T. and Oiwa, K. and Noji, H. and Kimura, S. and Muneyuki,
	E. and Yoshida, M. and Kinosita, K.},
  title = {{Chemomechanical coupling in F1-ATPase revealed by simultaneous observation
	of nucleotide kinetics and rotation}},
  journal = {Nat Struct Mol Biol},
  year = {2004},
  volume = {11},
  pages = {142-148},
  number = {2},
  month = {Feb},
  pmid = {14730353},
  url = {http://www.hubmed.org/display.cgi?uids=14730353}
}

@ARTICLE{okabe01,
  author = {Okabe, M. and Yakushi, T. and Asai, Y. and Homma, M.},
  title = {{Cloning and characterization of motX, a Vibrio alginolyticus sodium-driven
	flagellar motor gene}},
  journal = {J Biochem (Tokyo)},
  year = {2001},
  volume = {130},
  pages = {879-884},
  number = {6},
  month = {Dec},
  abstract = {{Four motor proteins, MotX, MotY, PomA, and PomB, have been identified
	as constituents of the Na(+)-driven flagellum of Vibrio species.
	In this study, the complete motX gene was cloned from Vibrio alginolyticus
	and shown to complement three mot mutations, motX94, motX115, and
	motX119, as well as a V. parahaemolyticus motX mutant. The motX94
	mutant contains a frameshift at Val86 of MotX, while the motX115
	and motX119 mutations comprise substitutions of Ala146 to Val and
	Gln 194 to amber, respectively. When MotX was overexpressed in Vibrio
	cells, the amount of MotY detected in the membrane fraction increased,
	and vice versa, suggesting that MotX and MotY mutually stabilize
	each other by interacting at the membrane level. When a plasmid containing
	the motX gene was introduced into motY mutants NMB117 (motY117) and
	VIO542 (motY542), the mutations were suppressed. In contrast, motY
	could not cause the recovery of any swarm-defective motX mutants
	studied. Considering the above evidence, we propose that MotX is
	more directly involved than MotY in the mechanical functioning of
	the Na(+)-type flagellar motor, and that MotY may stabilize MotX
	to support its interaction with other Mot proteins.}},
  pmid = {11726290},
  url = {http://www.hubmed.org/display.cgi?uids=11726290}
}

@ARTICLE{okabe05,
  author = {Okabe, M. and Yakushi, T. and Homma, M.},
  title = {{Interactions of MotX with MotY and with the PomA/PomB sodium ion
	channel complex of the Vibrio alginolyticus polar flagellum}},
  journal = {Annual Review of Microbiology},
  year = {2005},
  volume = {280},
  pages = {25659-25664},
  number = {27},
  month = {Jul},
  abstract = {{Rotation of the sodium ion-driven polar flagellum of Vibrio alginolyticus
	requires the inner membrane sodium ion channel complex PomA/PomB
	and the outer membrane components MotX and MotY. None of the detergents
	used in this study were able to solubilize MotX when it was expressed
	alone. However, when co-expressed with MotY, MotX was solubilized
	by some detergents. The change in the solubility of MotX suggests
	that MotY interacts with MotX. In agreement with this, a pull-down
	assay showed the association of MotY with MotX. Solubilized MotX
	and MotY eluted in the void volume from a gel-filtration column,
	suggesting that MotX and MotY form a large oligomeric structure(s).
	In the absence of MotY, MotX affected membrane localization of the
	PomA/PomB complex and of PomB alone but not of PomA alone, suggesting
	an interaction between MotX and PomB. We propose that MotX exhibits
	multiple interactions with the other motor components, first with
	MotY for its localization to the outer membrane and then with the
	PomA/PomB complex through PomB for the motor rotation.}},
  pmid = {15866878},
  url = {http://www.hubmed.org/display.cgi?uids=15866878}
}

@ARTICLE{okabe02,
  author = {Okabe, M. and Yakushi, T. and Kojima, M. and Homma, M.},
  title = {{MotX and MotY, specific components of the sodium-driven flagellar
	motor, colocalize to the outer membrane in Vibrio alginolyticus}},
  journal = {Molecular Microbiology},
  year = {2002},
  volume = {46},
  pages = {125-134},
  number = {1},
  month = {Oct},
  abstract = {{Rotation of the sodium-driven polar flagella of Vibrio alginolyticus
	requires four motor proteins: PomA, PomB, MotX and MotY. MotX and
	MotY, which are unique components of the sodium-driven motor of Vibrio,
	have been believed to be localized in the inner (cytoplasmic) membrane
	via their N-terminal hydrophobic segments. Here we show that MotX
	and MotY colocalize to the outer membrane. Both proteins, when expressed
	together, were detected in the outer membrane fraction separated
	by sucrose density gradient centrifugation. As mature MotX and MotY
	proteins do not have N-terminal hydrophobic segments, the N-termini
	of the primary translation products must have signal sequences that
	are removed upon translocation across the inner membrane. Moreover,
	MotX and MotY require each other for efficient localization to the
	outer membrane. Based on these lines of evidence, we propose that
	MotX and MotY form a complex in the outer membrane. This is the first
	case that describes motor proteins function in the outer membrane
	for flagellar rotation.}},
  pmid = {12366836},
  url = {http://www.hubmed.org/display.cgi?uids=12366836}
}

@ARTICLE{oster00,
  author = {Oster, G. and Wang, H. and Grabe, M.},
  title = {{How Fo-ATPase generates rotary torque}},
  journal = {Philosophical Transactions of the Royal Society of London B},
  year = {2000},
  volume = {355},
  pages = {523-528},
  number = {1396},
  month = {Apr},
  pmid = {10836505},
  url = {http://www.hubmed.org/display.cgi?uids=10836505}
}

@ARTICLE{Packer:1994:J-Bacteriol:8282697,
  author = {Packer, H.L. and Armitage, J.P.},
  title = {{The chemokinetic and chemotactic behavior of \normalfont{Rhodobacter
	sphaeroides}: \textit{two independent responses}}},
  journal = {Journal of Bacteriology},
  year = {1994},
  volume = {176},
  pages = {206-212},
  number = {1},
  month = {Jan},
  abstract = {Rhodobacter sphaeroides exhibits two behavioral responses when exposed
	to some compounds: (i) a chemotactic response that results in accumulation
	and (ii) a sustained increase in swimming speed. This latter chemokinetic
	response occurs without any apparent long-term change in the size
	of the electrochemical proton gradient. The results presented here
	show that the chemokinetic response is separate from the chemotactic
	response, although some compounds can induce both responses. Compounds
	that caused only chemokinesis induced a sustained increase in the
	rate of flagellar rotation, but chemoeffectors which were also chemotactic
	caused an additional short-term change in both the stopping frequency
	and the duration of stops and runs. The response to a change in chemoattractant
	concentration was a transient increase in the stopping frequency
	when the concentration was reduced, with adaptation taking between
	10 and 60 s. There was also a decrease in the stopping frequency
	when the concentration was increased, but adaptation took up to 60
	min. The nature and duration of both the chemotactic and chemokinetic
	responses were concentration dependent. Weak organic acids elicited
	the strongest chemokinetic responses, and although many also caused
	chemotaxis, there were conditions under which chemokinesis occurred
	in the absence of chemotaxis. The transportable succinate analog
	malonate caused chemokinesis but not chemotaxis, as did acetate when
	added to a mutant able to transport but not grow on acetate. Chemokinesis
	also occurred after incubation with arsenate, conditions under which
	chemotaxis was lost, indicating that phosphorylation at some level
	may have a role in chemotaxis. Aspartate was the only chemoattractant
	amino acid to cause chemokinesis. Glutamate caused chemotaxis but
	not chemokinesis. These data suggest that (i) chemotaxis and chemokinesis
	are separate responses, (ii) metabolism is required for chemotaxis
	but not chemokinesis, (iii) a reduction in chemoattractant concentration
	may cause the major chemotactic signal, and (iv) a specific transport
	pathway(s) may be involved in chemokinetic signalling in R. sphaeroides.},
  pmid = {8282697},
  url = {http://www.hubmed.org/display.cgi?uids=8282697}
}

@ARTICLE{packer93,
  author = {Packer, H.L. and Armitage, J.P.},
  title = {{The unidirectional flagellar motor of \normalfont{Rhodobacter sphaeroides}
	\textit{WS8 can rotate either clockwise or counterclockwise: characterization
	of the flagellum under both conditions by antibody decoration}}},
  journal = {Journal of Bacteriology},
  year = {1993},
  volume = {175},
  pages = {6041-6045},
  number = {18},
  month = {Sep},
  abstract = {{A variant of Rhodobacter sphaeroides WS8 has been isolated which
	when tethered has a cell body that rotates counterclockwise instead
	of clockwise. Antibody decoration in vivo has shown that the filament
	on the variant has handedness opposite to that of the normal form.
	In both cases the cell body is pushed by the rotating flagellum.}},
  pmid = {8376349},
  url = {http://www.hubmed.org/display.cgi?uids=8376349}
}

