Micron-scale plasma membrane curvature is recognized by the septin cytoskeleton

PubMed Central

Bridges, Andrew A.; Jentzsch, Maximilian S.; Oakes, Patrick W.; Occhipinti, Patricia

2016-01-01

Cells change shape in response to diverse environmental and developmental conditions, creating topologies with micron-scale features. Although individual proteins can sense nanometer-scale membrane curvature, it is unclear if a cell could also use nanometer-scale components to sense micron-scale contours, such as the cytokinetic furrow and base of neuronal branches. Septins are filament-forming proteins that serve as signaling platforms and are frequently associated with areas of the plasma membrane where there is micron-scale curvature, including the cytokinetic furrow and the base of cell protrusions. We report here that fungal and human septins are able to distinguish between different degrees of micron-scale curvature in cells. By preparing supported lipid bilayers on beads of different curvature, we reconstitute and measure the intrinsic septin curvature preference. We conclude that micron-scale curvature recognition is a fundamental property of the septin cytoskeleton that provides the cell with a mechanism to know its local shape. PMID:27044896

Blindness to Curvature and Blindness to Illusory Curvature.

PubMed

Bertamini, Marco; Kitaoka, Akiyoshi

2018-01-01

We compare two versions of two known phenomena, the Curvature blindness and the Kite mesh illusions, to highlight how similar manipulations lead to blindness to curvature and blindness to illusory curvature, respectively. The critical factor is a change in luminance polarity; this factor interferes with the computation of curvature along the contour, for both real and illusory curvature.

Curvature and torsion in growing actin networks

NASA Astrophysics Data System (ADS)

Shaevitz, Joshua W.; Fletcher, Daniel A.

2008-06-01

Intracellular pathogens such as Listeria monocytogenes and Rickettsia rickettsii move within a host cell by polymerizing a comet-tail of actin fibers that ultimately pushes the cell forward. This dense network of cross-linked actin polymers typically exhibits a striking curvature that causes bacteria to move in gently looping paths. Theoretically, tail curvature has been linked to details of motility by considering force and torque balances from a finite number of polymerizing filaments. Here we track beads coated with a prokaryotic activator of actin polymerization in three dimensions to directly quantify the curvature and torsion of bead motility paths. We find that bead paths are more likely to have low rather than high curvature at any given time. Furthermore, path curvature changes very slowly in time, with an autocorrelation decay time of 200 s. Paths with a small radius of curvature, therefore, remain so for an extended period resulting in loops when confined to two dimensions. When allowed to explore a three-dimensional (3D) space, path loops are less evident. Finally, we quantify the torsion in the bead paths and show that beads do not exhibit a significant left- or right-handed bias to their motion in 3D. These results suggest that paths of actin-propelled objects may be attributed to slow changes in curvature, possibly associated with filament debranching, rather than a fixed torque.

Curvature-Induced Instabilities of Shells

NASA Astrophysics Data System (ADS)

Pezzulla, Matteo; Stoop, Norbert; Steranka, Mark P.; Bade, Abdikhalaq J.; Holmes, Douglas P.

2018-01-01

Induced by proteins within the cell membrane or by differential growth, heating, or swelling, spontaneous curvatures can drastically affect the morphology of thin bodies and induce mechanical instabilities. Yet, the interaction of spontaneous curvature and geometric frustration in curved shells remains poorly understood. Via a combination of precision experiments on elastomeric spherical shells, simulations, and theory, we show how a spontaneous curvature induces a rotational symmetry-breaking buckling as well as a snapping instability reminiscent of the Venus fly trap closure mechanism. The instabilities, and their dependence on geometry, are rationalized by reducing the spontaneous curvature to an effective mechanical load. This formulation reveals a combined pressurelike term in the bulk and a torquelike term in the boundary, allowing scaling predictions for the instabilities that are in excellent agreement with experiments and simulations. Moreover, the effective pressure analogy suggests a curvature-induced subcritical buckling in closed shells. We determine the critical buckling curvature via a linear stability analysis that accounts for the combination of residual membrane and bending stresses. The prominent role of geometry in our findings suggests the applicability of the results over a wide range of scales.

Impact of membrane curvature on amyloid aggregation.

PubMed

Terakawa, Mayu S; Lin, Yuxi; Kinoshita, Misaki; Kanemura, Shingo; Itoh, Dai; Sugiki, Toshihiko; Okumura, Masaki; Ramamoorthy, Ayyalusamy; Lee, Young-Ho

2018-04-28

The misfolding, amyloid aggregation, and fibril formation of intrinsically disordered proteins/peptides (or amyloid proteins) have been shown to cause a number of disorders. The underlying mechanisms of amyloid fibrillation and structural properties of amyloidogenic precursors, intermediates, and amyloid fibrils have been elucidated in detail; however, in-depth examinations on physiologically relevant contributing factors that induce amyloidogenesis and lead to cell death remain challenging. A large number of studies have attempted to characterize the roles of biomembranes on protein aggregation and membrane-mediated cell death by designing various membrane components, such as gangliosides, cholesterol, and other lipid compositions, and by using various membrane mimetics, including liposomes, bicelles, and different types of lipid-nanodiscs. We herein review the dynamic effects of membrane curvature on amyloid generation and the inhibition of amyloidogenic proteins and peptides, and also discuss how amyloid formation affects membrane curvature and integrity, which are key for understanding relationships with cell death. Small unilamellar vesicles with high curvature and large unilamellar vesicles with low curvature have been demonstrated to exhibit different capabilities to induce the nucleation, amyloid formation, and inhibition of amyloid-β peptides and α-synuclein. Polymorphic amyloidogenesis in small unilamellar vesicles was revealed and may be viewed as one of the generic properties of interprotein interaction-dominated amyloid formation. Several mechanical models and phase diagrams are comprehensively shown to better explain experimental findings. The negative membrane curvature-mediated mechanisms responsible for the toxicity of pancreatic β cells by the amyloid aggregation of human islet amyloid polypeptide (IAPP) and binding of the precursors of the semen-derived enhancer of viral infection (SEVI) are also described. The curvature-dependent binding

Distributed mean curvature on a discrete manifold for Regge calculus

NASA Astrophysics Data System (ADS)

Conboye, Rory; Miller, Warner A.; Ray, Shannon

2015-09-01

The integrated mean curvature of a simplicial manifold is well understood in both Regge Calculus and Discrete Differential Geometry. However, a well motivated pointwise definition of curvature requires a careful choice of the volume over which to uniformly distribute the local integrated curvature. We show that hybrid cells formed using both the simplicial lattice and its circumcentric dual emerge as a remarkably natural structure for the distribution of this local integrated curvature. These hybrid cells form a complete tessellation of the simplicial manifold, contain a geometric orthonormal basis, and are also shown to give a pointwise mean curvature with a natural interpretation as the fractional rate of change of the normal vector.

Direct membrane binding by bacterial actin MreB.

PubMed

Salje, Jeanne; van den Ent, Fusinita; de Boer, Piet; Löwe, Jan

2011-08-05

Bacterial actin MreB is one of the key components of the bacterial cytoskeleton. It assembles into short filaments that lie just underneath the membrane and organize the cell wall synthesis machinery. Here we show that MreB from both T. maritima and E. coli binds directly to cell membranes. This function is essential for cell shape determination in E. coli and is proposed to be a general property of many, if not all, MreBs. We demonstrate that membrane binding is mediated by a membrane insertion loop in TmMreB and by an N-terminal amphipathic helix in EcMreB and show that purified TmMreB assembles into double filaments on a membrane surface that can induce curvature. This, the first example of a membrane-binding actin filament, prompts a fundamental rethink of the structure and dynamics of MreB filaments within cells. Copyright © 2011 Elsevier Inc. All rights reserved.

Mechanical influences in bacterial morphogenesis and cell division

NASA Astrophysics Data System (ADS)

Sun, Sean

2010-03-01

Bacterial cells utilize a ring-like organelle (the Z-ring) to accomplish cell division. The Z-ring actively generates a contractile force and influences cell wall growth. We will discuss a general model of bacterial morphogenesis where mechanical forces are coupled to the growth dynamics of the cell wall. The model suggests a physical mechanism that determines the shapes of bacteria cells. The roles of several bacterial cytoskeletal proteins and the Z-ring are discussed. We will also explore molecular mechanisms of force generation by the Z-ring and how cells can generate mechanical forces without molecular motors.

Can dead bacterial cells be defined and are genes expressed after cell death?

PubMed

Trevors, J T

2012-07-01

There is a paucity of knowledge on gene expression in dead bacterial cells. Why would this knowledge be useful? The cells are dead. However, the time duration of gene expression following cell death is often unknown, and possibly in the order of minutes. In addition, it is a challenge to determine if bacterial cells are dead, or viable but non-culturable (VBNC), and what is an agreed upon correct definition of dead bacteria. Cells in the bacterial population or community may die at different rates or times and this complicates both the viability and gene expression analysis. In this article, the definition of dead bacterial cells is discussed and its significance in continued gene expression in cells following death. The definition of living and dead has implications for possible, completely, synthetic bacterial cells that may be capable of growth and division. Copyright © 2012 Elsevier B.V. All rights reserved.

Mammalian phospholipid homeostasis: evidence that membrane curvature elastic stress drives homeoviscous adaptation in vivo

PubMed Central

2016-01-01

Several theories of phospholipid homeostasis have postulated that cells regulate the molecular composition of their bilayer membranes, such that a common biophysical membrane parameter is under homeostatic control. Two commonly cited theories are the intrinsic curvature hypothesis, which states that cells control membrane curvature elastic stress, and the theory of homeoviscous adaptation, which postulates cells control acyl chain packing order (membrane order). In this paper, we present evidence from data-driven modelling studies that these two theories correlate in vivo. We estimate the curvature elastic stress of mammalian cells to be 4–7 × 10−12 N, a value high enough to suggest that in mammalian cells the preservation of membrane order arises through a mechanism where membrane curvature elastic stress is controlled. These results emerge from analysing the molecular contribution of individual phospholipids to both membrane order and curvature elastic stress in nearly 500 cellular compositionally diverse lipidomes. Our model suggests that the de novo synthesis of lipids is the dominant mechanism by which cells control curvature elastic stress and hence membrane order in vivo. These results also suggest that cells can increase membrane curvature elastic stress disproportionately to membrane order by incorporating polyunsaturated fatty acids into lipids. PMID:27534697

Mammalian phospholipid homeostasis: evidence that membrane curvature elastic stress drives homeoviscous adaptation in vivo.

PubMed

Dymond, Marcus K

2016-08-01

Several theories of phospholipid homeostasis have postulated that cells regulate the molecular composition of their bilayer membranes, such that a common biophysical membrane parameter is under homeostatic control. Two commonly cited theories are the intrinsic curvature hypothesis, which states that cells control membrane curvature elastic stress, and the theory of homeoviscous adaptation, which postulates cells control acyl chain packing order (membrane order). In this paper, we present evidence from data-driven modelling studies that these two theories correlate in vivo. We estimate the curvature elastic stress of mammalian cells to be 4-7 × 10(-12) N, a value high enough to suggest that in mammalian cells the preservation of membrane order arises through a mechanism where membrane curvature elastic stress is controlled. These results emerge from analysing the molecular contribution of individual phospholipids to both membrane order and curvature elastic stress in nearly 500 cellular compositionally diverse lipidomes. Our model suggests that the de novo synthesis of lipids is the dominant mechanism by which cells control curvature elastic stress and hence membrane order in vivo These results also suggest that cells can increase membrane curvature elastic stress disproportionately to membrane order by incorporating polyunsaturated fatty acids into lipids. © 2016 The Author(s).

The Role of Membrane Curvature in Nanoscale Topography-Induced Intracellular Signaling.

PubMed

Lou, Hsin-Ya; Zhao, Wenting; Zeng, Yongpeng; Cui, Bianxiao

2018-05-15

Over the past decade, there has been growing interest in developing biosensors and devices with nanoscale and vertical topography. Vertical nanostructures induce spontaneous cell engulfment, which enhances the cell-probe coupling efficiency and the sensitivity of biosensors. Although local membranes in contact with the nanostructures are found to be fully fluidic for lipid and membrane protein diffusions, cells appear to actively sense and respond to the surface topography presented by vertical nanostructures. For future development of biodevices, it is important to understand how cells interact with these nanostructures and how their presence modulates cellular function and activities. How cells recognize nanoscale surface topography has been an area of active research for two decades before the recent biosensor works. Extensive studies show that surface topographies in the range of tens to hundreds of nanometers can significantly affect cell functions, behaviors, and ultimately the cell fate. For example, titanium implants having rough surfaces are better for osteoblast attachment and host-implant integration than those with smooth surfaces. At the cellular level, nanoscale surface topography has been shown by a large number of studies to modulate cell attachment, activity, and differentiation. However, a mechanistic understanding of how cells interact and respond to nanoscale topographic features is still lacking. In this Account, we focus on some recent studies that support a new mechanism that local membrane curvature induced by nanoscale topography directly acts as a biochemical signal to induce intracellular signaling, which we refer to as the curvature hypothesis. The curvature hypothesis proposes that some intracellular proteins can recognize membrane curvatures of a certain range at the cell-to-material interface. These proteins then recruit and activate downstream components to modulate cell signaling and behavior. We discuss current technologies

Tiny cells meet big questions: a closer look at bacterial cell biology.

PubMed

Goley, Erin D

2013-04-01

While studying actin assembly as a graduate student with Matt Welch at the University of California at Berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. Curiosity about these phenomena drew me to Lucy Shapiro's lab at Stanford University for my postdoctoral research. In the Shapiro lab, and now in my lab at Johns Hopkins, I have focused on investigating the mechanisms of bacterial cytokinesis. Spending time as both a eukaryotic cell biologist and a bacterial cell biologist has convinced me that bacterial cells present the same questions as eukaryotic cells: How are chromosomes organized and accurately segregated? How is force generated for cytokinesis? How is polarity established? How are signals transduced within and between cells? These problems are conceptually similar between eukaryotes and bacteria, although their solutions can differ significantly in specifics. In this Perspective, I provide a broad view of cell biological phenomena in bacteria, the technical challenges facing those of us who peer into bacterial cells, and areas of common ground as research in eukaryotic and bacterial cell biology moves forward.

The role of curvature in entanglement

NASA Astrophysics Data System (ADS)

Buck, Gregory

2015-10-01

Which tangles more readily: curly hair or straight hair? A perhaps natural thought, supported by some theoretical evidence, is to associate curvature and entanglement, and assume that they would grow together-that an increase in one fosters an increase in the other. However we have biological examples such as DNA in the chromosome, and mechanical examples such as coiled telephone cords, in which much more curvature is employed than is required for the packing, and in which tangling is presumably detrimental. We offer a resolution to this conundrum. We show, that at least for simple but generally applicable models, the relationship between curvature and entanglement is subtle: if we keep filament density constant and increase curvature, the entanglement initially increases, passes through a maximum, then decreases, so there is a regime where increasing curvature increases entanglement, and there is also a regime where increasing curvature decreases entanglement. This has implications for filament packing in many circumstances, and in particular for the compaction structure of DNA in the cell-it provides a straightforward argument for the view that one purpose of DNA coiling and supercoiling is to inhibit entanglement. It also tells us to expect that wavy hair-neither the straightest nor the curliest-tangles most readily.

Isolation of cell-free bacterial inclusion bodies.

PubMed

Rodríguez-Carmona, Escarlata; Cano-Garrido, Olivia; Seras-Franzoso, Joaquin; Villaverde, Antonio; García-Fruitós, Elena

2010-09-17

Bacterial inclusion bodies are submicron protein clusters usually found in recombinant bacteria that have been traditionally considered as undesirable products from protein production processes. However, being fully biocompatible, they have been recently characterized as nanoparticulate inert materials useful as scaffolds for tissue engineering, with potentially wider applicability in biomedicine and material sciences. Current protocols for inclusion body isolation from Escherichia coli usually offer between 95 to 99% of protein recovery, what in practical terms, might imply extensive bacterial cell contamination, not compatible with the use of inclusion bodies in biological interfaces. Using an appropriate combination of chemical and mechanical cell disruption methods we have established a convenient procedure for the recovery of bacterial inclusion bodies with undetectable levels of viable cell contamination, below 10⁻¹ cfu/ml, keeping the particulate organization of these aggregates regarding size and protein folding features. The application of the developed protocol allows obtaining bacterial free inclusion bodies suitable for use in mammalian cell cultures and other biological interfaces.

Molecular mechanisms of cell-cell spread of intracellular bacterial pathogens.

PubMed

Ireton, Keith

2013-07-17

Several bacterial pathogens, including Listeria monocytogenes, Shigella flexneri and Rickettsia spp., have evolved mechanisms to actively spread within human tissues. Spreading is initiated by the pathogen-induced recruitment of host filamentous (F)-actin. F-actin forms a tail behind the microbe, propelling it through the cytoplasm. The motile pathogen then encounters the host plasma membrane, forming a bacterium-containing protrusion that is engulfed by an adjacent cell. Over the past two decades, much progress has been made in elucidating mechanisms of F-actin tail formation. Listeria and Shigella produce tails of branched actin filaments by subverting the host Arp2/3 complex. By contrast, Rickettsia forms tails with linear actin filaments through a bacterial mimic of eukaryotic formins. Compared with F-actin tail formation, mechanisms controlling bacterial protrusions are less well understood. However, recent findings have highlighted the importance of pathogen manipulation of host cell-cell junctions in spread. Listeria produces a soluble protein that enhances bacterial protrusions by perturbing tight junctions. Shigella protrusions are engulfed through a clathrin-mediated pathway at 'tricellular junctions'--specialized membrane regions at the intersection of three epithelial cells. This review summarizes key past findings in pathogen spread, and focuses on recent developments in actin-based motility and the formation and internalization of bacterial protrusions.

Magnetic curvature effects on plasma interchange turbulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, B., E-mail: bli@pku.edu.cn; Liao, X.; Sun, C. K.

2016-06-15

The magnetic curvature effects on plasma interchange turbulence and transport in the Z-pinch and dipole-like systems are explored with two-fluid global simulations. By comparing the transport levels in the systems with a different magnetic curvature, we show that the interchange-mode driven transport strongly depends on the magnetic geometry. For the system with large magnetic curvature, the pressure and density profiles are strongly peaked in a marginally stable state and the nonlinear evolution of interchange modes produces the global convective cells in the azimuthal direction, which lead to the low level of turbulent convective transport.

Cellulose-ethylenediaminetetraacetic acid conjugates protect mammalian cells from bacterial cells.

PubMed

Luo, Jie; Lv, Wei; Deng, Ying; Sun, Yuyu

2013-04-08

Cellulose-ethylenediaminetetraacetic acid (EDTA) conjugates were synthesized by the esterification of cellulose with ethylenediaminetetraacetic dianhydride (EDTAD). The new materials provided potent antimicrobial activities against Staphylococcus aureus (S. aureus, Gram-positive bacteria) and Pseudomonas aeruginosa (P. aeruginosa, Gram-negative bacteria), and inhibited the formation of bacterial biofilms. The biocompatibility of the new cellulose-EDTA conjugates was evaluated with mouse skin fibroblasts for up to 14 days. SEM observation and DNA content analysis suggested that the new materials sustained the viability of fibroblast cells. Moreover, in mouse skin fibroblast-bacteria co-culture systems, the new cellulose-EDTA conjugates prevented bacterial biofilm formation and protected the mammalian cells from the bacterial cells for at least one day.

Bacterial spread from cell to cell: beyond actin-based motility.

PubMed

Kuehl, Carole J; Dragoi, Ana-Maria; Talman, Arthur; Agaisse, Hervé

2015-09-01

Several intracellular pathogens display the ability to propagate within host tissues by displaying actin-based motility in the cytosol of infected cells. As motile bacteria reach cell-cell contacts they form plasma membrane protrusions that project into adjacent cells and resolve into vacuoles from which the pathogen escapes, thereby achieving spread from cell to cell. Seminal studies have defined the bacterial and cellular factors that support actin-based motility. By contrast, the mechanisms supporting the formation of protrusions and their resolution into vacuoles have remained elusive. Here, we review recent advances in the field showing that Listeria monocytogenes and Shigella flexneri have evolved pathogen-specific mechanisms of bacterial spread from cell to cell. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gaussian curvature directs the distribution of spontaneous curvature on bilayer membrane necks.

PubMed

Chabanon, Morgan; Rangamani, Padmini

2018-03-28

Formation of membrane necks is crucial for fission and fusion in lipid bilayers. In this work, we seek to answer the following fundamental question: what is the relationship between protein-induced spontaneous mean curvature and the Gaussian curvature at a membrane neck? Using an augmented Helfrich model for lipid bilayers to include membrane-protein interaction, we solve the shape equation on catenoids to find the field of spontaneous curvature that satisfies mechanical equilibrium of membrane necks. In this case, the shape equation reduces to a variable coefficient Helmholtz equation for spontaneous curvature, where the source term is proportional to the Gaussian curvature. We show how this latter quantity is responsible for non-uniform distribution of spontaneous curvature in minimal surfaces. We then explore the energetics of catenoids with different spontaneous curvature boundary conditions and geometric asymmetries to show how heterogeneities in spontaneous curvature distribution can couple with Gaussian curvature to result in membrane necks of different geometries.

Surface Curvature Differentially Regulates Stem Cell Migration and Differentiation via Altered Attachment Morphology and Nuclear Deformation

PubMed Central

Werner, Maike; Blanquer, Sébastien B. G.; Haimi, Suvi P.; Korus, Gabriela; Dunlop, John W. C.; Duda, Georg N.; Grijpma, Dirk. W.

2016-01-01

Signals from the microenvironment around a cell are known to influence cell behavior. Material properties, such as biochemical composition and substrate stiffness, are today accepted as significant regulators of stem cell fate. The knowledge of how cell behavior is influenced by 3D geometric cues is, however, strongly limited despite its potential relevance for the understanding of tissue regenerative processes and the design of biomaterials. Here, the role of surface curvature on the migratory and differentiation behavior of human mesenchymal stem cells (hMSCs) has been investigated on 3D surfaces with well‐defined geometric features produced by stereolithography. Time lapse microscopy reveals a significant increase of cell migration speed on concave spherical compared to convex spherical structures and flat surfaces resulting from an upward‐lift of the cell body due to cytoskeletal forces. On convex surfaces, cytoskeletal forces lead to substantial nuclear deformation, increase lamin‐A levels and promote osteogenic differentiation. The findings of this study demonstrate a so far missing link between 3D surface curvature and hMSC behavior. This will not only help to better understand the role of extracellular matrix architecture in health and disease but also give new insights in how 3D geometries can be used as a cell‐instructive material parameter in the field of biomaterial‐guided tissue regeneration. PMID:28251054

Lipids, curvature, and nano-medicine*

PubMed Central

Mouritsen, Ole G

2011-01-01

The physical properties of the lamellar lipid-bilayer component of biological membranes are controlled by a host of thermodynamic forces leading to overall tensionless bilayers with a conspicuous lateral pressure profile and build-in curvature-stress instabilities that may be released locally or globally in terms of morphological changes. In particular, the average molecular shape and the propensity of the different lipid and protein species for forming non-lamellar and curved structures are a source of structural transitions and control of biological function. The effects of different lipids, sterols, and proteins on membrane structure are discussed and it is shown how one can take advantage of the curvature-stress modulations brought about by specific molecular agents, such as fatty acids, lysolipids, and other amphiphilic solutes, to construct intelligent drug-delivery systems that function by enzymatic triggering via curvature. Practical applications: The simple concept of lipid molecular shape and how it impacts on the structure of lipid aggregates, in particular the curvature and curvature stress in lipid bilayers and liposomes, can be exploited to construct liposome-based drug-delivery systems, e.g., for use as nano-medicine in cancer therapy. Non-lamellar-forming lysolipids and fatty acids, some of which may be designed to be prodrugs, can be created by phospholipase action in diseased tissues thereby providing for targeted drug release and proliferation of molecular entities with conical shape that break down the permeability barrier of the target cells and may hence enhance efficacy. PMID:22164124

Sequence-Specific Affinity Chromatography of Bacterial Small Regulatory RNA-Binding Proteins from Bacterial Cells.

PubMed

Gans, Jonathan; Osborne, Jonathan; Cheng, Juliet; Djapgne, Louise; Oglesby-Sherrouse, Amanda G

2018-01-01

Bacterial small RNA molecules (sRNAs) are increasingly recognized as central regulators of bacterial stress responses and pathogenesis. In many cases, RNA-binding proteins are critical for the stability and function of sRNAs. Previous studies have adopted strategies to genetically tag an sRNA of interest, allowing isolation of RNA-protein complexes from cells. Here we present a sequence-specific affinity purification protocol that requires no prior genetic manipulation of bacterial cells, allowing isolation of RNA-binding proteins bound to native RNA molecules.

Intestinal Epithelial Cells Modulate Antigen-Presenting Cell Responses to Bacterial DNA

PubMed Central

Campeau, J. L.; Salim, S. Y.; Albert, E. J.; Hotte, N.

2012-01-01

Intestinal epithelial cells and antigen-presenting cells orchestrate mucosal innate immunity. This study investigated the role of bacterial DNA in modulating epithelial and bone marrow-derived antigen-presenting cells (BM-APCs) and subsequent T-lymphocyte responses. Murine MODE-K epithelial cells and BM-APCs were treated with DNA from either Bifidobacterium breve or Salmonella enterica serovar Dublin directly and under coculture conditions with CD4+ T cells. Apical stimulation of MODE-K cells with S. Dublin DNA enhanced secretion of cytokines from underlying BM-APCs and induced interleukin-17 (IL-17) and gamma interferon (IFN-γ) secretion from CD4+ T cells. Bacterial DNA isolated from either strain induced maturation and increased cytokine secretion from BM-APCs. Conditioned medium from S. Dublin-treated MODE-K cells elicited an increase in cytokine secretion similar to that seen for S. Dublin DNA. Treatment of conditioned medium from MODE-K cells with RNase and protease prevented the S. Dublin-induced increased cytokine secretion. Oral feeding of mice with B. breve DNA resulted in enhanced levels of colonic IL-10 and transforming growth factor β (TGFβ) compared with what was seen for mice treated with S. Dublin DNA. In contrast, feeding mice with S. Dublin DNA increased levels of colonic IL-17 and IL-12p70. T cells from S. Dublin DNA-treated mice secreted high levels of IL-12 and IFN-γ compared to controls and B. breve DNA-treated mice. These results demonstrate that intestinal epithelial cells are able to modulate subsequent antigen-presenting and T-cell responses to bacterial DNA with pathogenic but not commensal bacterial DNA inducing effector CD4+ T lymphocytes. PMID:22615241

Coupling Bacterial Activity Measurements with Cell Sorting by Flow Cytometry.

PubMed

Servais; Courties; Lebaron; Troussellier

1999-08-01

> Abstract A new procedure to investigate the relationship between bacterial cell size and activity at the cellular level has been developed; it is based on the coupling of radioactive labeling of bacterial cells and cell sorting by flow cytometry after SYTO 13 staining. Before sorting, bacterial cells were incubated in the presence of tritiated leucine using a procedure similar to that used for measuring bacterial production by leucine incorporation and then stained with SYTO 13. Subpopulations of bacterial cells were sorted according to their average right-angle light scatter (RALS) and fluorescence. Average RALS was shown to be significantly related to the average biovolume. Experiments were performed on samples collected at different times in a Mediterranean seawater mesocosm enriched with nitrogen and phosphorus. At four sampling times, bacteria were sorted in two subpopulations (cells smaller and larger than 0.25 µm(3)). The results indicate that, at each sampling time, the growth rate of larger cells was higher than that of smaller cells. In order to confirm this tendency, cell sorting was performed on six subpopulations differing in average biovolume during the mesocosm follow-up. A clear increase of the bacterial growth rates was observed with increasing cell size for the conditions met in this enriched mesocosm.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p180.html

Curvature-Guided Motility of Microalgae in Geometric Confinement

NASA Astrophysics Data System (ADS)

Ostapenko, Tanya; Schwarzendahl, Fabian Jan; Böddeker, Thomas J.; Kreis, Christian Titus; Cammann, Jan; Mazza, Marco G.; Bäumchen, Oliver

2018-02-01

Microorganisms, such as bacteria and microalgae, often live in habitats consisting of a liquid phase and a plethora of interfaces. The precise ways in which these motile microbes behave in their confined environment remain unclear. Using experiments and Brownian dynamics simulations, we study the motility of a single Chlamydomonas microalga in an isolated microhabitat with controlled geometric properties. We demonstrate how the geometry of the habitat controls the cell's navigation in confinement. The probability of finding the cell swimming near the boundary increases with the wall curvature, as seen for both circular and elliptical chambers. The theory, utilizing an asymmetric dumbbell model of the cell and steric wall interactions, captures this curvature-guided navigation quantitatively with no free parameters.

Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers

PubMed Central

Tourdot, Richard W.; Ramakrishnan, N.; Radhakrishnan, Ravi

2015-01-01

Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and Exo70, are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can act as curvature sensors; they aggregate to membrane regions matching their intrinsic curvature; as well as induce curvature in cell membranes to stabilize emergent high curvature, nonspherical, structures such as tubules, discs, and caveolae. A definitive understanding of the interplay between protein recruitment and migration, the evolution of membrane curvature, and membrane morphological transitions is emerging but remains incomplete. Here, within a continuum framework and using the machinery of Monte Carlo simulations, we introduce and compare three free-energy methods to delineate the free-energy landscape of curvature-inducing proteins on bilayer membranes. We demonstrate the utility of the Widom test particle (or field) insertion methodology in computing the excess chemical potentials associated with curvature-inducing proteins on the membrane—in particular, we use this method to track the onset of morphological transitions in the membrane at elevated protein densities. We validate this approach by comparing the results from the Widom method with those of thermodynamic integration and Bennett acceptance ratio methods. Furthermore, the predictions from the Widom method have been tested against analytical calculations of the excess chemical potential at infinite dilution. Our results are useful in precisely quantifying the free-energy landscape, and also in determining the phase boundaries associated with curvature-induction, curvature-sensing, and morphological transitions. This approach can be extended to studies exploring the role of thermal fluctuations and other external (control) variables, such as membrane excess area, in shaping curvature-mediated interactions on bilayer

Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers.

PubMed

Tourdot, Richard W; Ramakrishnan, N; Radhakrishnan, Ravi

2014-08-01

Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and Exo70, are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can act as curvature sensors; they aggregate to membrane regions matching their intrinsic curvature; as well as induce curvature in cell membranes to stabilize emergent high curvature, nonspherical, structures such as tubules, discs, and caveolae. A definitive understanding of the interplay between protein recruitment and migration, the evolution of membrane curvature, and membrane morphological transitions is emerging but remains incomplete. Here, within a continuum framework and using the machinery of Monte Carlo simulations, we introduce and compare three free-energy methods to delineate the free-energy landscape of curvature-inducing proteins on bilayer membranes. We demonstrate the utility of the Widom test particle (or field) insertion methodology in computing the excess chemical potentials associated with curvature-inducing proteins on the membrane-in particular, we use this method to track the onset of morphological transitions in the membrane at elevated protein densities. We validate this approach by comparing the results from the Widom method with those of thermodynamic integration and Bennett acceptance ratio methods. Furthermore, the predictions from the Widom method have been tested against analytical calculations of the excess chemical potential at infinite dilution. Our results are useful in precisely quantifying the free-energy landscape, and also in determining the phase boundaries associated with curvature-induction, curvature-sensing, and morphological transitions. This approach can be extended to studies exploring the role of thermal fluctuations and other external (control) variables, such as membrane excess area, in shaping curvature-mediated interactions on bilayer

Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling.

