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1

Li, G., L. K. Tam, and J. X. Tang. "Amplified effect of Brownian motion in bacterial near-surface swimming." Proceedings of the National Academy of Sciences 105, no. 47 (November 17, 2008): 18355–59. http://dx.doi.org/10.1073/pnas.0807305105.

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2

Ishimoto, Kenta. "Bacterial spinning top." Journal of Fluid Mechanics 880 (October 10, 2019): 620–52. http://dx.doi.org/10.1017/jfm.2019.714.

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We have investigated the dynamics of a monotrichous bacteria cell near a wall boundary, taking elastic hook flexibility into consideration. Combining theoretical linear stability analysis and direct numerical computations via the boundary element method, we have found that the elastohydrodynamic coupling between the hook elasticity and cell rotational motion enables a stable vertical spinning behaviour like a low-Reynolds-number spinning top. The forwardly rotated flagellum, which generates the force exertion pushing towards the cell body, typically destabilizes the vertical upright position and leads to a boundary-following motion. In contrast, the backward rotation of the flagellum, generating a force pulling the cell body, contributes to stable upright behaviour in a large range of hook rigidity. Further numerical investigations have demonstrated that the non-spherical geometry of the cell body and boundary adhesive interactions affect the bacterial dynamics, leading to complex behaviours such as horizontal spinning and unstable vertical spinning motions, both of which are experimentally observed in Pseudomonas aeruginosa bacteria. These results highlight the rich diversity of bacterial surface motility emerging from mechanical boundary interactions coupled with the cell swimming and hook flexibility.
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3

Shum, H., E. A. Gaffney, and D. J. Smith. "Modelling bacterial behaviour close to a no-slip plane boundary: the influence of bacterial geometry." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 466, no. 2118 (January 13, 2010): 1725–48. http://dx.doi.org/10.1098/rspa.2009.0520.

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We describe a boundary-element method used to model the hydrodynamics of a bacterium propelled by a single helical flagellum. Using this model, we optimize the power efficiency of swimming with respect to cell body and flagellum geometrical parameters, and find that optima for swimming in unbounded fluid and near a no-slip plane boundary are nearly indistinguishable. We also consider the novel optimization objective of torque efficiency and find a very different optimal shape. Excluding effects such as Brownian motion and electrostatic interactions, it is demonstrated that hydrodynamic forces may trap the bacterium in a stable, circular orbit near the boundary, leading to the empirically observable surface accumulation of bacteria. Furthermore, the details and even the existence of this stable orbit depend on geometrical parameters of the bacterium, as described in this article. These results shed some light on the phenomenon of surface accumulation of micro-organisms and offer hydrodynamic explanations as to why some bacteria may accumulate more readily than others based on morphology.
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4

Lee, Calvin K., Jaime de Anda, Amy E. Baker, Rachel R. Bennett, Yun Luo, Ernest Y. Lee, Joshua A. Keefe, et al. "Multigenerational memory and adaptive adhesion in early bacterial biofilm communities." Proceedings of the National Academy of Sciences 115, no. 17 (March 20, 2018): 4471–76. http://dx.doi.org/10.1073/pnas.1720071115.

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Using multigenerational, single-cell tracking we explore the earliest events of biofilm formation byPseudomonas aeruginosa. During initial stages of surface engagement (≤20 h), the surface cell population of this microbe comprises overwhelmingly cells that attach poorly (∼95% stay <30 s, well below the ∼1-h division time) with little increase in surface population. If we harvest cells previously exposed to a surface and direct them to a virgin surface, we find that these surface-exposed cells and their descendants attach strongly and then rapidly increase the surface cell population. This “adaptive,” time-delayed adhesion requires determinants we showed previously are critical for surface sensing: type IV pili (TFP) and cAMP signaling via the Pil-Chp-TFP system. We show that these surface-adapted cells exhibit damped, coupled out-of-phase oscillations of intracellular cAMP levels and associated TFP activity that persist for multiple generations, whereas surface-naïve cells show uncorrelated cAMP and TFP activity. These correlated cAMP–TFP oscillations, which effectively impart intergenerational memory to cells in a lineage, can be understood in terms of a Turing stochastic model based on the Pil-Chp-TFP framework. Importantly, these cAMP–TFP oscillations create a state characterized by a suppression of TFP motility coordinated across entire lineages and lead to a drastic increase in the number of surface-associated cells with near-zero translational motion. The appearance of this surface-adapted state, which can serve to define the historical classification of “irreversibly attached” cells, correlates with family tree architectures that facilitate exponential increases in surface cell populations necessary for biofilm formation.
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5

Shrivastava, Abhishek, and Howard C. Berg. "A molecular rack and pinion actuates a cell-surface adhesin and enables bacterial gliding motility." Science Advances 6, no. 10 (March 2020): eaay6616. http://dx.doi.org/10.1126/sciadv.aay6616.

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The gliding bacterium Flavobacterium johnsoniae is known to have an adhesin, SprB, that moves along the cell surface on a spiral track. Following viscous shear, cells can be tethered by the addition of an anti-SprB antibody, causing spinning at 3 Hz. Labeling the type 9 secretion system (T9SS) with a YFP fusion of GldL showed a yellow fluorescent spot near the rotation axis, indicating that the motor driving the motion is associated with the T9SS. The distance between the rotation axis and the track (90 nm) was determined after adding a Cy3 label for SprB. A rotary motor spinning a pinion of radius 90 nm at 3 Hz would cause a spot on its periphery to move at 1.5 μm/s, the gliding speed. We suggest the pinion drives a flexible tread that carries SprB along a track fixed to the cell surface. Cells glide when this adhesin adheres to the solid substratum.
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6

Klebba, Phillip E. "ROSET Model of TonB Action in Gram-Negative Bacterial Iron Acquisition." Journal of Bacteriology 198, no. 7 (January 19, 2016): 1013–21. http://dx.doi.org/10.1128/jb.00823-15.