@ARTICLE{Packer:1996:Microbiology:8868434,
  author = {Packer, H.L. and Gauden, D.E. and Armitage, J.P.},
  title = {{The behavioural response of anaerobic \normalfont{Rhodobacter sphaeroides}
	\textit{to temporal stimuli}}},
  journal = {Microbiology},
  year = {1996},
  volume = {142},
  pages = {593-599},
  month = {Mar},
  abstract = {The behavioural response of Rhodobacter sphaeroides to temporal changes
	in the concentration of chemoeffectors, and to stimuli affecting
	electron transport, was analysed using tethered cells. Populations
	of photosynthetically grown tethered cells of R. sphaeroides showed
	a transient response, a stop followed by adaptation, to a stepwise
	reduction in the concentration of chemoattractants (such as organic
	acids or sugars) and terminal electron acceptors. A step-down response
	was also measured in free swimming cells to a reduction in light
	intensity. As this response appears to apply to all effectors this
	suggests that there is a sensory pathway in anaerobically grown R.
	sphaeroides which responds primarily to a reduction in a stimulus.
	R. sphaeroides therefore responds when moving down a concentration
	gradient. This is the inverse of the classical Escherichia coli-Salmonella
	typhimurium model of bacterial sensory behaviour in which bacteria
	respond primarily when there is an increase in an attractant concentration,
	i.e. when moving up a gradient. R. sphaeroides does show a chemokinetic
	response to an increase in concentration of a limited number of compounds
	but this response is sustained and accompanied by an increase in
	the rate of flagellar rotation and therefore not simply equivalent
	to the transient increase in smooth swimming measured in E. coli
	on addition of an attractant.},
  pmid = {8868434},
  url = {http://www.hubmed.org/display.cgi?uids=8868434}
}

@ARTICLE{packer1994epg,
  author = {Packer, H.L. and Harrison, D.M. and Dixon, R.M. and Armitage, J.P.},
  title = {{The effect of pH on the growth and motility of \normalfont{Rhodobacter
	sphaeroides} \textit{WS8N and the nature of the driving force of
	the flagellar motor}}},
  journal = {Biochimica et biophysica acta. Bioenergetics},
  year = {1994},
  volume = {1188},
  pages = {101-107},
  number = {1-2},
  publisher = {Elsevier Science}
}

@ARTICLE{Packer:1997:FEBS-Lett:9199499,
  author = {Packer, H.L. and Lawther, H. and Armitage, J.P.},
  title = {{The \normalfont{Rhodobacter sphaeroides} \textit{flagellar motor
	is a variable-speed rotor}}},
  journal = {FEBS Letters},
  year = {1997},
  volume = {409},
  pages = {37-40},
  number = {1},
  month = {Jun},
  abstract = {The rotation rate of the unidirectional stop/start motor of Rhodobacter
	sphaeroides was investigated using computerised motion analysis of
	tethered cells. The R. sphaeroides motor was found to have a variable
	rotation rate compared to the virtually constant-speed motor of wild-type
	and CheR mutant (smooth swimming) Escherichia coli. In addition,
	the dynamics of the R. sphaeroides motor during stopping was analysed
	with no consistent correlation behaviour. The motor could go from
	full rotation to stop, or stop to full rotation within one video
	frame, i.e. 0.02 s, but it could also slow down into a stop or restart
	slowly, taking up to 0.25 s. The R. sphaeroides motor under chemokinetic
	stimulation was also analysed and was found to show increased torque
	generation and reduced variation in rotation rate.},
  pmid = {9199499},
  url = {http://www.hubmed.org/display.cgi?uids=9199499}
}

@ARTICLE{padan01,
  author = {Padan, E. and Venturi, M. and Gerchman, Y. and Dover, N.},
  title = {{Na(+)/H(+) antiporters}},
  journal = {Biochimica et Biophysica},
  year = {2001},
  volume = {1505},
  pages = {144-157},
  number = {1},
  month = {May},
  abstract = {{Na(+)/H(+) antiporters are membrane proteins that play a major role
	in pH and Na(+) homeostasis of cells throughout the biological kingdom,
	from bacteria to humans and higher plants. The emerging genomic sequence
	projects already have started to reveal that the Na(+)/H(+) antiporters
	cluster in several families. Structure and function studies of a
	purified antiporter protein have as yet been conducted mainly with
	NhaA, the key Na(+)/H(+) antiporter of Escherichia coli. This antiporter
	has been overexpressed, purified and reconstituted in a functional
	form in proteoliposomes. It has recently been crystallized in both
	3D as well as 2D crystals. The NhaA 2D crystals were analyzed by
	cryoelectron microscopy and a density map at 4 A resolution was obtained
	and a 3D map was reconstructed. NhaA is shown to exist in the 2D
	crystals as a dimer of monomers each composed of 12 transmembrane
	segments with an asymmetric helix packing. This is the first insight
	into the structure of a polytopic membrane protein. Many Na(+)/H(+)
	antiporters are characterized by very dramatic sensitivity to pH,
	a property that corroborates their role in pH homeostasis. The molecular
	mechanism underlying this pH sensitivity has been studied in NhaA.
	Amino acid residues involved in the pH response have been identified.
	Conformational changes transducing the pH change into a change in
	activity were found in loop VIII-IX and at the N-terminus by probing
	trypsin digestion or binding of a specific monoclonal antibody respectively.
	Regulation by pH of the eukaryotic Na(+)/H(+) antiporters involves
	an intricate signal transduction pathway (recently reviewed by Yun
	et al., Am. J. Physiol. 269 (1995) G1-G11). The transcription of
	NhaA has been shown to be regulated by a novel Na(+)-specific regulatory
	network. It is envisaged that interdisciplinary approaches combining
	structure, molecular and cell biology as well as genomics should
	be applied in the future to the study of this important group of
	transporters.}},
  pmid = {11248196},
  url = {http://www.hubmed.org/display.cgi?uids=11248196}
}

@ARTICLE{paoli1998acg,
  author = {Paoli, G.C. and Tabita, F.R.},
  title = {{Aerobic chemolithoautotrophic growth and RubisCO function in \normalfont{Rhodobacter
	capsulatus} \textit{and a spontaneous gain of function mutant of}
	\normalfont{Rhodobacter sphaeroides}}},
  journal = {Archives of Microbiology},
  year = {1998},
  volume = {170},
  pages = {8-17},
  number = {1},
  publisher = {Springer}
}

@ARTICLE{parkinson1978caa,
  author = {Parkinson, J.S.},
  title = {{Complementation analysis and deletion mapping of \normalfont{Escherichia
	coli} \textit{mutants defective in chemotaxis}}},
  journal = {Journal of Bacteriology},
  year = {1978},
  volume = {135},
  pages = {45-53},
  number = {1},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{passmore2008aff,
  author = {Passmore, S.E. and Meas, R. and Marykwas, D.L.},
  title = {{Analysis of the FliM/FliG motor protein interaction by two-hybrid
	mutation suppression analysis}},
  journal = {Microbiology},
  year = {2008},
  volume = {154},
  pages = {714-724},
  number = {3},
  publisher = {Soc General Microbiol}
}

@ARTICLE{paul2006maf,
  author = {Paul, K. and Harmon, J.G. and Blair, D.F.},
  title = {{Mutational analysis of the flagellar rotor protein FliN: identification
	of surfaces important for flagellar assembly and switching}},
  journal = {Journal of Bacteriology},
  year = {2006},
  volume = {188},
  pages = {5240--5248},
  number = {14},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{penfold1992isv,
  author = {Penfold, R.J. and Pemberton, J.M.},
  title = {{An improved suicide vector for construction of chromosomal insertion
	mutations in bacteria}},
  journal = {Gene},
  year = {1992},
  volume = {118},
  pages = {145-146},
  number = {1}
}

@ARTICLE{peskin:93,
  author = {Peskin, Charles S. and Odell, Garrett M. and Oster, George F.},
  title = {Cellular Motions and Thermal Fluctuations: The Brownian Ratchet},
  journal = {Biophysical Journal},
  year = {1993},
  volume = {65},
  pages = {316-324},
  optnote = {models}
}

@ARTICLE{peterman:03,
  author = {Peterman, EJG. and Gittes, F. and Schmidt, CF.},
  title = {Laser-Induced heating in Optical Traps},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {84},
  pages = {1308-1316},
  month = {February}
}

@PHDTHESIS{pilizota,
  author = {Pilizota, T.},
  title = {{A programmable optical angle clamp for rotary molecular motors}},
  school = {University of Oxford},
  year = {2006},
  owner = {mostyn},
  timestamp = {2008.08.24}
}

@ARTICLE{pilizota2007poa,
  author = {Pilizota, T. and Bilyard, T. and Bai, F. and Futai, M. and Hosokawa,
	H. and Berry, R.M.},
  title = {{A programmable optical angle clamp for rotary molecular motors}},
  journal = {Biophysical Journal},
  year = {2007},
  volume = {93},
  pages = {264-275},
  number = {1},
  publisher = {Biophysical Soc}
}

@ARTICLE{poggio2007csf,
  author = {Poggio, S. and Abreu-Goodger, C. and Fabela, S. and Osorio, A. and
	Dreyfus, G. and Vinuesa, P. and Camarena, L.},
  title = {{A complete set of flagellar genes acquired by horizontal transfer
	coexists with the endogenous flagellar system in \normalfont{Rhodobacter
	sphaeroides}}},
  journal = {Journal of Bacteriology},
  year = {2007},
  volume = {189},
  pages = {3208-3216},
  number = {8},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{poggio2001ntf,
  author = {Poggio, S. and Osorio, A. and Corkidi, G. and Dreyfus, G. and Camarena,
	L.},
  title = {{The N terminus of FliM is essential to promote flagellar rotation
	in \normalfont{Rhodobacter sphaeroides}}},
  journal = {Journal of Bacteriology},
  year = {2001},
  volume = {183},
  pages = {3142-3148},
  number = {10},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{poole1991epm,
  author = {Poole, P.S. and Brown, S. and Counsell, D. and Armitage, J.P.},
  title = {{The effect of phosphate on the motility of \normalfont{Rhodobacter
	sphaeroides}}},
  journal = {FEMS Microbiology Letters},
  year = {1991},
  volume = {79},
  pages = {1-4},
  number = {1},
  publisher = {Blackwell Synergy}
}