PubMed

Elías-Wolff, Federico; Lindén, Martin; Lyubartsev, Alexander P; Brandt, Erik G

2018-03-13

Membrane curvature sensing, where the binding free energies of membrane-associated molecules depend on the local membrane curvature, is a key factor to modulate and maintain the shape and organization of cell membranes. However, the microscopic mechanisms are not well understood, partly due to absence of efficient simulation methods. Here, we describe a method to compute the curvature dependence of the binding free energy of a membrane-associated probe molecule that interacts with a buckled membrane, which has been created by lateral compression of a flat bilayer patch. This buckling approach samples a wide range of curvatures in a single simulation, and anisotropic effects can be extracted from the orientation statistics. We develop an efficient and robust algorithm to extract the motion of the probe along the buckled membrane surface, and evaluate its numerical properties by extensive sampling of three coarse-grained model systems: local lipid density in a curved environment for single-component bilayers, curvature preferences of individual lipids in two-component membranes, and curvature sensing by a homotrimeric transmembrane protein. The method can be used to complement experimental data from curvature partition assays and provides additional insight into mesoscopic theories and molecular mechanisms for curvature sensing.

Bacterial Actins.

PubMed

Izoré, Thierry; van den Ent, Fusinita

2017-01-01

A diverse set of protein polymers, structurally related to actin filaments contributes to the organization of bacterial cells as cytomotive or cytoskeletal filaments. This chapter describes actin homologs encoded by bacterial chromosomes. MamK filaments, unique to magnetotactic bacteria, help establishing magnetic biological compasses by interacting with magnetosomes. Magnetosomes are intracellular membrane invaginations containing biomineralized crystals of iron oxide that are positioned by MamK along the long-axis of the cell. FtsA is widespread across bacteria and it is one of the earliest components of the divisome to arrive at midcell, where it anchors the cell division machinery to the membrane. FtsA binds directly to FtsZ filaments and to the membrane through its C-terminus. FtsA shows altered domain architecture when compared to the canonical actin fold. FtsA's subdomain 1C replaces subdomain 1B of other members of the actin family and is located on the opposite side of the molecule. Nevertheless, when FtsA assembles into protofilaments, the protofilament structure is preserved, as subdomain 1C replaces subdomain IB of the following subunit in a canonical actin filament. MreB has an essential role in shape-maintenance of most rod-shaped bacteria. Unusually, MreB filaments assemble from two protofilaments in a flat and antiparallel arrangement. This non-polar architecture implies that both MreB filament ends are structurally identical. MreB filaments bind directly to membranes where they interact with both cytosolic and membrane proteins, thereby forming a key component of the elongasome. MreB filaments in cells are short and dynamic, moving around the long axis of rod-shaped cells, sensing curvature of the membrane and being implicated in peptidoglycan synthesis.

On the curvature effect of thin membranes

NASA Astrophysics Data System (ADS)

Wang, Duo; Jiao, Xiangmin; Conley, Rebecca; Glimm, James

2013-01-01

We investigate the curvature effect of a thin, curved elastic interface that separates two subdomains and exerts a pressure due to a curvature effect. This pressure, which we refer to as interface pressure, is similar to the surface tension in fluid mechanics. It is important in some applications, such as the canopy of parachutes, biological membranes of cells, balloons, airbags, etc., as it partially balances a pressure jump between the two sides of an interface. In this paper, we show that the interface pressure is equal to the trace of the matrix product of the curvature tensor and the Cauchy stress tensor in the tangent plane. We derive the theory for interfaces in both 2-D and 3-D, and present numerical discretizations for computing the quality over triangulated surfaces.

Growth mechanics of bacterial cell wall and morphology of bacteria

NASA Astrophysics Data System (ADS)

Jiang, Hongyuan; Sun, Sean

2010-03-01

The peptidoglycan cell wall of bacteria is responsible for maintaining the cell shape and integrity. During the bacterial life cycle, the growth of the cell wall is affected by mechanical stress and osmotic pressure internal to the cell. We develop a theory to describe cell shape changes under the influence of mechanical forces. We find that the theory predicts a steady state size and shape for bacterial cells ranging from cocci to spirillum. Moreover, the theory suggest a mechanism by which bacterial cytoskeletal proteins such as MreB and crescentin can maintain the shape of the cell. The theory can also explain the several recent experiments on growing bacteria in micro-environments.

Revised Model of Calcium and Magnesium Binding to the Bacterial Cell Wall

PubMed Central

Thomas, Kieth J.; Rice, Charles V.

2014-01-01

Metals bind to the bacterial cell wall yet the binding mechanisms and affinity constants are not fully understood. The cell wall of gram positive bacteria is characterized by a thick layer of peptidoglycan and anionic teichoic acids anchored in the cytoplasmic membrane (lipoteichoic acid) or covalently bound to the cell wall (wall teichoic acid). The polyphosphate groups of teichoic acid provide one-half of the metal binding sites for calcium and magnesium, contradicting previous reports that calcium binding is 100% dependent on teichoic acid. The remaining binding sites are formed with the carboxyl units of peptidoglycan. In this work we report equilibrium association constants and total metal binding capacities for the interaction of calcium and magnesium ions with the bacterial cell wall. Metal binding is much stronger and previously reported. Curvature of Scatchard plots from the binding data and the resulting two regions of binding affinity suggest the presence of negative cooperative binding, meaning that the binding affinity decreases as more ions become bound to the sample. For Ca2+, Region I has a KA = (1.0 ± 0.2) × 106 M−1 and Region II has a KA = (0.075 ± 0.058) × 106 M−1. For Mg2+, KA1 = (1.5 ± 0.1) × 106 and KA2 = (0.17 ± 0.10) × 106. A binding capacity (η) is reported for both regions. However, since binding is still occurring in Region II, the total binding capacity is denoted by η2, which are 0.70 ± 0.04 µmol/mg and 0.67 ± 0.03 µmol/mg for Ca2+ and Mg2+ respectively. These data contradict the current paradigm of there being a single metal affinity value that is constant over a range of concentrations. We also find that measurement of equilibrium binding constants is highly sample dependent, suggesting a role for diffusion of metals through heterogeneous cell wall fragments. As a result, we are able to reconcile many contradictory theories that describe binding affinity and the binding mode of divalent metal cations. PMID:25315444

Pattern formation by curvature-inducing proteins on spherical membranes

NASA Astrophysics Data System (ADS)

Agudo-Canalejo, Jaime; Golestanian, Ramin

2017-12-01

Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic mechanisms underlying spatial organisation in cells. In this work, we use a continuum model of membrane and protein dynamics to study the behaviour of curvature-inducing proteins on membranes of spherical shape, such as living cells or lipid vesicles. We show that the interplay between curvature energy, entropic forces, and the geometric constraints on the membrane can result in the formation of patterns of highly-curved/protein-rich and weakly-curved/protein-poor domains on the membrane. The spontaneous formation of such patterns can be triggered either by an increase in the average density of curvature-inducing proteins, or by a relaxation of the geometric constraints on the membrane imposed by the membrane tension or by the tethering of the membrane to a rigid cell wall or cortex. These parameters can also be tuned to select the size and number of the protein-rich domains that arise upon pattern formation. The very general mechanism presented here could be related to protein self-organisation in many biological processes, ranging from (proto)cell division to the formation of membrane rafts.

Incidence and Predictors of Bacterial infection in Febrile Children with Sickle Cell Disease.

PubMed

Morrissey, Benita J; Bycroft, Thomas P; Almossawi, Ofran; Wilkey, Olufunke B; Daniels, Justin G

2015-01-01

Children with sickle cell disease are at increased risk of developing bacteremia and other serious bacterial infections. Fever is a common symptom in sickle cell disease and can also occur with sickle cell crises and viral infections. We aimed to evaluate the incidence and predictors of bacteremia and bacterial infection in children with sickle cell disease presenting with fever to a district hospital and sickle cell center in London. A retrospective analysis was performed on all attendances of children (aged under 16 years) with sickle cell disease presenting with a fever of 38.5 °C or higher over a 1-year period. Confirmed bacterial infection was defined as bacteremia, bacterial meningitis, urinary tract infection (UTI), pneumonia, osteomyelitis or other bacterial infection with positive identification of organism. Children were defined as having a suspected bacterial infection if a bacterial infection was suspected clinically, but no organism was identified. Over a 1-year period there were 88 episodes analyzed in 59 children. Bacteremia occurred in 3.4% of episodes and confirmed bacterial infection in 7.0%. Suspected bacterial infection occurred in 33.0%. One death occurred from Salmonella typhirium septicemia. C-reactive protein (CRP) level and white blood cell (WBC) count were both significantly associated with bacterial infection (p = 0.004 and 0.02, respectively.) In conclusion, bacterial infections continue to be a significant problem in children with sickle cell disease. C-reactive protein was significantly associated with bacterial infections, and could be included in clinical risk criteria for febrile children with sickle cell disease.

Poisons, ruffles and rockets: bacterial pathogens and the host cell cytoskeleton.

PubMed

Steele-Mortimer, O; Knodler, L A; Finlay, B B

2000-02-01

The cytoskeleton of eukaryotic cells is affected by a number of bacterial and viral pathogens. In this review we consider three recurring themes of cytoskeletal involvement in bacterial pathogenesis: 1) the effect of bacterial toxins on actin-regulating small GTP-binding proteins; 2) the invasion of non-phagocytic cells by the bacterial induction of ruffles at the plasma membrane; 3) the formation of actin tails and pedestals by intracellular and extracellular bacteria, respectively. Considerable progress has been made recently in the characterization of these processes. It is becoming clear that bacterial pathogens have developed a variety of sophisticated mechanisms for utilizing the complex cytoskeletal system of host cells. These bacterially-induced processes are now providing unique insights into the regulation of fundamental eukaryotic mechanisms.

Proteomic analysis of the bacterial cell cycle

PubMed Central

Grünenfelder, Björn; Rummel, Gabriele; Vohradsky, Jiri; Röder, Daniel; Langen, Hanno; Jenal, Urs

2001-01-01

A global approach was used to analyze protein synthesis and stability during the cell cycle of the bacterium Caulobacter crescentus. Approximately one-fourth (979) of the estimated C. crescentus gene products were detected by two-dimensional gel electrophoresis, 144 of which showed differential cell cycle expression patterns. Eighty-one of these proteins were identified by mass spectrometry and were assigned to a wide variety of functional groups. Pattern analysis revealed that coexpression groups were functionally clustered. A total of 48 proteins were rapidly degraded in the course of one cell cycle. More than half of these unstable proteins were also found to be synthesized in a cell cycle-dependent manner, establishing a strong correlation between rapid protein turnover and the periodicity of the bacterial cell cycle. This is, to our knowledge, the first evidence for a global role of proteolysis in bacterial cell cycle control. PMID:11287652

Biosensors for Whole-Cell Bacterial Detection

PubMed Central

Rushworth, Jo V.; Hirst, Natalie A.; Millner, Paul A.

2014-01-01

SUMMARY Bacterial pathogens are important targets for detection and identification in medicine, food safety, public health, and security. Bacterial infection is a common cause of morbidity and mortality worldwide. In spite of the availability of antibiotics, these infections are often misdiagnosed or there is an unacceptable delay in diagnosis. Current methods of bacterial detection rely upon laboratory-based techniques such as cell culture, microscopic analysis, and biochemical assays. These procedures are time-consuming and costly and require specialist equipment and trained users. Portable stand-alone biosensors can facilitate rapid detection and diagnosis at the point of care. Biosensors will be particularly useful where a clear diagnosis informs treatment, in critical illness (e.g., meningitis) or to prevent further disease spread (e.g., in case of food-borne pathogens or sexually transmitted diseases). Detection of bacteria is also becoming increasingly important in antibioterrorism measures (e.g., anthrax detection). In this review, we discuss recent progress in the use of biosensors for the detection of whole bacterial cells for sensitive and earlier identification of bacteria without the need for sample processing. There is a particular focus on electrochemical biosensors, especially impedance-based systems, as these present key advantages in terms of ease of miniaturization, lack of reagents, sensitivity, and low cost. PMID:24982325

Elucidating Duramycin's Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope.

PubMed

Hasim, Sahar; Allison, David P; Mendez, Berlin; Farmer, Abigail T; Pelletier, Dale A; Retterer, Scott T; Campagna, Shawn R; Reynolds, Todd B; Doktycz, Mitchel J

2018-01-01

The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus -derived bacterial isolates to determine species selectivity. Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE) in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin's mode of action and a better understanding of its selectivity.

Generalized Boussinesq-Scriven surface fluid model with curvature dissipation for liquid surfaces and membranes.

PubMed

Aguilar Gutierrez, Oscar F; Herrera Valencia, Edtson E; Rey, Alejandro D

2017-10-01

Curvature dissipation is relevant in synthetic and biological processes, from fluctuations in semi-flexible polymer solutions, to buckling of liquid columns, tomembrane cell wall functioning. We present a micromechanical model of curvature dissipation relevant to fluid membranes and liquid surfaces based on a parallel surface parameterization and a stress constitutive equation appropriate for anisotropic fluids and fluid membranes.The derived model, aimed at high curvature and high rate of change of curvature in liquid surfaces and membranes, introduces additional viscous modes not included in the widely used 2D Boussinesq-Scriven rheological constitutive equation for surface fluids.The kinematic tensors that emerge from theparallel surface parameterization are the interfacial rate of deformation and the surface co-rotational Zaremba-Jaumann derivative of the curvature, which are used to classify all possibledissipative planar and non-planar modes. The curvature dissipation function that accounts for bending, torsion and twist rates is derived and analyzed under several constraints, including the important inextensional bending mode.A representative application of the curvature dissipation model to the periodic oscillation in nano-wrinkled outer hair cells show how and why curvature dissipation decreases with frequency, and why the 100kHz frequency range is selected. These results contribute to characterize curvature dissipation in membranes and liquid surfaces. Copyright © 2017 Elsevier Inc. All rights reserved.

Curved tails in polymerization-based bacterial motility

NASA Astrophysics Data System (ADS)

Rutenberg, Andrew D.; Grant, Martin

2001-08-01

The curved actin ``comet-tail'' of the bacterium Listeria monocytogenes is a visually striking signature of actin polymerization-based motility. Similar actin tails are associated with Shigella flexneri, spotted-fever Rickettsiae, the Vaccinia virus, and vesicles and microspheres in related in vitro systems. We show that the torque required to produce the curvature in the tail can arise from randomly placed actin filaments pushing the bacterium or particle. We find that the curvature magnitude determines the number of actively pushing filaments, independent of viscosity and of the molecular details of force generation. The variation of the curvature with time can be used to infer the dynamics of actin filaments at the bacterial surface.

Estimation of lactic acid bacterial cell number by DNA quantification.

PubMed

Ishii, Masaki; Matsumoto, Yasuhiko; Sekimizu, Kazuhisa

2018-01-01

Lactic acid bacteria are provided by fermented foods, beverages, medicines, and supplements. Because the beneficial effects of medicines and supplements containing functional lactic acid bacteria are related to the bacterial cell number, it is important to establish a simple method for estimating the total number of lactic acid bacterial cells in the products for quality control. Almost all of the lactic acid bacteria in the products are dead, however, making it difficult to estimate the total number of lactic acid bacterial cells in the products using a standard colony-counting method. Here we estimated the total lactic acid bacterial cell number in samples containing dead bacteria by quantifying the DNA. The number of viable Enterococcus faecalis 0831-07 cells decreased to less than 1 × 10 -8 by 15 min of heat treatment at 80°C. The amount of extracted DNA from heat-treated cells was 78% that of non-heated cells. The number of viable Lactobacillus paraplantarum 11-1 cells decreased to 1 × 10 -4 after 4 days culture. The amount of extracted DNA of the long-cultured cells, however, was maintained at 97%. These results suggest that cell number of lactic acid bacteria killed by heat-treatment or long-term culture can be estimated by DNA quantification.

A geometric construction of the Riemann scalar curvature in Regge calculus

NASA Astrophysics Data System (ADS)

McDonald, Jonathan R.; Miller, Warner A.

2008-10-01

The Riemann scalar curvature plays a central role in Einstein's geometric theory of gravity. We describe a new geometric construction of this scalar curvature invariant at an event (vertex) in a discrete spacetime geometry. This allows one to constructively measure the scalar curvature using only clocks and photons. Given recent interest in discrete pre-geometric models of quantum gravity, we believe is it ever so important to reconstruct the curvature scalar with respect to a finite number of communicating observers. This derivation makes use of a new fundamental lattice cell built from elements inherited from both the original simplicial (Delaunay) spacetime and its circumcentric dual (Voronoi) lattice. The orthogonality properties between these two lattices yield an expression for the vertex-based scalar curvature which is strikingly similar to the corresponding hinge-based expression in Regge calculus (deficit angle per unit Voronoi dual area). In particular, we show that the scalar curvature is simply a vertex-based weighted average of deficits per weighted average of dual areas.

Identification of individual biofilm-forming bacterial cells using Raman tweezers

NASA Astrophysics Data System (ADS)

Samek, Ota; Bernatová, Silvie; Ježek, Jan; Šiler, Martin; Šerý, Mojmir; Krzyžánek, Vladislav; Hrubanová, Kamila; Zemánek, Pavel; Holá, Veronika; Růžička, Filip

2015-05-01

A method for in vitro identification of individual bacterial cells is presented. The method is based on a combination of optical tweezers for spatial trapping of individual bacterial cells and Raman microspectroscopy for acquisition of spectral "Raman fingerprints" obtained from the trapped cell. Here, Raman spectra were taken from the biofilm-forming cells without the influence of an extracellular matrix and were compared with biofilm-negative cells. Results of principal component analyses of Raman spectra enabled us to distinguish between the two strains of Staphylococcus epidermidis. Thus, we propose that Raman tweezers can become the technique of choice for a clearer understanding of the processes involved in bacterial biofilms which constitute a highly privileged way of life for bacteria, protected from the external environment.

Identification of individual biofilm-forming bacterial cells using Raman tweezers.

PubMed

Samek, Ota; Bernatová, Silvie; Ježek, Jan; Šiler, Martin; Šerý, Mojmir; Krzyžánek, Vladislav; Hrubanová, Kamila; Zemánek, Pavel; Holá, Veronika; Růžička, Filip

2015-05-01

A method for in vitro identification of individual bacterial cells is presented. The method is based on a combination of optical tweezers for spatial trapping of individual bacterial cells and Raman microspectroscopy for acquisition of spectral “Raman fingerprints” obtained from the trapped cell. Here, Raman spectra were taken from the biofilm-forming cells without the influence of an extracellular matrix and were compared with biofilm-negative cells. Results of principal component analyses of Raman spectra enabled us to distinguish between the two strains of Staphylococcus epidermidis. Thus, we propose that Raman tweezers can become the technique of choice for a clearer understanding of the processes involved in bacterial biofilms which constitute a highly privileged way of life for bacteria, protected from the external environment.

Cell-to-Cell Heterogeneity in Cortical Tension Specifies Curvature of Contact Surfaces in Caenorhabditis elegans Embryos

PubMed Central

Fujita, Masashi; Onami, Shuichi

2012-01-01

In the two-cell stage embryos of Caenorhabditis elegans, the contact surface of the two blastomeres forms a curve that bulges from the AB blastomere to the P1 blastomere. This curve is a consequence of the high intracellular hydrostatic pressure of AB compared with that of P1. However, the higher pressure in AB is intriguing because AB has a larger volume than P1. In soap bubbles, which are a widely used model of cell shape, a larger bubble has lower pressure than a smaller bubble. Here, we reveal that the higher pressure in AB is mediated by its higher cortical tension. The cell fusion experiments confirmed that the curvature of the contact surface is related to the pressure difference between the cells. Chemical and genetic interferences showed that the pressure difference is mediated by actomyosin. Fluorescence imaging indicated that non-muscle myosin is enriched in the AB cortex. The cell killing experiments provided evidence that AB but not P1 is responsible for the pressure difference. Computer simulation clarified that the cell-to-cell heterogeneity of cortical tensions is indispensable for explaining the pressure difference. This study demonstrates that heterogeneity in surface tension results in significant deviations of cell behavior compared to simple soap bubble models, and thus must be taken into consideration in understanding cell shape within embryos. PMID:22253922

Membrane Curvature Sensing by Amphipathic Helices

PubMed Central

Jensen, Martin Borch; Bhatia, Vikram Kjøller; Jao, Christine C.; Rasmussen, Jakob Ewald; Pedersen, Søren L.; Jensen, Knud J.; Langen, Ralf; Stamou, Dimitrios

2011-01-01

Preferential binding of proteins on curved membranes (membrane curvature sensing) is increasingly emerging as a general mechanism whereby cells may effect protein localization and trafficking. Here we use a novel single liposome fluorescence microscopy assay to examine a common sensing motif, the amphipathic helix (AH), and provide quantitative measures describing and distinguishing membrane binding and sensing behavior. By studying two AH-containing proteins, α-synuclein and annexin B12, as well as a range of AH peptide mutants, we reveal that both the hydrophobic and hydrophilic faces of the helix greatly influence binding and sensing. Although increased hydrophobic and electrostatic interactions with the membrane both lead to greater densities of bound protein, the former yields membrane curvature-sensitive binding, whereas the latter is not curvature-dependent. However, the relative contributions of both components determine the sensing of AHs. In contrast, charge density in the lipid membrane seems important primarily in attracting AHs to the membrane but does not significantly influence sensing. These observations were made possible by the ability of our assay to distinguish within our samples liposomes with and without bound protein as well as the density of bound protein. Our findings suggest that the description of membrane curvature-sensing requires consideration of several factors such as short and long range electrostatic interactions, hydrogen bonding, and the volume and structure of inserted hydrophobic residues. PMID:21953452

Circular Dichroism studies on the interactions of antimicrobial peptides with bacterial cells

NASA Astrophysics Data System (ADS)

Avitabile, Concetta; D'Andrea, Luca Domenico; Romanelli, Alessandra

2014-03-01

Studying how antimicrobial peptides interact with bacterial cells is pivotal to understand their mechanism of action. In this paper we explored the use of Circular Dichroism to detect the secondary structure of two antimicrobial peptides, magainin 2 and cecropin A, with E. coli bacterial cells. The results of our studies allow us to gain two important information in the context of antimicrobial peptides- bacterial cells interactions: peptides fold mainly due to interaction with LPS, which is the main component of the Gram negative bacteria outer membrane and the time required for the folding on the bacterial cells depends on the peptide analyzed.

Curvature-undulation coupling as a basis for curvature sensing and generation in bilayer membranes.

PubMed

Bradley, Ryan P; Radhakrishnan, Ravi

2016-08-30

We present coarse-grained molecular dynamics simulations of the epsin N-terminal homology domain interacting with a lipid bilayer and demonstrate a rigorous theoretical formalism and analysis method for computing the induced curvature field in varying concentrations of the protein in the dilute limit. Our theory is based on the description of the height-height undulation spectrum in the presence of a curvature field. We formulated an objective function to compare the acquired undulation spectrum from the simulations to that of the theory. We recover the curvature field parameters by minimizing the objective function even in the limit where the protein-induced membrane curvature is of the same order as the amplitude due to thermal undulations. The coupling between curvature and undulations leads to significant predictions: (i) Under dilute conditions, the proteins can sense a site of spontaneous curvature at distances much larger than their size; (ii) as the density of proteins increases the coupling focuses and stabilizes the curvature field to the site of the proteins; and (iii) the mapping of the protein localization and the induction of a stable curvature is a cooperative process that can be described through a Hill function.

Single Lipid Molecule Dynamics on Supported Lipid Bilayers with Membrane Curvature.

PubMed

Cheney, Philip P; Weisgerber, Alan W; Feuerbach, Alec M; Knowles, Michelle K

2017-03-15

The plasma membrane is a highly compartmentalized, dynamic material and this organization is essential for a wide variety of cellular processes. Nanoscale domains allow proteins to organize for cell signaling, endo- and exocytosis, and other essential processes. Even in the absence of proteins, lipids have the ability to organize into domains as a result of a variety of chemical and physical interactions. One feature of membranes that affects lipid domain formation is membrane curvature. To directly test the role of curvature in lipid sorting, we measured the accumulation of two similar lipids, 1,2-Dihexadecanoyl- sn -glycero-3-phosphoethanolamine (DHPE) and hexadecanoic acid (HDA), using a supported lipid bilayer that was assembled over a nanopatterned surface to obtain regions of membrane curvature. Both lipids studied contain 16 carbon, saturated tails and a head group tag for fluorescence microscopy measurements. The accumulation of lipids at curvatures ranging from 28 nm to 55 nm radii was measured and fluorescein labeled DHPE accumulated more than fluorescein labeled HDA at regions of membrane curvature. We then tested whether single biotinylated DHPE molecules sense curvature using single particle tracking methods. Similar to groups of fluorescein labeled DHPE accumulating at curvature, the dynamics of single molecules of biotinylated DHPE was also affected by membrane curvature and highly confined motion was observed.

Membrane curvature and the Tol-Pal complex determine polar localization of the chemoreceptor Tar in E. coli.

PubMed

Saaki, Terrens N V; Strahl, Henrik; Hamoen, Leendert W

2018-02-20

Chemoreceptors are localized at the cell poles of Escherichia coli and other rod-shaped bacteria. Over the years different mechanisms have been put forward to explain this polar localization; from stochastic clustering, membrane curvature driven localization, interactions with the Tol-Pal complex, to nucleoid exclusion. To evaluate these mechanisms, we monitored the cellular localization of the aspartate chemoreceptor Tar in different deletion mutants. We did not find any indication for either stochastic cluster formation or nucleoid exclusion. However, the presence of a functional Tol-Pal complex appeared to be essential to retain Tar at cell poles. Interestingly, Tar still accumulated at midcell in tol and in pal deletion mutants. In these mutants, the protein appears to gather at the base of division septa, a region characterised by strong membrane curvature. Chemoreceptors, like Tar, form trimer-of-dimers that bend the cell membrane due to a rigid tripod structure. The curvature approaches the curvature of the cell membrane generated during cell division, and localization of chemoreceptor tripods at curved membrane areas is therefore energetically favourable as it lowers membrane tension. Indeed, when we introduced mutations in Tar that abolish the rigid tripod structure, the protein was no longer able to accumulate at midcell or cell poles. These findings favour a model where chemoreceptor localization in E. coli is driven by strong membrane curvature and association with the Tol-Pal complex. Importance Bacteria have exquisite mechanisms to sense and to adapt to the environment they live in. One such mechanism involves the chemotaxis signal transduction pathway, in which chemoreceptors specifically bind certain attracting or repelling molecules and transduce the signals to the cell. In different rod-shaped bacteria, these chemoreceptors localize specifically to cell poles. Here, we examined the polar localization of the aspartate chemoreceptor Tar in E. coli

Biolistic transformation of tobacco and maize suspension cells using bacterial cells as microprojectiles.

PubMed

Rasmussen, J L; Kikkert, J R; Roy, M K; Sanford, J C

1994-01-01

We have used both Escherichia coli cells and Agrobacterium tumefaciens cells as microprojectiles to deliver DNA into suspension-cultured tobacco (Nicotiana tabacum L. line NT1) cells using a helium powered biolistic device. In addition, E. coli cells were used as microprojectiles for the transformation of suspension-cultured maize (Zea mays cv. Black Mexican Sweet) cells. Pretreating the bacterial cells with phenol at a concentration of 1.0%, and combining the bacterial cells with tungsten particles increased the rates of transformation. In N. tabacum, we obtained hundreds of transient transformants per bombardment, but were unable to recover any stable transformants. In Z. mays we obtained thousands of transient transformants and an average of six stable transformants per bombardment. This difference is discussed.

Implementing quantum Ricci curvature

NASA Astrophysics Data System (ADS)

Klitgaard, N.; Loll, R.

2018-05-01

Quantum Ricci curvature has been introduced recently as a new, geometric observable characterizing the curvature properties of metric spaces, without the need for a smooth structure. Besides coordinate invariance, its key features are scalability, computability, and robustness. We demonstrate that these properties continue to hold in the context of nonperturbative quantum gravity, by evaluating the quantum Ricci curvature numerically in two-dimensional Euclidean quantum gravity, defined in terms of dynamical triangulations. Despite the well-known, highly nonclassical properties of the underlying quantum geometry, its Ricci curvature can be matched well to that of a five-dimensional round sphere.

Selection of peptidoglycan-specific aptamers for bacterial cells identification.

PubMed

Ferreira, Iêda Mendes; de Souza Lacerda, Camila Maria; de Faria, Lígia Santana; Corrêa, Cristiane Rodrigues; de Andrade, Antero Silva Ribeiro

2014-12-01

Peptidoglycan is a highly complex and essential macromolecule of bacterial outer cell wall; it is a heteropolymer made up of linear glycan strands cross-linked by peptides. Peptidoglycan has a particular composition which makes it a possible target for specific bacterial recognition. Aptamers are single-stranded DNA or RNA oligonucleotides that bind to target molecules with high affinity and specificity. Aptamers can be labeled with different radioisotopes and possess several properties that make them suitable for molecular imaging. The purpose of this study was to obtain aptamers for use as radiopharmaceutical in bacterial infection diagnosis. Two aptamers (Antibac1 and Antibac2) against peptidoglycan were selected through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology. The dissociation constant (Kd) for Antibac1 was 0.415 + 0.047 μM and for Antibac2 was 1.261 + 0.280 μM. These aptamers labeled with (32)P showed high affinity for Staphylococcus aureus cells. The binding to S. aureus and Escherichia coli in vitro were significantly higher than for Candida albicans and human fibroblasts, demonstrating their specificity for bacterial cells. These results point Antibac1 and Antibac2 as promising tools for bacterial infections identification.

Physical Sensing of Surface Properties by Microswimmers--Directing Bacterial Motion via Wall Slip.

PubMed

Hu, Jinglei; Wysocki, Adam; Winkler, Roland G; Gompper, Gerhard

2015-05-20

Bacteria such as Escherichia coli swim along circular trajectories adjacent to surfaces. Thereby, the orientation (clockwise, counterclockwise) and the curvature depend on the surface properties. We employ mesoscale hydrodynamic simulations of a mechano-elastic model of E. coli, with a spherocylindrical body propelled by a bundle of rotating helical flagella, to study quantitatively the curvature of the appearing circular trajectories. We demonstrate that the cell is sensitive to nanoscale changes in the surface slip length. The results are employed to propose a novel approach to directing bacterial motion on striped surfaces with different slip lengths, which implies a transformation of the circular motion into a snaking motion along the stripe boundaries. The feasibility of this approach is demonstrated by a simulation of active Brownian rods, which also reveals a dependence of directional motion on the stripe width.

Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope

DOE PAGES

Hasim, Sahar; Allison, David P.; Mendez, Berlin; ...

2018-02-14

The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus-derived bacterial isolates to determine species selectivity.more » Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE) in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin’s mode of action and a better understanding of its selectivity.« less

Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasim, Sahar; Allison, David P.; Mendez, Berlin

The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus-derived bacterial isolates to determine species selectivity.more » Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE) in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin’s mode of action and a better understanding of its selectivity.« less

Sensitive zone parameters and curvature radius evaluation for polymer optical fiber curvature sensors

NASA Astrophysics Data System (ADS)

Leal-Junior, Arnaldo G.; Frizera, Anselmo; José Pontes, Maria

2018-03-01

Polymer optical fibers (POFs) are suitable for applications such as curvature sensors, strain, temperature, liquid level, among others. However, for enhancing sensitivity, many polymer optical fiber curvature sensors based on intensity variation require a lateral section. Lateral section length, depth, and surface roughness have great influence on the sensor sensitivity, hysteresis, and linearity. Moreover, the sensor curvature radius increase the stress on the fiber, which leads on variation of the sensor behavior. This paper presents the analysis relating the curvature radius and lateral section length, depth and surface roughness with the sensor sensitivity, hysteresis and linearity for a POF curvature sensor. Results show a strong correlation between the decision parameters behavior and the performance for sensor applications based on intensity variation. Furthermore, there is a trade-off among the sensitive zone length, depth, surface roughness, and curvature radius with the sensor desired performance parameters, which are minimum hysteresis, maximum sensitivity, and maximum linearity. The optimization of these parameters is applied to obtain a sensor with sensitivity of 20.9 mV/°, linearity of 0.9992 and hysteresis below 1%, which represent a better performance of the sensor when compared with the sensor without the optimization.

Confinement Stabilizes a Bacterial Suspension into a Spiral Vortex

NASA Astrophysics Data System (ADS)

Wioland, Hugo; Woodhouse, Francis G.; Dunkel, Jörn; Kessler, John O.; Goldstein, Raymond E.