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Therotationalsurveillance andenergytransfer (ROSET) model of TonB action suggests a mechanism by which the electrochemical proton gradient across the Gram-negative bacterial inner membrane (IM) promotes the transport of iron through ligand-gated porins (LGP) in the outer membrane (OM). TonB associates with the IM by an N-terminal hydrophobic helix that forms a complex with ExbBD. It also contains a central extended length of rigid polypeptide that spans the periplasm and a dimericC-terminal-ββαβ-domain (CTD) with LysM motifs that binds the peptidoglycan (PG) layer beneath the OM bilayer. The TonB CTD forms a dimer with affinity for both PG- and TonB-independent OM proteins (e.g., OmpA), localizing it near the periplasmic interface of the OM bilayer. Porins and other OM proteins associate with PG, and this general affinity allows the TonB CTD dimer to survey the periplasmic surface of the OM bilayer. Energized rotational motion of the TonB N terminus in the fluid IM bilayer promotes the lateral movement of the TonB-ExbBD complex in the IM and of the TonB CTD dimer across the inner surface of the OM. When it encounters an accessible TonB box of a (ligand-bound) LGP, the monomeric form of the CTD binds and recruits it into a 4-stranded β-sheet. Because the CTD is rotating, this binding reaction transfers kinetic energy, created by the electrochemical proton gradient across the IM, through the periplasm to the OM protein. The equilibration of the TonB C terminus between the dimeric and monomeric forms that engage in different binding reactions allows the identification of iron-loaded LGP and then the internalization of iron through their trans-outer membrane β-barrels. Hence, the ROSET model postulates a mechanism for the transfer of energy from the IM to the OM, triggering iron uptake.
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7

Shum, Henry. "Microswimmer Propulsion by Two Steadily Rotating Helical Flagella." Micromachines 10, no. 1 (January 18, 2019): 65. http://dx.doi.org/10.3390/mi10010065.

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Many theoretical studies of bacterial locomotion adopt a simple model for the organism consisting of a spheroidal cell body and a single corkscrew-shaped flagellum that rotates to propel the body forward. Motivated by experimental observations of a group of magnetotactic bacterial strains, we extended the model by considering two flagella attached to the cell body and rotating about their respective axes. Using numerical simulations, we analyzed the motion of such a microswimmer in bulk fluid and close to a solid surface. We show that positioning the two flagella far apart on the cell body reduces the rate of rotation of the body and increases the swimming speed. Near surfaces, we found that swimmers with two flagella can swim in relatively straight trajectories or circular orbits in either direction. It is also possible for the swimmer to escape from surfaces, unlike a model swimmer of similar shape but with only a single flagellum. Thus, we conclude that there are important implications of swimming with two flagella or flagellar bundles rather than one. These considerations are relevant not only for understanding differences in bacterial morphology but also for designing microrobotic swimmers.
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8

Kinde, Monica N., Vasyl Bondarenko, Daniele Granata, Weiming Bu, Kimberly C. Grasty, Patrick J. Loll, Vincenzo Carnevale, et al. "Fluorine-19 NMR and computational quantification of isoflurane binding to the voltage-gated sodium channel NaChBac." Proceedings of the National Academy of Sciences 113, no. 48 (November 15, 2016): 13762–67. http://dx.doi.org/10.1073/pnas.1609939113.

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Voltage-gated sodium channels (NaV) play an important role in general anesthesia. Electrophysiology measurements suggest that volatile anesthetics such as isoflurane inhibit NaVby stabilizing the inactivated state or altering the inactivation kinetics. Recent computational studies suggested the existence of multiple isoflurane binding sites in NaV, but experimental binding data are lacking. Here we use site-directed placement of19F probes in NMR experiments to quantify isoflurane binding to the bacterial voltage-gated sodium channel NaChBac.19F probes were introduced individually to S129 and L150 near the S4–S5 linker, L179 and S208 at the extracellular surface, T189 in the ion selectivity filter, and all phenylalanine residues. Quantitative analyses of19F NMR saturation transfer difference (STD) spectroscopy showed a strong interaction of isoflurane with S129, T189, and S208; relatively weakly with L150; and almost undetectable with L179 and phenylalanine residues. An orientation preference was observed for isoflurane bound to T189 and S208, but not to S129 and L150. We conclude that isoflurane inhibits NaChBac by two distinct mechanisms: (i) as a channel blocker at the base of the selectivity filter, and (ii) as a modulator to restrict the pivot motion at the S4–S5 linker and at a critical hinge that controls the gating and inactivation motion of S6.
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9

Peng, Qingmei, Xin Zhou, Zhi Wang, Qingyi Xie, Chunfeng Ma, Guangzhao Zhang, and Xiangjun Gong. "Three-Dimensional Bacterial Motions near a Surface Investigated by Digital Holographic Microscopy: Effect of Surface Stiffness." Langmuir 35, no. 37 (August 18, 2019): 12257–63. http://dx.doi.org/10.1021/acs.langmuir.9b02103.

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10

Asghar, Z., and N. Ali. "A mathematical model of the locomotion of bacteria near an inclined solid substrate: effects of different waveforms and rheological properties of couple-stress slime." Canadian Journal of Physics 97, no. 5 (May 2019): 537–47. http://dx.doi.org/10.1139/cjp-2017-0906.