@ARTICLE{poole1993csr,
  author = {Poole, PS and Smith, MJ and Armitage, JP},
  title = {{Chemotactic signalling in Rhodobacter sphaeroides requires metabolism
	of attractants.}},
  journal = {Journal of Bacteriology},
  year = {1993},
  volume = {175},
  pages = {291--294},
  number = {1},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{poole1990crr,
  author = {Poole, P.S. and Williams, R.L. and Armitage, J.P.},
  title = {{Chemotactic responses of \normalfont{Rhodobacter sphaeroides} \textit{in
	the absence of apparent adaptation}}},
  journal = {Archives of Microbiology},
  year = {1990},
  volume = {153},
  pages = {368-372},
  number = {4},
  publisher = {Springer}
}

@PHDTHESIS{porter_thesis,
  author = {Porter, S.L.},
  title = {{The chemotaxis proteins of \textit{Rhodobacter sphaeroides}}},
  school = {University of Oxford},
  year = {2002},
  owner = {mostyn},
  timestamp = {2008.08.24}
}

@ARTICLE{porter2004crs,
  author = {Porter, S.L. and Armitage, J.P.},
  title = {{Chemotaxis in \normalfont{Rhodobacter sphaeroides} \textit{requires
	an atypical histidine protein kinase}}},
  journal = {Journal of Biological Chemistry},
  year = {2004},
  volume = {279},
  pages = {54573-54580},
  number = {52},
  publisher = {ASBMB}
}

@ARTICLE{porter2002prs,
  author = {Porter, S.L. and Armitage, J.P.},
  title = {{Phosphotransfer in \normalfont{Rhodobacter sphaeroides} \textit{chemotaxis}}},
  journal = {Journal of Molecular Biology},
  year = {2002},
  volume = {324},
  pages = {35-45},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{porter2008bkp,
  author = {Porter, S.L. and Roberts, M.A. and Manning, C.S. and Armitage, J.P.},
  title = {{A bifunctional kinase-phosphatase in bacterial chemotaxis}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {2008},
  volume = {105},
  pages = {18531-18536},
  number = {47},
  publisher = {Proc Natl Acad Sci USA}
}

@ARTICLE{porter2008rsc,
  author = {Porter, S.L. and Wadhams, G.H. and Armitage, J.P.},
  title = {{\normalfont{Rhodobacter sphaeroides}: \textit{complexity in chemotactic
	signalling}}},
  journal = {Trends in Microbiology},
  year = {2008},
  volume = {16},
  pages = {251-260},
  number = {6},
  publisher = {Elsevier}
}

@ARTICLE{porter2006crs,
  author = {Porter, S.L. and Wadhams, G.H. and Martin, A.C. and Byles, E.D. and
	Lancaster, D.E. and Armitage, J.P.},
  title = {{The CheYs of \normalfont{Rhodobacter sphaeroides}}},
  journal = {Journal of Biological Chemistry},
  year = {2006},
  volume = {281},
  pages = {32694-32704},
  number = {43},
  publisher = {ASBMB}
}

@ARTICLE{porter2002tcl,
  author = {Porter, S.L. and Warren, A.V. and Martin, A.C. and Armitage, J.P.},
  title = {{The third chemotaxis locus of \normalfont{Rhodobacter sphaeroides}
	\textit{is essential for chemotaxis}}},
  journal = {Molecular Microbiology},
  year = {2002},
  volume = {46},
  pages = {1081-1094},
  number = {4},
  publisher = {Blackwell Synergy}
}

@ARTICLE{pralle:99,
  author = {Pralle, N. and Prummer, M. and Florin, E. and Stelzaer, EH. and Horber,
	JKH.},
  title = {Three dimensional high resolution particle tracking for optical tweezers
	by forward scattered light},
  journal = {Microscopy research and technique},
  year = {1999},
  volume = {44},
  pages = {378-386},
  optnote = {tweezers}
}

@ARTICLE{puskas1997qss,
  author = {Puskas, A. and Greenberg, E.P. and Kaplan, S. and Schaefer, A.L.},
  title = {{A quorum-sensing system in the free-living photosynthetic bacterium
	\normalfont{Rhodobacter sphaeroides}}},
  journal = {Journal of Bacteriology},
  year = {1997},
  volume = {179},
  pages = {7530-7537},
  number = {23},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{ravid84,
  author = {Ravid, S. and Eisenbach, M.},
  title = {{Minimal requirements for rotation of bacterial flagella}},
  journal = {Journal of Bacteriology},
  year = {1984},
  volume = {158},
  pages = {1208-1210},
  number = {3},
  month = {Jun},
  abstract = {{An in vitro system of cell envelopes from Salmonella typhimurium
	with functional flagella was used to determine the minimal requirements
	for flagellar rotation. Rotation in the absence of cytoplasmic constituents
	could be driven either by respiration or by an artificially imposed
	chemical gradient of protons. No specific ionic requirements other
	than protons (or hydroxyls) were found for the motor function.}},
  pmid = {6373740},
  url = {http://www.hubmed.org/display.cgi?uids=6373740}
}

@ARTICLE{ravid86,
  author = {Ravid, S. and Matsumura, P. and Eisenbach, M.},
  title = {{Restoration of flagellar clockwise rotation in bacterial envelopes
	by insertion of the chemotaxis protein CheY}},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1986},
  volume = {83},
  pages = {7157-7161},
  number = {19},
  month = {Oct},
  abstract = {{When cells of the bacterium Salmonella typhimurium are incubated
	with penicillin and lysed in a dilute buffer, flagellated cytoplasm-free
	envelopes are formed. When the envelopes are tethered to glass by
	their flagella and then energized, some of them spin. The direction
	of rotation of wild-type envelopes is exclusively counterclockwise
	(CCW). We perturbed this system by including in the lysis medium
	(and hence in the envelopes) the chemotaxis protein CheY. As a result,
	some of the envelopes rotated exclusively clockwise (CW). The fraction
	of envelopes that did so increased with the concentration of CheY;
	at a concentration of 48 microM (pH 8), all functional envelopes
	spun CW. The fraction also increased with the pH of the lysis medium
	in the range of 6.6-8.4. The results were the same in the presence
	or absence of intracellular Ca2+. Reconstituted envelopes failed
	to respond to chemotactic stimuli. None of them changed the direction
	of their rotation. However, when the intracellular pH was lowered
	to 6.6 or below, envelopes that spun CW stopped rotating, while envelopes
	that spun CCW continued to rotate. This phenomenon was reversible.
	We conclude that CheY per se, without any additional free cytoplasmic
	mediators, interacts with a switch at the base of the flagellum to
	cause CW rotation.}},
  pmid = {3532103},
  url = {http://www.hubmed.org/display.cgi?uids=3532103}
}

@ARTICLE{reid2006mnt,
  author = {Reid, S.W. and Leake, M.C. and Chandler, J.H. and Lo, C.J. and Armitage,
	J.P. and Berry, R.M.},
  title = {{The maximum number of torque-generating units in the flagellar motor
	of \textnormal{Escherichia coli} is at least 11}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {2006},
  volume = {103},
  pages = {8066--8071},
  number = {21},
  publisher = {National Acad Sciences}
}

@ARTICLE{roman1992css,
  author = {Roman, S.J. and Meyers, M. and Volz, K. and Matsumura, P.},
  title = {{A chemotactic signaling surface on CheY defined by suppressors of
	flagellar switch mutations}},
  journal = {Journal of Bacteriology},
  year = {1992},
  volume = {174},
  pages = {6247-6255},
  number = {19},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{roujeinikova2008csc,
  author = {Roujeinikova, A.},
  title = {{Crystal structure of the cell wall anchor domain of MotB, a stator
	component of the bacterial flagellar motor: Implications for peptidoglycan
	recognition}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {2008},
  volume = {105},
  pages = {10348-10353},
  number = {30},
  publisher = {National Acad Sciences}
}

@PHDTHESIS{rowe,
  author = {Rowe, A.D.},
  title = {{Rotation of the sodium driven bacterial flagellar motor}},
  school = {University of Oxford},
  year = {2005},
  owner = {mostyn},
  timestamp = {2008.08.20}
}

@ARTICLE{rowe:03,
  author = {Rowe, A.D. and Leake, M.C. and Morgan, H. and Berry, R.M.},
  title = {Rapid rotation of micron and sub-micron dielectric particles measured
	using optical tweezers},
  journal = {Journal of Modern Optics},
  year = {2003},
  volume = {50},
  pages = {1539-1554},
  number = {10},
  optnote = {tweezers}
}

@ARTICLE{ryu:00,
  author = {Ryu, W.S. and Berry, R.M. and Berg, H.C.},
  title = {Torque-generating units of the flagellar motor of \textnormal{Escherichia
	coli} have a high duty ratio},
  journal = {Nature},
  year = {2000},
  volume = {403},
  pages = {444-447},
  optnote = {ecoli}
}