2013-06-01

Confining surfaces play crucial roles in dynamics, transport, and order in many physical systems, but their effects on active matter, a broad class of dynamically self-organizing systems, are poorly understood. We investigate here the influence of global confinement and surface curvature on collective motion by studying the flow and orientational order within small droplets of a dense bacterial suspension. The competition between radial confinement, self-propulsion, steric interactions, and hydrodynamics robustly induces an intriguing steady single-vortex state, in which cells align in inward spiraling patterns accompanied by a thin counterrotating boundary layer. A minimal continuum model is shown to be in good agreement with these observations.

Structure of a bacterial cell surface decaheme electron conduit

USDA-ARS?s Scientific Manuscript database

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits...

The role of gravity in leaf blade curvatures

NASA Technical Reports Server (NTRS)

Hayes, A. B.

1984-01-01

In the past year we have gained useful information on several aspects of leaf blade growth. The most important observations are as follows: The C(14)-1AA moves preferentially in a gravipositive dorsiventral direction through the blade. This movement is inhibited by inversion of the blade. The responding cells in leaf blade hyponasty are in the lower epidermis and bundle sheath cells. Two additional responses in the leaf were characterized. In addition to blade curvature, the leaf shows petiole curvature and changes in the liminal angle subtended by the pulvinus. Ethylene production was studied under a number of conditions. The blade, rather than the petiole or pulvinus, is the principal site of auxin-promoted ethylene synthesis. The effects of a variety of agents on the blade, including gibberellic acid, abscisic acid, vanadate, low pH buffers, and blue light were reviewed.

Cosmic curvature tested directly from observations

NASA Astrophysics Data System (ADS)

Denissenya, Mikhail; Linder, Eric V.; Shafieloo, Arman

2018-03-01

Cosmic spatial curvature is a fundamental geometric quantity of the Universe. We investigate a model independent, geometric approach to measure spatial curvature directly from observations, without any derivatives of data. This employs strong lensing time delays and supernova distance measurements to measure the curvature itself, rather than just testing consistency with flatness. We define two curvature estimators, with differing error propagation characteristics, that can crosscheck each other, and also show how they can be used to map the curvature in redshift slices, to test constancy of curvature as required by the Robertson-Walker metric. Simulating realizations of redshift distributions and distance measurements of lenses and sources, we estimate uncertainties on the curvature enabled by next generation measurements. The results indicate that the model independent methods, using only geometry without assuming forms for the energy density constituents, can determine the curvature at the ~6×10‑3 level.

Bacterial cell identification in differential interference contrast microscopy images.

PubMed

Obara, Boguslaw; Roberts, Mark A J; Armitage, Judith P; Grau, Vicente

2013-04-23

Microscopy image segmentation lays the foundation for shape analysis, motion tracking, and classification of biological objects. Despite its importance, automated segmentation remains challenging for several widely used non-fluorescence, interference-based microscopy imaging modalities. For example in differential interference contrast microscopy which plays an important role in modern bacterial cell biology. Therefore, new revolutions in the field require the development of tools, technologies and work-flows to extract and exploit information from interference-based imaging data so as to achieve new fundamental biological insights and understanding. We have developed and evaluated a high-throughput image analysis and processing approach to detect and characterize bacterial cells and chemotaxis proteins. Its performance was evaluated using differential interference contrast and fluorescence microscopy images of Rhodobacter sphaeroides. Results demonstrate that the proposed approach provides a fast and robust method for detection and analysis of spatial relationship between bacterial cells and their chemotaxis proteins.

Comparison of the cytotoxic effect of polystyrene latex nanoparticles on planktonic cells and bacterial biofilms

NASA Astrophysics Data System (ADS)

Nomura, Toshiyuki; Fujisawa, Eri; Itoh, Shikibu; Konishi, Yasuhiro

2016-06-01

The cytotoxic effect of positively charged polystyrene latex nanoparticles (PSL NPs) was compared between planktonic bacterial cells and bacterial biofilms using confocal laser scanning microscopy, atomic force microscopy, and a colony counting method. Pseudomonas fluorescens, which is commonly used in biofilm studies, was employed as the model bacteria. We found that the negatively charged bacterial surface of the planktonic cells was almost completely covered with positively charged PSL NPs, leading to cell death, as indicated by the NP concentration being greater than that required to achieve single layer coverage. In addition, the relationship between surface coverage and cell viability of P. fluorescens cells correlated well with the findings in other bacterial cells ( Escherichia coli and Lactococcus lactis). However, most of the bacterial cells that formed the biofilm were viable despite the positively charged PSL NPs being highly toxic to planktonic bacterial cells. This indicated that bacterial cells embedded in the biofilm were protected by self-produced extracellular polymeric substances (EPS) that provide resistance to antibacterial agents. In conclusion, mature biofilms covered with EPS exhibit resistance to NP toxicity as well as antibacterial agents.

Physical Sensing of Surface Properties by Microswimmers – Directing Bacterial Motion via Wall Slip

PubMed Central

Hu, Jinglei; Wysocki, Adam; Winkler, Roland G.; Gompper, Gerhard

2015-01-01

Bacteria such as Escherichia coli swim along circular trajectories adjacent to surfaces. Thereby, the orientation (clockwise, counterclockwise) and the curvature depend on the surface properties. We employ mesoscale hydrodynamic simulations of a mechano-elastic model of E. coli, with a spherocylindrical body propelled by a bundle of rotating helical flagella, to study quantitatively the curvature of the appearing circular trajectories. We demonstrate that the cell is sensitive to nanoscale changes in the surface slip length. The results are employed to propose a novel approach to directing bacterial motion on striped surfaces with different slip lengths, which implies a transformation of the circular motion into a snaking motion along the stripe boundaries. The feasibility of this approach is demonstrated by a simulation of active Brownian rods, which also reveals a dependence of directional motion on the stripe width. PMID:25993019

Harnessing cell-to-cell variations to probe bacterial structure and biophysics

NASA Astrophysics Data System (ADS)

Cass, Julie A.

Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

Note: An automated image analysis method for high-throughput classification of surface-bound bacterial cell motions.

PubMed

Shen, Simon; Syal, Karan; Tao, Nongjian; Wang, Shaopeng

2015-12-01

We present a Single-Cell Motion Characterization System (SiCMoCS) to automatically extract bacterial cell morphological features from microscope images and use those features to automatically classify cell motion for rod shaped motile bacterial cells. In some imaging based studies, bacteria cells need to be attached to the surface for time-lapse observation of cellular processes such as cell membrane-protein interactions and membrane elasticity. These studies often generate large volumes of images. Extracting accurate bacterial cell morphology features from these images is critical for quantitative assessment. Using SiCMoCS, we demonstrated simultaneous and automated motion tracking and classification of hundreds of individual cells in an image sequence of several hundred frames. This is a significant improvement from traditional manual and semi-automated approaches to segmenting bacterial cells based on empirical thresholds, and a first attempt to automatically classify bacterial motion types for motile rod shaped bacterial cells, which enables rapid and quantitative analysis of various types of bacterial motion.

Different binarization processes validated against manual counts of fluorescent bacterial cells.

PubMed

Tamminga, Gerrit G; Paulitsch-Fuchs, Astrid H; Jansen, Gijsbert J; Euverink, Gert-Jan W

2016-09-01

State of the art software methods (such as fixed value approaches or statistical approaches) to create a binary image of fluorescent bacterial cells are not as accurate and precise as they should be for counting bacteria and measuring their area. To overcome these bottlenecks, we introduce biological significance to obtain a binary image from a greyscale microscopic image. Using our biological significance approach we are able to automatically count about the same number of cells as an individual researcher would do by manual/visual counting. Using the fixed value or statistical approach to obtain a binary image leads to about 20% less cells in automatic counting. In our procedure we included the area measurements of the bacterial cells to determine the right parameters for background subtraction and threshold values. In an iterative process the threshold and background subtraction values were incremented until the number of particles smaller than a typical bacterial cell is less than the number of bacterial cells with a certain area. This research also shows that every image has a specific threshold with respect to the optical system, magnification and staining procedure as well as the exposure time. The biological significance approach shows that automatic counting can be performed with the same accuracy, precision and reproducibility as manual counting. The same approach can be used to count bacterial cells using different optical systems (Leica, Olympus and Navitar), magnification factors (200× and 400×), staining procedures (DNA (Propidium Iodide) and RNA (FISH)) and substrates (polycarbonate filter or glass). Copyright © 2016 Elsevier B.V. All rights reserved.

Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells.

PubMed

Peternel, Spela; Komel, Radovan

2010-09-10

In recent years bacterial inclusion bodies (IBs) were recognised as highly pure deposits of active proteins inside bacterial cells. Such active nanoparticles are very interesting for further downstream protein isolation, as well as for many other applications in nanomedicine, cosmetic, chemical and pharmaceutical industry.To prepare large quantities of a high quality product, the whole bioprocess has to be optimised. This includes not only the cultivation of the bacterial culture, but also the isolation step itself, which can be of critical importance for the production process.To determine the most appropriate method for the isolation of biologically active nanoparticles, three methods for bacterial cell disruption were analyzed. In this study, enzymatic lysis and two mechanical methods, high-pressure homogenization and sonication, were compared.During enzymatic lysis the enzyme lysozyme was found to attach to the surface of IBs, and it could not be removed by simple washing. As this represents an additional impurity in the engineered nanoparticles, we concluded that enzymatic lysis is not the most suitable method for IBs isolation.During sonication proteins are released (lost) from the surface of IBs and thus the surface of IBs appears more porous when compared to the other two methods. We also found that the acoustic output power needed to isolate the IBs from bacterial cells actually damages proteins structures, thereby causing a reduction in biological activity.High-pressure homogenization also caused some damage to IBs, however the protein loss from the IBs was negligible. Furthermore, homogenization had no side-effects on protein biological activity. The study shows that among the three methods tested, homogenization is the most appropriate method for the isolation of active nanoparticles from bacterial cells.

MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis

PubMed Central

Szwedziak, Piotr; Wong, Felix; Schaefer, Kaitlin; Izoré, Thierry; Renner, Lars D; Holmes, Matthew J; Sun, Yingjie; Bisson-Filho, Alexandre W; Walker, Suzanne; Amir, Ariel; Löwe, Jan

2018-01-01

MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape of Bacillus subtilis. MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomes in vitro, orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape. PMID:29469806

Evidence of Cholesterol Accumulated in High Curvature Regions: Implication ot the Curvature Elastic Energy for Lipid Mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang,W.; Yang, L.; Huang, H.

2007-01-01

Recent experiments suggested that cholesterol and other lipid components of high negative spontaneous curvature facilitate membrane fusion. This is taken as evidence supporting the stalk-pore model of membrane fusion in which the lipid bilayers go through intermediate structures of high curvature. How do the high-curvature lipid components lower the free energy of the curved structure? Do the high-curvature lipid components modify the average spontaneous curvature of the relevant monolayer, thereby facilitate its bending, or do the lipid components redistribute in the curved structure so as to lower the free energy? This question is fundamental to the curvature elastic energy formore » lipid mixtures. Here we investigate the lipid distribution in a monolayer of a binary lipid mixture before and after bending, or more precisely in the lamellar, hexagonal, and distorted hexagonal phases. The lipid mixture is composed of 2:1 ratio of brominated di18:0PC and cholesterol. Using a newly developed procedure for the multiwavelength anomalous diffraction method, we are able to isolate the bromine distribution and reconstruct the electron density distribution of the lipid mixture in the three phases. We found that the lipid distribution is homogenous and uniform in the lamellar and hexagonal phases. But in the distorted hexagonal phase, the lipid monolayer has nonuniform curvature, and cholesterol almost entirely concentrates in the high curvature region. This finding demonstrates that the association energies between lipid molecules vary with the curvature of membrane. Thus, lipid components in a mixture may redistribute under conditions of nonuniform curvature, such as in the stalk structure. In such cases, the spontaneous curvature depends on the local lipid composition and the free energy minimum is determined by lipid distribution as well as curvature.« less

From voxel to curvature

NASA Astrophysics Data System (ADS)

Monga, Olivier; Ayache, Nicholas; Sander, Peter T.

1991-09-01

Modern medical image techniques, such as magnetic resonance image (MRI) or x-ray computed tomography provide three dimensional images of internal structures of the body, usually by means of a stack of tomographic images. The first stage in the automatic analysis of such data is 3-D edge detection1,2 which provides points corresponding to the boundaries of the surfaces forming the 3-D structure. The next stage is to characterize the local geometry of these surfaces in order to extract points or lines on which registration and/or tracking procedures can rely.3,4,5,6 This paper presents a pipeline of processes which define a hierarchical description of the second order differential characteristics of the surfaces. The focus is on the theoretical coherence of these levels of representation. Using uncertainty, a link is established between the edge detection and the local surface approximation by addressing the uncertainties inherent to edge detection in 2-D or 3-D images; and how to incorporate these uncertainties into the computation of local geometric models. In particular, calculate the uncertainty of edge location, direction, and magnitude for the 3-D Deriche operator is calculated.1,2 Statistical results are then used as a solid theoretical foundation on which to base subsequent computations, such as the determination of local surface curvature using local geometric models for surface segmentation. From the local fitting, for each edge point the mean and Gaussian curvature, principal curvatures and directions, curvature singularities, lines of curvature singularities, and covariance matrices defining the uncertainties are calculated. Experimental results for real data using two 3-D scanner images of the same organ taken at different positions demonstrate the stability of the mean and Gaussian curvatures. Experimental results for real data showing the determination of local curvature extremes of surfaces extracted from MR images are presented.

The transport along membrane nanotubes driven by the spontaneous curvature of membrane components.

PubMed

Kabaso, Doron; Bobrovska, Nataliya; Góźdź, Wojciech; Gongadze, Ekaterina; Kralj-Iglič, Veronika; Zorec, Robert; Iglič, Aleš

2012-10-01

Intercellular membrane nanotubes (ICNs) serve as a very specific transport system between neighboring cells. The underlying mechanisms responsible for the transport of membrane components and vesicular dilations along the ICNs are not clearly understood. The present study investigated the spatial distribution of anisotropic membrane components of tubular shapes and isotropic membrane components of spherical shapes. Experimental results revealed the preferential distribution of CTB (cholera toxin B)-GM1 complexes mainly on the spherical cell membrane, and cholesterol-sphingomyelin at the membrane leading edge and ICNs. In agreement with previous studies, we here propose that the spatial distribution of CTB-GM1 complexes and cholesterol-sphingomyelin rafts were due to their isotropic and anisotropic shapes, respectively. To elucidate the relationship between a membrane component shape and its spatial distribution, a two-component computational model was constructed. The minimization of the membrane bending (free) energy revealed the enrichment of the anisotropic component along the ICN and the isotropic component in the parent cell membrane, which was due to the curvature mismatch between the ICN curvature and the spontaneous curvature of the isotropic component. The equations of motion, derived from the differentiation of the membrane free energy, revealed a curvature-dependent flux of the isotropic component and a curvature-dependent force exerted on a vesicular dilation along the ICN. Finally, the effects of possible changes in the orientational ordering of the anisotropic component attendant to the transport of the vesicular dilation were discussed with connection to the propagation of electrical and chemical signals. Copyright © 2012 Elsevier B.V. All rights reserved.

Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy†

PubMed Central

Gunsolus, Ian L.; Hu, Dehong; Mihai, Cosmin; Lohse, Samuel E.; Lee, Chang-soo; Torelli, Marco D.; Hamers, Robert J.; Murhpy, Catherine J.; Orr, Galya

2015-01-01

A method to fluorescently stain the surfaces of both Gram-negative and Gram-positive bacterial cells compatible with super-resolution fluorescence microscopy is presented. This method utilizes a commercially-available fluorescent probe to label primary amines at the surface of the cell. We demonstrate eficient staining of two bacterial strains, the Gram-negative Shewanella oneidensis MR-1 and the Gram-positive Bacillus subtilis 168. Using structured illumination microscopy and stochastic optical reconstruction microscopy, which require high quantum yield or specialized dyes, we show that this staining method may be used to resolve the bacterial cell surface with sub-diffraction-limited resolution. We further use this method to identify localization patterns of nanomaterials, specifically cadmium selenide quantum dots, following interaction with bacterial cells. PMID:24816810

Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunsolus, Ian L.; Hu, Dehong; Mihai, Cosmin

A method to fluorescently stain the surfaces of both Gram-negative and Gram-positive bacterial cells compatible with super-resolution fluorescence microscopy is presented. This method utilizes a commercially-available fluorescent probe to label primary amines at the surface of the cell. We demonstrate efficient staining of two bacterial strains, the Gram-negative Shewanella oneidensis MR-1 and the Gram-positive Bacillus subtilis 168. Using structured illumination microscopy and stochastic optical reconstruction microscopy, which require high quantum yield or specialized dyes, we show that this staining method may be used to resolve the bacterial cell surface with sub-diffraction-limited resolution. We further use this method to identify localizationmore » patterns of nanomaterials, specifically cadmium selenide quantum dots, following interaction with bacterial cells.« less

Myeloid-Derived Suppressor Cells in Bacterial Infections

PubMed Central

Ost, Michael; Singh, Anurag; Peschel, Andreas; Mehling, Roman; Rieber, Nikolaus; Hartl, Dominik

2016-01-01

Myeloid-derived suppressor cells (MDSCs) comprise monocytic and granulocytic innate immune cells with the capability of suppressing T- and NK-cell responses. While the role of MDSCs has been studied in depth in malignant diseases, the understanding of their regulation and function in infectious disease conditions has just begun to evolve. Here we summarize and discuss the current view how MDSCs participate in bacterial infections and how this knowledge could be exploited for potential future therapeutics. PMID:27066459

Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells

PubMed Central

2010-01-01

Background In recent years bacterial inclusion bodies (IBs) were recognised as highly pure deposits of active proteins inside bacterial cells. Such active nanoparticles are very interesting for further downstream protein isolation, as well as for many other applications in nanomedicine, cosmetic, chemical and pharmaceutical industry. To prepare large quantities of a high quality product, the whole bioprocess has to be optimised. This includes not only the cultivation of the bacterial culture, but also the isolation step itself, which can be of critical importance for the production process. To determine the most appropriate method for the isolation of biologically active nanoparticles, three methods for bacterial cell disruption were analyzed. Results In this study, enzymatic lysis and two mechanical methods, high-pressure homogenization and sonication, were compared. During enzymatic lysis the enzyme lysozyme was found to attach to the surface of IBs, and it could not be removed by simple washing. As this represents an additional impurity in the engineered nanoparticles, we concluded that enzymatic lysis is not the most suitable method for IBs isolation. During sonication proteins are released (lost) from the surface of IBs and thus the surface of IBs appears more porous when compared to the other two methods. We also found that the acoustic output power needed to isolate the IBs from bacterial cells actually damages proteins structures, thereby causing a reduction in biological activity. High-pressure homogenization also caused some damage to IBs, however the protein loss from the IBs was negligible. Furthermore, homogenization had no side-effects on protein biological activity. Conclusions The study shows that among the three methods tested, homogenization is the most appropriate method for the isolation of active nanoparticles from bacterial cells. PMID:20831775

Electroporation of Functional Bacterial Effectors into Mammalian Cells

DOE PAGES

Sontag, Ryan L.; Mihai, Cosmin; Orr, Galya; ...

2015-01-19

Electroporation was used to insert purified bacterial virulence effector proteins directly into living eukaryotic cells. Protein localization was monitored by confocal immunofluorescence microscopy. This method allows for studies on trafficking, function, and protein-protein interactions using active exogenous proteins, avoiding the need for heterologous expression in eukaryotic cells.

Measuring the Scalar Curvature with Clocks and Photons: Voronoi-Delaunay Lattices in Regge Calculus

NASA Astrophysics Data System (ADS)

Miller, Warner; McDonald, Jonathan

2008-04-01

The Riemann scalar curvature plays a central role in Einstein's geometric theory of gravity. We describe a new geometric construction of this scalar curvature invariant at an event (vertex) in a discrete spacetime geometry. This allows one to constructively measure the scalar curvature using only clocks and photons. Given recent interest in discrete pre-geometric models of quantum gravity, we believe it is ever so important to reconstruct the curvature scalar with respect to a finite number of communicating observers. This derivation makes use of a fundamental lattice cell built from elements inherited from both the original simplicial (Delaunay) spacetime and its circumcentric dual (Voronoi) lattice. The orthogonality properties between these two lattices yield an expression for the vertex-based scalar curvature which is strikingly similar to the corresponding hinge-based expression in Regge Calculus (deficit angle per unit Voronoi dual area). In particular, we show that the scalar curvature is simply a vertex-based weighted average of deficits per weighted average of dual areas.

Do bacterial cell numbers follow a theoretical Poisson distribution? Comparison of experimentally obtained numbers of single cells with random number generation via computer simulation.

PubMed

Koyama, Kento; Hokunan, Hidekazu; Hasegawa, Mayumi; Kawamura, Shuso; Koseki, Shigenobu

2016-12-01

We investigated a bacterial sample preparation procedure for single-cell studies. In the present study, we examined whether single bacterial cells obtained via 10-fold dilution followed a theoretical Poisson distribution. Four serotypes of Salmonella enterica, three serotypes of enterohaemorrhagic Escherichia coli and one serotype of Listeria monocytogenes were used as sample bacteria. An inoculum of each serotype was prepared via a 10-fold dilution series to obtain bacterial cell counts with mean values of one or two. To determine whether the experimentally obtained bacterial cell counts follow a theoretical Poisson distribution, a likelihood ratio test between the experimentally obtained cell counts and Poisson distribution which parameter estimated by maximum likelihood estimation (MLE) was conducted. The bacterial cell counts of each serotype sufficiently followed a Poisson distribution. Furthermore, to examine the validity of the parameters of Poisson distribution from experimentally obtained bacterial cell counts, we compared these with the parameters of a Poisson distribution that were estimated using random number generation via computer simulation. The Poisson distribution parameters experimentally obtained from bacterial cell counts were within the range of the parameters estimated using a computer simulation. These results demonstrate that the bacterial cell counts of each serotype obtained via 10-fold dilution followed a Poisson distribution. The fact that the frequency of bacterial cell counts follows a Poisson distribution at low number would be applied to some single-cell studies with a few bacterial cells. In particular, the procedure presented in this study enables us to develop an inactivation model at the single-cell level that can estimate the variability of survival bacterial numbers during the bacterial death process. Copyright © 2016 Elsevier Ltd. All rights reserved.

x-y curvature wavefront sensor.

PubMed

Cagigal, Manuel P; Valle, Pedro J

2015-04-15

In this Letter, we propose a new curvature wavefront sensor based on the principles of optical differentiation. The theoretically modeled setup consists of a diffractive optical mask placed at the intermediate plane of a classical two-lens coherent optical processor. The resulting image is composed of a number of local derivatives of the entrance pupil function whose proper combination provides the wavefront curvature. In contrast to the common radial curvature sensors, this one is able to provide the x and y wavefront curvature maps simultaneously. The sensor offers other additional advantages like having high spatial resolution, adjustable dynamic range, and not being sensitive to misalignment.

Biomechanics of phalangeal curvature.

PubMed

Richmond, Brian G

2007-12-01

Phalangeal curvature has been widely cited in primate functional morphology and is one of the key traits in the ongoing debate about whether the locomotion of early hominins included a significant degree of arboreality. This study examines the biomechanics of phalangeal curvature using data on hand posture, muscle recruitment, and anatomical moment arms to develop a finite element (FE) model of a siamang manual proximal phalanx during suspensory grasping. Strain patterns from experiments on intact cadaver forelimbs validated the model. The strain distribution in the curved siamang phalanx FE model was compared to that in a mathematically straight rendition in order to test the hypotheses that curvature: 1) reduces strain and 2) results in lower bending strains but relatively higher compression. In the suspensory posture, joint reaction forces load the articular ends of the phalanx in compression and dorsally, while muscle forces acting through the flexor sheath pull the mid-shaft palmarly. These forces compress the phalanx dorsally and tense it palmarly, effectively bending it 'open.' Strains in the curved model were roughly half that of the straight model despite equivalent lengths, areas, mechanical properties, and loading conditions in the two models. The curved model also experienced a higher ratio of compressive to tensile strains. Curvature reduces strains during grasping hand postures because the curved bone is more closely aligned with the joint reaction forces. Therefore, phalangeal curvature reduces the strains associated with arboreal, and especially suspensory, activity involving flexed digits. These results offer a biomechanical explanation for the observed association between phalangeal curvature and arboreality.

Host-induced bacterial cell wall decomposition mediates pattern-triggered immunity in Arabidopsis

PubMed Central

Liu, Xiaokun; Grabherr, Heini M; Willmann, Roland; Kolb, Dagmar; Brunner, Frédéric; Bertsche, Ute; Kühner, Daniel; Franz-Wachtel, Mirita; Amin, Bushra; Felix, Georg; Ongena, Marc; Nürnberger, Thorsten; Gust, Andrea A

2014-01-01

Peptidoglycans (PGNs) are immunogenic bacterial surface patterns that trigger immune activation in metazoans and plants. It is generally unknown how complex bacterial structures such as PGNs are perceived by plant pattern recognition receptors (PRRs) and whether host hydrolytic activities facilitate decomposition of bacterial matrices and generation of soluble PRR ligands. Here we show that Arabidopsis thaliana, upon bacterial infection or exposure to microbial patterns, produces a metazoan lysozyme-like hydrolase (lysozyme 1, LYS1). LYS1 activity releases soluble PGN fragments from insoluble bacterial cell walls and cleavage products are able to trigger responses typically associated with plant immunity. Importantly, LYS1 mutant genotypes exhibit super-susceptibility to bacterial infections similar to that observed on PGN receptor mutants. We propose that plants employ hydrolytic activities for the decomposition of complex bacterial structures, and that soluble pattern generation might aid PRR-mediated immune activation in cell layers adjacent to infection sites. DOI: http://dx.doi.org/10.7554/eLife.01990.001 PMID:24957336

Determining wave direction using curvature parameters.

PubMed

de Queiroz, Eduardo Vitarelli; de Carvalho, João Luiz Baptista

2016-01-01

The curvature of the sea wave was tested as a parameter for estimating wave direction in the search for better results in estimates of wave direction in shallow waters, where waves of different sizes, frequencies and directions intersect and it is difficult to characterize. We used numerical simulations of the sea surface to determine wave direction calculated from the curvature of the waves. Using 1000 numerical simulations, the statistical variability of the wave direction was determined. The results showed good performance by the curvature parameter for estimating wave direction. Accuracy in the estimates was improved by including wave slope parameters in addition to curvature. The results indicate that the curvature is a promising technique to estimate wave directions.•In this study, the accuracy and precision of curvature parameters to measure wave direction are analyzed using a model simulation that generates 1000 wave records with directional resolution.•The model allows the simultaneous simulation of time-series wave properties such as sea surface elevation, slope and curvature and they were used to analyze the variability of estimated directions.•The simultaneous acquisition of slope and curvature parameters can contribute to estimates wave direction, thus increasing accuracy and precision of results.

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

PubMed Central

Ramakrishnan, N.; Sunil Kumar, P. B.; Radhakrishnan, Ravi

2014-01-01

Biological membranes constitute boundaries of cells and cell organelles. These membranes are soft fluid interfaces whose thermodynamic states are dictated by bending moduli, induced curvature fields, and thermal fluctuations. Recently, there has been a flood of experimental evidence highlighting active roles for these structures in many cellular processes ranging from trafficking of cargo to cell motility. It is believed that the local membrane curvature, which is continuously altered due to its interactions with myriad proteins and other macromolecules attached to its surface, holds the key to the emergent functionality in these cellular processes. Mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. Interactions at the molecular scale can be computationally probed by all atom and coarse grained molecular dynamics (MD, CGMD), as well as dissipative particle dynamics (DPD) simulations, which we only describe in passing. We choose to focus on several continuum approaches extending the Canham - Helfrich elastic energy model for membranes to include the effect of curvature-inducing proteins and explore the conformational phase space of such systems. In this

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins.

PubMed

Ramakrishnan, N; Sunil Kumar, P B; Radhakrishnan, Ravi

2014-10-01

Biological membranes constitute boundaries of cells and cell organelles. These membranes are soft fluid interfaces whose thermodynamic states are dictated by bending moduli, induced curvature fields, and thermal fluctuations. Recently, there has been a flood of experimental evidence highlighting active roles for these structures in many cellular processes ranging from trafficking of cargo to cell motility. It is believed that the local membrane curvature, which is continuously altered due to its interactions with myriad proteins and other macromolecules attached to its surface, holds the key to the emergent functionality in these cellular processes. Mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. Interactions at the molecular scale can be computationally probed by all atom and coarse grained molecular dynamics (MD, CGMD), as well as dissipative particle dynamics (DPD) simulations, which we only describe in passing. We choose to focus on several continuum approaches extending the Canham - Helfrich elastic energy model for membranes to include the effect of curvature-inducing proteins and explore the conformational phase space of such systems. In this

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

NASA Astrophysics Data System (ADS)

Ramakrishnan, N.; Sunil Kumar, P. B.; Radhakrishnan, Ravi

2014-10-01

Biological membranes constitute boundaries of cells and cell organelles. These membranes are soft fluid interfaces whose thermodynamic states are dictated by bending moduli, induced curvature fields, and thermal fluctuations. Recently, there has been a flood of experimental evidence highlighting active roles for these structures in many cellular processes ranging from trafficking of cargo to cell motility. It is believed that the local membrane curvature, which is continuously altered due to its interactions with myriad proteins and other macromolecules attached to its surface, holds the key to the emergent functionality in these cellular processes. Mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. Interactions at the molecular scale can be computationally probed by all atom and coarse grained molecular dynamics (MD, CGMD), as well as dissipative particle dynamics (DPD) simulations, which we only describe in passing. We choose to focus on several continuum approaches extending the Canham-Helfrich elastic energy model for membranes to include the effect of curvature-inducing proteins and explore the conformational phase space of such systems. In this description, the

Self-organization and positioning of bacterial protein clusters

NASA Astrophysics Data System (ADS)

Murray, Seán M.; Sourjik, Victor

2017-10-01

Many cellular processes require proteins to be precisely positioned within the cell. In some cases this can be attributed to passive mechanisms such as recruitment by other proteins in the cell or by exploiting the curvature of the membrane. However, in bacteria, active self-positioning is likely to play a role in multiple processes, including the positioning of the future site of cell division and cytoplasmic protein clusters. How can such dynamic clusters be formed and positioned? Here, we present a model for the self-organization and positioning of dynamic protein clusters into regularly repeating patterns based on a phase-locked Turing pattern. A single peak in the concentration is always positioned at the midpoint of the model cell, and two peaks are positioned at the midpoint of each half. Furthermore, domain growth results in peak splitting and pattern doubling. We argue that the model may explain the regular positioning of the highly conserved structural maintenance of chromosomes complexes on the bacterial nucleoid and that it provides an attractive mechanism for the self-positioning of dynamic protein clusters in other systems.

EAU guidelines on penile curvature.