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Morphological mutations in bacterial cell make them the most miscellaneous microscopic group. Their non-flagellated species known as gliding bacteria exhibit self-powered motion and leave an adhesive trail of slime. The self-propelled motion in some gliding bacteria is achieved as a result of backward surface wave in the cell envelope. Motivated by this fact, an undulating surface on a layer of couple-stress fluid is used to model the motion of such gliding bacteria. Five different wave profiles, namely, sawtooth, sinusoidal, triangular, trapezoidal, and square profiles are used to model the waveform of the undulating wave in the outer cell surface. The inclination of the surface is also integrated into the model. The flow equations are set up under the lubrication assumption. Stream function is derived as an elementary function of an organism’s speed, undulation amplitude, and couple-stress parameter with its flow rate. Speed of the glider and flow rate (satisfying equilibrium conditions) are computed by employing modified Newton–Raphson method. These refined values are further utilized to compute the power dissipation. Effects of different waveforms, inclination angle, gravitational and couple-stress parameters on the speed of the microorganism and rate of energy expended are also quantified. Slime velocity is also plotted for fixed glider. In addition, making use of the obtained realistic set of values of the organism’s speed, flow rate, occlusion parameter, and couple-stress parameter, streamline patterns of the slime are plotted and discussed in detail.
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11

Münster, Anja-K., Matthias Eckhardt, Barry Potvin, Martina Mühlenhoff, Pamela Stanley, and Rita Gerardy-Schahn. "Mammalian cytidine 5′-monophosphateN-acetylneuraminic acid synthetase: A nuclear protein with evolutionarily conserved structural motifs." Proceedings of the National Academy of Sciences 95, no. 16 (August 4, 1998): 9140–45. http://dx.doi.org/10.1073/pnas.95.16.9140.

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Sialic acids of cell surface glycoproteins and glycolipids play a pivotal role in the structure and function of animal tissues. The pattern of cell surface sialylation is species- and tissue-specific, is highly regulated during embryonic development, and changes with stages of differentiation. A prerequisite for the synthesis of sialylated glycoconjugates is the activated sugar-nucleotide cytidine 5′-monophosphateN-acetylneuraminic acid (CMP-Neu5Ac), which provides a substrate for Golgi sialyltransferases. Although a mammalian enzymatic activity responsible for the synthesis of CMP-Neu5Ac has been described and the enzyme has been purified to near homogeneity, sequence information is restricted to bacterial CMP-Neu5Ac synthetases. In this paper, we describe the molecular characterization, functional expression, and subcellular localization of murine CMP-Neu5Ac synthetase. Cloning was achieved by complementation of the Chinese hamster ovarylec32mutation that causes a deficiency in CMP-Neu5Ac synthetase activity. A murine cDNA encoding a protein of 432 amino acids rescued thelec32mutation and also caused polysialic acid to be expressed in the capsule of the CMP-Neu5Ac synthetase negativeEscherichia colimutant EV5. Three potential nuclear localization signals were found in the murine synthetase, and immunofluorescence studies confirmed predominantly nuclear localization of an N-terminally Flag-tagged molecule. Four stretches of amino acids that occur in the N-terminal region are highly conserved in bacterial CMP-Neu5Ac synthetases, providing evidence for an ancestral relationship between the sialylation pathways of bacterial and animal cells.
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12

Pietrocola, Giampiero, Angelica Pellegrini, Mariangela J. Alfeo, Loredana Marchese, Timothy J. Foster, and Pietro Speziale. "The iron-regulated surface determinant B (IsdB) protein from Staphylococcus aureus acts as a receptor for the host protein vitronectin." Journal of Biological Chemistry 295, no. 29 (June 4, 2020): 10008–22. http://dx.doi.org/10.1074/jbc.ra120.013510.

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Staphylococcus aureus is an important bacterial pathogen that can cause a wide spectrum of diseases in humans and other animals. S. aureus expresses a variety of virulence factors that promote infection with this pathogen. These include cell-surface proteins that mediate adherence of the bacterial cells to host extracellular matrix components, such as fibronectin and fibrinogen. Here, using immunoblotting, ELISA, and surface plasmon resonance analysis, we report that the iron-regulated surface determinant B (IsdB) protein, besides being involved in heme transport, plays a novel role as a receptor for the plasma and extracellular matrix protein vitronectin (Vn). Vn-binding activity was expressed by staphylococcal strains grown under iron starvation conditions when Isd proteins are expressed. Recombinant IsdB bound Vn dose dependently and specifically. Both near-iron transporter motifs NEAT1 and NEAT2 of IsdB individually bound Vn in a saturable manner, with KD values in the range of 16–18 nm. Binding of Vn to IsdB was specifically blocked by heparin and reduced at high ionic strength. Furthermore, IsdB-expressing bacterial cells bound significantly higher amounts of Vn from human plasma than did an isdB mutant. Adherence to and invasion of epithelial and endothelial cells by IsdB-expressing S. aureus cells was promoted by Vn, and an αvβ3 integrin-blocking mAb or cilengitide inhibited adherence and invasion by staphylococci, suggesting that Vn acts as a bridge between IsdB and host αvβ3 integrin.
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13

Dryla, Agnieszka, Bernd Hoffmann, Dieter Gelbmann, Carmen Giefing, Markus Hanner, Andreas Meinke, Annaliesa S. Anderson, et al. "High-Affinity Binding of the Staphylococcal HarA Protein to Haptoglobin and Hemoglobin Involves a Domain with an Antiparallel Eight-Stranded β-Barrel Fold." Journal of Bacteriology 189, no. 1 (October 13, 2006): 254–64. http://dx.doi.org/10.1128/jb.01366-06.