@ARTICLE{sakamoto:00,
  author = {Sakamoto, T. and Amitani, I. and Yokota, E. and Ando, T.},
  title = {Direct observation of processive movement by individual myosin-V
	molecules},
  journal = {Biochemical and Biophysical Research Communications},
  year = {2000},
  optnote = {myosin},
  optnumber = {272},
  optpages = {586-590}
}

@ARTICLE{samatey04,
  author = {Samatey, F.A. and Matsunami, H. and Imada, K. and Nagashima, S. and
	Shaikh, T.R. and Thomas, D.R. and Chen, J.Z. and Derosier, D.J. and
	Kitao, A. and Namba, K.},
  title = {{Structure of the bacterial flagellar hook and implication for the
	molecular universal joint mechanism}},
  journal = {Nature},
  year = {2004},
  volume = {431},
  pages = {1062-1068},
  number = {7012},
  month = {Oct},
  abstract = {{The bacterial flagellum is a motile organelle, and the flagellar
	hook is a short, highly curved tubular structure that connects the
	flagellar motor to the long filament acting as a helical propeller.
	The hook is made of about 120 copies of a single protein, FlgE, and
	its function as a nano-sized universal joint is essential for dynamic
	and efficient bacterial motility and taxis. It transmits the motor
	torque to the helical propeller over a wide range of its orientation
	for swimming and tumbling. Here we report a partial atomic model
	of the hook obtained by X-ray crystallography of FlgE31, a major
	proteolytic fragment of FlgE lacking unfolded terminal regions, and
	by electron cryomicroscopy and three-dimensional helical image reconstruction
	of the hook. The model reveals the intricate molecular interactions
	and a plausible switching mechanism for the hook to be flexible in
	bending but rigid against twisting for its universal joint function.}},
  pmid = {15510139},
  url = {http://www.hubmed.org/display.cgi?uids=15510139}
}

@BOOK{sambrook2001mcl,
  title = {{Molecular Cloning: A Laboratory Manual}},
  publisher = {CSHL Press},
  year = {2001},
  author = {Sambrook, J. and Russell, D.W.}
}

@ARTICLE{samuel96,
  author = {Samuel, AD. and Berg, HC.},
  title = {{Torque-generating units of the bacterial flagellar motor step independently}},
  journal = {Biophysical Journal},
  year = {1996},
  volume = {71},
  pages = {918-923},
  number = {2},
  month = {Aug},
  abstract = {{Measurements of the variance in rotation period of tethered cells
	as a function of mean rotation rate have shown that the flagellar
	motor of Escherichia coli is a stepping motor. Here, by measurement
	of the variance in rotation period as a function of the number of
	active torque-generating units, it is shown that each unit steps
	independently.}},
  pmid = {8842231},
  url = {http://www.hubmed.org/display.cgi?uids=8842231}
}

@ARTICLE{samuel:95,
  author = {Samuel, AD. and Berg, HC.},
  title = {Fluctuation analysis of rotational speeds of the bacterial flagellar
	motor},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1995},
  volume = {92},
  pages = {3502-3506},
  optnote = {general motors}
}

@ARTICLE{sato:00feb,
  author = {Sato, K. and Homma, M.},
  title = {Functional Reconstitution of the Na+ -driven Polar Flagellar Motor
	Component of {\it Vibrio alginolyticus}},
  journal = {Journal of Biological Chemistry},
  year = {2000},
  volume = {275},
  pages = {5718-5722},
  number = {8},
  optnote = {structure}
}

@ARTICLE{sato:00jun,
  author = {Sato, K. and Homma, M.},
  title = {Multimeric structure of PomA, a component of the Na+ driven polar
	flagellar motor of \textit{Vibrio alginolyticus}},
  journal = {Journal of Biological Chemistry},
  year = {2000},
  optnote = {structure},
  optnumber = {26},
  optpages = {20223-20228},
  optvolume = {275}
}

@ARTICLE{schafer1994smm,
  author = {Schafer, A. and Tauch, A. and Jager, W. and Kalinowski, J. and Thierbach,
	G. and Puhler, A.},
  title = {{Small mobilizable multi-purpose cloning vectors derived from the
	\normalfont{Escherichia coli} \textit{plasmids pK18 and pK19: selection
	of defined deletions in the chromosome of} \normalfont{Corynebacterium
	glutamicum}}},
  journal = {Gene},
  year = {1994},
  volume = {145},
  pages = {69-73},
  number = {1}
}

@ARTICLE{scharf98,
  author = {Scharf, BE. and Fahrner, KA. and Turner, L. and Berg, HC.},
  title = {{Control of direction of flagellar rotation in bacterial chemotaxis}},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1998},
  volume = {95},
  pages = {201-206},
  number = {1},
  month = {Jan},
  abstract = {{The motile behavior of the bacterium Escherichia coli depends on
	the direction of rotation of its flagellar motors. Binding of the
	phosphorylated signaling molecule CheY to a motor component FliM
	is known to enhance clockwise rotation. It is difficult to study
	this interaction in vivo, because the dynamics of phosphorylation
	of CheY by its kinase CheA and the hydrolysis of CheY (accelerated
	by CheZ) are not under direct experimental control. Here, we examine
	instead the interaction with the flagellar motor of a double mutant
	CheY13DK106YW that is active without phosphorylation. The behavioral
	assays were carried out on tethered cells lacking CheA and CheZ.
	The effects of variation in intracellular concentration of the mutant
	protein were highly nonlinear. However, they can be explained by
	a thermal isomerization model in which the free energies of clockwise
	and counterclockwise states depend linearly on the amount of CheY
	bound.}},
  pmid = {9419353},
  url = {http://www.hubmed.org/display.cgi?uids=9419353}
}

@ARTICLE{schnitzer97,
  author = {Schnitzer, MJ. and Block, SM.},
  title = {{Kinesin hydrolyses one ATP per 8-nm step}},
  journal = {Nature},
  year = {1997},
  volume = {388},
  pages = {386-390},
  number = {6640},
  month = {Jul},
  abstract = {{Kinesin is a two-headed, ATP-dependent motor protein that moves along
	microtubules in discrete steps of 8 nm. In vitro, single molecules
	produce processive movement; motors typically take approximately
	100 steps before releasing from a microtubule. A central question
	relates to mechanochemical coupling in this enzyme: how many molecules
	of ATP are consumed per step? For the actomyosin system, experimental
	approaches to this issue have generated considerable controversy.
	Here we take advantage of the processivity of kinesin to determine
	the coupling ratio without recourse to direct measurements of ATPase
	activity, which are subject to large experimental uncertainties.
	Beads carrying single molecules of kinesin moving on microtubules
	were tracked with high spatial and temporal resolution by interferometry.
	Statistical analysis of the intervals between steps at limiting ATP,
	and studies of fluctuations in motor speed as a function of ATP concentration,
	allow the coupling ratio to be determined. At near-zero load, kinesin
	molecules hydrolyse a single ATP molecule per 8-nm advance. This
	finding excludes various one-to-many and many-to-one coupling schemes,
	analogous to those advanced for myosin, and places severe constraints
	on models for movement.}},
  pmid = {9237757},
  url = {http://www.hubmed.org/display.cgi?uids=9237757}
}

@ARTICLE{schuster2000csb,
  author = {Schuster, M. and Zhao, R. and Bourret, R.B. and Collins, E.J.},
  title = {{Correlated switch binding and signaling in bacterial chemotaxis}},
  journal = {Journal of Biological Chemistry},
  year = {2000},
  volume = {275},
  pages = {19752-19758},
  number = {26},
  publisher = {ASBMB}
}

@ARTICLE{segall1986tcb,
  author = {Segall, J.E. and Block, S.M. and Berg, H.C.},
  title = {{Temporal comparisons in bacterial chemotaxis}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {1986},
  volume = {83},
  pages = {8987--8991},
  number = {23},
  publisher = {National Acad Sciences}
}

@BOOK{Serway2003,
  title = {Physics for Scientists and Engineers},
  publisher = {Brooks Cole},
  year = {2003},
  author = {Serway, R. A. and Jewett, Jr. J. W.},
  edition = {6th Ed.},
  owner = {mostyn},
  timestamp = {2008.12.16}
}

@ARTICLE{shah2000ifc,
  author = {Shah, D.S.H. and Porter, S.L. and Harris, D.C. and Wadhams, G.H.
	and Hamblin, P.A. and Armitage, J.P.},
  title = {{Identification of a fourth \normalfont{cheY} \textit{gene in} \normalfont{Rhodobacter
	sphaeroides} \textit{and interspecies interaction within the bacterial
	chemotaxis signal transduction pathway}}},
  journal = {Molecular Microbiology},
  year = {2000},
  volume = {35},
  pages = {101-112},
  number = {1},
  publisher = {Blackwell Synergy}
}

@ARTICLE{shah2000ftb,
  author = {Shah, D.S.H. and Porter, S.L. and Martin, A.C. and Hamblin, P.A.
	and Armitage, J.P.},
  title = {{Fine tuning bacterial chemotaxis: analysis of \normalfont{Rhodobacter
	sphaeroides} \textit{behaviour under aerobic and anaerobic conditions
	by mutation of the major chemotaxis operons and} \normalfont{cheY}
	\textit{genes}}},
  journal = {The EMBO Journal},
  year = {2000},
  volume = {19},
  pages = {4601-4613}
}