PubMed

Hatzimouratidis, Konstantinos; Eardley, Ian; Giuliano, François; Hatzichristou, Dimitrios; Moncada, Ignacio; Salonia, Andrea; Vardi, Yoram; Wespes, Eric

2012-09-01

Penile curvature can be congenital or acquired. Acquired curvature is secondary due to La Peyronie (Peyronie's) disease. To provide clinical guidelines on the diagnosis and treatment of penile curvature. A systematic literature search on the epidemiology, diagnosis, and treatment of penile curvature was performed. Articles with the highest evidence available were selected and formed the basis for assigning levels of evidence and grades of recommendations. The pathogenesis of congenital penile curvature is unknown. Peyronie's disease is a poorly understood connective tissue disorder most commonly attributed to repetitive microvascular injury or trauma during intercourse. Diagnosis is based on medical and sexual histories, which are sufficient to establish the diagnosis. Physical examination includes assessment of palpable nodules and penile length. Curvature is best documented by a self-photograph or pharmacologically induced erection. The only treatment option for congenital penile curvature is surgery based on plication techniques. Conservative treatment for Peyronie's disease is associated with poor outcomes. Pharmacotherapy includes oral potassium para-aminobenzoate, intralesional treatment with verapamil, clostridial collagenase or interferon, topical verapamil gel, and iontophoresis with verapamil and dexamethasone. They can be efficacious in some patients, but none of these options carry a grade A recommendation. Steroids, vitamin E, and tamoxifen cannot be recommended. Extracorporeal shock wave treatment and penile traction devices may only be used to treat penile pain and reduce penile deformity, respectively. Surgery is indicated when Peyronie's disease is stable for at least 3 mo. Tunical shortening procedures, especially plication techniques, are the first treatment options. Tunical lengthening procedures are preferred in more severe curvatures or in complex deformities. Penile prosthesis implantation is recommended in patients with erectile dysfunction

Curvature bound from gravitational catalysis

NASA Astrophysics Data System (ADS)

Gies, Holger; Martini, Riccardo

2018-04-01

We determine bounds on the curvature of local patches of spacetime from the requirement of intact long-range chiral symmetry. The bounds arise from a scale-dependent analysis of gravitational catalysis and its influence on the effective potential for the chiral order parameter, as induced by fermionic fluctuations on a curved spacetime with local hyperbolic properties. The bound is expressed in terms of the local curvature scalar measured in units of a gauge-invariant coarse-graining scale. We argue that any effective field theory of quantum gravity obeying this curvature bound is safe from chiral symmetry breaking through gravitational catalysis and thus compatible with the simultaneous existence of chiral fermions in the low-energy spectrum. With increasing number of dimensions, the curvature bound in terms of the hyperbolic scale parameter becomes stronger. Applying the curvature bound to the asymptotic safety scenario for quantum gravity in four spacetime dimensions translates into bounds on the matter content of particle physics models.

Comparison Of Pre-Operative Curvature With Postoperative Curvature In Root Canals Treated With K-3 Rotary Systems.

PubMed

Nagi, Sana Ehsen; Khan, Farhan Raza

2017-01-01

With root canal treatment, the organic debris and micro-organisms from pulp space is removed and an ideal canal preparation is achieved that is conducive of hermetic obturation. The purpose of this study was to correlate the pre-operative canal curvature with the postoperative curvature in human extracted teeth prepared with K-3 rotary systems. The root canal preparation was carried out on extracted human molars and premolars using K-3 endodontic rotary files. A pre and post-operative image of the teeth using digital radiograph were taken in order to compare pre and post-operative canal curvature. The images were saved in an images retrieval system (Gendex software, USA). Change in the canal curvature was measured using the software measuring tool (Vixwin software, USA). Student paired t-test and Pearson correlation test was applied at 0.05 level of significance. There is a statistically significant difference between pre-operative and post-operative canal curvature (p-value <0.001) and a strong positive correlation (91% correlation) between pre-operative and post-operative canal curvature in teeth prepared with the K-3 rotary files. A significant difference between pre and post instrumentation curvature was found. Degree of canal curvature was not correlated with time taken for canal preparation.

Curvature capillary migration of microspheres.

PubMed

Sharifi-Mood, Nima; Liu, Iris B; Stebe, Kathleen J

2015-09-14

We address the question: how does capillarity propel microspheres along curvature gradients? For a particle on a fluid interface, there are two conditions that can apply at the three phase contact line: either the contact line adopts an equilibrium contact angle, or it can be pinned by kinetic trapping, e.g. at chemical heterogeneities, asperities, or other pinning sites on the particle surface. We formulate the curvature capillary energy for both scenarios for particles smaller than the capillary length and far from any pinning boundaries. The scale and range of the distortion made by the particle are set by the particle radius; we use singular perturbation methods to find the distortions and to rigorously evaluate the associated capillary energies. For particles with equilibrium contact angles, contrary to the literature, we find that the capillary energy is negligible, with the first contribution bounded to fourth order in the product of the particle radius and the deviatoric curvature of the host interface. For pinned contact lines, we find curvature capillary energies that are finite, with a functional form investigated previously by us for disks and microcylinders on curved interfaces. In experiments, we show microspheres migrate along deterministic trajectories toward regions of maximum deviatoric curvature with curvature capillary energies ranging from 6 × 10(3)-5 × 10(4)kBT. These data agree with the curvature capillary energy for the case of pinned contact lines. The underlying physics of this migration is a coupling of the interface deviatoric curvature with the quadrupolar mode of nanometric disturbances in the interface owing to the particle's contact line undulations. This work is an example of the major implications of nanometric roughness and contact line pinning for colloidal dynamics.

Bacterial effectors target the plant cell nucleus to subvert host transcription.

PubMed

Canonne, Joanne; Rivas, Susana

2012-02-01

In order to promote virulence, Gram-negative bacteria have evolved the ability to inject so-called type III effector proteins into host cells. The plant cell nucleus appears to be a subcellular compartment repeatedly targeted by bacterial effectors. In agreement with this observation, mounting evidence suggests that manipulation of host transcription is a major strategy developed by bacteria to counteract plant defense responses. It has been suggested that bacterial effectors may adopt at least three alternative, although not mutually exclusive, strategies to subvert host transcription. T3Es may (1) act as transcription factors that directly activate transcription in host cells, (2) affect histone packing and chromatin configuration, and/or (3) target host transcription factor activity. Here, we provide an overview on how all these strategies may lead to host transcriptional re-programming and, as a result, to improved bacterial multiplication inside plant cells.

Stimulation of root elongation and curvature by calcium

NASA Technical Reports Server (NTRS)

Takahashi, H.; Scott, T. K.; Suge, H.

1992-01-01

Ca2+ has been proposed to mediate inhibition of root elongation. However, exogenous Ca2+ at 10 or 20 millimolar, applied directly to the root cap, significantly stimulated root elongation in pea (Pisum sativum L.) and corn (Zea mays L.) seedlings. Furthermore, Ca2+ at 1 to 20 millimolar, applied unilaterally to the caps of Alaska pea roots, caused root curvature away from the Ca2+ source, which was caused by an acceleration of elongation growth on the convex side (Ca2+ side) of the roots. Roots of an agravitropic pea mutant, ageotropum, responded to a greater extent. Roots of Merit and Silver Queen corn also responded to Ca2+ in similar ways but required a higher Ca2+ concentration than that of pea roots. Roots of all other cultivars tested (additional four cultivars of pea and one of corn) curved away from the unilateral Ca2+ source as well. The Ca(2+)-stimulated curvature was substantially enhanced by light. A Ca2+ ionophore, A23187, at 20 micromolar or abscisic acid at 0.1 to 100 micromolar partially substituted for the light effect and enhanced the Ca(2+)-stimulated curvature in the dark. Unilateral application of Ca2+ to the elongation zone of intact roots or to the cut end of detipped roots caused either no curvature or very slight curvature toward the Ca2+. Thus, Ca2+ action on root elongation differs depending on its site of application. The stimulatory action of Ca2+ may involve an elevation of cytoplasmic Ca2+ in root cap cells and may partipate in root tropisms.

Surface Curvatures Computation from Equidistance Contours

NASA Astrophysics Data System (ADS)

Tanaka, Hiromi T.; Kling, Olivier; Lee, Daniel T. L.

1990-03-01

The subject of our research is on the 3D shape representation problem for a special class of range image, one where the natural mode of the acquired range data is in the form of equidistance contours, as exemplified by a moire interferometry range system. In this paper we present a novel surface curvature computation scheme that directly computes the surface curvatures (the principal curvatures, Gaussian curvature and mean curvature) from the equidistance contours without any explicit computations or implicit estimates of partial derivatives. We show how the special nature of the equidistance contours, specifically, the dense information of the surface curves in the 2D contour plane, turns into an advantage for the computation of the surface curvatures. The approach is based on using simple geometric construction to obtain the normal sections and the normal curvatures. This method is general and can be extended to any dense range image data. We show in details how this computation is formulated and give an analysis on the error bounds of the computation steps showing that the method is stable. Computation results on real equidistance range contours are also shown.

Stoichiometry of mercury-thiol complexes on bacterial cell envelopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Bhoopesh; Shoenfelt, Elizabeth; Yu, Qiang

We have examined the speciation of Hg(II) complexed with intact cell suspensions (1013 cells L- 1) of Bacillus subtilis, a common gram-positive soil bacterium, Shewanella oneidensis MR-1, a facultative gram-negative aquatic organism, and Geobacter sulfurreducens, a gram-negative anaerobic bacterium capable of Hg-methylation at Hg(II) loadings spanning four orders of magnitude (120 nM to 350 μM) at pH 5.5 (± 0.2). The coordination environments of Hg on bacterial cells were analyzed using synchrotron based X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy at the Hg LIII edge. The abundance of thiols on intact cells wasmore » determined by a fluorescence-spectroscopy based method using a soluble bromobimane, monobromo(trimethylammonio)bimane (qBBr) to block thiol sites, and potentiometric titrations of biomass with and without qBBr treatment. The chemical forms of S on intact bacterial cells were determined using S k-edge XANES spectroscopy.« less

Multi-scale curvature for automated identification of glaciated mountain landscapes

NASA Astrophysics Data System (ADS)

Prasicek, Günther; Otto, Jan-Christoph; Montgomery, David R.; Schrott, Lothar

2014-03-01

Erosion by glacial and fluvial processes shapes mountain landscapes in a long-recognized and characteristic way. Upland valleys incised by fluvial processes typically have a V-shaped cross-section with uniform and moderately steep slopes, whereas glacial valleys tend to have a U-shaped profile with a changing slope gradient. We present a novel regional approach to automatically differentiate between fluvial and glacial mountain landscapes based on the relation of multi-scale curvature and drainage area. Sample catchments are delineated and multiple moving window sizes are used to calculate per-cell curvature over a variety of scales ranging from the vicinity of the flow path at the valley bottom to catchment sections fully including valley sides. Single-scale curvature can take similar values for glaciated and non-glaciated catchments but a comparison of multi-scale curvature leads to different results according to the typical cross-sectional shapes. To adapt these differences for automated classification of mountain landscapes into areas with V- and U-shaped valleys, curvature values are correlated with drainage area and a new and simple morphometric parameter, the Difference of Minimum Curvature (DMC), is developed. At three study sites in the western United States the DMC thresholds determined from catchment analysis are used to automatically identify 5 × 5 km quadrats of glaciated and non-glaciated landscapes and the distinctions are validated by field-based geological and geomorphological maps. Our results demonstrate that DMC is a good predictor of glacial imprint, allowing automated delineation of glacially and fluvially incised mountain landscapes.

Multi-scale curvature for automated identification of glaciated mountain landscapes☆

PubMed Central

Prasicek, Günther; Otto, Jan-Christoph; Montgomery, David R.; Schrott, Lothar

2014-01-01

Erosion by glacial and fluvial processes shapes mountain landscapes in a long-recognized and characteristic way. Upland valleys incised by fluvial processes typically have a V-shaped cross-section with uniform and moderately steep slopes, whereas glacial valleys tend to have a U-shaped profile with a changing slope gradient. We present a novel regional approach to automatically differentiate between fluvial and glacial mountain landscapes based on the relation of multi-scale curvature and drainage area. Sample catchments are delineated and multiple moving window sizes are used to calculate per-cell curvature over a variety of scales ranging from the vicinity of the flow path at the valley bottom to catchment sections fully including valley sides. Single-scale curvature can take similar values for glaciated and non-glaciated catchments but a comparison of multi-scale curvature leads to different results according to the typical cross-sectional shapes. To adapt these differences for automated classification of mountain landscapes into areas with V- and U-shaped valleys, curvature values are correlated with drainage area and a new and simple morphometric parameter, the Difference of Minimum Curvature (DMC), is developed. At three study sites in the western United States the DMC thresholds determined from catchment analysis are used to automatically identify 5 × 5 km quadrats of glaciated and non-glaciated landscapes and the distinctions are validated by field-based geological and geomorphological maps. Our results demonstrate that DMC is a good predictor of glacial imprint, allowing automated delineation of glacially and fluvially incised mountain landscapes. PMID:24748703

Microspectrometric insights on the uptake of antibiotics at the single bacterial cell level

PubMed Central

Cinquin, Bertrand; Maigre, Laure; Pinet, Elizabeth; Chevalier, Jacqueline; Stavenger, Robert A.; Mills, Scott; Réfrégiers, Matthieu; Pagès, Jean-Marie

2015-01-01

Bacterial multidrug resistance is a significant health issue. A key challenge, particularly in Gram-negative antibacterial research, is to better understand membrane permeation of antibiotics in clinically relevant bacterial pathogens. Passing through the membrane barrier to reach the required concentration inside the bacterium is a pivotal step for most antibacterials. Spectrometric methodology has been developed to detect drugs inside bacteria and recent studies have focused on bacterial cell imaging. Ultimately, we seek to use this method to identify pharmacophoric groups which improve penetration, and therefore accumulation, of small-molecule antibiotics inside bacteria. We developed a method to quantify the time scale of antibiotic accumulation in living bacterial cells. Tunable ultraviolet excitation provided by DISCO beamline (synchrotron Soleil) combined with microscopy allows spectroscopic analysis of the antibiotic signal in individual bacterial cells. Robust controls and measurement of the crosstalk between fluorescence channels can provide real time quantification of drug. This technique represents a new method to assay drug translocation inside the cell and therefore incorporate rational drug design to impact antibiotic uptake. PMID:26656111

Curvature Analysis of Cardiac Excitation Wavefronts

DTIC Science & Technology

2013-04-01

required at this level either. To enable this kind of analysis, a type field is added to the polyline data structure, too. The downside of reusing the...GPU-based parallel methods. The wave curvature and the refractory period of the cardiac cells influence the motion of cardiac waves. The role of...propagation speed, the action potential duration, and the refractory period is studied. In the recent work of [26], multiple spirals and their

Multi-scale curvature for automated identification of glaciated mountain landscapes

NASA Astrophysics Data System (ADS)

Prasicek, Günther; Otto, Jan-Christoph; Montgomery, David; Schrott, Lothar

2014-05-01

Automated morphometric interpretation of digital terrain data based on impartial rule sets holds substantial promise for large dataset processing and objective landscape classification. However, the geomorphological realm presents tremendous complexity in the translation of qualitative descriptions into geomorphometric semantics. Here, the simple, conventional distinction of V-shaped fluvial and U-shaped glacial valleys is analyzed quantitatively using the relation of multi-scale curvature and drainage area. Glacial and fluvial erosion shapes mountain landscapes in a long-recognized and characteristic way. Valleys incised by fluvial processes typically have V-shaped cross-sections with uniform and moderately steep slopes, whereas glacial valleys tend to have U-shaped profiles and topographic gradients steepening with distance from valley floor. On a DEM, thalweg cells are determined by a drainage area cutoff and multiple moving window sizes are used to derive per-cell curvature over a variety of scales ranging from the vicinity of the flow path at the valley bottom to catchment sections fully including valley sides. The relation of the curvatures calculated for the user-defined minimum scale and the automatically detected maximum scale is presented as a novel morphometric variable termed Difference of Minimum Curvature (DMC). DMC thresholds determined from typical glacial and fluvial sample catchments are employed to identify quadrats of glaciated and non-glaciated mountain landscapes and the distinctions are validated by field-based geological and geomorphological maps. A first test of the novel algorithm at three study sites in the western United States and a subsequent application to Europe and western Asia demonstrate the transferability of the approach.

Total Mean Curvature, Scalar Curvature, and a Variational Analog of Brown-York Mass

NASA Astrophysics Data System (ADS)

Mantoulidis, Christos; Miao, Pengzi

2017-06-01

We study the supremum of the total mean curvature on the boundary of compact, mean-convex 3-manifolds with nonnegative scalar curvature, and a prescribed boundary metric. We establish an additivity property for this supremum and exhibit rigidity for maximizers assuming the supremum is attained. When the boundary consists of 2-spheres, we demonstrate that the finiteness of the supremum follows from the previous work of Shi-Tam and Wang-Yau on the quasi-local mass problem in general relativity. In turn, we define a variational analog of Brown-York quasi-local mass without assuming that the boundary 2-sphere has positive Gauss curvature.

Genetic reprogramming of host cells by bacterial pathogens.

PubMed

Tran Van Nhieu, Guy; Arbibe, Laurence

2009-10-29

During the course of infection, pathogens often induce changes in gene expression in host cells and these changes can be long lasting and global or transient and of limited amplitude. Defining how, when, and why bacterial pathogens reprogram host cells represents an exciting challenge that opens up the opportunity to grasp the essence of pathogenesis and its molecular details.

Spline-Based Smoothing of Airfoil Curvatures

NASA Technical Reports Server (NTRS)

Li, W.; Krist, S.

2008-01-01

Constrained fitting for airfoil curvature smoothing (CFACS) is a splinebased method of interpolating airfoil surface coordinates (and, concomitantly, airfoil thicknesses) between specified discrete design points so as to obtain smoothing of surface-curvature profiles in addition to basic smoothing of surfaces. CFACS was developed in recognition of the fact that the performance of a transonic airfoil is directly related to both the curvature profile and the smoothness of the airfoil surface. Older methods of interpolation of airfoil surfaces involve various compromises between smoothing of surfaces and exact fitting of surfaces to specified discrete design points. While some of the older methods take curvature profiles into account, they nevertheless sometimes yield unfavorable results, including curvature oscillations near end points and substantial deviations from desired leading-edge shapes. In CFACS as in most of the older methods, one seeks a compromise between smoothing and exact fitting. Unlike in the older methods, the airfoil surface is modified as little as possible from its original specified form and, instead, is smoothed in such a way that the curvature profile becomes a smooth fit of the curvature profile of the original airfoil specification. CFACS involves a combination of rigorous mathematical modeling and knowledge-based heuristics. Rigorous mathematical formulation provides assurance of removal of undesirable curvature oscillations with minimum modification of the airfoil geometry. Knowledge-based heuristics bridge the gap between theory and designers best practices. In CFACS, one of the measures of the deviation of an airfoil surface from smoothness is the sum of squares of the jumps in the third derivatives of a cubicspline interpolation of the airfoil data. This measure is incorporated into a formulation for minimizing an overall deviation- from-smoothness measure of the airfoil data within a specified fitting error tolerance. CFACS has been

Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation.

PubMed

Boix-Amorós, Alba; Collado, Maria C; Mira, Alex

2016-01-01

Human breast milk is considered the optimal nutrition for infants, providing essential nutrients and a broad range of bioactive compounds, as well as its own microbiota. However, the interaction among those components and the biological role of milk microorganisms is still uncovered. Thus, our aim was to identify the relationships between milk microbiota composition, bacterial load, macronutrients, and human cells during lactation. Bacterial load was estimated in milk samples from a total of 21 healthy mothers through lactation time by bacteria-specific qPCR targeted to the single-copy gene fusA. Milk microbiome composition and diversity was estimated by 16S-pyrosequencing and the structure of these bacteria in the fluid was studied by flow cytometry, qPCR, and microscopy. Fat, protein, lactose, and dry extract of milk as well as the number of somatic cells were also analyzed. We observed that milk bacterial communities were generally complex, and showed individual-specific profiles. Milk microbiota was dominated by Staphylococcus, Pseudomonas, Streptococcus, and Acinetobacter. Staphylococcus aureus was not detected in any of these samples from healthy mothers. There was high variability in composition and number of bacteria per milliliter among mothers and in some cases even within mothers at different time points. The median bacterial load was 10(6) bacterial cells/ml through time, higher than those numbers reported by 16S gene PCR and culture methods. Furthermore, milk bacteria were present in a free-living, "planktonic" state, but also in equal proportion associated to human immune cells. There was no correlation between bacterial load and the amount of immune cells in milk, strengthening the idea that milk bacteria are not sensed as an infection by the immune system.

Bacterial cell wall composition and the influence of antibiotics by cell-wall and whole-cell NMR

PubMed Central

Romaniuk, Joseph A. H.; Cegelski, Lynette

2015-01-01

The ability to characterize bacterial cell-wall composition and structure is crucial to understanding the function of the bacterial cell wall, determining drug modes of action and developing new-generation therapeutics. Solid-state NMR has emerged as a powerful tool to quantify chemical composition and to map cell-wall architecture in bacteria and plants, even in the context of unperturbed intact whole cells. In this review, we discuss solid-state NMR approaches to define peptidoglycan composition and to characterize the modes of action of old and new antibiotics, focusing on examples in Staphylococcus aureus. We provide perspectives regarding the selected NMR strategies as we describe the exciting and still-developing cell-wall and whole-cell NMR toolkit. We also discuss specific discoveries regarding the modes of action of vancomycin analogues, including oritavancin, and briefly address the reconsideration of the killing action of β-lactam antibiotics. In such chemical genetics approaches, there is still much to be learned from perturbations enacted by cell-wall assembly inhibitors, and solid-state NMR approaches are poised to address questions of cell-wall composition and assembly in S. aureus and other organisms. PMID:26370936

Lipid membrane-mediated attraction between curvature inducing objects

NASA Astrophysics Data System (ADS)

van der Wel, Casper; Vahid, Afshin; Šarić, Anđela; Idema, Timon; Heinrich, Doris; Kraft, Daniela J.

2016-09-01

The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membrane curvature energy. Here, we present a combined experimental and numerical study in which we quantify these interactions directly for the first time. In our experimental model system we control the deformation of a lipid membrane by adhering colloidal particles. Using confocal microscopy, we establish that these membrane deformations cause an attractive interaction force leading to reversible binding. The attraction extends over 2.5 times the particle diameter and has a strength of three times the thermal energy (-3.3 kBT). Coarse-grained Monte-Carlo simulations of the system are in excellent agreement with the experimental results and prove that the measured interaction is independent of length scale. Our combined experimental and numerical results reveal membrane curvature as a common physical origin for interactions between any membrane-deforming objects, from nanometre-sized proteins to micrometre-sized particles.

Membrane tension controls the assembly of curvature-generating proteins

PubMed Central

Simunovic, Mijo; Voth, Gregory A.

2015-01-01

Proteins containing a Bin/Amphiphysin/Rvs (BAR) domain regulate membrane curvature in the cell. Recent simulations have revealed that BAR proteins assemble into linear aggregates, strongly affecting membrane curvature and its in-plane stress profile. Here, we explore the opposite question: do mechanical properties of the membrane impact protein association? By using coarse-grained molecular dynamics simulations, we show that increased surface tension significantly impacts the dynamics of protein assembly. While tensionless membranes promote a rapid formation of long-living linear aggregates of N-BAR proteins, increase in tension alters the geometry of protein association. At high tension, protein interactions are strongly inhibited. Increasing surface density of proteins leads to a wider range of protein association geometries, promoting the formation of meshes, which can be broken apart with membrane tension. Our work indicates that surface tension may play a key role in recruiting proteins to membrane-remodelling sites in the cell. PMID:26008710

Compound curvature laser window development

NASA Technical Reports Server (NTRS)

Verhoff, Vincent G.

1993-01-01

The NASA Lewis Research Center has developed and implemented a unique process for forming flawless compound curvature laser windows. These windows represent a major part of specialized, nonintrusive laser data acquisition systems used in a variety of compressor and turbine research test facilities. This report summarizes the main aspects of compound curvature laser window development. It is an overview of the methodology and the peculiarities associated with the formulation of these windows. Included in this discussion is new information regarding procedures for compound curvature laser window development.

Current-controlled curvature of coated micromirrors

NASA Astrophysics Data System (ADS)

Liu, Wei; Talghader, Joseph J.

2003-06-01

Precise control of micromirror curvature is critical in many optical microsystems. Micromirrors with current-controlled curvature are demonstrated. The working principle is that resistive heating changes the temperature of the micromirrors and thermal expansion induces a controlled curvature whose magnitude is determined by coating design. For example, for wide focal-length tuning, the radius of curvature of a gold-coated mirror was tuned from 2.5 to 8.2 mm over a current-induced temperature range from 22° to 72 °C. For fine focal-length tuning, the radius of curvature of a dielectric-coated (SiO2/Y2O3 λ/4 pairs) mirror was tuned from -0.68 to -0.64 mm over a current-induced temperature range from 22 to 84 °C. These results should be readily extendable to mirror flattening or real-time adaptive shape control.

Disinfection byproduct formation from chlorination of pure bacterial cells and pipeline biofilms.

PubMed

Wang, Jun-Jian; Liu, Xin; Ng, Tsz Wai; Xiao, Jie-Wen; Chow, Alex T; Wong, Po Keung

2013-05-15

Disinfection byproduct (DBP) formation is commonly attributed to the reaction between natural organic matters and disinfectants, yet few have considered the contribution from disinfecting bacterial materials - the essential process of water disinfection. Here, we explored the DBP formation from chlorination and chloramination of Escherichia coli and found that most selected DBPs were detectable, including trihalomethanes, haloacetonitriles, chloral hydrate, chloropicrin, and 1,1,1-trichloro-2-propanone. A positive correlation (P = 0.08-0.09) between DBP formation and the log reduction of E. coli implied that breaking down of bacterial cells released precursors for DBP formation. As Pseudomonas aeruginosa is a dominant bacterial species in pipeline biofilms, the DBP formation potentials (DBPFPs) from its planktonic cells and biofilms were characterized. Planktonic cells formed 7-11 times greater trihalomethanes per carbon of those from biofilms but significantly lower (P < 0.05) chloral hydrate, highlighting the bacterial phenotype's impact on the bacteria-derived DBPFP. Pipe material appeared to affect the DBPFP of bacteria, with 4-28% lower bromine incorporation factor for biofilms on polyvinyl chloride compared to that on galvanized zinc. This study revealed both the in situ disinfection of bacterial planktonic cells in source water and ex situ reaction between biofilms and residual chlorine in pipeline networks as hitherto unknown DBP sources in drinking water. Copyright © 2013 Elsevier Ltd. All rights reserved.

Spontaneous-curvature theory of clathrin-coated membranes.

PubMed Central

Mashl, R J; Bruinsma, R F

1998-01-01

Clathrin-coated membranes are precursors to coated vesicles in the receptor-mediated endocytic pathway. In this paper we present a physical model for the first steps of the transformation of a clathrin-coated membrane into a coated vesicle. The theory is based on in vitro cytoplasmic acidification experiments of Heuser (J. Cell Biol. 108:401-411) that suggest the transformation proceeds by changes in the chemical environment of the clathrin lattice, wherein the chemical environment determines the amount of intrinsic, or spontaneous, curvature of the network. We show that a necessary step of the transformation, formation of free pentagons in the clathrin network, can proceed via dislocation unbinding, driven by changes in the spontaneous curvature. Dislocation unbinding is shown to favor formation of coated vesicles that are quite small compared to those predicted by the current continuum theories, which do not include the topology of the clathrin lattice. PMID:9635740

Curvature induced by amyloplast magnetophoresis in protonemata of the moss Ceratodon purpureus

NASA Technical Reports Server (NTRS)

Kuznetsov, O. A.; Schwuchow, J.; Sack, F. D.; Hasenstein, K. H.

1999-01-01

After gravistimulation of Ceratodon purpureus (Hedw.) Brid. protonemata in the dark, amyloplast sedimentation was followed by upward curvature in the wild-type (WT) and downward curvature in the wwr mutant (wrong way response). We used ponderomotive forces induced by high-gradient magnetic fields (HGMF) to simulate the effect of gravity and displace the presumptive statoliths. The field was applied by placing protonemata either between two permanent magnets at the edge of the gap, close to the edge of a magnetized ferromagnetic wedge, or close to a small (<1 mm) permanent magnet. Continuous application of an HGMF in all three configurations resulted in plastid displacement and induced curvature in tip cells of WT and wwr protonemata. WT cells curved toward the HGMF, and wwr cells curved away from the HGMF, comparable to gravitropism. Plastids isolated from protonemal cultures had densities ranging from 1.24 to 1.38 g cm-3. Plastid density was similar for both genotypes, but the mutant contained larger plastids than the WT. The size difference might explain the stronger response of the wwr protonemata to the HGMF. Our data support the plastid-based theory of gravitropic sensing and suggest that HGMF-induced ponderomotive forces can substitute for gravity.

Sigma models with negative curvature

DOE PAGES

Alonso, Rodrigo; Jenkins, Elizabeth E.; Manohar, Aneesh V.

2016-03-16

Here, we construct Higgs Effective Field Theory (HEFT) based on the scalar manifold Hn, which is a hyperbolic space of constant negative curvature. The Lagrangian has a non-compact O(n, 1) global symmetry group, but it gives a unitary theory as long as only a compact subgroup of the global symmetry is gauged. Whether the HEFT manifold has positive or negative curvature can be tested by measuring the S-parameter, and the cross sections for longitudinal gauge boson and Higgs boson scattering, since the curvature (including its sign) determines deviations from Standard Model values.

Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation

PubMed Central

Boix-Amorós, Alba; Collado, Maria C.; Mira, Alex

2016-01-01

Human breast milk is considered the optimal nutrition for infants, providing essential nutrients and a broad range of bioactive compounds, as well as its own microbiota. However, the interaction among those components and the biological role of milk microorganisms is still uncovered. Thus, our aim was to identify the relationships between milk microbiota composition, bacterial load, macronutrients, and human cells during lactation. Bacterial load was estimated in milk samples from a total of 21 healthy mothers through lactation time by bacteria-specific qPCR targeted to the single-copy gene fusA. Milk microbiome composition and diversity was estimated by 16S-pyrosequencing and the structure of these bacteria in the fluid was studied by flow cytometry, qPCR, and microscopy. Fat, protein, lactose, and dry extract of milk as well as the number of somatic cells were also analyzed. We observed that milk bacterial communities were generally complex, and showed individual-specific profiles. Milk microbiota was dominated by Staphylococcus, Pseudomonas, Streptococcus, and Acinetobacter. Staphylococcus aureus was not detected in any of these samples from healthy mothers. There was high variability in composition and number of bacteria per milliliter among mothers and in some cases even within mothers at different time points. The median bacterial load was 106 bacterial cells/ml through time, higher than those numbers reported by 16S gene PCR and culture methods. Furthermore, milk bacteria were present in a free-living, “planktonic” state, but also in equal proportion associated to human immune cells. There was no correlation between bacterial load and the amount of immune cells in milk, strengthening the idea that milk bacteria are not sensed as an infection by the immune system. PMID:27148183

Bacterial Cell Enlargement Requires Control of Cell Wall Stiffness Mediated by Peptidoglycan Hydrolases.

PubMed

Wheeler, Richard; Turner, Robert D; Bailey, Richard G; Salamaga, Bartłomiej; Mesnage, Stéphane; Mohamad, Sharifah A S; Hayhurst, Emma J; Horsburgh, Malcolm; Hobbs, Jamie K; Foster, Simon J

2015-07-28

Most bacterial cells are enclosed in a single macromolecule of the cell wall polymer, peptidoglycan, which is required for shape determination and maintenance of viability, while peptidoglycan biosynthesis is an important antibiotic target. It is hypothesized that cellular enlargement requires regional expansion of the cell wall through coordinated insertion and hydrolysis of peptidoglycan. Here, a group of (apparent glucosaminidase) peptidoglycan hydrolases are identified that are together required for cell enlargement and correct cellular morphology of Staphylococcus aureus, demonstrating the overall importance of this enzyme activity. These are Atl, SagA, ScaH, and SagB. The major advance here is the explanation of the observed morphological defects in terms of the mechanical and biochemical properties of peptidoglycan. It was shown that cells lacking groups of these hydrolases have increased surface stiffness and, in the absence of SagB, substantially increased glycan chain length. This indicates that, beyond their established roles (for example in cell separation), some hydrolases enable cellular enlargement by making peptidoglycan easier to stretch, providing the first direct evidence demonstrating that cellular enlargement occurs via modulation of the mechanical properties of peptidoglycan. Understanding bacterial growth and division is a fundamental problem, and knowledge in this area underlies the treatment of many infectious diseases. Almost all bacteria are surrounded by a macromolecule of peptidoglycan that encloses the cell and maintains shape, and bacterial cells must increase the size of this molecule in order to enlarge themselves. This requires not only the insertion of new peptidoglycan monomers, a process targeted by antibiotics, including penicillin, but also breakage of existing bonds, a potentially hazardous activity for the cell. Using Staphylococcus aureus, we have identified a set of enzymes that are critical for cellular enlargement. We

Mirror with thermally controlled radius of curvature

DOEpatents

Neil, George R.; Shinn, Michelle D.