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ABSTRACT Iron scavenging from the host is essential for the growth of pathogenic bacteria. In this study, we further characterized two staphylococcal cell wall proteins previously shown to bind hemoproteins. HarA and IsdB harbor homologous ligand binding domains, the so called NEAT domain (for “near transporter”) present in several surface proteins of gram-positive pathogens. Surface plasmon resonance measurements using glutathione S-transferase (GST)-tagged HarAD1, one of the ligand binding domains of HarA, and GST-tagged full-length IsdB proteins confirmed high-affinity binding to hemoglobin and haptoglobin-hemoglobin complexes with equilibrium dissociation constants (KD ) of 5 to 50 nM. Haptoglobin binding could be detected only with HarA and was in the low micromolar range. In order to determine the fold of this evolutionarily conserved ligand binding domain, the untagged HarAD1 protein was subjected to nuclear magnetic resonance spectroscopy, which revealed an eight-stranded, purely antiparallel β-barrel with the strand order (-β1↓-β2↑-β3↓-β6↑-β5↓-β4↑-β7↓-β8↑), forming two Greek key motifs. Based on structural-homology searches, the topology of the HarAD1 domain resembles that of the immunoglobulin (Ig) fold family, whose members are involved in protein-protein interactions, but with distinct structural features. Therefore, we consider that the HarAD1/NEAT domain fold is a novel variant of the Ig fold that has not yet been observed in other proteins.
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14

Li, Tong, Anthony Suen, Michael Winkler, and Chuan Xue. "Global small-data solutions of a two-dimensional chemotaxis system with rotational flux terms." Mathematical Models and Methods in Applied Sciences 25, no. 04 (January 19, 2015): 721–46. http://dx.doi.org/10.1142/s0218202515500177.

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We study non-negative solutions to the chemotaxis system [Formula: see text] under no-flux boundary conditions in a bounded planar convex domain with smooth boundary, where f and S are given parameter functions on Ω × [0, ∞)2 with values in [0, ∞) and ℝ2×2, respectively, which are assumed to satisfy certain regularity assumptions and growth restrictions. Systems of type (⋆), in the special case [Formula: see text] reducing to a version of the standard Keller–Segel system with signal consumption, have recently been proposed as a model for swimming bacteria near a surface, with the sensitivity tensor then given by [Formula: see text], reflecting rotational chemotactic motion. It is shown that for any choice of suitably regular initial data (u0, v0) fulfilling a smallness condition on the norm of v0 in L∞(Ω), the corresponding initial-boundary value problem associated with (⋆) possesses a globally defined classical solution which is bounded. This result is achieved through the derivation of a series of a priori estimates involving an interpolation inequality of Gagliardo–Nirenberg type which appears to be new in this context. It is next proved that all corresponding solutions approach a spatially homogeneous steady state of the form (u, v) ≡ (μ, κ) in the large time limit, with μ := fΩu0 and some κ ≥ 0. A mild additional assumption on the positivity of f is shown to guarantee that κ = 0. Finally, numerical solutions are presented which suggest the occurrence of wave-like solution behavior.
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15

Ostberg, Karen L., Amanda J. DeRocco, Shreni D. Mistry, Mary Kathryne Dickinson, and Cynthia Nau Cornelissen. "Conserved Regions of Gonococcal TbpB Are Critical for Surface Exposure and Transferrin Iron Utilization." Infection and Immunity 81, no. 9 (July 8, 2013): 3442–50. http://dx.doi.org/10.1128/iai.00280-13.

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ABSTRACTThe transferrin-binding proteins TbpA and TbpB enableNeisseria gonorrhoeaeto obtain iron from human transferrin. The lipoprotein TbpB facilitates, but is not strictly required for, TbpA-mediated iron acquisition. The goal of the current study was to determine the contribution of two conserved regions within TbpB to the function of this protein. Using site-directed mutagenesis, the first mutation we constructed replaced the lipobox (LSAC) of TbpB with a signal I peptidase cleavage site (LAAA), while the second mutation deleted a conserved stretch of glycine residues immediately downstream of the lipobox. We then evaluated the resulting mutants for effects on TbpB expression, surface exposure, and transferrin iron utilization. Western blot analysis and palmitate labeling indicated that the lipobox, but not the glycine-rich motif, is required for lipidation of TbpB and tethering to the outer membrane. TbpB was released into the supernatant by the mutant that produces TbpB LSAC. Neither mutation disrupted the transport of TbpB across the bacterial cell envelope. When these mutant TbpB proteins were produced in a strain expressing a form of TbpA that requires TbpB for iron acquisition, growth on transferrin was either abrogated or dramatically diminished. We conclude that surface tethering of TbpB is required for optimal performance of the transferrin iron acquisition system, while the presence of the polyglycine stretch near the amino terminus of TbpB contributes significantly to transferrin iron transport function. Overall, these results provide important insights into the functional roles of two conserved motifs of TbpB, enhancing our understanding of this critical iron uptake system.
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16

MRŠA HABER, IVA, TARZAN LEGOVIĆ, LADO KRANJČEVIĆ, and MARIJAN CUKROV. "Simulation of pollutants spreading from a sewage outfall in the Rijeka Bay." Mediterranean Marine Science 21, no. 1 (March 30, 2020): 116. http://dx.doi.org/10.12681/mms.20467.