@ARTICLE{shimada:87,
  author = {Shimada, K. and Berg, H.C.},
  title = {Response of the flagellar rotary motor to abrupt changes in extracellular
	pH},
  journal = {Journal of Molecular Biology},
  year = {1987},
  optnote = {pmf},
  optpages = {585-589},
  optvolume = {193}
}

@ARTICLE{shioi:80,
  author = {Shioi, J.I. and Matsuura, S. and Imae, Y.},
  title = {Quantitative measurements of proton motive force and motility in
	\textit{Bacillus subtilis}},
  journal = {Journal of Bacteriology},
  year = {1980},
  optnote = {pmf},
  optnumber = {3},
  optpages = {891-897},
  optvolume = {144}
}

@ARTICLE{silverman:74,
  author = {Silverman, M. and Simon, M.},
  title = {Flagellar rotation and the mechanism of bacterial motility},
  journal = {Nature},
  year = {1974},
  volume = {249},
  pages = {73-74},
  optnote = {general motors}
}

@ARTICLE{simmons:96,
  author = {Simmons, RM. and Finer, JT. and Chu, S. and Spudich, JA.},
  title = {Quantitative measurements of force and displacement using an optical
	trap},
  journal = {Biophysical Journal},
  year = {1996},
  volume = {70},
  pages = {1813-1822},
  optnote = {tweezers}
}

@ARTICLE{slovak2005lmr,
  author = {Slovak, P.M. and Wadhams, G.H. and Armitage, J.P.},
  title = {{Localization of MreB in \normalfont{Rhodobacter sphaeroides} \textit{under
	conditions causing changes in cell shape and membrane structure}}},
  journal = {Journal of Bacteriology},
  year = {2005},
  volume = {187},
  pages = {54-64},
  number = {1},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{sockett1992maf,
  author = {Sockett, H. and Yamaguchi, S. and Kihara, M. and Irikura, V.M. and
	Macnab, R.M.},
  title = {{Molecular analysis of the flagellar switch protein FliM of \normalfont{Salmonella
	typhimurium}}},
  journal = {Journal of Bacteriology},
  year = {1992},
  volume = {174},
  pages = {793-806},
  number = {3},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{sockett1991ica,
  author = {Sockett, R.E. and Armitage, J.P.},
  title = {{Isolation, characterization, and complementation of a paralyzed
	flagellar mutant of \normalfont{Rhodobacter sphaeroides} \textit{WS8}}},
  journal = {Journal of Bacteriology},
  year = {1991},
  volume = {173},
  pages = {2786-2790},
  number = {9},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{sourjik2002bec,
  author = {Sourjik, V. and Berg, H.C.},
  title = {{Binding of the \normalfont{Escherichia coli} \textit{response regulator
	CheY to its target measured} \normalfont{in vivo} \textit{by fluorescence
	resonance energy transfer}}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {2002},
  volume = {99},
  pages = {12669-12674},
  number = {20},
  publisher = {National Acad Sciences}
}

@ARTICLE{sourjik1998pbc,
  author = {Sourjik, V. and Schmitt, R.},
  title = {{Phosphotransfer between CheA, CheY$_1$, and CheY$_2$ in the chemotaxis
	signal transduction chain of \normalfont{Rhizobium meliloti}}},
  journal = {Biochemistry},
  year = {1998},
  volume = {37},
  pages = {2327-2335},
  number = {8}
}

@ARTICLE{sourjik1996drc,
  author = {Sourjik, V. and Schmitt, R.},
  title = {{Different roles of CheY$_1$ and CheY$_2$ in the chemotaxis of \normalfont{Rhizobium
	meliloti}}},
  journal = {Molecular Microbiology},
  year = {1996},
  volume = {22},
  pages = {427-436},
  number = {3},
  publisher = {Blackwell Synergy}
}

@ARTICLE{sowa2008bfm,
  author = {Sowa, Y. and Berry, R.M.},
  title = {{Bacterial flagellar motor}},
  journal = {Quarterly Reviews of Biophysics},
  year = {2008},
  volume = {41},
  pages = {1--30},
  publisher = {Cambridge University Press}
}

@ARTICLE{sowa:03,
  author = {Sowa, Y. and Hotta, H. and Homma, M. and Ishijima, A.},
  title = {{Torque-Speed relationship of the Na+ driven flagellar motor of \textnormal{Vibrio
	alginolyticus}}},
  journal = {Journal of Molecular Biology},
  year = {2003},
  volume = {327},
  pages = {1043-1051},
  optnote = {vibrio}
}

@ARTICLE{rowe05,
  author = {Sowa, Y. and Rowe, A.D. and Leake, M.C. and Yakushi, T. and Homma,
	M. and Ishijima, A. and Berry, R.M.},
  title = {{Direct observation of steps in rotation of the bacterial flagellar
	motor}},
  journal = {Nature},
  year = {2005},
  volume = {437},
  pages = {916-919},
  number = {7060},
  month = {Oct},
  abstract = {{The bacterial flagellar motor is a rotary molecular machine that
	rotates the helical filaments that propel many species of swimming
	bacteria. The rotor is a set of rings up to 45 nm in diameter in
	the cytoplasmic membrane; the stator contains about ten torque-generating
	units anchored to the cell wall at the perimeter of the rotor. The
	free-energy source for the motor is an inward-directed electrochemical
	gradient of ions across the cytoplasmic membrane, the protonmotive
	force or sodium-motive force for H(+)-driven and Na(+)-driven motors,
	respectively. Here we demonstrate a stepping motion of a Na(+)-driven
	chimaeric flagellar motor in Escherichia coli at low sodium-motive
	force and with controlled expression of a small number of torque-generating
	units. We observe 26 steps per revolution, which is consistent with
	the periodicity of the ring of FliG protein, the proposed site of
	torque generation on the rotor. Backwards steps despite the absence
	of the flagellar switching protein CheY indicate a small change in
	free energy per step, similar to that of a single ion transit.}},
  pmid = {16208378},
  url = {http://www.hubmed.org/display.cgi?uids=16208378}
}

@ARTICLE{steffen:01,
  author = {Steffen, W. and Smith, D. and Simmons, R. and Sleep, J.},
  title = {Mapping the actin filament with myosin},
  journal = {Proceedings of the National Academy of Science USA},
  year = {2001},
  volume = {98},
  pages = {14949-14954},
  number = {26},
  optnote = {myosin}
}

@ARTICLE{steuber00,
  author = {Steuber, J. and Schmid, C. and Rufibach, M. and Dimroth, P.},
  title = {{Na+ translocation by complex I (NADH:quinone oxidoreductase) of
	\textnormal{Escherichia coli}}},
  journal = {Molecular Microbiology},
  year = {2000},
  volume = {35},
  pages = {428-434},
  number = {2},
  month = {Jan},
  abstract = {{Following on from our previous discovery of Na+ pumping by the NADH:ubiquinone
	oxidoreductase (complex I) of Klebsiella pneumoniae, we show here
	that complex I from Escherichia coli is a Na+ pump as well. Our study
	object was the Escherichia coli mutant EP432, which lacks the Na+/H+
	antiporter genes nhaA and nhaB and is therefore unable to grow on
	LB medium at elevated Na+ concentrations. During growth on mineral
	medium, the Na+ tolerance of E. coli EP432 was influenced by the
	organic substrate. NaCl up to 450 mM did not affect growth on glycerol
	and fumarate, but growth on glucose was inhibited. Correlated to
	the Na+ tolerance was an increased synthesis of complex I in the
	glycerol/fumarate medium. Inverted membrane vesicles catalysed respiratory
	Na+ uptake with NADH as electron donor. The sodium ion transport
	activity of vesicles from glycerol/fumarate-grown cells was 40 nmol
	mg-1 min-1 and was resistant to the uncoupler carbonyl-cyanide m-chlorophenylhydrazone
	(CCCP), but was inhibited by the complex I-specific inhibitor rotenone.
	With an E. coli mutant deficient in complex I, the Na+ transport
	activity was low (1-3 nmol mg-1 min-1), and rotenone was without
	effect.}},
  pmid = {10652103},
  url = {http://www.hubmed.org/display.cgi?uids=10652103}
}

@BOOK{stryer,
  title = {Biochemistry},
  publisher = {Freeman},
  year = {1995},
  author = {Stryer, Lubert},
  optedition = {4},
  optkey = {0-7167-2009-4},
  optnote = {textbook}
}

@ARTICLE{svoboda:94,
  author = {Svoboda, K. and Block, SM.},
  title = {Biological applications of optical forces},
  journal = {Annual review of Biophysical and Biomolecular Structure},
  year = {1994},
  volume = {23},
  pages = {247-285},
  optnote = {tweezers}
}

@ARTICLE{svoboda:93,
  author = {Svoboda, K. and Schmidt, CF. and Schnapp, BJ. and Block, SM.},
  title = {Direct observation of kinesin stepping by optical trapping interferometry},
  journal = {Nature},
  year = {1993},
  volume = {365},
  pages = {721-727},
  month = {October}
}

@ARTICLE{tanaka:02,
  author = {Tanaka, H. and Homma, K. and Iwane, A.H. and Katayama, E. and Ikebe,
	R. and Saito, J. and Yanagida, T. and Ikebe, M.},
  title = {The motor domain determines the large step of myosin-V},
  journal = {Nature},
  year = {2002},
  optnote = {myosin},
  optpages = {192-195},
  optvolume = {415}
}