2010-06-22

A radius of curvature controlled mirror for controlling precisely the focal point of a laser beam or other light beam. The radius of curvature controlled mirror provides nearly spherical distortion of the mirror in response to differential expansion between the front and rear surfaces of the mirror. The radius of curvature controlled mirror compensates for changes in other optical components due to heating or other physical changes. The radius of curvature controlled mirror includes an arrangement for adjusting the temperature of the front surface and separately adjusting the temperature of the rear surface to control the radius of curvature. The temperature adjustment arrangements can include cooling channels within the mirror body or convection of a gas upon the surface of the mirror. A control system controls the differential expansion between the front and rear surfaces to achieve the desired radius of curvature.

Bacterial Cell Growth Inhibitors Targeting Undecaprenyl Diphosphate Synthase and Undecaprenyl Diphosphate Phosphatase.

PubMed

Wang, Yang; Desai, Janish; Zhang, Yonghui; Malwal, Satish R; Shin, Christopher J; Feng, Xinxin; Sun, Hong; Liu, Guizhi; Guo, Rey-Ting; Oldfield, Eric

2016-10-19

We synthesized a series of benzoic acids and phenylphosphonic acids and investigated their effects on the growth of Staphylococcus aureus and Bacillus subtilis. One of the most active compounds, 5-fluoro-2-(3-(octyloxy)benzamido)benzoic acid (7, ED 50 ∼0.15 μg mL -1 ) acted synergistically with seven antibiotics known to target bacterial cell-wall biosynthesis (a fractional inhibitory concentration index (FICI) of ∼0.35, on average) but had indifferent effects in combinations with six non-cell-wall biosynthesis inhibitors (average FICI∼1.45). The most active compounds were found to inhibit two enzymes involved in isoprenoid/bacterial cell-wall biosynthesis: undecaprenyl diphosphate synthase (UPPS) and undecaprenyl diphosphate phosphatase (UPPP), but not farnesyl diphosphate synthase, and there were good correlations between bacterial cell growth inhibition, UPPS inhibition, and UPPP inhibition. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sonication reduces the attachment of Salmonella Typhimurium ATCC 14028 cells to bacterial cellulose-based plant cell wall models and cut plant material.

PubMed

Tan, Michelle S F; Rahman, Sadequr; Dykes, Gary A

2017-04-01

This study investigated the removal of bacterial surface structures, particularly flagella, using sonication, and examined its effect on the attachment of Salmonella Typhimurium ATCC 14028 cells to plant cell walls. S. Typhimurium ATCC 14028 cells were subjected to sonication at 20 kHz to remove surface structures without affecting cell viability. Effective removal of flagella was determined by staining flagella of sonicated cells with Ryu's stain and enumerating the flagella remaining by direct microscopic counting. The attachment of sonicated S. Typhimurium cells to bacterial cellulose-based plant cell wall models and cut plant material (potato, apple, lettuce) was then evaluated. Varying concentrations of pectin and/or xyloglucan were used to produce a range of bacterial cellulose-based plant cell wall models. As compared to the non-sonicated controls, sonicated S. Typhimurium cells attached in significantly lower numbers (between 0.5 and 1.0 log CFU/cm 2 ) to all surfaces except to the bacterial cellulose-only composite without pectin and xyloglucan. Since attachment of S. Typhimurium to the bacterial cellulose-only composite was not affected by sonication, this suggests that bacterial surface structures, particularly flagella, could have specific interactions with pectin and xyloglucan. This study indicates that sonication may have potential applications for reducing Salmonella attachment during the processing of fresh produce. Copyright © 2016 Elsevier Ltd. All rights reserved.

Incorporating contact angles in the surface tension force with the ACES interface curvature scheme

NASA Astrophysics Data System (ADS)

Owkes, Mark

2017-11-01

In simulations of gas-liquid flows interacting with solid boundaries, the contact line dynamics effect the interface motion and flow field through the surface tension force. The surface tension force is directly proportional to the interface curvature and the problem of accurately imposing a contact angle must be incorporated into the interface curvature calculation. Many commonly used algorithms to compute interface curvatures (e.g., height function method) require extrapolating the interface, with defined contact angle, into the solid to allow for the calculation of a curvature near a wall. Extrapolating can be an ill-posed problem, especially in three-dimensions or when multiple contact lines are near each other. We have developed an accurate methodology to compute interface curvatures that allows for contact angles to be easily incorporated while avoiding extrapolation and the associated challenges. The method, known as Adjustable Curvature Evaluation Scale (ACES), leverages a least squares fit of a polynomial to points computed on the volume-of-fluid (VOF) representation of the gas-liquid interface. The method is tested by simulating canonical test cases and then applied to simulate the injection and motion of water droplets in a channel (relevant to PEM fuel cells).

Streamline-curvature effect in three-dimensional boundary layers

NASA Technical Reports Server (NTRS)

Reed, Helen L.; Lin, Ray-Sing; Petraglia, Media M.

1992-01-01

The effect of including wall and streamline curvature terms in swept-wing boundary-layer stability calculations is studied. The linear disturbance equations are cast on a fixed, body-intrinsic, curvilinear coordinate system. Those nonparallel terms which contribute mainly to the streamline-curvature effect are retained in this formulation and approximated by their local finite-difference values. Convex-wall curvature has a stabilizing effect, while streamline curvature is destabilizing if the curvature exceeds a critical value.

The concept of geodesic curvature applied to optical surfaces.

PubMed

Barbero, Sergio

2015-07-01

To propose geodesic curvature as a metric to characterise how an optical surface locally differs from axial symmetry. To derive equations to evaluate geodesic curvatures of arbitrary surfaces expressed in polar coordinates. The concept of geodesic curvature is explained in detail as compared to other curvature-based metrics. Starting with the formula representing a surface as function of polar coordinates, an equation for the geodesic curvature is obtained depending only on first and second radial and first order angular derivatives of the surface function. The potential of the geodesic curvature is illustrated using different surface tests. Geodesic curvature reveals local axial asymmetries more sharply than other types of curvatures such as normal curvatures. Geodesic curvature maps could be used to characterise local axial asymmetries for relevant optometry applications such as corneal topography anomalies (keratoconus) or ophthalmic lens metrology. © 2015 The Authors Ophthalmic & Physiological Optics © 2015 The College of Optometrists.

The disruptive effect of lysozyme on the bacterial cell wall explored by an in-silico structural outlook.

PubMed

Primo, Emiliano D; Otero, Lisandro H; Ruiz, Francisco; Klinke, Sebastián; Giordano, Walter

2018-01-01

The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine. Such exercises typically do not include structural data. We describe here a sequence of computer tasks designed to illustrate and reinforce both physiological and structural concepts involved in lysozyme effects on the bacterial cell-wall structure. This lab class usually lasts 3.5 hours. First, the instructor presents introductory concepts of the bacterial cell wall and the effect of lysozyme on its structure. Then, students are taught to use computer modeling to visualize the three-dimensional structure of a lysozyme in complex with bacterial cell-wall fragments. Finally, the lysozyme inhibitory effect on a bacterial culture is optionally proposed as a simple microbiological assay. The computer lab exercises described here give students a realistic understanding of the disruptive effect of lysozymes on the bacterial cell wall, a crucial component in bacterial survival. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):83-90, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

Bacterial safety of cell-based therapeutic preparations, focusing on haematopoietic progenitor cells.

PubMed

Störmer, M; Wood, E M; Schurig, U; Karo, O; Spreitzer, I; McDonald, C P; Montag, T

2014-05-01

Bacterial safety of cellular preparations, especially haematopoietic progenitor cells (HPCs), as well as advanced therapy medicinal products (ATMPs) derived from stem cells of various origins, present a challenge for physicians, manufacturers and regulators. The article describes the background and practical issues in this area and illustrates why sterility of these products cannot currently be guaranteed. Advantages and limitations of approaches both for classical sterility testing and for microbiological control using automated culture systems are discussed. The review considers novel approaches for growth-based rapid microbiological control with high sensitivity and faster availability of results, as well as new methods for rapid bacterial detection in cellular preparations enabling meaningful information about product contamination within one to two hours. Generally, however, these direct rapid methods are less sensitive and have greater sampling error compared with the growth-based methods. Opportunities for pyrogen testing of cell therapeutics are also discussed. There is an urgent need for development of novel principles and methods applicable to bacterial safety of cellular therapeutics. We also need a major shift in approach from the traditional view of sterility evaluation (identify anything and everything) to a new thinking about how to find what is clinically relevant within the time frame available for the special clinical circumstances in which these products are used. The review concludes with recommendations for optimization of microbiological control of cellular preparations, focusing on HPCs. © 2013 International Society of Blood Transfusion.

Mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights.

PubMed

Jiang, Chao; Caccamo, Paul D; Brun, Yves V

2015-04-01

How Darwin's "endless forms most beautiful" have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating "evolutionary thinking" into bacterial cell biology in the genomic era. © 2015 WILEY Periodicals, Inc.

Biophysical model of bacterial cell interactions with nanopatterned cicada wing surfaces.

PubMed

Pogodin, Sergey; Hasan, Jafar; Baulin, Vladimir A; Webb, Hayden K; Truong, Vi Khanh; Phong Nguyen, The Hong; Boshkovikj, Veselin; Fluke, Christopher J; Watson, Gregory S; Watson, Jolanta A; Crawford, Russell J; Ivanova, Elena P

2013-02-19

The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of biomaterials that can kill bacteria on contact based solely on their physical surface structure. The wings provide a model for the development of novel functional surfaces that possess an increased resistance to bacterial contamination and infection. We propose a biophysical model of the interactions between bacterial cells and cicada wing surface structures, and show that mechanical properties, in particular cell rigidity, are key factors in determining bacterial resistance/sensitivity to the bactericidal nature of the wing surface. We confirmed this experimentally by decreasing the rigidity of surface-resistant strains through microwave irradiation of the cells, which renders them susceptible to the wing effects. Our findings demonstrate the potential benefits of incorporating cicada wing nanopatterns into the design of antibacterial nanomaterials. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The actin homologue MreB organizes the bacterial cell membrane

PubMed Central

Strahl, Henrik; Bürmann, Frank; Hamoen, Leendert W.

2014-01-01

The eukaryotic cortical actin cytoskeleton creates specific lipid domains, including lipid rafts, which determine the distribution of many membrane proteins. Here we show that the bacterial actin homologue MreB displays a comparable activity. MreB forms membrane-associated filaments that coordinate bacterial cell wall synthesis. We noticed that the MreB cytoskeleton influences fluorescent staining of the cytoplasmic membrane. Detailed analyses combining an array of mutants, using specific lipid staining techniques and spectroscopic methods, revealed that MreB filaments create specific membrane regions with increased fluidity (RIFs). Interference with these fluid lipid domains (RIFs) perturbs overall lipid homeostasis and affects membrane protein localization. The influence of MreB on membrane organization and fluidity may explain why the active movement of MreB stimulates membrane protein diffusion. These novel MreB activities add additional complexity to bacterial cell membrane organization and have implications for many membrane-associated processes. PMID:24603761

The actin homologue MreB organizes the bacterial cell membrane.

PubMed

Strahl, Henrik; Bürmann, Frank; Hamoen, Leendert W

2014-03-07

The eukaryotic cortical actin cytoskeleton creates specific lipid domains, including lipid rafts, which determine the distribution of many membrane proteins. Here we show that the bacterial actin homologue MreB displays a comparable activity. MreB forms membrane-associated filaments that coordinate bacterial cell wall synthesis. We noticed that the MreB cytoskeleton influences fluorescent staining of the cytoplasmic membrane. Detailed analyses combining an array of mutants, using specific lipid staining techniques and spectroscopic methods, revealed that MreB filaments create specific membrane regions with increased fluidity (RIFs). Interference with these fluid lipid domains (RIFs) perturbs overall lipid homeostasis and affects membrane protein localization. The influence of MreB on membrane organization and fluidity may explain why the active movement of MreB stimulates membrane protein diffusion. These novel MreB activities add additional complexity to bacterial cell membrane organization and have implications for many membrane-associated processes.

Process to Selectively Distinguish Viable from Non-Viable Bacterial Cells

NASA Technical Reports Server (NTRS)

LaDuc, Myron T.; Bernardini, Jame N.; Stam, Christina N.

2010-01-01

The combination of ethidium monoazide (EMA) and post-fragmentation, randomly primed DNA amplification technologies will enhance the analytical capability to discern viable from non-viable bacterial cells in spacecraft-related samples. Intercalating agents have been widely used since the inception of molecular biology to stain and visualize nucleic acids. Only recently, intercalating agents such as EMA have been exploited to selectively distinguish viable from dead bacterial cells. Intercalating dyes can only penetrate the membranes of dead cells. Once through the membrane and actually inside the cell, they intercalate DNA and, upon photolysis with visible light, produce stable DNA monoadducts. Once the DNA is crosslinked, it becomes insoluble and unable to be fragmented for post-fragmentation, randomly primed DNA library formation. Viable organisms DNA remains unaffected by the intercalating agents, allowing for amplification via post-fragmentation, randomly primed technologies. This results in the ability to carry out downstream nucleic acid-based analyses on viable microbes to the exclusion of all non-viable cells.

The lemon illusion: seeing curvature where there is none.

PubMed

Strother, Lars; Killebrew, Kyle W; Caplovitz, Gideon P

2015-01-01

Curvature is a highly informative visual cue for shape perception and object recognition. We introduce a novel illusion-the Lemon Illusion-in which subtle illusory curvature is perceived along contour regions that are devoid of physical curvature. We offer several perceptual demonstrations and observations that lead us to conclude that the Lemon Illusion is an instance of a more general illusory curvature phenomenon, one in which the presence of contour curvature discontinuities lead to the erroneous extension of perceived curvature. We propose that this erroneous extension of perceived curvature results from the interaction of neural mechanisms that operate on spatially local contour curvature signals with higher-tier mechanisms that serve to establish more global representations of object shape. Our observations suggest that the Lemon Illusion stems from discontinuous curvature transitions between rectilinear and curved contour segments. However, the presence of curvature discontinuities is not sufficient to produce the Lemon Illusion, and the minimal conditions necessary to elicit this subtle and insidious illusion are difficult to pin down.

[Influence of human gastrointestinal tract bacterial pathogens on host cell apoptosis].

PubMed

Wronowska, Weronika; Godlewska, Renata; Jagusztyn-Krynicka, Elzbieta Katarzyna

2005-01-01

Several pathogenic bacteria are able to trigger apoptosis in the host cell, but the mechanisms by which it occurs differ, and the resulting pathology can take different courses. Induction and/or blockage of programmed cell death upon infection is a result of complex interaction of bacterial proteins with cellular proteins involved in signal transduction and apoptosis. In this review we focus on pro/anti-apoptotic activities exhibited by two enteric pathogens Salmonella enterica, Yersinia spp. and gastric pathogen Helicobacter pylori. We present current knowledge on how interaction between mammalian and bacterial cell relates to the molecular pathways of apoptosis, and what is the role of apoptosis in pathogenesis.

The impact of metabolic state on Cd adsorption onto bacterial cells

USGS Publications Warehouse

Johnson, K.J.; Ams, D.A.; Wedel, A.N.; Szymanowski, J.E.S.; Weber, D.L.; Schneegurt, M.A.; Fein, J.B.

2007-01-01

This study examines the effect of bacterial metabolism on the adsorption of Cd onto Gram-positive and Gram-negative bacterial cells. Metabolically active Gram-positive cells adsorbed significantly less Cd than non-metabolizing cells. Gram-negative cells, however, showed no systematic difference in Cd adsorption between metabolizing and non-metabolizing cells. The effect of metabolism on Cd adsorption to Gram-positive cells was likely due to an influx of protons in and around the cell wall from the metabolic proton motive force, promoting competition between Cd and protons for adsorption sites on the cell wall. The relative lack of a metabolic effect on Cd adsorption onto Gram-negative compared to Gram-positive cells suggests that Cd binding in Gram-negative cells is focused in a region of the cell wall that is not reached, or is unaffected by this proton flux. Thermodynamic modeling was used to estimate that proton pumping causes the pH in the cell wall of metabolizing Gram-positive bacteria to decrease from the bulk solution value of 7.0 to approximately 5.7. ?? 2007 The Authors.

Pattern Transitions in Bacterial Oscillating System under Nanofluidic Confinement

NASA Astrophysics Data System (ADS)

Shen, Jie-Pan; Chou, Chia-Fu

2011-03-01

Successful binary fission in E. coli relies on remarkable oscillatory behavior of the MinCDE protein system to determine the exact division site. The most favorable models to explain this fascinating spatiotemporal regulation on dynamic MinDE pattern formation in cells are based on reaction-diffusion scenario. Although not fully understood, geometric factors caused by bacterial morphology play a crucial role in MinDE dynamics. In the present study, bacteria were cultured, confined and reshaped in various micro/nanofluidic devices, to mimic either curvature changes of cell peripherals. Fluorescence imaging was utilized to detail the mode transitions in multiple MinDE patterns. The understanding of the physics in multiple pattern formations is further complemented via in silico modeling. The study synergizes the join merits of in vivo, in vitro and in silico approaches, to grasp the insight of stochastic dynamics inherited from the noisy mesoscopic biophysics. We acknowledge support from the Foresight Project, Academia Sinica.

Chemically synthesized silver nanoparticles as cell lysis agent for bacterial genomic DNA isolation

NASA Astrophysics Data System (ADS)

Goswami, Gunajit; Boruah, Himangshu; Gautom, Trishnamoni; Jyoti Hazarika, Dibya; Barooah, Madhumita; Boro, Robin Chandra

2017-12-01

Silver nanoparticles (AgNPs) have seen a recent spurt of use in varied fields of science. In this paper, we showed a novel application of AgNP as a promising microbial cell-lysis agent for genomic DNA isolation. We utilized chemically synthesized AgNPs for lysing bacterial cells to isolate their genomic DNA. The AgNPs efficiently lysed bacterial cells to yield good quality DNA that could be subsequently used for several molecular biology works.

PGE2 suppresses intestinal T cell function in thermal injury: a cause of enhanced bacterial translocation.

PubMed

Choudhry, M A; Fazal, N; Namak, S Y; Haque, F; Ravindranath, T; Sayeed, M M

2001-09-01

Increased gut bacterial translocation in burn and trauma patients has been demonstrated in a number of previous studies, however, the mechanism for such an increased gut bacterial translocation in injured patients remains poorly understood. Utilizing a rat model of burn injury, in the present study we examined the role of intestinal immune defense by analyzing the T cell functions. We investigated if intestinal T cells dysfunction contributes to bacterial translocation after burn injury. Also our study determined if burn-mediated alterations in intestinal T cell functions are related to enhanced release of PGE2. Finally, we examined whether or not burn-related alterations in intestinal T cell function are due to inappropriate activation of signaling molecule P59fyn, which is required for T cell activation and proliferation. The results presented here showed an increase in gut bacterial accumulation in mesenteric lymph nodes after thermal injury. This was accompanied by a decrease in the intestinal T cell proliferative responses. Furthermore, the treatments of burn-injured animals with PGE2 synthesis blocker (indomethacin or NS398) prevented both the decrease in intestinal T cell proliferation and enhanced bacterial translocation. Finally, our data suggested that the inhibition of intestinal T cell proliferation could result via PGE2-mediated down-regulation of the T cell activation-signaling molecule P59fyn. These findings support a role of T cell-mediated immune defense against bacterial translocation in burn injury.

Interplay between membrane curvature and protein conformational equilibrium investigated by solid-state NMR.

PubMed

Liao, Shu Y; Lee, Myungwoon; Hong, Mei

2018-03-01

Many membrane proteins sense and induce membrane curvature for function, but structural information about how proteins modulate their structures to cause membrane curvature is sparse. We review our recent solid-state NMR studies of two virus membrane proteins whose conformational equilibrium is tightly coupled to membrane curvature. The influenza M2 proton channel has a drug-binding site in the transmembrane (TM) pore. Previous chemical shift data indicated that this pore-binding site is lost in an M2 construct that contains the TM domain and a curvature-inducing amphipathic helix. We have now obtained chemical shift perturbation, protein-drug proximity, and drug orientation data that indicate that the pore-binding site is restored when the full cytoplasmic domain is present. This finding indicates that the curvature-inducing amphipathic helix distorts the TM structure to interfere with drug binding, while the cytoplasmic tail attenuates this effect. In the second example, we review our studies of a parainfluenza virus fusion protein that merges the cell membrane and the virus envelope during virus entry. Chemical shifts of two hydrophobic domains of the protein indicate that both domains have membrane-dependent backbone conformations, with the β-strand structure dominating in negative-curvature phosphatidylethanolamine (PE) membranes. 31 P NMR spectra and 1 H- 31 P correlation spectra indicate that the β-strand-rich conformation induces saddle-splay curvature to PE membranes and dehydrates them, thus stabilizing the hemifusion state. These results highlight the indispensable role of solid-state NMR to simultaneously determine membrane protein structures and characterize the membrane curvature in which these protein structures exist. Copyright © 2018 Elsevier Inc. All rights reserved.

Spatial Patterning of Newly-Inserted Material during Bacterial Cell Growth

NASA Astrophysics Data System (ADS)

Ursell, Tristan

2012-02-01

In the life cycle of a bacterium, rudimentary microscopy demonstrates that cell growth and elongation are essential characteristics of cellular reproduction. The peptidoglycan cell wall is the main load-bearing structure that determines both cell shape and overall size. However, simple imaging of cellular growth gives no indication of the spatial patterning nor mechanism by which material is being incorporated into the pre-existing cell wall. We employ a combination of high-resolution pulse-chase fluorescence microscopy, 3D computational microscopy, and detailed mechanistic simulations to explore how spatial patterning results in uniform growth and maintenance of cell shape. We show that growth is happening in discrete bursts randomly distributed over the cell surface, with a well-defined mean size and average rate. We further use these techniques to explore the effects of division and cell wall disrupting antibiotics, like cephalexin and A22, respectively, on the patterning of cell wall growth in E. coli. Finally, we explore the spatial correlation between presence of the bacterial actin-like cytoskeletal protein, MreB, and local cell wall growth. Together these techniques form a powerful method for exploring the detailed dynamics and involvement of antibiotics and cell wall-associated proteins in bacterial cell growth.[4pt] In collaboration with Kerwyn Huang, Stanford University.

Conventional CD4+ T cells present bacterial antigens to induce cytotoxic and memory CD8+ T cell responses.

PubMed

Cruz-Adalia, Aránzazu; Ramirez-Santiago, Guillermo; Osuna-Pérez, Jesús; Torres-Torresano, Mónica; Zorita, Virgina; Martínez-Riaño, Ana; Boccasavia, Viola; Borroto, Aldo; Martínez Del Hoyo, Gloria; González-Granado, José María; Alarcón, Balbino; Sánchez-Madrid, Francisco; Veiga, Esteban

2017-11-17

Bacterial phagocytosis and antigen cross-presentation to activate CD8 + T cells are principal functions of professional antigen presenting cells. However, conventional CD4 + T cells also capture and kill bacteria from infected dendritic cells in a process termed transphagocytosis (also known as transinfection). Here, we show that transphagocytic T cells present bacterial antigens to naive CD8 + T cells, which proliferate and become cytotoxic in response. CD4 + T-cell-mediated antigen presentation also occurs in vivo in the course of infection, and induces the generation of central memory CD8 + T cells with low PD-1 expression. Moreover, transphagocytic CD4 + T cells induce protective anti-tumour immune responses by priming CD8 + T cells, highlighting the potential of CD4 + T cells as a tool for cancer immunotherapy.

The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis

PubMed Central

Zhou, Zhou; Munteanu, Emilia Laura; He, Jun; Ursell, Tristan; Bathe, Mark; Huang, Kerwyn Casey; Chang, Fred

2015-01-01

The functions of the actin-myosin–based contractile ring in cytokinesis remain to be elucidated. Recent findings show that in the fission yeast Schizosaccharomyces pombe, cleavage furrow ingression is driven by polymerization of cell wall fibers outside the plasma membrane, not by the contractile ring. Here we show that one function of the ring is to spatially coordinate septum cell wall assembly. We develop an improved method for live-cell imaging of the division apparatus by orienting the rod-shaped cells vertically using microfabricated wells. We observe that the septum hole and ring are circular and centered in wild-type cells and that in the absence of a functional ring, the septum continues to ingress but in a disorganized and asymmetric manner. By manipulating the cleavage furrow into different shapes, we show that the ring promotes local septum growth in a curvature-dependent manner, allowing even a misshapen septum to grow into a more regular shape. This curvature-dependent growth suggests a model in which contractile forces of the ring shape the septum cell wall by stimulating the cell wall machinery in a mechanosensitive manner. Mechanical regulation of the cell wall assembly may have general relevance to the morphogenesis of walled cells. PMID:25355954

On turbulent flows dominated by curvature effects

NASA Technical Reports Server (NTRS)

Cheng, G. C.; Farokhi, S.

1992-01-01

A technique for improving the numerical predictions of turbulent flows with the effect of streamline curvature is developed. Separated flows and the flow in a curved duct are examples of flowfields where streamline curvature plays a dominant role. New algebraic formulations for the eddy viscosity incorporating the k-epsilon turbulence model are proposed to account for various effects of streamline curvature. The loci of flow reversal of the separated flows over various backward-facing steps are employed to test the capability of the proposed turbulence model in capturing the effect of local curvature.

Osmotic Pressure, Bacterial Cell Walls, and Penicillin: A Demonstration.

ERIC Educational Resources Information Center

Lennox, John E.

1984-01-01

An easily constructed apparatus that models the effect of penicillin on the structure of bacterial cells is described. Background information and procedures for using the apparatus during a classroom demonstration are included. (JN)

Curvature Induced by Amyloplast Magnetophoresis in Protonemata of the Moss Ceratodon purpureus1

PubMed Central

Kuznetsov, Oleg A.; Schwuchow, Jochen; Sack, Fred D.; Hasenstein, Karl H.

1999-01-01

After gravistimulation of Ceratodon purpureus (Hedw.) Brid. protonemata in the dark, amyloplast sedimentation was followed by upward curvature in the wild-type (WT) and downward curvature in the wwr mutant (wrong way response). We used ponderomotive forces induced by high-gradient magnetic fields (HGMF) to simulate the effect of gravity and displace the presumptive statoliths. The field was applied by placing protonemata either between two permanent magnets at the edge of the gap, close to the edge of a magnetized ferromagnetic wedge, or close to a small (<1 mm) permanent magnet. Continuous application of an HGMF in all three configurations resulted in plastid displacement and induced curvature in tip cells of WT and wwr protonemata. WT cells curved toward the HGMF, and wwr cells curved away from the HGMF, comparable to gravitropism. Plastids isolated from protonemal cultures had densities ranging from 1.24 to 1.38 g cm−3. Plastid density was similar for both genotypes, but the mutant contained larger plastids than the WT. The size difference might explain the stronger response of the wwr protonemata to the HGMF. Our data support the plastid-based theory of gravitropic sensing and suggest that HGMF-induced ponderomotive forces can substitute for gravity. PMID:9952461

Control of actin polymerization via the coincidence of phosphoinositides and high membrane curvature

PubMed Central

Daste, Frederic; Walrant, Astrid; Mason, Julia; Lee, Ji-Eun; Brook, Daniel; Mettlen, Marcel; Larsson, Elin; Lee, Steven F.; Lundmark, Richard

2017-01-01

The conditional use of actin during clathrin-mediated endocytosis in mammalian cells suggests that the cell controls whether and how actin is used. Using a combination of biochemical reconstitution and mammalian cell culture, we elucidate a mechanism by which the coincidence of PI(4,5)P2 and PI(3)P in a curved vesicle triggers actin polymerization. At clathrin-coated pits, PI(3)P is produced by the INPP4A hydrolysis of PI(3,4)P2, and this is necessary for actin-driven endocytosis. Both Cdc42⋅guanosine triphosphate and SNX9 activate N-WASP–WIP- and Arp2/3-mediated actin nucleation. Membrane curvature, PI(4,5)P2, and PI(3)P signals are needed for SNX9 assembly via its PX–BAR domain, whereas signaling through Cdc42 is activated by PI(4,5)P2 alone. INPP4A activity is stimulated by high membrane curvature and synergizes with SNX9 BAR domain binding in a process we call curvature cascade amplification. We show that the SNX9-driven actin comets that arise on human disease–associated oculocerebrorenal syndrome of Lowe (OCRL) deficiencies are reduced by inhibiting PI(3)P production, suggesting PI(3)P kinase inhibitors as a therapeutic strategy in Lowe syndrome. PMID:28923975

On the Weyl curvature hypothesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoica, Ovidiu Cristinel, E-mail: holotronix@gmail.com

2013-11-15

The Weyl curvature hypothesis of Penrose attempts to explain the high homogeneity and isotropy, and the very low entropy of the early universe, by conjecturing the vanishing of the Weyl tensor at the Big-Bang singularity. In previous papers it has been proposed an equivalent form of Einstein’s equation, which extends it and remains valid at an important class of singularities (including in particular the Schwarzschild, FLRW, and isotropic singularities). Here it is shown that if the Big-Bang singularity is from this class, it also satisfies the Weyl curvature hypothesis. As an application, we study a very general example of cosmologicalmore » models, which generalizes the FLRW model by dropping the isotropy and homogeneity constraints. This model also generalizes isotropic singularities, and a class of singularities occurring in Bianchi cosmologies. We show that the Big-Bang singularity of this model is of the type under consideration, and satisfies therefore the Weyl curvature hypothesis. -- Highlights: •The singularities we introduce are described by finite geometric/physical objects. •Our singularities have smooth Riemann and Weyl curvatures. •We show they satisfy Penrose’s Weyl curvature hypothesis (Weyl=0 at singularities). •Examples: FLRW, isotropic singularities, an extension of Schwarzschild’s metric. •Example: a large class of singularities which may be anisotropic and inhomogeneous.« less

Integration of length and curvature in haptic perception.

PubMed

Panday, Virjanand; Tiest, Wouter M Bergmann; Kappers, Astrid M L

2014-01-24

We investigated if and how length and curvature information are integrated when an object is explored in one hand. Subjects were asked to explore four types of objects between thumb and index finger. Objects differed in either length, curvature, both length and curvature correlated as in a circle, or anti-correlated. We found that when both length and curvature are present, performance is significantly better than when only one of the two cues is available. Therefore, we conclude that there is integration of length and curvature. Moreover, if the two cues are correlated in a circular cross-section instead of in an anti-correlated way, performance is better than predicted by a combination of two independent cues. We conclude that integration of curvature and length is highly efficient when the cues in the object are combined as in a circle, which is the most common combination of curvature and length in daily life.

Nonadditive Compositional Curvature Energetics of Lipid Bilayers

NASA Astrophysics Data System (ADS)

Sodt, A. J.; Venable, R. M.; Lyman, E.; Pastor, R. W.

2016-09-01

The unique properties of the individual lipids that compose biological membranes together determine the energetics of the surface. The energetics of the surface, in turn, govern the formation of membrane structures and membrane reshaping processes, and thus they will underlie cellular-scale models of viral fusion, vesicle-dependent transport, and lateral organization relevant to signaling. The spontaneous curvature, to the best of our knowledge, is always assumed to be additive. We describe observations from simulations of unexpected nonadditive compositional curvature energetics of two lipids essential to the plasma membrane: sphingomyelin and cholesterol. A model is developed that connects molecular interactions to curvature stress, and which explains the role of local composition. Cholesterol is shown to lower the number of effective Kuhn segments of saturated acyl chains, reducing lateral pressure below the neutral surface of bending and favoring positive curvature. The effect is not observed for unsaturated (flexible) acyl chains. Likewise, hydrogen bonding between sphingomyelin lipids leads to positive curvature, but only at sufficient concentration, below which the lipid prefers negative curvature.

In vitro bacterial cytotoxicity of CNTs: reactive oxygen species mediate cell damage edges over direct physical puncturing.