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Results from a 3D numerical simulation of wind-induced currents and pollution spreading from a sewage outfall are described.The goal was to predict seawater sanitary quality in the Rijeka Bay, Adriatic Sea. A sea motion model was coupled with a modelof transport and chemical reactions of fecal coliforms (FC), fecal streptococci (FS) and dissolved oxygen. The selected simulationperiod of 36 hours following wastewater discharge was found to be sufficient for a significant extinction of bacteria. The simulationwas carried out for eight wind directions and two intensities (moderate and high). Mesh convergence was obtained. Twomesh sizes were coupled: coarse, for the whole Bay, and fine, for the northern part of the Bay, close to the sewage discharge ofthe Rijeka city.For all considered wind directions, the pollution plume with a concentration higher than 100 FC and 100 FS per 100 ml of seawateris conveyed mostly parallel to the coast in either north-west or south-east directions. The plume does not rise to the surfacebut stays at the depth of 10 to 20 meters. This is a consequence of the hydrodynamics of the Rijeka Bay: the bora wind carriesthe surface water layer out of the Bay through the Middle and Great Gates, while cold water enters the Bay from the layer belowthe thermocline. During the southern wind (jugo), the situation is reversed: warmer surface water enters the Bay through eitherthe Middle Gate or the Great Gate, while cold seawater exits through the bottom layer, accumulating warmer seawater in the Bay.The conclusion is that the Rijeka city sewage discharge Delta is well-designed, and the microorganism concentration is wellwithin the suggested regulatory range. The discharge site is far enough from the coast, where local streamlines are mostly parallelto the coast, hence the elevated pollution concentration does not come close to swimming and recreational areas. Even if thedischarge increases by 50%, which is unlikely in the near future, the pollution at beaches will stay within regulatory boundaries.
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17

Hook, Andrew L., James L. Flewellen, Jean-Frédéric Dubern, Alessandro M. Carabelli, Irwin M. Zaid, Richard M. Berry, Ricky D. Wildman, Noah Russell, Paul Williams, and Morgan R. Alexander. "Simultaneous Tracking of Pseudomonas aeruginosa Motility in Liquid and at the Solid-Liquid Interface Reveals Differential Roles for the Flagellar Stators." mSystems 4, no. 5 (September 24, 2019). http://dx.doi.org/10.1128/msystems.00390-19.

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ABSTRACT Bacteria sense chemicals, surfaces, and other cells and move toward some and away from others. Studying how single bacterial cells in a population move requires sophisticated tracking and imaging techniques. We have established quantitative methodology for label-free imaging and tracking of individual bacterial cells simultaneously within the bulk liquid and at solid-liquid interfaces by utilizing the imaging modes of digital holographic microscopy (DHM) in three dimensions (3D), differential interference contrast (DIC), and total internal reflectance microscopy (TIRM) in two dimensions (2D) combined with analysis protocols employing bespoke software. To exemplify and validate this methodology, we investigated the swimming behavior of a Pseudomonas aeruginosa wild-type strain and isogenic flagellar stator mutants (motAB and motCD) within the bulk liquid and at the surface at the single-cell and population levels. Multiple motile behaviors were observed that could be differentiated by speed and directionality. Both stator mutants swam slower and were unable to adjust to the near-surface environment as effectively as the wild type, highlighting differential roles for the stators in adapting to near-surface environments. A significant reduction in run speed was observed for the P. aeruginosa mot mutants, which decreased further on entering the near-surface environment. These results are consistent with the mot stators playing key roles in responding to the near-surface environment. IMPORTANCE We have established a methodology to enable the movement of individual bacterial cells to be followed within a 3D space without requiring any labeling. Such an approach is important to observe and understand how bacteria interact with surfaces and form biofilm. We investigated the swimming behavior of Pseudomonas aeruginosa, which has two flagellar stators that drive its swimming motion. Mutants that had only either one of the two stators swam slower and were unable to adjust to the near-surface environment as effectively as the wild type. These results are consistent with the mot stators playing key roles in responding to the near-surface environment and could be used by bacteria to sense via their flagella when they are near a surface.
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18

Makarchuk, Stanislaw, Vasco C. Braz, Nuno A. M. Araújo, Lena Ciric, and Giorgio Volpe. "Enhanced propagation of motile bacteria on surfaces due to forward scattering." Nature Communications 10, no. 1 (September 11, 2019). http://dx.doi.org/10.1038/s41467-019-12010-1.

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Abstract How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell’s propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells’ motion. Here, we show that micro-obstacles influence the propagation of peritrichously flagellated bacteria on a flat surface in a non-monotonic way. Instead of hindering it, an optimal, relatively low obstacle density can significantly enhance cells’ propagation on surfaces due to individual forward-scattering events. This finding provides insight on the emerging dynamics of chiral active matter in complex environments and inspires possible routes to control microbial ecology in natural habitats.
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19

Liu, Yue, Xiaoyun Zhou, Wenbo Liu, and Weiguo Miao. "The stability of the coiled-coil structure near to N-terminus influence the heat resistance of harpin proteins from Xanthomonas." BMC Microbiology 20, no. 1 (November 12, 2020). http://dx.doi.org/10.1186/s12866-020-02029-6.