@ARTICLE{thomas2006tds,
  author = {Thomas, D.R. and Francis, N.R. and Xu, C. and DeRosier, D.J.},
  title = {{The three-dimensional structure of the flagellar rotor from a clockwise-locked
	mutant of \normalfont{Salmonella enterica Serovar Typhimurium}}},
  journal = {Journal of Bacteriology},
  year = {2006},
  volume = {188},
  pages = {7039-7048},
  number = {20},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{thomas01,
  author = {Thomas, D. and Morgan, DG. and DeRosier, DJ.},
  title = {{Structures of bacterial flagellar motors from two FliF-FliG gene
	fusion mutants}},
  journal = {Journal of Bacteriology},
  year = {2001},
  volume = {183},
  pages = {6404-6412},
  number = {21},
  month = {Nov},
  pmid = {11591685},
  url = {http://www.hubmed.org/display.cgi?uids=11591685}
}

@ARTICLE{thomas99,
  author = {Thomas, DR. and Morgan, DG. and DeRosier, DJ.},
  title = {{Rotational symmetry of the C ring and a mechanism for the flagellar
	rotary motor}},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1999},
  volume = {96},
  pages = {10134-10139},
  number = {18},
  month = {Aug},
  abstract = {{FliG, FliM, and FliN, key proteins for torque generation, are located
	in two rings. The first protein is in the M ring and the last two
	are in the C ring. The rotational symmetries of the C and M rings
	have been determined to be about 34 (this paper) and 26 (previous
	work), respectively. The mechanism proposed here depends on the symmetry
	mismatch between the rings: the C ring extends 34 levers, of which
	26 can bind to the 26 equivalent sites on the M ring. The remaining
	8 levers bind to proton-pore complexes (studs) to form 8 torque generators.
	Movement results from the swapping of stud-bound levers with M ring-bound
	levers. The model predicts that both the M and C rings rotate in
	the same direction but at different speeds.}},
  pmid = {10468575},
  url = {http://www.hubmed.org/display.cgi?uids=10468575}
}

@ARTICLE{tokuda88,
  author = {Tokuda, H. and Asano, M. and Shimamura, Y. and Unemoto, T. and Sugiyama,
	S. and Imae, Y.},
  title = {{Roles of the respiratory Na+ pump in bioenergetics of Vibrio alginolyticus}},
  journal = {J Biochem (Tokyo)},
  year = {1988},
  volume = {103},
  pages = {650-655},
  number = {4},
  month = {Apr},
  abstract = {{Bioenergetic characteristics of Na+ pump-defective mutants of a marine
	bacterium Vibrio alginolyticus were compared with those of the wild
	type and revertant. Generation of membrane potential and motility
	at pH 8.5 in the mutants were completely inhibited by a proton conductor,
	carbonylcyanide m-chlorophenylhydrazone, whereas those in the wild
	type or revertant were resistant to the inhibitor. Motility and amino
	acid transport were driven by the electrochemical potential of Na+
	not only in the wild type or revertant but also in the mutants. In
	the absence of the proton conductor, motility and amino acid transport
	of the mutants did not significantly differ from those of the wild
	type or revertant even at pH 8.5, where the Na+ pump has maximum
	activity. Therefore, the electrochemical potential of Na+ in the
	mutants seemed to be maintained at a normal level by a respiration-dependent
	H+ pump and Na+/H+ antiporter. On the other hand, growth of the mutants
	became defective as the medium pH increased, especially on minimal
	medium. These results indicate that the Na+ pump is an important
	energy-generating mechanism when nutrients are limited at alkaline
	pH.}},
  pmid = {3170506},
  url = {http://www.hubmed.org/display.cgi?uids=3170506}
}

@ARTICLE{tokuda85,
  author = {Tokuda, H. and Udagawa, T. and Unemoto, T.},
  title = {{Generation of the electrochemical potential of Na+ by the Na+-motive
	NADH oxidase in inverted membrane vesicles of Vibrio alginolyticus}},
  journal = {FEBS Lett},
  year = {1985},
  volume = {183},
  pages = {95-98},
  number = {1},
  month = {Apr},
  abstract = {{Inverted membrane vesicles prepared from Vibrio alginolyticus generated
	a membrane potential (positive inside) and accumulated Na+ by the
	oxidation of NADH. Generation of the membrane potential required
	Na+ and was inhibited by 2-heptyl-4-hydroxyquinoline N-oxide, a specific
	inhibitor of the Na+-dependent NADH oxidase. Collapse of the membrane
	potential by valinomycin stimulated the uptake of Na+. In contrast,
	accumulation of H+ was not detected under all the conditions tested.
	These results suggest that only Na+ is translocated by the Na+-dependent
	NADH oxidase of V. alginolyticus.}},
  pmid = {2579856},
  url = {http://www.hubmed.org/display.cgi?uids=2579856}
}

@ARTICLE{tokuda84,
  author = {Tokuda, H. and Unemoto, T.},
  title = {{Na+ is translocated at NADH:quinone oxidoreductase segment in the
	respiratory chain of Vibrio alginolyticus}},
  journal = {Journal of Biological Chemistry},
  year = {1984},
  volume = {259},
  pages = {7785-7790},
  number = {12},
  month = {Jun},
  abstract = {{The coupling site of the Na+ pump to the respiratory chain of Vibrio
	alginolyticus was examined using membrane fractions prepared from
	the wild type, Na+ pump-deficient mutants, and spontaneous revertant.
	NADH oxidase of the wild type and revertant specifically required
	NA+ for maximum activity, whereas Na+ was not essential for the NADH
	oxidase of mutants. Similar to the Na+ pump in whole cells, the Na+-dependent
	NADH oxidase in membranes had a pH optimum in the alkaline region.
	A respiratory inhibitor, 2-heptyl-4-hydroxyquinoline-N-oxide (HQNO),
	inhibited the Na+-dependent NADH oxidase but had little effect on
	the NA+-independent activity of mutant membranes. NADH:quinone oxidoreductase
	was found to be the Na+-dependent HQNO-sensitive site of the NADH
	oxidase. In the wild type cells, HQNO was also found to cause a strong
	inhibition of the Na+ pump with little effect on the overall H+ extrusion
	by respiration. The inhibition of the Na+ pump by HQNO was overcome
	by oxidized, but not reduced, N,N,N',N'-tetra-methyl-p-phenylenediamine
	(TMPD). In the presence of oxidised TMPD, the electron flow NADH
	to oxygen seemed to bypass the HQNO-sensitive site and energize the
	Na+ pump. From these results, it was concluded that the Na+ pump
	is coupled to the respiratory chain at the step of NADH:quinone oxidoreductase.}},
  pmid = {6736026},
  url = {http://www.hubmed.org/display.cgi?uids=6736026}
}

@ARTICLE{tokuda82,
  author = {Tokuda, H. and Unemoto, T.},
  title = {{Characterization of the respiration-dependent Na+ pump in the marine
	bacterium Vibrio alginolyticus}},
  journal = {Journal of Biological Chemistry},
  year = {1982},
  volume = {257},
  pages = {10007-10014},
  number = {17},
  month = {Sep},
  abstract = {{}},
  pmid = {7107593},
  url = {http://www.hubmed.org/display.cgi?uids=7107593}
}

@ARTICLE{towbin1979etp,
  author = {Towbin, H. and Staehelin, T. and Gordon, J.},
  title = {{Electrophoretic Transfer of Proteins from Polyacrylamide Gels to
	Nitrocellulose Sheets: Procedure and Some Applications}},
  journal = {Proceedings of the National Academy of Sciences},
  year = {1979},
  volume = {76},
  pages = {4350--4354},
  number = {9},
  publisher = {National Acad Sciences}
}

@ARTICLE{trachtenberg1987tds,
  author = {Trachtenberg, S. and DeRosier, D.J.},
  title = {{Three-dimensional structure of the frozen-hydrated flagellar filament:
	the left-handed filament of \normalfont{Salmonella typhimurium}}},
  journal = {Journal of Molecular Biology},
  year = {1987},
  volume = {195},
  pages = {581-601},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{turberfield03,
  author = {Turberfield, AJ. and Mitchell, JC. and Yurke, B. and Mills, AP. and
	Blakey, MI. and Simmel, FC.},
  title = {{DNA fuel for free-running nanomachines}},
  journal = {Physical Review Letters},
  year = {2003},
  volume = {90},
  pages = {118102-118102},
  number = {11},
  month = {Mar},
  pmid = {12688969},
  url = {http://www.hubmed.org/display.cgi?uids=12688969}
}

@ARTICLE{turner:00,
  author = {Turner, L. and Ryu, W.S. and Berg, H.C.},
  title = {Real time imaging of fluorescent flagellar filaments},
  journal = {Journal of Bacteriology},
  year = {2000},
  volume = {182},
  pages = {2793-2801},
  number = {10},
  optnote = {structure}
}

@ARTICLE{unger:00,
  author = {Unger, M.A. and Chou, H-P. and Thorsen, T. and Scherer, A. and Quake,
	S.R.},
  title = {Monolithic microfabricated valves and pumps by multilayer soft lithography},
  journal = {Science},
  year = {2000},
  optnote = {nano fab},
  optpages = {113-116},
  optvolume = {288}
}