PubMed

Rajavel, Krishnamoorthy; Gomathi, Rajkumar; Manian, Sellamuthu; Rajendra Kumar, Ramasamy Thangavelu

2014-01-21

Understanding the bacterial cytotoxicity of CNTs is important for a wide variety of applications in the biomedical, environmental, and health sectors. A majority of the earlier reports attributed the bactericidal cytotoxicity of CNTs to bacterial cell membrane damage by direct physical puncturing. Our results reveal that bacterial cell death via bacterial cell membrane damage is induced by reactive oxygen species (ROS) produced from CNTs and is not due to direct physical puncturing by CNTs. To understand the actual mechanism of bacterial killing, we elucidated the bacterial cytotoxicity of SWCNTs and MWCNTs against Gram-negative human pathogenic bacterial species Escherichia coli, Shigella sonnei, Klebsiella pneumoniae, and Pseudomonas aeruginosa and its amelioration upon functionalizing the CNTs with antioxidant tannic acid (TA). Interestingly, the bacterial cells treated with CNTs exhibited severe cell damage under laboratory (ambient) and sunlight irradiation conditions. However, CNTs showed no cytotoxicity to the bacterial cells when incubated in the dark. The quantitative assessments carried out by us made it explicit that CNTs are effective generators of ROS such as (1)O2, O2(•-), and (•)OH in an aqueous medium under both ambient and sunlight-irradiated conditions. Both naked and TA-functionalized CNTs showed negligible ROS production in the dark. Furthermore, strong correlations were obtained between ROS produced by CNTs and the bacterial cell mortality (with the correlation coefficient varying between 0.7618 and 0.9891) for all four tested pathogens. The absence of bactericidal cytotoxicity in both naked and functionalized CNTs in the dark reveals that the presence of ROS is the major factor responsible for the bactericidal action compared to direct physical puncturing. This understanding of the bactericidal activity of the irradiated CNTs, mediated through the generation of ROS, could be interesting for novel applications such as regulated ROS delivery

Autologous tumor cells engineered to express bacterial antigens.

PubMed

Ramiya, Vijayakumar K; Jerald, Maya M; Lawman, Patricia D; Lawman, Michael J P

2014-01-01

Cancer immunotherapies are emerging as promising treatment modalities in the management of the disease. As a result, cancer vaccines are considered to be immensely crucial in preventing recurrence, a well-known nemesis in cancer patients because they have the potential to activate memory antitumor immunity. Due to poor antigenicity and self-tolerance, most tumor antigens require interventional vaccine therapies to provide an adequate "danger" signal to the immune system in order to activate a robust, clinically meaningful antitumor immunity. It has been postulated that this requirement may be achieved by providing bacterial and/or viral immunogens to prime this type of immune response. Briefly, we provide here a method of transfecting whole tumor cells with plasmid DNA encoding an immunogenic bacterial protein such as Emm55, which was derived from Streptococcus pyogenes (S. pyogenes). Subsequent inactivation of the transfected cells by irradiation (100 Gray) prevents replication. This type of whole-cell vaccine, e.g., ImmuneFx™, has demonstrated activity in a murine neuroblastoma model, in canine lymphoma patients with naturally occurring disease, and in many cancer types in companion animals. The protocols described in this chapter provide the necessary materials and methodologies to manufacture such a vaccine.

Active matter and Curvature

NASA Astrophysics Data System (ADS)

Sknepnek, Rastko

Coupling between active motion and curvature is an integral part of many fundamental biological processes such as gastrulation and intestinal crypt fission. However, to date very little is known about how curvature affects active motion. Here we use a particle-based model to study the interplay between activity and curvature in dense systems. Using detailed numerical simulations and simple physical arguments, we show that the presence of curvature results in a number of steady-state configurations that have no analogues in flat geometries. These states are particularly interesting if topological constraints require the presence of defects in the ground states in the passive limit. We focus on polar and nematic active systems confined to move on the surface of a sphere and show that activity can lead to the formation of moving band and multidefect states. We extend our model to self-propelled filaments confined to a plane or the surface of a sphere. We show that the activity leads to an effective softening of the polymer chain. As a result of this softening, with the increase in activity, the system transitions between a jammed polymer-melt state, an active turbulent state characterised by a proliferation of hair-pin defects, to a region dominated by phase segregation (MIPS), finally followed by the onset of a homogenous state characterised by spiral motion of individual polymers. UK EPSRC EP/M009599/1.

Rumen Bacterial Degradation of Forage Cell Walls Investigated by Electron Microscopy

PubMed Central

Akin, Danny E.; Amos, Henry E.

1975-01-01

The association of rumen bacteria with specific leaf tissues of the forage grass Kentucky-31 tall fescue (Festuca arundinacea Schreb.) during in vitro degradation was investigated by transmission and scanning electron microscopy. Examination of degraded leaf cross-sections revealed differential rates of tissue degradation in that the cell walls of the mesophyll and pholem were degraded prior to those of the outer bundle sheath and epidermis. Rumen bacteria appeared to degrade the mesophyll, in some cases, and phloem without prior attachment to the plant cell walls. The degradation of bundle sheath and epidermal cell walls appeared to be preceded by attachment of bacteria to the plant cell wall. Ultrastructural features apparently involved in the adhesion of large cocci to plant cells were observed by transmission and scanning electron microscopy. The physical association between plant and rumen bacterial cells during degradation apparently varies with tissue types. Bacterial attachment, by extracellular features in some microorganisms, is required prior to degradation of the more resistant tissues. Images PMID:16350017

Modeling the Mechanics of Cell Division: Influence of Spontaneous Membrane Curvature, Surface Tension, and Osmotic Pressure

PubMed Central

Beltrán-Heredia, Elena; Almendro-Vedia, Víctor G.; Monroy, Francisco; Cao, Francisco J.

2017-01-01

Many cell division processes have been conserved throughout evolution and are being revealed by studies on model organisms such as bacteria, yeasts, and protozoa. Cellular membrane constriction is one of these processes, observed almost universally during cell division. It happens similarly in all organisms through a mechanical pathway synchronized with the sequence of cytokinetic events in the cell interior. Arguably, such a mechanical process is mastered by the coordinated action of a constriction machinery fueled by biochemical energy in conjunction with the passive mechanics of the cellular membrane. Independently of the details of the constriction engine, the membrane component responds against deformation by minimizing the elastic energy at every constriction state following a pathway still unknown. In this paper, we address a theoretical study of the mechanics of membrane constriction in a simplified model that describes a homogeneous membrane vesicle in the regime where mechanical work due to osmotic pressure, surface tension, and bending energy are comparable. We develop a general method to find approximate analytical expressions for the main descriptors of a symmetrically constricted vesicle. Analytical solutions are obtained by combining a perturbative expansion for small deformations with a variational approach that was previously demonstrated valid at the reference state of an initially spherical vesicle at isotonic conditions. The analytic approximate results are compared with the exact solution obtained from numerical computations, getting a good agreement for all the computed quantities (energy, area, volume, constriction force). We analyze the effects of the spontaneous curvature, the surface tension and the osmotic pressure in these quantities, focusing especially on the constriction force. The more favorable conditions for vesicle constriction are determined, obtaining that smaller constriction forces are required for positive spontaneous

Interaction of Defensins with Model Cell Membranes

NASA Astrophysics Data System (ADS)

Sanders, Lori K.; Schmidt, Nathan W.; Yang, Lihua; Mishra, Abhijit; Gordon, Vernita D.; Selsted, Michael E.; Wong, Gerard C. L.

2009-03-01

Antimicrobial peptides (AMPs) comprise a key component of innate immunity for a wide range of multicellular organisms. For many AMPs, activity comes from their ability to selectively disrupt and lyse bacterial cell membranes. There are a number of proposed models for this action, but the detailed molecular mechanism of selective membrane permeation remains unclear. Theta defensins are circularized peptides with a high degree of selectivity. We investigate the interaction of model bacterial and eukaryotic cell membranes with theta defensins RTD-1, BTD-7, and compare them to protegrin PG-1, a prototypical AMP, using synchrotron small angle x-ray scattering (SAXS). The relationship between membrane composition and peptide induced changes in membrane curvature and topology is examined. By comparing the membrane phase behavior induced by these different peptides we will discuss the importance of amino acid composition and placement on membrane rearrangement.

Amplified effect of Brownian motion in bacterial near-surface swimming

PubMed Central

Li, Guanglai; Tam, Lick-Kong; Tang, Jay X.

2008-01-01

Brownian motion influences bacterial swimming by randomizing displacement and direction. Here, we report that the influence of Brownian motion is amplified when it is coupled to hydrodynamic interaction. We examine swimming trajectories of the singly flagellated bacterium Caulobacter crescentus near a glass surface with total internal reflection fluorescence microscopy and observe large fluctuations over time in the distance of the cell from the solid surface caused by Brownian motion. The observation is compared with computer simulation based on analysis of relevant physical factors, including electrostatics, van der Waals force, hydrodynamics, and Brownian motion. The simulation reproduces the experimental findings and reveals contribution from fluctuations of the cell orientation beyond the resolution of present observation. Coupled with hydrodynamic interaction between the bacterium and the boundary surface, the fluctuations in distance and orientation subsequently lead to variation of the swimming speed and local radius of curvature of swimming trajectory. These results shed light on the fundamental roles of Brownian motion in microbial motility, nutrient uptake, and adhesion. PMID:19015518

Differentiation of epithelial cells to M cells in response to bacterial colonization on the follicle-associated epithelium of Peyer's patch in rat small intestine.

PubMed

Chin, Keigi; Onishi, Sachiko; Yuji, Midori; Inamoto, Tetsurou; Qi, Wang-Mei; Warita, Katsuhiko; Yokoyama, Toshifumi; Hoshi, Nobuhiko; Kitagawa, Hiroshi

2006-10-01

To clarify the relationship between M cells and intestinal microflora, histoplanimetrical investigation into the bacterial colonization and the differentiation to M cells was carried out in rat Peyer's patch under physiological conditions. The follicle-associated epithelium (FAE), except for the narrow area of apical region, was closely covered with both neighboring intestinal villi and a thick mucous layer, the latter of which also filled the intervillous spaces as well as the space between the FAE and the neighboring intestinal villi. Indigenous bacteria adhered almost constantly to the narrow areas of apical regions of both intestinal villi and the FAE. Bacterial colonies were occasionally located on the basal to middle region of FAE, where M cells also appeared, forming large pockets. When bacterial colonies were located on the basal to middle region of FAE, bacteria with the same morphological characteristics also proliferated in the intervillous spaces neighboring the Peyer's patch. In cases with no bacterial colonies on the basal to middle region of FAE, however, M cells were rare in the FAE. Histoplanimetrical analysis showed the similar distribution pattern of bacterial colonies on the FAE and M cells in the FAE. M cells ultrastructurally engulfed indigenous bacteria, which were then transported to the pockets. These results suggest that indigenous bacterial colonization on the FAE stimulates the differentiation of M cells in the FAE under physiological conditions. The uptake of bacteria by M cells might contribute the regulation of the development of indigenous bacterial colonies in the small intestine.

Eddy-Current Measurement Of Turning Or Curvature

NASA Technical Reports Server (NTRS)

Chern, Engmin J.

1993-01-01

Rotatable conductive plate covers sensing coil to varying degree. Curvature of pipe at remote or otherwise inaccessible location inside pipe measured using relatively simple angular-displacement eddy-current probe. Crawler and sensor assemblies move along inside of pipe on wheels. Conductive plate pivots to follow curvature of pipe, partly covering one of eddy-current coils to degree depending on local curvature on pipe.

New Application of Hyperspectral Imaging for Bacterial Cell Classification

USDA-ARS?s Scientific Manuscript database

Hyperspectral microscopy has shown potential as a method for rapid detection of foodborne pathogenic bacteria with spectral characteristics from bacterial cells. Hyperspectral microscope images (HMIs) are collected from broiler chicken isolates of Salmonella serotypes Enteritidis, Typhimurium, Infa...

Curvature-processing network in macaque visual cortex

PubMed Central

Yue, Xiaomin; Pourladian, Irene S.; Tootell, Roger B. H.; Ungerleider, Leslie G.

2014-01-01

Our visual environment abounds with curved features. Thus, the goal of understanding visual processing should include the processing of curved features. Using functional magnetic resonance imaging in behaving monkeys, we demonstrated a network of cortical areas selective for the processing of curved features. This network includes three distinct hierarchically organized regions within the ventral visual pathway: a posterior curvature-biased patch (PCP) located in the near-foveal representation of dorsal V4, a middle curvature-biased patch (MCP) located on the ventral lip of the posterior superior temporal sulcus (STS) in area TEO, and an anterior curvature-biased patch (ACP) located just below the STS in anterior area TE. Our results further indicate that the processing of curvature becomes increasingly complex from PCP to ACP. The proximity of the curvature-processing network to the well-known face-processing network suggests a possible functional link between them. PMID:25092328

Cell shape can mediate the spatial organization of the bacterial cytoskeleton

NASA Astrophysics Data System (ADS)

Wang, Siyuan; Wingreen, Ned

2013-03-01

The bacterial cytoskeleton guides the synthesis of cell wall and thus regulates cell shape. Since spatial patterning of the bacterial cytoskeleton is critical to the proper control of cell shape, it is important to ask how the cytoskeleton spatially self-organizes in the first place. In this work, we develop a quantitative model to account for the various spatial patterns adopted by bacterial cytoskeletal proteins, especially the orientation and length of cytoskeletal filaments such as FtsZ and MreB in rod-shaped cells. We show that the combined mechanical energy of membrane bending, membrane pinning, and filament bending of a membrane-attached cytoskeletal filament can be sufficient to prescribe orientation, e.g. circumferential for FtsZ or helical for MreB, with the accuracy of orientation increasing with the length of the cytoskeletal filament. Moreover, the mechanical energy can compete with the chemical energy of cytoskeletal polymerization to regulate filament length. Notably, we predict a conformational transition with increasing polymer length from smoothly curved to end-bent polymers. Finally, the mechanical energy also results in a mutual attraction among polymers on the same membrane, which could facilitate tight polymer spacing or bundling. The predictions of the model can be verified through genetic, microscopic, and microfluidic approaches.

Morphology, Growth, and Size Limit of Bacterial Cells

NASA Astrophysics Data System (ADS)

Jiang, Hongyuan; Sun, Sean X.

2010-07-01

Bacterial cells utilize a living peptidoglycan network (PG) to separate the cell interior from the surroundings. The shape of the cell is controlled by PG synthesis and cytoskeletal proteins that form bundles and filaments underneath the cell wall. The PG layer also resists turgor pressure and protects the cell from osmotic shock. We argue that mechanical influences alter the chemical equilibrium of the reversible PG assembly and determine the cell shape and cell size. Using a mechanochemical approach, we show that the cell shape can be regarded as a steady state of a growing network under the influence of turgor pressure and mechanical stress. Using simple elastic models, we predict the size of common spherical and rodlike bacteria. The influence of cytoskeletal bundles such as crescentin and MreB are discussed within the context of our model.

Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging

PubMed Central

Yaginuma, Hideyuki; Kawai, Shinnosuke; Tabata, Kazuhito V.; Tomiyama, Keisuke; Kakizuka, Akira; Komatsuzaki, Tamiki; Noji, Hiroyuki; Imamura, Hiromi

2014-01-01

Recent advances in quantitative single-cell analysis revealed large diversity in gene expression levels between individual cells, which could affect the physiology and/or fate of each cell. In contrast, for most metabolites, the concentrations were only measureable as ensemble averages of many cells. In living cells, adenosine triphosphate (ATP) is a critically important metabolite that powers many intracellular reactions. Quantitative measurement of the absolute ATP concentration in individual cells has not been achieved because of the lack of reliable methods. In this study, we developed a new genetically-encoded ratiometric fluorescent ATP indicator “QUEEN”, which is composed of a single circularly-permuted fluorescent protein and a bacterial ATP binding protein. Unlike previous FRET-based indicators, QUEEN was apparently insensitive to bacteria growth rate changes. Importantly, intracellular ATP concentrations of numbers of bacterial cells calculated from QUEEN fluorescence were almost equal to those from firefly luciferase assay. Thus, QUEEN is suitable for quantifying the absolute ATP concentration inside bacteria cells. Finally, we found that, even for a genetically-identical Escherichia coli cell population, absolute concentrations of intracellular ATP were significantly diverse between individual cells from the same culture, by imaging QUEEN signals from single cells. PMID:25283467

The effect of antibacterial acting extracorporeal shockwaves on bacterial cell integrity.

PubMed

Horn, Carsten; Mengele, Karin; Gerdesmeyer, Ludger; Gradinger, Reiner; Gollwitzer, Hans

2009-12-01

Antibacterial effects of extracorporeal shockwaves (ESWs) have been demonstrated in vitro against bacteria under static and dynamic growth conditions. This study assessed the effects of ESWs on the cell wall integrity of bacteria. Standardized suspensions of Staphylococcus aureus were exposed to various shockwave impulses (2000-12,000) of different energy flux densities (EFD, 0.38-0.96 mJ/mm(2)). Bacterial suspensions of equal concentration that had been permeabilized (to >99%) with isopropanol were used as positive controls. The bacteria of all groups were stained with Sytox Green nucleic acid stain. The fluorescence of the shockwave-treated, permeabilized, and untreated suspensions was measured and compared for bacterial survival, quantified by colony-forming units after plating. Although ESWs showed a significant energy-dependent antibacterial effect that reduced CFUs in the treated suspensions by between 56% and 99%, only maximum energies (4000 impulses at 0.96 mJ/mm(2) and 12,000 impulses at 0.59 mJ/mm(2)) were followed by a significant increase in fluorescence compared with the untreated control (p<0.05). However, the fluorescence of these treated groups was still far less than that of the alcohol-permeabilized positive control groups (p<0.05). Lower energies and impulse rates did not show increased intracellular uptake of the fluorescent dye (p>0.05). This is the first study to assess bacterial cell wall permeability after ESW treatment. It was found that the permeabilization of bacterial cells after ESW treatment was far less than expected due to the corresponding antibacterial effect. Other mechanisms, such as intracellular effects, might be involved in bacterial killing after ESWs and still must be elucidated.

Effect of cell physicochemical characteristics and motility on bacterial transport in groundwater

USGS Publications Warehouse

Becker, M.W.; Collins, S.A.; Metge, D.W.; Harvey, R.W.; Shapiro, A.M.

2004-01-01

The influence of physicochemical characteristics and motility on bacterial transport in groundwater were examined in flow-through columns. Four strains of bacteria isolated from a crystalline rock groundwater system were investigated, with carboxylate-modified and amidine-modified latex microspheres and bromide as reference tracers. The bacterial isolates included a gram-positive rod (ML1), a gram-negative motile rod (ML2), a nonmotile mutant of ML2 (ML2m), and a gram-positive coccoid (ML3). Experiments were repeated at two flow velocities, in a glass column packed with glass beads, and in another packed with iron-oxyhydroxide coated glass beads. Bacteria breakthrough curves were interpreted using a transport equation that incorporates a sorption model from microscopic observation of bacterial deposition in flow-cell experiments. The model predicts that bacterial desorption rate will decrease exponentially with the amount of time the cell is attached to the solid surface. Desorption kinetics appeared to influence transport at the lower flow rate, but were not discernable at the higher flow rate. Iron-oxyhydroxide coatings had a lower-than-expected effect on bacterial breakthrough and no effect on the microsphere recovery in the column experiments. Cell wall type and shape also had minor effects on breakthrough. Motility tended to increase the adsorption rate, and decrease the desorption rate. The transport model predicts that at field scale, desorption rate kinetics may be important to the prediction of bacteria transport rates. ?? 2003 Elsevier B.V. All rights reserved.

Curvature of the localized surface plasmon resonance peak.

PubMed

Chen, Peng; Liedberg, Bo

2014-08-05

Localized surface plasmon resonance (LSPR) occurring in noble metal nanoparticles (e.g., Au) is a widely used phenomenon to report molecular interactions. Traditional LSPR sensors typically monitor shifts in the peak position or extinction in response to local refractive index changes in the close vicinity of the nanoparticle surface. The ability to resolve minute shifts/extinction changes is to a large extent limited by instrumental noise. A new strategy to evaluate LSPR responses utilizing changes in the shape of the extinction spectrum (the curvature) is proposed. The response of curvature to refractive index changes is investigated theoretically using Mie theory and an analytical expression relating the curvature to the refractive index is presented. The experimentally derived curvatures for 13 nm spherical gold nanoparticles (AuNPs) exposed to solvents with different bulk refractive indices confirm the theoretical predictions. Moreover, both the calculated and experimental findings suggest that the curvature is approximately a linear function of refractive index in regimes relevant to bio and chemical sensing. We demonstrate that curvature is superior over peak shift and extinction both in terms of signal-to-noise (S/N) ratio and reliability of LSPR sensors. With a curvature, one could readily monitor submonolayer adsorption of a low molecular weight thiol molecule (M(w) = 458.6) onto 13 nm AuNPs. It is also worthwhile mentioning that curvature is virtually insensitive to instrumental instabilities and artifacts occurring during measurement. Instabilities such as baseline tilt and shift, shift in peak position as well as sharp spikes/steps in the extinction spectra do not induce artifacts in the sensorgrams of curvature.

Magnetophoretic induction of curvature in coleoptiles and hypocotyls

NASA Technical Reports Server (NTRS)

Kuznetsov, O. A.; Hasenstein, K. H.

1997-01-01

Coleoptiles of barley (Hordeum vulgare) were positioned in a high gradient magnetic field (HGMF, dynamic factor gradient of H(2)/2 of 10(9)-10(10) Oe2 cm-1), generated by a ferromagnetic wedge in a uniform magnetic field and rotated on a 1 rpm clinostat. After 4 h 90% of coleoptiles had curved toward the HGMF. The cells affected by HGMF showed clear intracellular displacement of amyloplasts. Coleoptiles in a magnetic field next to a non-ferromagnetic wedge showed no preferential curvature. The small size of the area of nonuniformity of the HGMF allowed mapping of the sensitivity of the coleoptiles by varying the initial position of the wedge relative to the coleoptile apex. When the ferromagnetic wedge was placed 1 mm below the coleoptile tip only 58% of the coleoptiles curved toward the wedge indicating that the cells most sensitive to intracellular displacement of amyloplasts and thus gravity sensing are confined to the top 1 mm portion of barley coleoptiles. Similar experiments with tomato hypocotyls (Lycopersicum esculentum) also resulted in curvature toward the HGMF. The data strongly support the amyloplast-based gravity-sensing system in higher plants and the usefulness of HGMF to substitute gravity in shoots.

Curvature-Mediated Assembly of Janus Nanoparticles on Membrane Vesicles.

PubMed

Bahrami, Amir Houshang; Weikl, Thomas R

2018-02-14

Besides direct particle-particle interactions, nanoparticles adsorbed to biomembranes experience indirect interactions that are mediated by the membrane curvature arising from particle adsorption. In this Letter, we show that the curvature-mediated interactions of adsorbed Janus particles depend on the initial curvature of the membrane prior to adsorption, that is, on whether the membrane initially bulges toward or away from the particles in our simulations. The curvature-mediated interaction can be strongly attractive for Janus particles adsorbed to the outside of a membrane vesicle, which initially bulges away from the particles. For Janus particles adsorbed to the vesicle inside, in contrast, the curvature-mediated interactions are repulsive. We find that the area fraction of the adhesive Janus particle surface is an important control parameter for the curvature-mediated interaction and assembly of the particles, besides the initial membrane curvature.

Radius of Curvature of Off-Axis Paraboloids

NASA Technical Reports Server (NTRS)

Robinson, Brian; Reardon, Patrick; Hadaway, James; Geary, Joseph; Russell, Kevin (Technical Monitor)

2002-01-01

We present several methods for measuring the vertex radius of curvature of off-axis paraboloidal mirrors. One is based on least-squares fitting of interferometer output, one on comparison of sagittal and tangential radii of curvature, and another on measurement of displacement of the nulled test article from the ideal reference wave. Each method defines radius of curvature differently and, as a consequence, produces its own sort of errors.

Corneal curvature, pachymetry, and endothelial cell density in Marfan syndrome.

PubMed

Konradsen, Tiina R; Koivula, Annemari; Kugelberg, Maria; Zetterström, Charlotta

2012-06-01

To evaluate corneal curvature, pachymetry, and endothelial cell density (ECD) in Marfan syndrome (MFS). A case-control study in which K values, pachymetry, and ECD were compared in 39 MFS eyes and 40 control eyes matched for age and refraction was conducted. MFS eyes with lens subluxation also were compared with eyes without subluxation. The mean K(med) value in MFS eyes was lower than in the control eyes, 42.2 ± 1.9 versus 43.4 ± 1.4 dioptres (D), respectively (p = 0.02). Fifteen MFS eyes (38%) and three control eyes (8%) had K(med) values below 41.5 D (p = 0.0012). MFS eyes had generally more corneal astigmatism than control eyes, 1.1 ± 0.9 versus 0.8 ± 0.4 D (p = 0.035), and MFS eyes with lens subluxation had more corneal astigmatism than those without, 1.6 ± 1.1 versus 0.6 ± 0.3 D (p = 0.0002). Nine MFS eyes with corneal astigmatism exceeding 1.5 D also had a subluxated lens. No eyes had keratoconus. The mean pachymetry value was lower in MFS eyes compared to the controls, 485 ± 54.5 versus 514 ± 37.3 μm (p = 0.007); 24 MFS eyes (62%) and 10 control eyes (25%) had measurements below 500 μm (p = 0.01). The mean ECD values were similar in MFS and control eyes, 2815 ± 430 versus 2858 ± 458 cells/mm(2) (p = 0.66). The mean K value, pachymetry, and ECD values did not differ between MFS eyes with and without lens subluxation. Decreased K values and pachymetry could indicate MFS regardless of subluxation. High corneal astigmatism is associated with subluxation in MFS. Subluxation should be identified in MFS eyes with high corneal astigmatism. © 2010 The Authors. Journal compilation © 2010 Acta Ophthalmol.

Long-time behavior of material-surface curvature in isotropic turbulence

NASA Technical Reports Server (NTRS)

Girimaji, S. S.

1992-01-01

The behavior at large times of the curvature of material elements in turbulence is investigated using Lagrangian velocity-gradient time series obtained from direct numerical simulations of isotropic turbulence. The main objectives are: to study the asymptotic behavior of the pdf curvature as a function of initial curvature and shape; and to establish whether the curvature of an initially plane material element goes to a stationary probability distribution. The evidence available in the literature about the asymptotic curvature-pdf of initially flat surfaces is ambiguous, and the conjecture is that it is quasi-stationary. In this work several material-element ensembles of different initial curvatures and shapes are studied. It is found that, at long times the moments of the logarithm of curvature are independent of the initial pdf of curvature. This, it is argued, supports the view that the curvature attains a stationary distribution at long times. It is also shown that, irrespective of initial shape or curvature, the shape of any material element at long times is cylindrical with a high probability.

Turbulent boundary layers subjected to multiple curvatures and pressure gradients

NASA Technical Reports Server (NTRS)

Bandyopadhyay, Promode R.; Ahmed, Anwar

1993-01-01

The effects of abruptly applied cycles of curvatures and pressure gradients on turbulent boundary layers are examined experimentally. Two two-dimensional curved test surfaces are considered: one has a sequence of concave and convex longitudinal surface curvatures and the other has a sequence of convex and concave curvatures. The choice of the curvature sequences were motivated by a desire to study the asymmetric response of turbulent boundary layers to convex and concave curvatures. The relaxation of a boundary layer from the effects of these two opposite sequences has been compared. The effect of the accompaying sequences of pressure gradient has also been examined but the effect of curvature dominates. The growth of internal layers at the curvature junctions have been studied. Measurements of the Gortler and corner vortex systems have been made. The boundary layer recovering from the sequence of concave to convex curvature has a sustained lower skin friction level than in that recovering from the sequence of convex to concave curvature. The amplification and suppression of turbulence due to the curvature sequences have also been studied.

Evaluation of the sensitivity of bacterial and yeast cells to cold atmospheric plasma jet treatments.

PubMed

Sharkey, Michael A; Chebbi, Ahmed; McDonnell, Kevin A; Staunton, Claire; Dowling, Denis P

2015-06-07

The focus of this research was first to determine the influence of the atmospheric plasma drive frequency on the generation of atomic oxygen species and its correlation with the reduction of bacterial load after treatment in vitro. The treatments were carried out using a helium-plasma jet source called PlasmaStream™. The susceptibility of multiple microbial cell lines was investigated in order to compare the response of gram-positive and gram-negative bacteria, as well as a yeast cell line to the atmospheric plasma treatment. It was observed for the source evaluated that at a frequency of 160 kHz, increased levels of oxygen-laden active species (i.e., OH, NO) were generated. At this frequency, the maximum level of bacterial inactivation in vitro was also achieved. Ex vivo studies (using freshly excised porcine skin as a human analog) were also carried out to verify the antibacterial effect of the plasma jet treatment at this optimal operational frequency and to investigate the effect of treatment duration on the reduction of bacterial load. The plasma jet treatment was found to yield a 4 log reduction in bacterial load after 6 min of treatment, with no observable adverse effects on the treatment surface. The gram-negative bacterial cell lines were found to be far more susceptible to the atmospheric plasma treatments than the gram-positive bacteria. Flow cytometric analysis of plasma treated bacterial cells (Escherichia coli) was conducted in order to attain a fundamental understanding of the mode of action of the treatment on bacteria at a cellular level. This study showed that after treatment with the plasma jet, E. coli cells progressed through the following steps of cell death; the inactivation of transport systems, followed by depolarization of the cytoplasmic membrane, and finally permeabilization of the cell wall.

Ultrastructure of Bacterial Cells Infected with Bacteriophage PM2, a Lipid-containing Bacterial Virus

PubMed Central

Cota-Robles, Eugene; Espejo, Romilio Torres; Haywood, Patricia Williams

1968-01-01

The cytological pattern of infection of a host pseudomonad with PM2, a lipid-containing bacterial virus, was investigated by electron microscopy. Normal and infected cells frequently contain a myelin figure, which is found in the nucleoid region or at the periphery of the cell. The most striking finding in this investigation was that completed virions are found in the cell adjacent to or in association with the cytoplasmic membrane. This localization is precise; virions are not found elsewhere in infected cells. The completed virions occasionally appear to be attached to the cytoplasmic membrane. The virus contains a darkly staining core surrounded by a tripartite envelope of a thickness of approximately 70 A, which is identical to the thickness of the cytoplasmic membrane. Lysing cells appear to undergo extensive damage of the cytoplasmic membrane prior to rupture of the L layer of the cell wall. Images PMID:5742028

The development of curvature in the porcine radioulna

PubMed Central

Pantinople, Jess; McCabe, Kyle; Henderson, Keith; Milne, Nick

2017-01-01

Long bone curvature in animal limbs has long been a subject of interest and much work has explored why long bones should be curved. However, the ‘when’ and ‘how’ of curvature development is poorly understood. It has been shown that the rat tibia fails to attain its normal curvature if the action of muscles is removed early in life, but it is not clear if this is because the curvature fails to develop or if the bone becomes straighter without the action of muscles. No studies have examined the development of bone curvature in a normally developing quadruped, so this study tracks the course of curvature formation in the radioulna in a series of growing pigs. We also histologically examined the epiphyseal growth plates of these bones to determine if they contribute to the formation of curvature. In all three epiphyseal plates examined, the proliferative zone is thicker and more densely populated with chondrocytes on the cranial (convex) side than the caudal (concave) side. Frost’s chondral modelling theory would suggest that the cranial side of the bone is under more compression than the caudal side, and we conclude that this is due to the action of triceps extending the elbow by pulling on the olecranon process. These results support the idea that bone curvature is an adaptation to habitual loading, where longitudinal loads acting on the curved bone cause bending strains that counter the bending resulting from the habitual muscle action. PMID:28584714

The development of curvature in the porcine radioulna.