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Abstract Background Heat resistance is a common characteristic of harpins, a class of proteins found in Gram-negative bacteria, which may be related to the stability of coiled-coil (CC) structure. The CC structure is a ubiquitous protein folding and assembly motif made of α-helices wrapping around each other forming a supercoil. Specifically, whether the stability of the CC structure near to N-terminus of four selected harpin proteins from Xanthomonas (hereafter referred to as Hpa1) would influence their characteristics of heat resistance was investigated. We used bioinformatics approach to predict the structure of Hpa1, used the performance of hypersensitive response (HR)-induction activity of Hpa1 and circular dichroism (CD) spectral analyses to detect the relationship between the stability of the CC structure of Hpa1 and heat resistance. Results Each of four-selected Hpa1 has two α-helical regions with one in their N-terminus that could form CC structure, and the other in their C-terminus that could not. And the important amino acid residues involved in the CC motifs are located on helices present on the surface of these proteins, indicating they may engage in the formation of oligo mericaggregates, which may be responsible for HR elicitation by harpins and their high thermal stability. Increased or decreased the probability of forming a CC could either induce a stronger HR response or eliminate the ability to induce HR in tobacco after high temperature treatment. In addition, although the four Hpa1 mutants had little effect on the induction of HR by Hpa1, its thermal stability was significantly decreased. The α-helical content increased with increasing temperature, and the secondary structures of Hpa1 became almost entirely α-helices when the temperature reached 200 °C. Moreover, the stability of the CC structure near to N-terminus was found to be positively correlated with the heat resistance of Hpa1. Conclusions The stability of the CC structure might sever as an inner drive for mediating the heat resistance of harpin proteins. Our results offer a new insight into the interpretation of the mechanism involved in the heat resistance of harpin protein and provide a theoretical basis for further harpin function investigations and structure modifications.
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Orel, Brigita. "The Language of Food." M/C Journal 16, no. 3 (June 23, 2013). http://dx.doi.org/10.5204/mcj.636.