@ARTICLE{VanWay:2004,
  author = {Van Way, S.M. and Millas, S.G. and Lee, A.H. and Manson, M.D.},
  title = {{Rusty, jammed, and well-oiled hinges: mutations affecting the interdomain
	region of FliG, a rotor element of the \normalfont{Escherichia coli}
	\textit{flagellar motor}}},
  journal = {Journal of Bacteriology},
  year = {2004},
  volume = {186},
  pages = {3173-3181},
  number = {10},
  month = {May},
  abstract = {The FliG protein is a central component of the bacterial flagellar
	motor. It is one of the first proteins added during assembly of the
	flagellar basal body, and there are 26 copies per motor. FliG interacts
	directly with the Mot protein complex of the stator to generate torque,
	and it is a crucial player in switching the direction of flagellar
	rotation from clockwise (CW) to counterclockwise and vice versa.
	A primarily helical linker joins the N-terminal assembly domain of
	FliG, which is firmly attached to the FliF protein of the MS ring
	of the basal body, to the motility domain that interacts with MotA/MotB.
	We report here the results of a mutagenic analysis focused on what
	has been called the hinge region of the linker. Residue substitutions
	in this region generate a diversity of phenotypes, including motors
	that are strongly CW biased, infrequent switchers, rapid switchers,
	and transiently or permanently paused. Isolation of these mutants
	was facilitated by a "sensitizing" mutation (E232G) outside of the
	hinge region that was accidentally introduced during cloning of the
	chromosomal fliG gene into our vector plasmid. This mutation partially
	interferes with flagellar assembly and accentuates the defects associated
	with mutations that by themselves have little phenotypic consequence.
	The effects of these mutations are analyzed in the context of a conformational-coupling
	model for motor switching and with respect to the structure of the
	C-terminal 70% of FliG from Thermotoga maritima.},
  pmid = {15126479},
  url = {http://www.hubmed.org/display.cgi?uids=15126479}
}

@ARTICLE{veigel05,
  author = {Veigel, C. and Schmitz, S. and Wang, F. and Sellers, JR.},
  title = {{Load-dependent kinetics of myosin-V can explain its high processivity}},
  journal = {Nature Cell Biology},
  year = {2005},
  volume = {7},
  pages = {861-869},
  number = {9},
  month = {Sep},
  abstract = {{Recent studies provide strong evidence that single myosin class V
	molecules transport vesicles and organelles processively along F-actin,
	taking several 36-nm steps, 'hand over hand', for each diffusional
	encounter. The mechanisms regulating myosin-V's processivity remain
	unknown. Here, we have used an optical-tweezers-based transducer
	to measure the effect of load on the mechanical interactions between
	rabbit skeletal F-actin and a single head of mouse brain myosin-V,
	which produces its working stroke in two phases. We found that the
	lifetimes of the first phase of the working stroke changed exponentially
	and about 10-fold over a range of pushing and pulling forces of +/-
	1.5 pN. Stiffness measurements suggest that intramolecular forces
	could approach 3.6 pN when both heads are bound to F-actin, in which
	case extrapolation would predict the detachment kinetics of the front
	head to slow down 50-fold and the kinetics of the rear head to accelerate
	respectively. This synchronizing effect on the chemo-mechanical cycles
	of the heads increases the probability of the trail head detaching
	first and causes a strong increase in the number of forward steps
	per diffusional encounter over a system with no strain dependence.}},
  pmid = {16100513},
  url = {http://www.hubmed.org/display.cgi?uids=16100513}
}

@ARTICLE{veigel:02,
  author = {Veigel, C. and Wang, F. and Bartoo, ML. and Sellers, JR. and Molloy,
	JE.},
  title = {{The gated gait of the processive molecular motor, myosin V}},
  journal = {Nature Cell Biology},
  year = {2002},
  volume = {4},
  pages = {59-65},
  optnote = {myosin}
}

@BOOK{voet,
  title = {Biochemistry},
  publisher = {Wiley},
  year = {1990},
  author = {Voet, Donald and Voet, Judith G.},
  volume = {1},
  optedition = {4},
  optkey = {0-471-51287-7},
  optnote = {textbook}
}

@BOOK{vogel1994lmf,
  title = {{Life in Moving Fluids}},
  publisher = {Princeton University Press},
  year = {1994},
  author = {Vogel, S.}
}

@ARTICLE{wadhams04,
  author = {Wadhams, G.H. and Armitage, J.P.},
  title = {{Making sense of it all: bacterial chemotaxis}},
  journal = {Nature Reviews Molecular Cell Biology},
  year = {2004},
  volume = {5},
  pages = {1024-1037},
  number = {12},
  month = {Dec},
  abstract = {{Bacteria must be able to respond to a changing environment, and one
	way to respond is to move. The transduction of sensory signals alters
	the concentration of small phosphorylated response regulators that
	bind to the rotary flagellar motor and cause switching. This simple
	pathway has provided a paradigm for sensory systems in general. However,
	the increasing number of sequenced bacterial genomes shows that although
	the central sensory mechanism seems to be common to all bacteria,
	there is added complexity in a wide range of species.}},
  pmid = {15573139},
  url = {http://www.hubmed.org/display.cgi?uids=15573139}
}

@ARTICLE{wadhams2003tts,
  author = {Wadhams, G.H. and Warren, A.V. and Martin, A.C. and Armitage, J.P.},
  title = {{Targeting of two signal transduction pathways to different regions
	of the bacterial cell}},
  journal = {Molecular Microbiology},
  year = {2003},
  volume = {50},
  pages = {763-770},
  number = {3},
  publisher = {Blackwell Synergy}
}

@ARTICLE{walker:00,
  author = {Walker, ML. and Burgess, SA. and Sellers, JR. and Wang, F. and Hammer,
	JA. and Trinick, J. and Knight, PJ.},
  title = {{Two-headed binding of a processive myosin to F-actin}},
  journal = {Nature},
  year = {2000},
  volume = {405},
  pages = {804-807},
  optnote = {myosin}
}

@ARTICLE{walz:00,
  author = {Walz, Dieter and Caplan, S. Roy},
  title = {An electrostatic mechanism closely reproducing observed behavior
	in the bacterial flagellar motor},
  journal = {Biophysical Journal},
  year = {2000},
  volume = {78},
  pages = {626-651},
  optnote = {models}
}

@ARTICLE{wang,
  author = {Wang, H. and Oster, G.},
  title = {The stokes efficiency for molecular motors and its applications},
  journal = {Europhysics Letters},
  optnote = {models}
}

@ARTICLE{welch1993pdb,
  author = {Welch, M. and Oosawa, K. and Aizawa, S. and Eisenbach, M.},
  title = {{Phosphorylation-dependent binding of a signal molecule to the flagellar
	switch of bacteria}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {1993},
  volume = {90},
  pages = {8787--8791},
  number = {19},
  publisher = {National Acad Sciences}
}

@ARTICLE{wikstrom:00,
  author = {Wikstrom, M.},
  title = {Mechanism of proton translocation by cytochrome c oxidase: a new
	four stroke histidine cycle},
  journal = {Biochimica et Biophysica Acta},
  year = {2000},
  optnote = {intracellular proteins},
  optpages = {188-198},
  optvolume = {1458}
}

@ARTICLE{wolfe1989mbs,
  author = {Wolfe, A.J. and Berg, H.C.},
  title = {{Migration of bacteria in semisolid agar}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {1989},
  volume = {86},
  pages = {6973-6977},
  number = {18},
  publisher = {National Acad Sciences}
}

@ARTICLE{wolgemuth:00,
  author = {Wolgemuth, C.W. and Powers, T.R. and Goldstein, R.E.},
  title = {Twirling and whirling: viscous dynamics of rotating elastic filaments},
  journal = {Physical Review Letters},
  year = {2000},
  optnote = {structure},
  optnumber = {7},
  optpages = {1623-1626},
  optvolume = {84}
}

@ARTICLE{xing04,
  author = {Xing, J. and Wang, H. and von Ballmoos, C. and Dimroth, P. and Oster,
	G.},
  title = {{Torque generation by the Fo motor of the sodium ATPase}},
  journal = {Biophysical Journal},
  year = {2004},
  volume = {87},
  pages = {2148-2163},
  number = {4},
  month = {Oct},
  abstract = {{Based on recent structural and functional findings, we have constructed
	a mathematical model for the sodium-driven Fo motor of the F1Fo-ATPase
	from the anaerobic bacterium Propionigenium modestum. The model reveals
	the mechanochemical principles underlying the Fo motor's operation,
	and explains all of the existing experimental data on wild-type and
	mutant Fo motors. In particular, the model predicts a nonmonotonic
	dependence of the ATP hydrolysis activity on the sodium concentration,
	a prediction confirmed by new experiments. To explain experimental
	observations, the positively charged stator residue (R227) must assume
	different positions in the ATP synthesis and hydrolysis directions.
	This work also illustrates how to extract a motor mechanism from
	dynamical experimental observations in the absence of complete structural
	information.}},
  pmid = {15454418},
  url = {http://www.hubmed.org/display.cgi?uids=15454418}
}