PubMed

Pantinople, Jess; McCabe, Kyle; Henderson, Keith; Richards, Hazel L; Milne, Nick

2017-01-01

Long bone curvature in animal limbs has long been a subject of interest and much work has explored why long bones should be curved. However, the 'when' and 'how' of curvature development is poorly understood. It has been shown that the rat tibia fails to attain its normal curvature if the action of muscles is removed early in life, but it is not clear if this is because the curvature fails to develop or if the bone becomes straighter without the action of muscles. No studies have examined the development of bone curvature in a normally developing quadruped, so this study tracks the course of curvature formation in the radioulna in a series of growing pigs. We also histologically examined the epiphyseal growth plates of these bones to determine if they contribute to the formation of curvature. In all three epiphyseal plates examined, the proliferative zone is thicker and more densely populated with chondrocytes on the cranial (convex) side than the caudal (concave) side. Frost's chondral modelling theory would suggest that the cranial side of the bone is under more compression than the caudal side, and we conclude that this is due to the action of triceps extending the elbow by pulling on the olecranon process. These results support the idea that bone curvature is an adaptation to habitual loading, where longitudinal loads acting on the curved bone cause bending strains that counter the bending resulting from the habitual muscle action.

SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells.

PubMed

Stylianidou, Stella; Brennan, Connor; Nissen, Silas B; Kuwada, Nathan J; Wiggins, Paul A

2016-11-01

Many quantitative cell biology questions require fast yet reliable automated image segmentation to identify and link cells from frame-to-frame, and characterize the cell morphology and fluorescence. We present SuperSegger, an automated MATLAB-based image processing package well-suited to quantitative analysis of high-throughput live-cell fluorescence microscopy of bacterial cells. SuperSegger incorporates machine-learning algorithms to optimize cellular boundaries and automated error resolution to reliably link cells from frame-to-frame. Unlike existing packages, it can reliably segment microcolonies with many cells, facilitating the analysis of cell-cycle dynamics in bacteria as well as cell-contact mediated phenomena. This package has a range of built-in capabilities for characterizing bacterial cells, including the identification of cell division events, mother, daughter and neighbouring cells, and computing statistics on cellular fluorescence, the location and intensity of fluorescent foci. SuperSegger provides a variety of postprocessing data visualization tools for single cell and population level analysis, such as histograms, kymographs, frame mosaics, movies and consensus images. Finally, we demonstrate the power of the package by analyzing lag phase growth with single cell resolution. © 2016 John Wiley & Sons Ltd.

Activation of mouse liver natural killer cells and NK1.1(+) T cells by bacterial superantigen-primed Kupffer cells.

PubMed

Dobashi, H; Seki, S; Habu, Y; Ohkawa, T; Takeshita, S; Hiraide, H; Sekine, I

1999-08-01

Although bacterial superantigens have been well characterized as potent stimulators of T cells, their role in natural killer (NK)-type cells remains largely unknown. In the present study, we examined the effect of bacterial superantigens on mouse liver NK cells and NK1.1 Ag(+) (NK1(+)) T cells. C57BL/6 mice were intravenously injected with staphylococcal enterotoxin B (SEB) or streptococcal pyrogenic exotoxin A (SPE-A), and mononuclear cells (MNC) of various organs were obtained from mice 4 hours after being injected with superantigen. MNC were cultured for 48 hours, and interferon gamma (IFN-gamma) levels of supernatants were measured. The antitumor cytotoxicities of the liver and spleen MNC were also evaluated 24 hours after the mice were injected with superantigen. Liver MNC produced more IFN-gamma than did splenocytes, and peripheral blood and lung MNC did not produce any detectable IFN-gamma. In addition, liver MNC acquired a potent antitumor cytotoxicity by the SEB injection, and both NK cells and NK1(+)T cells but not cluster of differentiation (CD)8(+) T cells were responsible for the cytotoxicity as demonstrated by either in vivo or in vitro cell depletion experiments, and the NK-type cells were partly responsible for the increased serum IFN-gamma. Activation of liver NK-type cells was also supported by the fact that liver NK cells proportionally increased and NK1(+) T cells augmented their CD11a expressions after SEB injection. The pretreatment of mice with anti-IFN-gamma Ab and/or with anti-interleukin-12 (IL-12) Ab diminished the SEB-induced cytotoxicity of liver MNC. Furthermore, the in vivo depletion of Kupffer cells decreased the SEB-induced cytotoxicity of liver MNC. Consistent with these results, liver MNC stimulated with superantigens in the presence of Kupffer cells in vitro produced a greater amount of IFN-gamma than did the liver MNC without Kupffer cells or splenocytes. Our results suggest that bacterial superantigen-primed Kupffer cells

Bacterial Cell Production from Hexadecane at High Temperatures

PubMed Central

Sukatsch, Dieter A.; Johnson, Marvin J.

1972-01-01

On mineral medium with hexadecane as the sole carbon source, stable mixed bacterial enrichment cultures were obtained from soil inoculum at 25, 35, 45, 55, and 65 C. Cell yields (grams of dry cells per gram of hexadecane) were determined for each of the enrichment cultures grown at the temperature at which they were enriched, and also for the 55 and 65 C cultures grown at various temperatures. In all cases, cell yields decreased with increasing growth temperature. The highest yield obtained at 65 C was 0.26, and the lowest yield obtained at 25 or 35 C was 1.02. Slower growth was observed at higher temperatures. PMID:5021971

Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

NASA Astrophysics Data System (ADS)

Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

2017-01-01

Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

In situ probing the interior of single bacterial cells at nanometer scale

NASA Astrophysics Data System (ADS)

Liu, Boyin; Hemayet Uddin, Md; Ng, Tuck Wah; Paterson, David L.; Velkov, Tony; Li, Jian; Fu, Jing

2014-10-01

We report a novel approach to probe the interior of single bacterial cells at nanometre resolution by combining focused ion beam (FIB) and atomic force microscopy (AFM). After removing layers of pre-defined thickness in the order of 100 nm on the target bacterial cells with FIB milling, AFM of different modes can be employed to probe the cellular interior under both ambient and aqueous environments. Our initial investigations focused on the surface topology induced by FIB milling and the hydration effects on AFM measurements, followed by assessment of the sample protocols. With fine-tuning of the process parameters, in situ AFM probing beneath the bacterial cell wall was achieved for the first time. We further demonstrate the proposed method by performing a spatial mapping of intracellular elasticity and chemistry of the multi-drug resistant strain Klebsiella pneumoniae cells prior to and after it was exposed to the ‘last-line’ antibiotic polymyxin B. Our results revealed increased stiffness occurring in both surface and interior regions of the treated cells, suggesting loss of integrity of the outer membrane from polymyxin treatments. In addition, the hydrophobicity measurement using a functionalized AFM tip was able to highlight the evident hydrophobic portion of the cell such as the regions containing cell membrane. We expect that the proposed FIB-AFM platform will help in gaining deeper insights of bacteria-drug interactions to develop potential strategies for combating multi-drug resistance.

In-vitro analysis of APA microcapsules for oral delivery of live bacterial cells.

PubMed

Chen, H; Ouyang, W; Jones, M; Haque, T; Lawuyi, B; Prakash, S

2005-08-01

Oral administration of microcapsules containing live bacterial cells has potential as an alternative therapy for several diseases. This article evaluates the suitability of the alginate-poly-L-lysine-alginate (APA) microcapsules for oral delivery of live bacterial cells, in-vitro, using a dynamic simulated human gastro-intestinal (GI) model. Results showed that the APA microcapsules were morphologically stable in the simulated stomach conditions, but did not retain their structural integrity after a 3-day exposure in simulated human GI media. The microbial populations of the tested bacterial cells and the activities of the tested enzymes in the simulated human GI suspension were not substantially altered by the presence of the APA microcapsules, suggesting that there were no significant adverse effects of oral administration of the APA microcapsules on the flora of the human gastrointestinal tract. When the APA microcapsules containing Lactobacillus plantarum 80 (LP80) were challenged in the simulated gastric medium (pH = 2.0), 80.0% of the encapsulated cells remained viable after a 5-min incubation; however, the viability decreased considerably (8.3%) after 15 min and dropped to 2.6% after 30 min and lower than 0.2% after 60 min, indicating the limitations of the currently obtainable APA membrane for oral delivery of live bacteria. Further in-vivo studies are required before conclusions can be made concerning the inadequacy of APA microcapsules for oral delivery of live bacterial cells.

Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells.

PubMed

Spahn, Christoph; Glaesmann, Mathilda; Gao, Yunfeng; Foo, Yong Hwee; Lampe, Marko; Kenney, Linda J; Heilemann, Mike

2017-01-01

Despite their small size and the lack of compartmentalization, bacteria exhibit a striking degree of cellular organization, both in time and space. During the last decade, a group of new microscopy techniques emerged, termed super-resolution microscopy or nanoscopy, which facilitate visualizing the organization of proteins in bacteria at the nanoscale. Single-molecule localization microscopy (SMLM) is especially well suited to reveal a wide range of new information regarding protein organization, interaction, and dynamics in single bacterial cells. Recent developments in click chemistry facilitate the visualization of bacterial chromatin with a resolution of ~20 nm, providing valuable information about the ultrastructure of bacterial nucleoids, especially at short generation times. In this chapter, we describe a simple-to-realize protocol that allows determining precise structural information of bacterial nucleoids in fixed cells, using direct stochastic optical reconstruction microscopy (dSTORM). In combination with quantitative photoactivated localization microscopy (PALM), the spatial relationship of proteins with the bacterial chromosome can be studied. The position of a protein of interest with respect to the nucleoids and the cell cylinder can be visualized by super-resolving the membrane using point accumulation for imaging in nanoscale topography (PAINT). The combination of the different SMLM techniques in a sequential workflow maximizes the information that can be extracted from single cells, while maintaining optimal imaging conditions for each technique.

Intrinsic DNA curvature in trypanosomes.

PubMed

Smircich, Pablo; El-Sayed, Najib M; Garat, Beatriz

2017-11-09

Trypanosoma cruzi and Trypanosoma brucei are protozoan parasites causing Chagas disease and African sleeping sickness, displaying unique features of cellular and molecular biology. Remarkably, no canonical signals for RNA polymerase II promoters, which drive protein coding genes transcription, have been identified so far. The secondary structure of DNA has long been recognized as a signal in biological processes and more recently, its involvement in transcription initiation in Leishmania was proposed. In order to study whether this feature is conserved in trypanosomatids, we undertook a genome wide search for intrinsic DNA curvature in T. cruzi and T. brucei. Using a region integrated intrinsic curvature (RIIC) scoring that we previously developed, a non-random distribution of sequence-dependent curvature was observed. High RIIC scores were found to be significantly correlated with transcription start sites in T. cruzi, which have been mapped in divergent switch regions, whereas in T. brucei, the high RIIC scores correlated with sites that have been involved not only in RNA polymerase II initiation but also in termination. In addition, we observed regions with high RIIC score presenting in-phase tracts of Adenines, in the subtelomeric regions of the T. brucei chromosomes that harbor the variable surface glycoproteins genes. In both T. cruzi and T. brucei genomes, a link between DNA conformational signals and gene expression was found. High sequence dependent curvature is associated with transcriptional regulation regions. High intrinsic curvature also occurs at the T. brucei chromosome subtelomeric regions where the recombination processes involved in the evasion of the immune host system take place. These findings underscore the relevance of indirect DNA readout in these ancient eukaryotes.

Effects of Iris Surface Curvature on Iris Recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Joseph T; Flynn, Patrick J; Bowyer, Kevin W

To focus on objects at various distances, the lens of the eye must change shape to adjust its refractive power. This change in lens shape causes a change in the shape of the iris surface which can be measured by examining the curvature of the iris. This work isolates the variable of iris curvature in the recognition process and shows that differences in iris curvature degrade matching ability. To our knowledge, no other work has examined the effects of varying iris curvature on matching ability. To examine this degradation, we conduct a matching experiment across pairs of images with varyingmore » degrees of iris curvature differences. The results show a statistically signi cant degradation in matching ability. Finally, the real world impact of these ndings is discussed« less

Hair curvature: a natural dialectic and review.

PubMed

Nissimov, Joseph N; Das Chaudhuri, Asit Baran

2014-08-01

Although hair forms (straight, curly, wavy, etc.) are present in apparently infinite variations, each fibre can be reduced to a finite sequence of tandem segments of just three types: straight, bent/curly, or twisted. Hair forms can thus be regarded as resulting from genetic pathways that induce, reverse or modulate these basic curvature modes. However, physical interconversions between twists and curls demonstrate that strict one-to-one correspondences between them and their genetic causes do not exist. Current hair-curvature theories do not distinguish between bending and twisting mechanisms. We here introduce a multiple papillary centres (MPC) model which is particularly suitable to explain twisting. The model combines previously known features of hair cross-sectional morphology with partially/completely separated dermal papillae within single follicles, and requires such papillae to induce differential growth rates of hair cortical material in their immediate neighbourhoods. The MPC model can further help to explain other, poorly understood, aspects of hair growth and morphology. Separate bending and twisting mechanisms would be preferentially affected at the major or minor ellipsoidal sides of fibres, respectively, and together they exhaust the possibilities for influencing hair-form phenotypes. As such they suggest dialectic for hair-curvature development. We define a natural-dialectic (ND) which could take advantage of speculative aspects of dialectic, but would verify its input data and results by experimental methods. We use this as a top-down approach to first define routes by which hair bending or twisting may be brought about and then review evidence in support of such routes. In particular we consider the wingless (Wnt) and mammalian target of rapamycin (mTOR) pathways as paradigm pathways for molecular hair bending and twisting mechanisms, respectively. In addition to the Wnt canonical pathway, the Wnt/Ca(2+) and planar cell polarity (PCP) pathways

Further consideration of the curvature of the Neandertal Femur.

PubMed

Chapman, Tara; Sholukha, Victor; Semal, Patrick; Louryan, Stéphane; Van Sint Jan, Serge

2018-01-01

Neandertal femora are particularly known for having a marked sagittal femoral curvature. This study examined femoral curvature in Neandertals in comparison to a modern human population from Belgium by the use of three-dimensional (3D) quadric surfaces modeled from the bone surface. 3D models provide detailed information and enabled femoral curvature to be analyzed in conjunction with other morphological parameters. 3D models were created from CT scans of 75 modern human femora and 7 Neandertal femora. Quadric surfaces (QS) were created from the triangulated surface vertices in all areas of interest (neck, head, diaphyseal shaft, condyles) extracted from previously placed anatomical landmarks. The diaphyseal shaft was divided into five QS shapes and curvature was measured by degrees of difference between QS shapes. Each bone was placed in a local coordinate system enabling each bone to be analyzed in the same way. The use of 3D quadric surface fitting allowed the distribution of curvature with similarly curved femora to be analyzed and the different patterns of curvature between the two groups to be determined. The Neandertals were shown to have a higher degree of femoral curvature and a more distal point of femoral curvature than the modern human population from Belgium. Morphological aspects of the Neandertal femur are different from this modern human population although mainly seem unrelated to femoral curvature. The relative lack of correlations with other femoral bony morphological factors suggests femoral curvature variations may be related to other aspects. © 2017 Wiley Periodicals, Inc.

Curvature Constraints from the Causal Entropic Principle

NASA Astrophysics Data System (ADS)

Bozek, Brandon

2010-01-01

Current cosmological observations indicate a preference for a cosmological constant that is drastically smaller than what can be explained by conventional particle physics. The Causal Entropic Principle (Bousso, et al.) provides an alternative approach to anthropic attempts to predict our observed value of the cosmological constant by calculating the entropy created within a causal diamond. We have extended this work to use the Causal Entropic Principle to predict the preferred curvature within the "multiverse." We have found that values larger than ρk = 40*ρm are disfavored by more than 99.99% and a peak value at ρΛ = 7.9*10-123 and ρk =4.3*ρm for open universes. For universes that allow only positive curvature or both positive and negative curvature, we find a correlation between curvature and dark energy that leads to an extended region of preferred values. Our universe is found to be disfavored to an extent depending on the priors on curvature. We also provide a comparison to previous anthropic constraints on open universes and discuss future directions for this work.

Curvature constraints from the causal entropic principle

NASA Astrophysics Data System (ADS)

Bozek, Brandon; Albrecht, Andreas; Phillips, Daniel

2009-07-01

Current cosmological observations indicate a preference for a cosmological constant that is drastically smaller than what can be explained by conventional particle physics. The causal entropic principle (Bousso et al.) provides an alternative approach to anthropic attempts to predict our observed value of the cosmological constant by calculating the entropy created within a causal diamond. We have extended this work to use the causal entropic principle to predict the preferred curvature within the “multiverse.” We have found that values larger than ρk=40ρm are disfavored by more than 99.99% peak value at ρΛ=7.9×10-123 and ρk=4.3ρm for open universes. For universes that allow only positive curvature or both positive and negative curvature, we find a correlation between curvature and dark energy that leads to an extended region of preferred values. Our universe is found to be disfavored to an extent depending on the priors on curvature. We also provide a comparison to previous anthropic constraints on open universes and discuss future directions for this work.

FY 2016 Status Report: CIRFT Testing Data Analyses and Updated Curvature Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jy-An John; Wang, Hong

This report provides a detailed description of FY15 test result corrections/analysis based on the FY16 Cyclic Integrated Reversible-Bending Fatigue Tester (CIRFT) test program methodology update used to evaluate the vibration integrity of spent nuclear fuel (SNF) under normal transportation conditions. The CIRFT consists of a U-frame testing setup and a real-time curvature measurement method. The three-component U-frame setup of the CIRFT has two rigid arms and linkages to a universal testing machine. The curvature of rod bending is obtained through a three-point deflection measurement method. Three linear variable differential transformers (LVDTs) are used and clamped to the side connecting platesmore » of the U-frame to capture the deformation of the rod. The contact-based measurement, or three-LVDT-based curvature measurement system, on SNF rods has been proven to be quite reliable in CIRFT testing. However, how the LVDT head contacts the SNF rod may have a significant effect on the curvature measurement, depending on the magnitude and direction of rod curvature. It has been demonstrated that the contact/curvature issues can be corrected by using a correction on the sensor spacing. The sensor spacing defines the separation of the three LVDT probes and is a critical quantity in calculating the rod curvature once the deflections are obtained. The sensor spacing correction can be determined by using chisel-type probes. The method has been critically examined this year and has been shown to be difficult to implement in a hot cell environment, and thus cannot be implemented effectively. A correction based on the proposed equivalent gauge-length has the required flexibility and accuracy and can be appropriately used as a correction factor. The correction method based on the equivalent gauge length has been successfully demonstrated in CIRFT data analysis for the dynamic tests conducted on Limerick (LMK) (17 tests), North Anna (NA) (6 tests), and Catawba mixed oxide

Determinants of Curvature-Sensing Behavior for MARCKS-Fragment Peptides.

PubMed

de Jesus, Armando J; White, Ormacinda R; Flynn, Aaron D; Yin, Hang

2016-05-10

It is increasingly recognized that membrane curvature plays an important role in various cellular activities such as signaling and trafficking, as well as key issues involving health and disease development. Thus, curvature-sensing peptides are essential to the study and detection of highly curved bilayer structures. The effector domain of myristoylated alanine-rich C-kinase substrate (MARCKS-ED) has been demonstrated to have curvature-sensing ability. Research of the MARCKS-ED has further revealed that its Lys and Phe residues play an essential role in how MARCKS-ED detects and binds to curved bilayers. MARCKS-ED has the added property of being a lower-molecular-weight curvature sensor, which offers advantages in production. With that in mind, this work investigates peptide-sequence-related factors that influence curvature sensing and explores whether peptide fragments of even shorter length can function as curvature sensors. Using both experimental and computational methods, we studied the curvature-sensing capabilities of seven fragments of MARCKS-ED. Two of the longer fragments were designed from approximately the two halves of the full-length peptide whereas the five shorter fragments were taken from the central stretch of MARCKS-ED. Fully atomistic molecular dynamics simulations show that the fragments that remain bound to the bilayer exhibit interactions with the bilayer similar to that of the full-length MARCKS-ED peptide. Fluorescence enhancement and anisotropy assays, meanwhile, reveal that five of the MARCKS fragments possess the ability to sense membrane curvature. Based on the sequences of the curvature-sensing fragments, it appears that the ability to sense curvature involves a balance between the numbers of positively charged residues and hydrophobic anchoring residues. Together, these findings help crystallize our understanding of the molecular mechanisms underpinning the curvature-sensing behaviors of peptides, which will prove useful in the

Procalcitonin as a Biomarker of Bacterial Infection in Sickle Cell Vaso-Occlusive Crisis

PubMed Central

Patel, Dilip Kumar; Mohapatra, Manoj Kumar; Thomas, Ancil George; Patel, Siris; Purohit, Prasanta

2014-01-01

Sickle cell anaemia (SCA) patients with vaso-occlusive crisis (VOC) have signs of inflammation and it is often difficult to diagnose a bacterial infection in them. This study was undertaken to evaluate the role of serum procalcitonin (PCT) as a biomarker of bacterial infection in acute sickle cell vaso-occlusive crisis. Hundred homozygous SCA patients were studied at Sickle Cell Clinic and Molecular Biology Laboratory, V.S.S. Medical College, Burla, Odisha, India. All the patients were divided into three categories namely category-A (VOC/ACS with SIRS but without evidence of bacterial infection - 66 patients), category-B (VOC/ACS with SIRS and either proven or suspected bacterial infection - 24 patients) and category-C (SCA patients in steady state without VOC/ACS or SIRS - 10 patients). Complete blood count, C-reactive protein (CRP) estimation and PCT measurement were done in all the patients. There was no significant difference in TLC and CRP values between category-A and B. In category-A, the PCT level was <0.5 ng/mL in 83.3% and 0.5–2 ng/mL in 16.7% of cases. In category-B, all the patients had PCT value >0.5 ng/mL with 87.5% of patients having >2 ng/mL. In category-C, PCT value was <0.5 ng/mL. PCT had a high sensitivity (100%) and negative predictive value (100%) for bacterial infection at a cutoff value of 0.5 ng/mL; whereas the specificity is excellent at a cut-off value of 2 ng/mL. SCA patients with VOC/ACS and SIRS having a PCT level of <0.5 ng/mL have a low probability of bacterial infection whereas PCT value of >2 ng/mL is indicative of bacterial infection necessitating early antimicrobial therapy. PMID:24678395

Nanoscale Membrane Curvature detected by Polarized Localization Microscopy

NASA Astrophysics Data System (ADS)

Kelly, Christopher; Maarouf, Abir; Woodward, Xinxin

Nanoscale membrane curvature is a necessary component of countless cellular processes. Here we present Polarized Localization Microscopy (PLM), a super-resolution optical imaging technique that enables the detection of nanoscale membrane curvature with order-of-magnitude improvements over comparable optical techniques. PLM combines the advantages of polarized total internal reflection fluorescence microscopy and fluorescence localization microscopy to reveal single-fluorophore locations and orientations without reducing localization precision by point spread function manipulation. PLM resolved nanoscale membrane curvature of a supported lipid bilayer draped over polystyrene nanoparticles on a glass coverslip, thus creating a model membrane with coexisting flat and curved regions and membrane radii of curvature as small as 20 nm. Further, PLM provides single-molecule trajectories and the aggregation of curvature-inducing proteins with super-resolution to reveal the correlated effects of membrane curvature, dynamics, and molecular sorting. For example, cholera toxin subunit B has been observed to induce nanoscale membrane budding and concentrate at the bud neck. PLM reveals a previously hidden and critical information of membrane topology.

Curvature constraints from large scale structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dio, Enea Di; Montanari, Francesco; Raccanelli, Alvise

We modified the CLASS code in order to include relativistic galaxy number counts in spatially curved geometries; we present the formalism and study the effect of relativistic corrections on spatial curvature. The new version of the code is now publicly available. Using a Fisher matrix analysis, we investigate how measurements of the spatial curvature parameter Ω {sub K} with future galaxy surveys are affected by relativistic effects, which influence observations of the large scale galaxy distribution. These effects include contributions from cosmic magnification, Doppler terms and terms involving the gravitational potential. As an application, we consider angle and redshift dependentmore » power spectra, which are especially well suited for model independent cosmological constraints. We compute our results for a representative deep, wide and spectroscopic survey, and our results show the impact of relativistic corrections on spatial curvature parameter estimation. We show that constraints on the curvature parameter may be strongly biased if, in particular, cosmic magnification is not included in the analysis. Other relativistic effects turn out to be subdominant in the studied configuration. We analyze how the shift in the estimated best-fit value for the curvature and other cosmological parameters depends on the magnification bias parameter, and find that significant biases are to be expected if this term is not properly considered in the analysis.« less

Glycerol Monolaurate Inhibits Lipase Production by Clinical Ocular Isolates Without Affecting Bacterial Cell Viability.

PubMed

Flanagan, Judith Louise; Khandekar, Neeta; Zhu, Hua; Watanabe, Keizo; Markoulli, Maria; Flanagan, John Terence; Papas, Eric

2016-02-01

We sought to determine the relative lipase production of a range of ocular bacterial isolates and to assess the efficacy of glycerol monolaurate (GML) in inhibiting this lipase production in high lipase-producing bacteria without affecting bacterial cell growth. Staphylococcus aureus,Staphylococcus epidermidis,Propionibacterium acnes, and Corynebacterium spp. were inoculated at a density of 10(6)/mL in varying concentrations of GML up to 25 μg/mL for 24 hours at 37 °C with constant shaking. Bacterial suspensions were centrifuged, bacterial cell density was determined, and production of bacterial lipase was quantified using a commercial lipase assay kit. Staphylococcus spp. produced high levels of lipase activity compared with P. acnes and Corynebacterium spp. GML inhibited lipase production by Staphylococcal spp. in a dose-dependent manner, with S. epidermidis lipase production consistently more sensitive to GML than S. aureus. Glycerol monolaurate showed significant (P < 0.05) lipase inhibition above concentrations of 15 μg/mL in S. aureus and was not cytotoxic up to 25 μg/mL. For S. epidermidis, GML showed significant (P < 0.05) lipase inhibition above 7.5 μg/mL. Lipase activity varied between species and between strains. Staphylococcal spp. produced higher lipase activity compared with P. acnes and Corynebacterium spp. Glycerol monolaurate inhibited lipase production by S. aureus and S. epidermidis at concentrations that did not adversely affect bacterial cell growth. GML can be used to inhibit ocular bacterial lipase production without proving detrimental to commensal bacteria viability.

Space Curvature and the "Heavy Banana 'Paradox.'"

ERIC Educational Resources Information Center

Gruber, Ronald P.; And Others

1991-01-01

Two ways to visually enhance the concept of space curvature are described. Viewing space curvature as a meterstick contraction and the heavy banana "paradox" are discussed. The meterstick contraction is mathematically explained. (KR)

Contribution of bacterial cells to lacustrine organic matter based on amino sugars and D-amino acids

NASA Astrophysics Data System (ADS)

Carstens, Dörte; Köllner, Krista E.; Bürgmann, Helmut; Wehrli, Bernhard; Schubert, Carsten J.

2012-07-01

Amino sugars (ASs), D-amino acids (D-AAs), and bacterial cell counts were measured in two Swiss lakes to study the contribution of bacterial cells to organic matter (OM) and the fate of ASs and bacterial amino biomarkers during OM degradation. Concentrations of individual ASs (glucosamine, galactosamine, muramic acid, and mannosamine) in the particulate and total OM pools were analyzed in water-column profiles of Lake Brienz (oligotrophic and oxic throughout the entire water column) and Lake Zug (eutrophic, stratified, and permanently anoxic below 170 m) in spring and in fall. Generally, carbon-normalized AS concentrations decreased with water depth, indicating the preferential decomposition of ASs. For Lake Brienz the relative loss of particulate ASs was higher than in Lake Zug, suggesting enhanced AS turnover in an oligotrophic environment. AS ratio changes in the water column revealed a replacement of plankton biomass with OM from heterotrophic microorganisms with increasing water depth. Similar to the ASs, highest carbon normalized D-AA concentrations were found in the upper water column with decreasing concentrations with depth and an increase close to the sediments. In Lake Zug, an increase in the percentage of D-AAs also showed the involvement of bacteria in OM degradation. Estimations of OM derived from bacterial cells using cell counts and the bacterial biomarkers muramic acid and D-AAs gave similar results. For Lake Brienz 0.2-14% of the organic carbon pool originated from bacterial cells, compared to only 0.1-5% in Lake Zug. Based on our estimates, muramic acid appeared primarily associated with bacterial biomass and not with refractory bacterial necromass. Our study underscores that bacteria are not only important drivers of OM degradation in lacustrine systems, they also represent a significant source of OM themselves, especially in oligotrophic lakes.

Robust estimation of adaptive tensors of curvature by tensor voting.

PubMed

Tong, Wai-Shun; Tang, Chi-Keung

2005-03-01

Although curvature estimation from a given mesh or regularly sampled point set is a well-studied problem, it is still challenging when the input consists of a cloud of unstructured points corrupted by misalignment error and outlier noise. Such input is ubiquitous in computer vision. In this paper, we propose a three-pass tensor voting algorithm to robustly estimate curvature tensors, from which accurate principal curvatures and directions can be calculated. Our quantitative estimation is an improvement over the previous two-pass algorithm, where only qualitative curvature estimation (sign of Gaussian curvature) is performed. To overcome misalignment errors, our improved method automatically corrects input point locations at subvoxel precision, which also rejects outliers that are uncorrectable. To adapt to different scales locally, we define the RadiusHit of a curvature tensor to quantify estimation accuracy and applicability. Our curvature estimation algorithm has been proven with detailed quantitative experiments, performing better in a variety of standard error metrics (percentage error in curvature magnitudes, absolute angle difference in curvature direction) in the presence of a large amount of misalignment noise.

Compensation of Gaussian curvature in developable cones is local

NASA Astrophysics Data System (ADS)

Wang, Jin W.; Witten, Thomas A.

2009-10-01

We use the angular deficit scheme [V. Borrelli, F. Cazals, and J.-M. Morvan, Comput. Aided Geom. Des. 20, 319 (2003)] to determine the distribution of Gaussian curvature in developable cones (d-cones) [E. Cerda, S. Chaieb, F. Melo, and L. Mahadevan, Nature (London) 401, 46 (1999)] numerically. These d-cones are formed by pushing a thin elastic sheet into a circular container. Negative Gaussian curvatures are identified at the rim where the sheet touches the container. Around the rim there are two narrow bands with positive Gaussian curvatures. The integral of the (negative) Gaussian curvature near the rim is almost completely compensated by that of the two adjacent bands. This suggests that the Gauss-Bonnet theorem which constrains the integral of Gaussian curvature globally does not explain the spontaneous curvature cancellation phenomenon [T. Liang and T. A. Witten, Phys. Rev. E 73, 046604 (2006)]. The locality of the compensation seems to increase for decreasing d-cone thickness. The angular deficit scheme also provides a way to confirm the curvature cancellation phenomenon.

Graph Curvature for Differentiating Cancer Networks

PubMed Central

Sandhu, Romeil; Georgiou, Tryphon; Reznik, Ed; Zhu, Liangjia; Kolesov, Ivan; Senbabaoglu, Yasin; Tannenbaum, Allen

2015-01-01

Cellular interactions can be modeled as complex dynamical systems represented by weighted graphs. The functionality of such networks, including measures of robustness, reliability, performance, and efficiency, are intrinsically tied to the topology and geometry of the underlying graph. Utilizing recently proposed geometric notions of curvature on weighted graphs, we investigate the features of gene co-expression networks derived from large-scale genomic studies of cancer. We find that the curvature of these networks reliably distinguishes between cancer and normal samples, with cancer networks exhibiting higher curvature than their normal counterparts. We establish a quantitative relationship between our findings and prior investigations of network entropy. Furthermore, we demonstrate how our approach yields additional, non-trivial pair-wise (i.e. gene-gene) interactions which may be disrupted in cancer samples. The mathematical formulation of our approach yields an exact solution to calculating pair-wise changes in curvature which was computationally infeasible using prior methods. As such, our findings lay the foundation for an analytical approach to studying complex biological networks. PMID:26169480

New method for estimating bacterial cell abundances in natural samples by use of sublimation

NASA Technical Reports Server (NTRS)

Glavin, Daniel P.; Cleaves, H. James; Schubert, Michael; Aubrey, Andrew; Bada, Jeffrey L.

2004-01-01

We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500 degrees C for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from approximately 10(5) to 10(9) E. coli cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DAPI (4,6-diamidino-2-phenylindole) staining.