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Hors d’oeuvre The popularity of cookbooks and culinary television shows in the last few years has been the origin of all sorts of new phenomena, such as literature crossing the bridge from cookbooks to such subgenres as food memoirs and culinary travelogues, or the discovery of new food cultures and food vocabulary. We can now cook the Basque menestra following the recipe of the famous blogger and cookbook author, Aran Goayaga, or try our hand at the Chinese soup tangyuan from Leslie Li’s Daughter of Heaven regardless of where we live. But how well does food translate across languages and cultures? I know what to expect from menestra as I am familiar with the Italian minestrone, which was introduced into the western dialects of Slovene as mineštra. But when reading about tangyuan, there is no mental image, much less a taste imprint, accompanying the word. Language and food are closely linked, if for nothing else, for the fact that the mouth is instrumental in both. For language, the oral cavity is the means of expression, for food it is the means for reception and tasting. It is like an intersection where language and food meet. When we reminisce about a favourite childhood dish or food, we can virtually taste it only by saying the word. The senses, supported by emotions, are a powerful tool, a reliable memory. It is for this reason that sometimes emotions are more easily expressed through food than with words, such as Tita’s longing and desperation in Laura Esquivel’s Like Water for Chocolate. It is perhaps because of this inability to truly verbalise the wonder and deliciousness of food that when translating food between different languages and cultures, meanings and tastes can become unclear or lost. Appetiser In less exact culinary genres, such as food memoirs, difficult translations can be tackled by using approximate and roundabout descriptions. “Metaphors are very plentiful, evocative, and useful in food memoirs. They are often created to explain exotic foods and culinary practices in terms that are more familiar to [...] readers” (Waxman 373). Similarly, in an interview about multiculturalism and identity, Homi Bhabha suggests that “all forms of culture are in some ways related to each other” and thus translatable (Rutherford 209–10). However, Bhabha is also referring to metaphors, myths, and symbols. Food, however, is a very particular ingredient of culture that cannot be always expressed with metaphors when translated. Cookbooks require an exact terminology; metaphors are of little help when a soufflé collapses or steaks end up overdone. Yet despite cultural, ethnic, religious, and other differences, there are certain concepts, such as beauty, that can be almost universally appreciated. Kant’s notion of “common sense“ explains what enables us to comprehend and appreciate beauty. By this universal communicability Kant “means that humans all must have a kind of sensing ability which operates the same way” (Burnham). This sensing ability could easily be expanded onto the beauty (and deliciousness) of food. After all, just as everyone can appreciate the magnificence of a Renoir, they can enjoy the satisfying mix of spices and herbs in a steak tartare, regardless of their mother tongue. And yet, when food is transformed into a written recipe and the language becomes a barrier, the opportunity for misunderstanding becomes greater. Walter Benjamin maintains that in translation, “the transfer can never be total [...] Even when all the surface content has been extracted and transmitted, the primary concern of the genuine translator remains elusive. Unlike the words of the original, it is not translatable, because the relationship between content and language is quite different in the original and the translation” (19). Furthermore, translation “implies adapting the meaning of a proposition, enabling it to pass from one code to another” (Bourriaud 30). If translation means adaptation, then in the process we lose the nuances of dishes that differ from one village to the next, not to mention from one nation to another at the other end of the world. And with this, we can lose subtle “insights into cultures” (Waxman 364). Brett Jocelyn Epstein, a translator and editor of a number of cookbooks, enumerates several issues that cause trouble when translating culinary texts, among them the availability of ingredients, different cuts of meats, measurements, and the kitchen equipment. While all are of equal importance for the translation of a text, let us focus on the difficulties that can arise when translating the ingredients that can sometimes be essential for a dish but difficult to find in a foreign country. Epstein emphasizes that simply substituting an ingredient with a more easily obtainable one is not an appropriate solution if this is repeated throughout a cookbook for recipe after recipe, ingredient after ingredient. There are limits to the changes a translator can make in a text; limits that turn one dish into an entirely new fare with a host of new ingredients. Instead, Epstein suggests keeping the original ingredients, but adding a list of possible substitutes. National Dish Let us have a look at an edible example. In France, crème fraîche is a naturally fermented thick cream, but the version sold in the UK is fermented by adding sour cream, buttermilk, or yoghurt. In North Wales it is known as “croghurt“ (a portmanteau word for “cream and yoghurt“) (Ayto 103). Crème fraîche, although slightly sour with pH of about 4.5, is not sour cream, but in many countries sour cream is used as a substitute because the French version is unobtainable. On the contrary, in Italy, it is near impossible to find sour cream. There is no tradition of using it in Italian cuisine, and it is mostly immigrants from other countries, such as Ukrainians, Poles, or Slovenians, who use it in their cooking. Panna acida or panna agra, as sour cream is known in Italy, is being imported and only sold in selected shops. As another example, the Swedes use filmjölk and gräddfil which are most often translated as yoghurt and cultivated buttermilk respectively, although these translations are mere approximations. Filmjölk may resemble yoghurt in consistency but it is fermented by different bacteria that give it a less sour taste. Gräddfil is a little thicker than yoghurt and also not as sour. Then there are kefir, piimä, kumis, lassi, ayran, and clabber, to mention just a few related, but different, products. How do such untranslatable ingredients affect the final outcome? Crêpes with fruit and sour cream are not quite the same as with crème fraîche; sour cream lacks the creaminess of the crème and has a tangier taste. Worse still, sour cream can curdle when added to a soup and heated, while crème fraîche does not. It is evident then, that culinary translation affects more than just words. This is not, however, only a matter for chefs and cooks to consider; it is also an issue when an author wants to share traditional dishes with readers of other nationalities and especially when the core ingredients of their (or their country’s) signature dishes are not available globally. I am not here referring only to such unusual ingredients as the honeypot ants used in bush tucker. Some foods, despite the logistics accessibility of every nook and cranny of our world, are sometimes still difficult or impossible to obtain outside their place of origin simply for the lack of a high enough demand. Is it, then, better to stick to the original ingredients and keep the integrity of the recipe, or is it better to adapt the dish to another culture or let it exist between cultures? Would we rather our recipe remain a “wannabe dish” because readers are unable to find the ingredients for it, or would we prefer for them to enjoy an approximation of our creation? Linguist, anthropologist, and renowned chef, Rick Bayless, tackles the translation of food the same way he would translate languages. He introduced countless Mexican dishes into the North American cuisine through his award-winning Mexican restaurants, cookbooks, and his television show Mexico–One Plate at a Time. He looks at the issue of translation not solely from the point of view of the original cuisine, but also from the perspective of the target audience. “You have to really understand both cultures. Not just the words, not just the ingredients or the dishes out of context, but you have to understand it on a much broader perspective” (Translating Food). He is trying to present traditional Mexican dishes in a way that will make them “understandable“ in the American context. Bayless maintains that “people will cook a dish exactly the way it's done in the host culture,” but that makes it “this sort of relic that’s not understandable” in the target culture’s context. Or as German writer and poet, Rudolf Pannwitz, stated, “our translations, even the best ones, proceed from a wrong premise. They want to turn Hindi, Greek, English into German instead of turning German into Hindi, Greek, English” (qtd. in Benjamin 22). The more ingredients, the more complex the situation becomes, and sometimes a dish is near impossible to translate because of its cultural specificity. Mostly, such names of dishes are kept in the original, like polenta, sushi, or the already mentioned tangyuan. But particularly smaller nations, with subsequently smaller languages, feel the need to make their dishes more recognisable. For example, certain Slovenian dishes, such as idrijski žlikrofi, are registered as a traditional speciality (TSG) at the European Commission but even as such they often have poor recognisability. The same is true of other typical Slovenian dishes; while well known and appreciated at home, they are often quite unknown outside the country’s borders. Consequently, to reach higher recognisability, we often over-translate. Fig. 1. The Making of idrijski žlikrofi. 