@ARTICLE{yakushi04,
  author = {Yakushi, T. and Kojima, M. and Homma, M.},
  title = {{Isolation of Vibrio alginolyticus sodium-driven flagellar motor
	complex composed of PomA and PomB solubilized by sucrose monocaprate}},
  journal = {Microbiology},
  year = {2004},
  volume = {150},
  pages = {911-920},
  number = {Pt 4},
  month = {Apr},
  abstract = {{The polar flagella of Vibrio alginolyticus have sodium-driven motors,
	and four membrane proteins, PomA, PomB, MotX and MotY, are essential
	for torque generation of the motor. PomA and PomB are believed to
	form a sodium-conducting channel. This paper reports the purification
	of the motor complex by using sucrose monocaprate, a non-ionic detergent,
	to solubilize the complex. Plasmid pKJ301, which encodes intact PomA,
	and PomB tagged with a C-terminal hexahistidine that does not interfere
	with PomB function, was constructed. The membrane fraction of cells
	transformed with pKJ301 was solubilized with sucrose monocaprate,
	and the solubilized materials were applied to a Ni-NTA column. The
	imidazole eluate contained both PomA and PomB, which were further
	purified by anion-exchange chromatography. Gel-filtration chromatography
	was used to investigate the apparent molecular size of the complex;
	the PomA/PomB complex was eluted as approx. 900 kDa and PomB alone
	was eluted as approx. 260 kDa. These findings suggest that the motor
	complex may have a larger structure than previously assumed.}},
  pmid = {15073300},
  url = {http://www.hubmed.org/display.cgi?uids=15073300}
}

@ARTICLE{yamamoto1990rrf,
  author = {Yamamoto, K. and Macnab, RM and Imae, Y.},
  title = {{Repellent response functions of the Trg and Tap chemoreceptors of
	Escherichia coli}},
  journal = {{Journal of Bacteriology}},
  year = {1990},
  volume = {172},
  pages = {383--388},
  number = {1},
  owner = {mostyn},
  timestamp = {2008.09.05}
}

@ARTICLE{yasuda98,
  author = {Yasuda, R. and Noji, H. and Kinosita, K. and Yoshida, M.},
  title = {{F1-ATPase is a highly efficient molecular motor that rotates with
	discrete 120 degree steps}},
  journal = {Cell},
  year = {1998},
  volume = {93},
  pages = {1117-1124},
  number = {7},
  month = {Jun},
  abstract = {{A single molecule of F1-ATPase, a portion of ATP synthase, is by
	itself a rotary motor in which a central gamma subunit rotates against
	a surrounding cylinder made of alpha3beta3 subunits. Driven by three
	catalytic betas, each fueled with ATP, gamma makes discrete 120 degree
	steps, occasionally stepping backward. The work done in each step
	is constant over a broad range of imposed load and is close to the
	free energy of hydrolysis of one ATP molecule.}},
  pmid = {9657145},
  url = {http://www.hubmed.org/display.cgi?uids=9657145}
}

@ARTICLE{yasuda:01,
  author = {Yasuda, R. and Noji, H. and Yoshida, M. and Kinosita, K. and Itoh,
	H.},
  title = {{Resolution of distinct rotational substeps by submillisecond kinetic
	analysis of F1-ATPase}},
  journal = {Nature},
  year = {2001},
  volume = {410},
  pages = {898-904},
  optnote = {f1fo}
}

@ARTICLE{yin04,
  author = {Yin, P. and Yan, H. and Daniell, XG. and Turberfield, AJ. and Reif,
	JH.},
  title = {{A unidirectional DNA walker that moves autonomously along a track}},
  journal = {Angewandte Chemie International Edition English},
  year = {2004},
  volume = {43},
  pages = {4906-4911},
  number = {37},
  month = {Sep},
  pmid = {15372637},
  url = {http://www.hubmed.org/display.cgi?uids=15372637}
}

@ARTICLE{yorimitsu:00oct,
  author = {Yorimitsu, T. and Asai, Y. and Sato, K. and Homma, M.},
  title = {Intermolecular cross-linking between the periplasmic loop regions
	of PomA, a component of the Na+ driven flagellar motor of \textit{Vibrio
	alginolyticus}},
  journal = {Journal of Biological Chemistry},
  year = {2000},
  optnote = {structure},
  optnumber = {40},
  optpages = {31387-31391},
  optvolume = {275}
}

@ARTICLE{yorimitsu:00,
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  title = {Na+ -driven flagellar motor of {\it Vibrio}},
  journal = {Biochimica et Biophysica Acta},
  year = {2000},
  volume = {1505},
  pages = {82-93},
  optnote = {vibrio}
}

@ARTICLE{yorimitsu:02,
  author = {Yorimitsu, T. and Sowa, Y. and Ishijima, A. and Yakushi, T. and Homma,
	M.},
  title = {The systematic substitution around the conserved charged residues
	of the cytoplasmic loop of Na+ driven flagellar motor component PomA},
  journal = {Journal of Molecular Biology},
  year = {2002},
  volume = {320},
  pages = {403-413},
  optnote = {structure}
}

@ARTICLE{yoshida:01,
  author = {Yoshida, M. and Muneyuki, E. and Hisabori, T.},
  title = {ATP Synthase - A Marvellous Rotary Engine of the Cell},
  journal = {Nature Reviews},
  year = {2001},
  optnote = {f1fo},
  optpages = {669-677},
  optvolume = {2}
}

@ARTICLE{yoshida:90,
  author = {Yoshida, S. and Sugiyama, S. and Hojo, Y. and Tokuda, H. and Imae,
	Y.},
  title = {Intracellular Na+ Kinetically Interferes with the Rotation of the
	Na+ driven Flagellar Motors of {\it Vibrio alginolyticus}},
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  year = {1990},
  volume = {265},
  pages = {20346-20350},
  number = {33},
  optnote = {vibrio}
}

@ARTICLE{young03,
  author = {Young, HS. and Dang, H. and Lai, Y. and DeRosier, DJ. and Khan, S.},
  title = {{Variable symmetry in Salmonella typhimurium flagellar motors}},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {84},
  pages = {571-577},
  number = {1},
  month = {Jan},
  abstract = {{Electron cryomicroscopy of rotor complexes of the Salmonella typhimurium
	flagellar motor, overproduced in a nonmotile Escherichia coli host,
	has revealed a variation in subunit symmetry of the cytoplasmic ring
	(C ring) module. C rings with subunit symmetries ranging from 31
	to 38 were found. They formed a Gaussian distribution around a mean
	between 34 and 35, a similar number to that determined for native
	C rings. C-ring diameter scaled with the number of subunits, indicating
	that the elliptical-shaped subunits maintained constant intersubunit
	spacing. Taken together with evidence that the M ring does not correspondingly
	increase in size, this finding indicates that rotor assembly does
	not require strict stoichiometric interactions between the M- and
	C-ring subunits. Implications for motor function are discussed.}},
  pmid = {12524310},
  url = {http://www.hubmed.org/display.cgi?uids=12524310}
}

@BOOK{young,
  title = {University Physics with Modern Physics},
  publisher = {Addison-Wesley},
  year = {2000},
  author = {Young, Hugh D. and Freedman, Roger A.},
  optedition = {10},
  optkey = {0-201-60336-5},
  optnote = {textbook}
}

@ARTICLE{yurke00,
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	Neumann, JL.},
  title = {{A DNA-fuelled molecular machine made of DNA}},
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  year = {2000},
  volume = {406},
  pages = {605-608},
  number = {6796},
  month = {Aug},
  pmid = {10949296},
  url = {http://www.hubmed.org/display.cgi?uids=10949296}
}

@ARTICLE{zaslavsky:99,
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  year = {1999},
  optnote = {energetics},
  optnumber = {1458},
  optpages = {164-179}
}

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	S.},
  title = {{Direct visualization of \normalfont{Escherichia coli} \textit{chemotaxis
	receptor arrays using cryo-electron microscopy}}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {2007},
  volume = {104},
  pages = {3777-3781},
  number = {10},
  publisher = {National Acad Sciences}
}

@ARTICLE{zhao1996faf,
  author = {Zhao, R. and Amsler, C.D. and Matsumura, P. and Khan, S.},
  title = {{FliG and FliM distribution in the \normalfont{Salmonella typhimurium}
	\textit{cell and flagellar basal bodies}}},
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  volume = {178},
  pages = {258-265},
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}

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  title = {Residues of the cytoplasmic domain of MotA essential for torque generation
	in the bacterial flagellar motor},
  journal = {Journal of Molecular Biology},
  year = {1997},
  optnote = {structure},
  optpages = {428-439},
  optvolume = {273}
}

@ARTICLE{zhou:98,
  author = {Zhou, J. and Lloyd, SA. and Blair, DF.},
  title = {Electrostatic interactions between rotor and stator in the bacterial
	flagellar motor},
  journal = {Proceedings of the National Academy of Science USA},
  year = {1998},
  volume = {95},
  pages = {6436-6441},
  optnote = {general motors}
}

@ARTICLE{zhou1998fpr,
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	S. and Braun, T.F. and Blair, D.F.},
  title = {{Function of protonatable residues in the flagellar motor of \normalfont{Escherichia
	coli}: \textit{a critical role for Asp-32 of MotB}}},
  journal = {Journal of Bacteriology},
  year = {1998},
  volume = {180},
  pages = {2729-2735},
  number = {10},
  publisher = {Am Soc Microbiol}
}

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  year = {1997},
  volume = {272},
  pages = {5000-5006},
  number = {8}
}

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  optnote = {pmf},
  optnumber = {1},
  optpages = {246-252},
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}

@INBOOK{oster,
  chapter = {13},
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  altauthor = {Oster, G.},
  optnote = {models},
  optpages = {356-380}
}