2013. The Author. An example of this is a Slovenian dessert whose established name in English is the “Prekmurian layer cake“ (a layered cake with apples, poppy seeds, cottage cheese and walnuts from the Prekmurje region, a region across the river Mura). However, it happens quite often that you will receive a decidedly different translation if you ask a waiter in a restaurant or people on the street what prekmurska gibanica is. Someone at some point literally translated it as the “over Mura moving cake“ (gibanica contains the morpheme gib- meaning “movement, motion“, hence “moving cake“, although it has nothing to do with moving). The wrong translation is probably mentioned more often than the correct one and it is so nonsensical that it has been preserved as a running joke, while some still think it is a correct translation. Another quandary for the translator is the existence of words that denote different dishes in one language. Within hundred kilometres of my hometown, the name fancelj refers to three different culinary delights. We use it to denote an omelette-like dish of beaten eggs with yarrow, lemon balm or other herbs occasionally added to it. In the upper Soča valley, it is known to denote doughnuts. Further to the south, fancelj stands for deep-fried buns similar to what the French call pets-de-nonne (literally “nun’s farts“). Similarly, in Swedish, the terms kaka and tårta quite often overlap in their usage and thus cause confusion when being translated into English (as cake and torte, and sometimes even as cookie, depending on the type of pastry in the original recipe). If one is not familiar with such dialectal distinctions or cultural peculiarities, it is difficult to avoid mistranslations. Such delicate translations also include the Turkish coffee that becomes Greek coffee in Greek bars, French toast that is called pain perdu in France, or Russian salad, called salade russe by the French, but French salad by Slovenians (and salat oliv’e by the Russians). Furthermore, if you order à la mode in France, you will be served beef braised with vegetables. In the US, however, you can only order à la mode for dessert as it means an apple pie or similar dessert served with ice cream (Ayto). These examples are often due to disagreements and misconceptions about who created a certain dish, and wrong usage can cause resentment among the (presumably) wronged parties. Sometimes, delicious bits of information get lost in translation. A Slovenian dialectal word knedelj is usually translated into English as dumpling, a neat and straightforward translation. But in the original word knedelj that was borrowed from the German knödel, related to kneten (Snoj 209), one can detect traces of Proto-Germanic knedanan that developed through Old Saxon knedan into Old English cnedan and today’s knead (Online Etymology Dictionary). The two words, one English and the other dialectal Slovene, originate in the same ancient expression. But I suppose only linguists would find this information worth mulling over for a few seconds before tucking into a wholesome serving of plum dumplings. Considering the aforementioned difficulties of culinary translation, it is not surprising that certain words are often simply left in the original. This is especially true of Italian dishes, such as types of pasta, or certain Asian fares (for more on translating Chinese dishes see Mu 2010). Consequently, many are now familiar with calzone, bento, farfalle, sashimi, zucchini, and zabaglione (the latter of which is also known as sabayon, zabaione, and zabajone). Even once the words find their place in their adoptive language and the users become wholly familiarised with their meaning and thus the problem of translation is avoided, another difficulty arises—that of adapting the word (morphologically) to the new language. Pine nuts in American English are also called pignoli, a word borrowed from Italian. There seems to be considerable confusion as to the plural form of the word in its English usage. Pignoli, originally a plural form of pignolo, “hovers between singular and plural in English”, where subsequently two other plural forms have appeared—pignolia and pignolis (Ayto 277). Dessert For readers, getting to know about other cultures’s foods and their preparation can be very enriching for gaining an understanding of both those particular cultures and, in turn, their own (Waxman), but for writers and translators of cookbooks, food memoirs, culinary travelogues, and other such culturally and culinary specific genres (and especially those from smaller countries), translating food expressions can be challenging. There is no simple rule that helps translate every expression or ingredient. Translations must be carried out on a case-to-case basis, sometimes compromising the food, sometimes the translation. Similarly, as more and more people become nomads in the 21st century, immigrating for economic or political reasons, family, or simply for fun, in the same way food too is becoming a “portable practice” (Bourriaud 33) that crosses boundaries, cultures, and languages. Due to this, food is taking on a new role; its functions “both unifying and divisive” (Waxman 366). The culinary translator’s task should be to translate in such a way that the divisive effect is minimised as much as possible and yet the text retains its cultural flavour. This is difficult, and requires knowledge of both the source and target languages and cultures, but ultimately it can be done. Food and language are like a pair of tango dancers—caught in a passionate embrace, but bickering constantly nonetheless, their tastes too dissimilar. Or, as Isabel Allende suggests, to seduce a lover one needs both food and words: “language is also aphrodisiac in regard to food; commenting on the dishes, their flavours and perfumes, is a sensual exercise for which we have a vast vocabulary filled with wit, metaphors, references, humour, word games, and subtleties” (106). But to seduce with words, we must first taste the food. Perhaps translators and authors of culinary texts are not all accomplished cooks, but it is of great help if they can prepare and taste the dishes and ingredients that they are attempting to adapt to new cultures and environments. References Allende, Isabel. Aphrodite, A Memoir of the Senses. New York: HarperCollins Publishers, 1998. Ayto, John. The Diner’s Dictionary: Word Origins of Food & Drink. UK: Oxford UP, 2012. Benjamin, Walter. “The Task of the Translator.” The Translation Studies Reader. Ed. Lawrence Venuti. London: Routledge, 2004. 15–25. Bourriaud, Nicolas. The Radicant. New York: Lukas & Sternberg, 2010. Burnham, Douglas. “Kant’s Aesthetics.” Internet Encyclopedia of Philosophy 30 Jun. 2005. 7 Apr. 2013 ‹http://www.iep.utm.edu/kantaest›. Epstein, Brett Jocelyn. “What’s Cooking: Translating Food.” Translation Journal, 13.3 (2009). 11 Mar. 2013 ‹http://www.bokorlang.com/journal/49cooking.htm›. Esquivel, Laura. Like Water for Chocolate. USA: Transworld Publishers, 1989. Goayaga, Aran. Small Plates & Sweet Treats: My Family’s Journey to Gluten-free Cooking. New York: Little, Brown & Company, 2012. Li, Leslie. Daughter of Heaven: A Memoir of Earthly Recipes. New York: Arcade, 2005. Mu, John Congjun. “English Translation of Chinese Dish Names.” Translation Journal 14.4 (Oct. 2010). 8 Apr. 2013 ‹http://www.translationjournal.net/journal/54dishes.htm›. Online Etymology Dictionary. 12 Feb. 2013 ‹http://www.etymonline.com/index.php?term=knead&allowed_in_frame=0›. Rutherford, Jonathan. “The Third Space: Interview with Homi Bhabha.” Identity: Community, Culture, Difference. Ed. Jonathan Rutherford. London: Lawrence and Wishart, 1990. 207–221. Snoj, Marko. Slovenski etimološki slovar. Ljubljana: Modrijan založba, 2009. “Translating Food.” Visual Thesaurus 23 May 2007. 11 Mar. 2013 ‹https://www.visualthesaurus.com/cm/wc/translating-food›. Waxman, Barbara Frey. “Food Memoirs: What They Are, Why They Are Popular, and Why They Belong in the Literature Classroom.” College English 70.4 (2008): 363–82.
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