Seasonal Bacterial Production in a Dimictic Lake as Measured by Increases in Cell Numbers and Thymidine Incorporation

PubMed Central

Lovell, Charles R.; Konopka, Allan

1985-01-01

Rates of primary and bacterial production in Little Crooked Lake were calculated from the rates of incorporation of H14CO3− and [methyl-3H]thymidine, respectively. Growth rates of bacteria in diluted natural samples were determined for epilimnetic and metalimnetic bacterial populations during the summers of 1982 and 1983. Exponential growth was observed in these diluted samples, with increases in cell numbers of 30 to 250%. No lag was observed in bacterial growth in 14 of 16 experiments. Correlation of bacterial growth rates to corresponding rates of thymidine incorporation by natural samples produced a conversion factor of 2.2 × 1018 cells produced per mole of thymidine incorporated. The mass of the average bacterial cell in the lake was 1.40 × 10−14 ± 0.05 × 10−14 g of C cell−1. Doubling times of natural bacteria calculated from thymidine incorporation rates and in situ cell numbers ranged from 0.35 to 12.00 days (median, 1.50 days). Bacterial production amounted to 66.7 g of C m−2 from April through September, accounting for 29.4% of total (primary plus bacterial) production during this period. The vertical and seasonal distribution of bacterial production in Little Crooked Lake was strongly influenced by the distribution of primary production. From April through September 1983, the depth of maximum bacterial production rates in the water column was related to the depth of high rates of primary production. On a seasonal basis, primary production increased steadily from May through September, and bacterial production increased from May through August and then decreased in September. PMID:16346743

Vehicles, Replicators, and Intercellular Movement of Genetic Information: Evolutionary Dissection of a Bacterial Cell

PubMed Central

Jalasvuori, Matti

2012-01-01

Prokaryotic biosphere is vastly diverse in many respects. Any given bacterial cell may harbor in different combinations viruses, plasmids, transposons, and other genetic elements along with their chromosome(s). These agents interact in complex environments in various ways causing multitude of phenotypic effects on their hosting cells. In this discussion I perform a dissection for a bacterial cell in order to simplify the diversity into components that may help approach the ocean of details in evolving microbial worlds. The cell itself is separated from all the genetic replicators that use the cell vehicle for preservation and propagation. I introduce a classification that groups different replicators according to their horizontal movement potential between cells and according to their effects on the fitness of their present host cells. The classification is used to discuss and improve the means by which we approach general evolutionary tendencies in microbial communities. Moreover, the classification is utilized as a tool to help formulating evolutionary hypotheses and to discuss emerging bacterial pathogens as well as to promote understanding on the average phenotypes of different replicators in general. It is also discussed that any given biosphere comprising prokaryotic cell vehicles and genetic replicators may naturally evolve to have horizontally moving replicators of various types. PMID:22567533

Curvature Continuous and Bounded Path Planning for Fixed-Wing UAVs.

PubMed

Wang, Xiaoliang; Jiang, Peng; Li, Deshi; Sun, Tao

2017-09-19

Unmanned Aerial Vehicles (UAVs) play an important role in applications such as data collection and target reconnaissance. An accurate and optimal path can effectively increase the mission success rate in the case of small UAVs. Although path planning for UAVs is similar to that for traditional mobile robots, the special kinematic characteristics of UAVs (such as their minimum turning radius) have not been taken into account in previous studies. In this paper, we propose a locally-adjustable, continuous-curvature, bounded path-planning algorithm for fixed-wing UAVs. To deal with the curvature discontinuity problem, an optimal interpolation algorithm and a key-point shift algorithm are proposed based on the derivation of a curvature continuity condition. To meet the upper bound for curvature and to render the curvature extrema controllable, a local replanning scheme is designed by combining arcs and Bezier curves with monotonic curvature. In particular, a path transition mechanism is built for the replanning phase using minimum curvature circles for a planning philosophy. Numerical results demonstrate that the analytical planning algorithm can effectively generate continuous-curvature paths, while satisfying the curvature upper bound constraint and allowing UAVs to pass through all predefined waypoints in the desired mission region.

Seeking Beta: Experimental Considerations and Theoretical Implications Regarding the Detection of Curvature in Dose-Response Relationships for Chromosome Aberrations.

PubMed

Shuryak, Igor; Loucas, Bradford D; Cornforth, Michael N

2017-01-01

The concept of curvature in dose-response relationships figures prominently in radiation biology, encompassing a wide range of interests including radiation protection, radiotherapy and fundamental models of radiation action. In this context, the ability to detect even small amounts of curvature becomes important. Standard (ST) statistical approaches used for this purpose typically involve least-squares regression, followed by a test on sums of squares. Because we have found that these methods are not particularly robust, we investigated an alternative information theoretic (IT) approach, which involves Poisson regression followed by information-theoretic model selection. Our first objective was to compare the performances of the ST and IT methods by using them to analyze mFISH data on gamma-ray-induced simple interchanges in human lymphocytes, and on Monte Carlo simulated data. Real and simulated data sets that contained small-to-moderate curvature were deliberately selected for this exercise. The IT method tended to detect curvature with higher confidence than the ST method. The finding of curvature in the dose response for true simple interchanges is discussed in the context of fundamental models of radiation action. Our second objective was to optimize the design of experiments aimed specifically at detecting curvature. We used Monte Carlo simulation to investigate the following parameters. Constrained by available resources (i.e., the total number of cells to be scored) these include: the optimal number of dose points to use; the best way to apportion the total number of cells among these dose points; and the spacing of dose intervals. Counterintuitively, our simulation results suggest that 4-5 radiation doses were typically optimal, whereas adding more dose points may actually prove detrimental. Superior results were also obtained by implementing unequal dose spacing and unequal distributions in the number of cells scored at each dose.

Novel tilt-curvature coupling in lipid membranes

NASA Astrophysics Data System (ADS)

Terzi, M. Mert; Deserno, Markus

2017-08-01

On mesoscopic scales, lipid membranes are well described by continuum theories whose main ingredients are the curvature of a membrane's reference surface and the tilt of its lipid constituents. In particular, Hamm and Kozlov [Eur. Phys. J. E 3, 323 (2000)] have shown how to systematically derive such a tilt-curvature Hamiltonian based on the elementary assumption of a thin fluid elastic sheet experiencing internal lateral pre-stress. Performing a dimensional reduction, they not only derive the basic form of the effective surface Hamiltonian but also express its emergent elastic couplings as trans-membrane moments of lower-level material parameters. In the present paper, we argue, though, that their derivation unfortunately missed a coupling term between curvature and tilt. This term arises because, as one moves along the membrane, the curvature-induced change of transverse distances contributes to the area strain—an effect that was believed to be small but nevertheless ends up contributing at the same (quadratic) order as all other terms in their Hamiltonian. We illustrate the consequences of this amendment by deriving the monolayer and bilayer Euler-Lagrange equations for the tilt, as well as the power spectra of shape, tilt, and director fluctuations. A particularly curious aspect of our new term is that its associated coupling constant is the second moment of the lipid monolayer's lateral stress profile—which within this framework is equal to the monolayer Gaussian curvature modulus, κ¯ m. On the one hand, this implies that many theoretical predictions now contain a parameter that is poorly known (because the Gauss-Bonnet theorem limits access to the integrated Gaussian curvature); on the other hand, the appearance of κ¯ m outside of its Gaussian curvature provenance opens opportunities for measuring it by more conventional means, for instance by monitoring a membrane's undulation spectrum at short scales.

Novel tilt-curvature coupling in lipid membranes.

PubMed

Terzi, M Mert; Deserno, Markus

2017-08-28

On mesoscopic scales, lipid membranes are well described by continuum theories whose main ingredients are the curvature of a membrane's reference surface and the tilt of its lipid constituents. In particular, Hamm and Kozlov [Eur. Phys. J. E 3, 323 (2000)] have shown how to systematically derive such a tilt-curvature Hamiltonian based on the elementary assumption of a thin fluid elastic sheet experiencing internal lateral pre-stress. Performing a dimensional reduction, they not only derive the basic form of the effective surface Hamiltonian but also express its emergent elastic couplings as trans-membrane moments of lower-level material parameters. In the present paper, we argue, though, that their derivation unfortunately missed a coupling term between curvature and tilt. This term arises because, as one moves along the membrane, the curvature-induced change of transverse distances contributes to the area strain-an effect that was believed to be small but nevertheless ends up contributing at the same (quadratic) order as all other terms in their Hamiltonian. We illustrate the consequences of this amendment by deriving the monolayer and bilayer Euler-Lagrange equations for the tilt, as well as the power spectra of shape, tilt, and director fluctuations. A particularly curious aspect of our new term is that its associated coupling constant is the second moment of the lipid monolayer's lateral stress profile-which within this framework is equal to the monolayer Gaussian curvature modulus, κ¯ m . On the one hand, this implies that many theoretical predictions now contain a parameter that is poorly known (because the Gauss-Bonnet theorem limits access to the integrated Gaussian curvature); on the other hand, the appearance of κ¯ m outside of its Gaussian curvature provenance opens opportunities for measuring it by more conventional means, for instance by monitoring a membrane's undulation spectrum at short scales.

Gut microbial translocation corrupts myeloid cell function to control bacterial infection during liver cirrhosis.

PubMed

Hackstein, Carl-Philipp; Assmus, Lisa Mareike; Welz, Meike; Klein, Sabine; Schwandt, Timo; Schultze, Joachim; Förster, Irmgard; Gondorf, Fabian; Beyer, Marc; Kroy, Daniela; Kurts, Christian; Trebicka, Jonel; Kastenmüller, Wolfgang; Knolle, Percy A; Abdullah, Zeinab

2017-03-01

Patients with liver cirrhosis suffer from increased susceptibility to life-threatening bacterial infections that cause substantial morbidity. Experimental liver fibrosis in mice induced by bile duct ligation or CCl 4 application was used to characterise the mechanisms determining failure of innate immunity to control bacterial infections. In murine liver fibrosis, translocation of gut microbiota induced tonic type I interferon (IFN) expression in the liver. Such tonic IFN expression conditioned liver myeloid cells to produce high concentrations of IFN upon intracellular infection with Listeria that activate cytosolic pattern recognition receptors. Such IFN-receptor signalling caused myeloid cell interleukin (IL)-10 production that corrupted antibacterial immunity, leading to loss of infection-control and to infection-associated mortality. In patients with liver cirrhosis, we also found a prominent liver IFN signature and myeloid cells showed increased IL-10 production after bacterial infection. Thus, myeloid cells are both source and target of IFN-induced and IL-10-mediated immune dysfunction. Antibody-mediated blockade of IFN-receptor or IL-10-receptor signalling reconstituted antibacterial immunity and prevented infection-associated mortality in mice with liver fibrosis. In severe liver fibrosis and cirrhosis, failure to control bacterial infection is caused by augmented IFN and IL-10 expression that incapacitates antibacterial immunity of myeloid cells. Targeted interference with the immune regulatory host factors IL-10 and IFN reconstitutes antibacterial immunity and may be used as therapeutic strategy to control bacterial infections in patients with liver cirrhosis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Cervical curvature variations in patients with infraocclusion.

PubMed

Ando, E; Shigeta, Y; Hirabayashi, R; Ikawa, T; Hirai, S; Katsumura, S; Ogawa, T

2014-08-01

The purpose of this study was to observe the variations of cervical curvature in patients with infraocclusion, and to compare this with the controls. In this study, the infraocclusion criteria were defined with the Pr-id as <17 mm on the cephalometric image. The subjects were 32 patients with infraocclusion, and 28 controls which matched the distribution for gender and age. The six points of inquiry were as follows: (i) cervical vertebra height, (ii) neck alignment, (iii) ratio of lower facial height, (iv) vertical dimension of occlusion, (v) cervical angle and (vi) occlusal angle. In over 90% of the patients with infraocclusion, the cervical curvature was classified as straight or kyphosis. Conversely, in 36% of the control subjects, the cervical curvature was classified as lordosis. There was a weak positive correlation between the vertical dimension of occlusion and the cervical curvature in all subjects. In the control group, there was a significant and strong positive correlation between the age and cervical curvature, and a strong negative correlation between age and cervical angle and occlusal angle. Conversely, in the patients with infraocclusion, age was only correlated with the ratio of lower facial height. The prevalence of non-lordosis in the patients with infraocclusion was higher in comparison with the control group in our study, and the previous large-scale study of Japanese. However, there was merely a weak positive correlation between the cervical curvature and the vertical dimension of occlusion. © 2014 John Wiley & Sons Ltd.

[Changes and clinical significance of peripheral blood natural killer cells in neonates with bacterial pneumonia].

PubMed

Li, Qiuling; Weng, Kaizhi; Zhu, Ling; Mei, Xuqiao; Xu, Liping; Lin, Jiehua

2014-10-01

To detect the percentage of total natural killer (NK) cells and its different populations in the peripheral blood from neonates with bacterial pneumonia and discuss the clinical significance of NK cells in the pathogenesis of bacterial pneumonia. Flow cytometry was performed to detect the percentages of NK cells and its subsets in peripheral blood lymphocytes from 38 cases of neonatal bacterial pneumonias and 18 cases of normal neonates. Patients recruited were divided into two groups according to hospitalization days and numbers of peripheral leukocytes: hospitalization days within 10 days (including 10 days) as group A, and more than 10 days as group B; the number of peripheral blood leukocytes <5.0×10(9)/L or >20.0×10(9)/L as severe infection group, and 5.0×10(9)/L< number of peripheral blood leukocytes <20.0×10(9)/L as mild infection group. The percentages of peripheral blood NK cells and CD3(-)CD56(neg)CD16(bright) subset in the neonates with bacterial pneumonia were significantly lower than those of the normal newborns (P<0.01), but there were no statistically significant differences in CD3(-)CD56(bright)CD16(neg/dim) and CD3(-)CD56(dim)CD16(bright) subsets. The percentage of CD3(-)CD56(neg)CD16(bright) subset in group A was significantly lower than that of the normal newborns (P<0.01), while the percentages of the total NK cells and other subsets had no statistical significance. The neonates with bacterial pneumonia had significantly lower percentages of the total NK cells and CD3(-)CD56(neg)CD16(bright) subset in group B as compared with the normal neonates (P<0.01). And the percentages of the total NK cells and its subsets in group B were also lower than those in group A (P<0.05). The percentages of NK cells and each subset in severe infection group were significantly lower than those in mild infection group (P<0.05). To the neonates who suffer from bacterial pneumonia, the more serious and the longer hospital stay, the lower the percentages of NK

Curvature constraints from the causal entropic principle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozek, Brandon; Albrecht, Andreas; Phillips, Daniel

2009-07-15

Current cosmological observations indicate a preference for a cosmological constant that is drastically smaller than what can be explained by conventional particle physics. The causal entropic principle (Bousso et al.) provides an alternative approach to anthropic attempts to predict our observed value of the cosmological constant by calculating the entropy created within a causal diamond. We have extended this work to use the causal entropic principle to predict the preferred curvature within the 'multiverse'. We have found that values larger than {rho}{sub k}=40{rho}{sub m} are disfavored by more than 99.99% peak value at {rho}{sub {lambda}}=7.9x10{sup -123} and {rho}{sub k}=4.3{rho}{sub m}more » for open universes. For universes that allow only positive curvature or both positive and negative curvature, we find a correlation between curvature and dark energy that leads to an extended region of preferred values. Our universe is found to be disfavored to an extent depending on the priors on curvature. We also provide a comparison to previous anthropic constraints on open universes and discuss future directions for this work.« less

Quantifying phalangeal curvature: an empirical comparison of alternative methods.

PubMed

Stern, J T; Jungers, W L; Susman, R L

1995-05-01

It has been generally assumed and theoretically argued that the curvature of finger and toe bones seen in some nonhuman primates is associated with cheiridial use in an arboreal setting. Assessment of such curvature in fossil primates has been used to infer the positional behavior of these animals. Several methods of quantifying curvature of bones have been proposed. The measure most commonly applied to phalanges is that of included angle, but this has come under some criticism. We consider various other approaches for quantifying phalangeal curvature, demonstrating that some are equivalent to use of included angle, but that one--normalized curvature moment arm (NCMA)--represents a true alternative. A comparison of NCMA to included angle, both calculated on manual and pedal proximal phalanges of humans, apes, some monkeys, and the Hadar fossils, revealed that these two different measures of curvature are highly correlated and result in very similar distributional patterns.

Negative Gaussian curvature induces significant suppression of thermal conduction in carbon crystals.

PubMed

Zhang, Zhongwei; Chen, Jie; Li, Baowen

2017-09-28

From the mathematic category of surface Gaussian curvature, carbon allotropes can be classified into three types: zero curvature, positive curvature, and negative curvature. By performing Green-Kubo equilibrium molecular dynamics simulations, we found that surface curvature has a significant impact on the phonon vibration and thermal conductivity (κ) of carbon crystals. When curving from zero curvature to negative or positive curvature structures, κ is reduced by several orders of magnitude. Interestingly, we found that κ of negatively curved carbon crystals exhibits a monotonic dependence on curvature. Through phonon mode analysis, we show that curvature induces remarkable phonon softening in phonon dispersion, which results in the reduction of phonon group velocity and flattening of phonon band structure. Furthermore, the curvature was found to induce phonon mode hybridization, leading to the suppression of phonon relaxation time. Our study provides physical insight into thermal transport in curvature materials, and will be valuable in the modulation of phonon activity through surface curvature.

Biosensors of bacterial cells.

PubMed

Burlage, Robert S; Tillmann, Joshua

2017-07-01

Biosensors are devices which utilize both an electrical component (transducer) and a biological component to study an environment. They are typically used to examine biological structures, organisms and processes. The field of biosensors has now become so large and varied that the technology can often seem impenetrable. Yet the principles which underlie the technology are uncomplicated, even if the details of the mechanisms are elusive. In this review we confine our analysis to relatively current advancements in biosensors for the detection of whole bacterial cells. This includes biosensors which rely on an added labeled component and biosensors which do not have a labeled component and instead detect the binding event or bound structure on the transducer. Methods to concentrate the bacteria prior to biosensor analysis are also described. The variety of biosensor types and their actual and potential uses are described. Copyright © 2016 Elsevier B.V. All rights reserved.

The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis.

PubMed

Zhou, Zhou; Munteanu, Emilia Laura; He, Jun; Ursell, Tristan; Bathe, Mark; Huang, Kerwyn Casey; Chang, Fred

2015-01-01

The functions of the actin-myosin-based contractile ring in cytokinesis remain to be elucidated. Recent findings show that in the fission yeast Schizosaccharomyces pombe, cleavage furrow ingression is driven by polymerization of cell wall fibers outside the plasma membrane, not by the contractile ring. Here we show that one function of the ring is to spatially coordinate septum cell wall assembly. We develop an improved method for live-cell imaging of the division apparatus by orienting the rod-shaped cells vertically using microfabricated wells. We observe that the septum hole and ring are circular and centered in wild-type cells and that in the absence of a functional ring, the septum continues to ingress but in a disorganized and asymmetric manner. By manipulating the cleavage furrow into different shapes, we show that the ring promotes local septum growth in a curvature-dependent manner, allowing even a misshapen septum to grow into a more regular shape. This curvature-dependent growth suggests a model in which contractile forces of the ring shape the septum cell wall by stimulating the cell wall machinery in a mechanosensitive manner. Mechanical regulation of the cell wall assembly may have general relevance to the morphogenesis of walled cells. © 2015 Zhou et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Bench-to-bedside review: Quorum sensing and the role of cell-to-cell communication during invasive bacterial infection

PubMed Central

Asad, Shadaba; Opal, Steven M

2008-01-01

Bacteria communicate extensively with each other and employ a communal approach to facilitate survival in hostile environments. A hierarchy of cell-to-cell signaling pathways regulates bacterial growth, metabolism, biofilm formation, virulence expression, and a myriad of other essential functions in bacterial populations. The notion that bacteria can signal each other and coordinate their assault patterns against susceptible hosts is now well established. These signaling networks represent a previously unrecognized survival strategy by which bacterial pathogens evade antimicrobial defenses and overwhelm the host. These quorum sensing communication signals can transgress species barriers and even kingdom barriers. Quorum sensing molecules can regulate human transcriptional programs to the advantage of the pathogen. Human stress hormones and cytokines can be detected by bacterial quorum sensing systems. By this mechanism, the pathogen can detect the physiologically stressed host, providing an opportunity to invade when the patient is most vulnerable. These rather sophisticated, microbial communication systems may prove to be a liability to pathogens as they make convenient targets for therapeutic intervention in our continuing struggle to control microbial pathogens. PMID:19040778

Potential effect of cationic liposomes on interactions with oral bacterial cells and biofilms.

PubMed

Sugano, Marika; Morisaki, Hirobumi; Negishi, Yoichi; Endo-Takahashi, Yoko; Kuwata, Hirotaka; Miyazaki, Takashi; Yamamoto, Matsuo

2016-01-01

Although oral infectious diseases have been attributed to bacteria, drug treatments remain ineffective because bacteria and their products exist as biofilms. Cationic liposomes have been suggested to electrostatically interact with the negative charge on the bacterial surface, thereby improving the effects of conventional drug therapies. However, the electrostatic interaction between oral bacteria and cationic liposomes has not yet been examined in detail. The aim of the present study was to examine the behavior of cationic liposomes and Streptococcus mutans in planktonic cells and biofilms. Liposomes with or without cationic lipid were prepared using a reverse-phase evaporation method. The zeta potentials of conventional liposomes (without cationic lipid) and cationic liposomes were -13 and 8 mV, respectively, and both had a mean particle size of approximately 180 nm. We first assessed the interaction between liposomes and planktonic bacterial cells with a flow cytometer. We then used a surface plasmon resonance method to examine the binding of liposomes to biofilms. We confirmed the binding behavior of liposomes with biofilms using confocal laser scanning microscopy. The interactions between cationic liposomes and S. mutans cells and biofilms were stronger than those of conventional liposomes. Microscopic observations revealed that many cationic liposomes interacted with the bacterial mass and penetrated the deep layers of biofilms. In this study, we demonstrated that cationic liposomes had higher affinity not only to oral bacterial cells, but also biofilms than conventional liposomes. This electrostatic interaction may be useful as a potential drug delivery system to biofilms.

Asymptotic behavior of curvature of surface elements in isotropic turbulence

NASA Technical Reports Server (NTRS)

Girimaji, S. S.

1991-01-01

The asymptotic behavior of the curvature of material elements in turbulence is investigated using Lagrangian velocity-gradient time series obtained from direct numerical simulations of isotropic turbulence. Several material-element ensembles of different initial curvatures and shapes are studied. It is found that, at long times, the (first five) moments of the logarithm of characteristic curvature and shape factor asymptote to values that are independent of the initial curvature or shape. This evidence strongly suggests that the asymptotic pdf's of the curvature and shape of material elements are stationary and independent of initial conditions. Irrespective of initial curvature or shape, the asymptotic shape of a material surface is cylindrical with a high probability.

Robust pupil center detection using a curvature algorithm

NASA Technical Reports Server (NTRS)

Zhu, D.; Moore, S. T.; Raphan, T.; Wall, C. C. (Principal Investigator)

1999-01-01

Determining the pupil center is fundamental for calculating eye orientation in video-based systems. Existing techniques are error prone and not robust because eyelids, eyelashes, corneal reflections or shadows in many instances occlude the pupil. We have developed a new algorithm which utilizes curvature characteristics of the pupil boundary to eliminate these artifacts. Pupil center is computed based solely on points related to the pupil boundary. For each boundary point, a curvature value is computed. Occlusion of the boundary induces characteristic peaks in the curvature function. Curvature values for normal pupil sizes were determined and a threshold was found which together with heuristics discriminated normal from abnormal curvature. Remaining boundary points were fit with an ellipse using a least squares error criterion. The center of the ellipse is an estimate of the pupil center. This technique is robust and accurately estimates pupil center with less than 40% of the pupil boundary points visible.

Do adult men with untreated ventral penile curvature have adverse outcomes?

PubMed

Menon, Vani; Breyer, Benjamin; Copp, Hillary L; Baskin, Laurence; Disandro, Michael; Schlomer, Bruce J

2016-02-01

Congenital ventral penile curvature without hypospadias is often treated surgically in childhood. The history of untreated ventral curvature is unknown. This study's aim was to examine the association of untreated ventral penile curvature with various sexual and psychosexual outcomes. An electronic survey was advertised to men older than 18 years on Facebook. Men with possible ventral penile curvature identified themselves by choosing sketches that most closely represented their anatomy. Outcomes assessed included: Sexual Health Inventory for Men, difficulty of intercourse because of curvature, International Prostate Symptom Score, Penile Perception Score, psychosexual milestones, paternity, infertility, sitting to urinate, and the CDC HRQOL-4 module. Among participants, 81 out of 684 men (11.8%) reported untreated ventral penile curvature. Participants with self-reported curvature noted more difficulty with intercourse because of curvature (4.5 vs 4.9, p < 0.001), more unhealthy mental days (8.6 vs 6.2, p = 0.02), and increased dissatisfaction with penile self-perception compared with men without reported curvature (8.6 vs 9.5, p < 0.001). Men with possible untreated ventral curvature reported worse penile perception scores, more mentally unhealthy days, and increased difficulty with intercourse secondary to curvature compared with men without curvature. A limitation to this study is selection bias; responses collected were self-reported from survey volunteers. Additionally, the question identifying ventral penile curvature is not validated but performed well in pretesting. Most questions were from validated surveys, but some were modeled after validated surveys and/or contained high face validity types of questions. Men with possible untreated ventral penile curvature reported more dissatisfaction with penile appearance, increased difficulty with intercourse, and more unhealthy mental days. Given high success rates, low complications, and improved outcomes after

Do adult men with untreated ventral penile curvature have adverse outcomes?

PubMed Central

Menon, Vani; Breyer, Benjamin; Copp, Hillary L.; Baskin, Laurence; Disandro, Michael; Schlomer, Bruce J.

2016-01-01

Summary Introduction Congenital ventral penile curvature without hypospadias is often treated surgically in childhood. The history of untreated ventral curvature is unknown. Objective This study’s aim was to examine the association of untreated ventral penile curvature with various sexual and psychosexual outcomes. Study design An electronic survey was advertised to men older than 18 years on Facebook. Men with possible ventral penile curvature identified themselves by choosing sketches that most closely represented their anatomy. Outcomes assessed included: Sexual Health Inventory for Men, difficulty of intercourse because of curvature, International Prostate Symptom Score, Penile Perception Score, psychosexual milestones, paternity, infertility, sitting to urinate, and the CDC HRQOL-4 module. Results Among participants, 81 out of 684 men (11.8%) reported untreated ventral penile curvature. Participants with self-reported curvature noted more difficulty with intercourse because of curvature (4.5 vs 4.9, p < 0.001), more unhealthy mental days (8.6 vs 6.2, p = 0.02), and increased dissatisfaction with penile self-perception compared with men without reported curvature (8.6 vs 9.5, p < 0.001). Discussion Men with possible untreated ventral curvature reported worse penile perception scores, more mentally unhealthy days, and increased difficulty with intercourse secondary to curvature compared with men without curvature. A limitation to this study is selection bias; responses collected were self-reported from survey volunteers. Additionally, the question identifying ventral penile curvature is not validated but performed well in pretesting. Most questions were from validated surveys, but some were modeled after validated surveys and/or contained high face validity types of questions. Conclusion Men with possible untreated ventral penile curvature reported more dissatisfaction with penile appearance, increased difficulty with intercourse, and more unhealthy mental

Curvature Continuous and Bounded Path Planning for Fixed-Wing UAVs

PubMed Central

Jiang, Peng; Li, Deshi; Sun, Tao

2017-01-01

Unmanned Aerial Vehicles (UAVs) play an important role in applications such as data collection and target reconnaissance. An accurate and optimal path can effectively increase the mission success rate in the case of small UAVs. Although path planning for UAVs is similar to that for traditional mobile robots, the special kinematic characteristics of UAVs (such as their minimum turning radius) have not been taken into account in previous studies. In this paper, we propose a locally-adjustable, continuous-curvature, bounded path-planning algorithm for fixed-wing UAVs. To deal with the curvature discontinuity problem, an optimal interpolation algorithm and a key-point shift algorithm are proposed based on the derivation of a curvature continuity condition. To meet the upper bound for curvature and to render the curvature extrema controllable, a local replanning scheme is designed by combining arcs and Bezier curves with monotonic curvature. In particular, a path transition mechanism is built for the replanning phase using minimum curvature circles for a planning philosophy. Numerical results demonstrate that the analytical planning algorithm can effectively generate continuous-curvature paths, while satisfying the curvature upper bound constraint and allowing UAVs to pass through all predefined waypoints in the desired mission region. PMID:28925960

Single-lipid tracking on nanoscale membrane buds: The effects of curvature on lipid diffusion and sorting.

PubMed

Woodward, Xinxin; Stimpson, Eric E; Kelly, Christopher V

2018-05-29

Nanoscale membrane curvature in cells is critical for endocytosis/exocytosis and membrane trafficking. However, the biophysical ramifications of nanoscale membrane curvature on the behavior of lipids remain poorly understood. Here, we created an experimental model system of membrane curvature at a physiologically-relevant scale and obtained nanoscopic information on single-lipid distributions and dynamics. Supported lipid bilayers were created over 50 and 70 nm radius nanoparticles to create membrane buds. Single-molecule localization microscopy was performed with diverse mixtures of fluorescent and non-fluorescent lipids. Variations in lipid acyl tales length, saturation, head-group, and fluorescent labeling strategy were tested while maintaining a single fluid lipid phase throughout the membrane. Monte Carlo simulations were used to fit our experimental results and quantify the effects of curvature on the lipid diffusion and sorting. Whereas varying the composition of the non-fluorescent lipids yielded minimal changes to the curvature effects, the labeling strategy of the fluorescent lipids yielded highly varying effects of curvature. Most conditions yield single-population Brownian diffusion throughout the membrane; however, curvature-induced lipid sorting, slowing, and aggregation were observed in some conditions. Head-group labeled lipids such as DPPE-Texas Red and POPE-Rhodamine diffused >2.4× slower on the curved vs. the planar membranes; tail-labeled lipids such as NBD-PPC, TopFluor-PPC, TopFluor-PIP2, DiIC 12 , and DiIC 18 displayed no significant changes in diffusion due to the membrane curvature. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo. Copyright © 2018. Published by Elsevier B.V.

Inverse curvature flows in asymptotically Robertson Walker spaces

NASA Astrophysics Data System (ADS)

Kröner, Heiko

2018-04-01

In this paper we consider inverse curvature flows in a Lorentzian manifold N which is the topological product of the real numbers with a closed Riemannian manifold and equipped with a Lorentzian metric having a future singularity so that N is asymptotically Robertson Walker. The flow speeds are future directed and given by 1 / F where F is a homogeneous degree one curvature function of class (K*) of the principal curvatures, i.e. the n-th root of the Gauss curvature. We prove longtime existence of these flows and that the flow hypersurfaces converge to smooth functions when they are rescaled with a proper factor which results from the asymptotics of the metric.

3D curvature of muscle fascicles in triceps surae

PubMed Central

Hamarneh, Ghassan; Wakeling, James M.

2014-01-01

Muscle fascicles curve along their length, with the curvatures occurring around regions of high intramuscular pressure, and are necessary for mechanical stability. Fascicles are typically considered to lie in fascicle planes that are the planes visualized during dissection or two-dimensional (2D) ultrasound scans. However, it has previously been predicted that fascicles must curve in three-dimensional (3D) and thus the fascicle planes may actually exist as 3D sheets. 3D fascicle curvatures have not been explored in human musculature. Furthermore, if the fascicles do not lie in 2D planes, then this has implications for architectural measures that are derived from 2D ultrasound scans. The purpose of this study was to quantify the 3D curvatures of the muscle fascicles and fascicle sheets within the triceps surae muscles and to test whether these curvatures varied among different contraction levels, muscle length, and regions within the muscle. Six male subjects were tested for three torque levels (0, 30, and 60% maximal voluntary contraction) and four ankle angles (−15, 0, 15, and 30° plantar flexion), and fascicles were imaged using 3D ultrasound techniques. The fascicle curvatures significantly increased at higher ankle torques and shorter muscle lengths. The fascicle sheet curvatures were of similar magnitude to the fascicle curvatures but did not vary between contractions. Fascicle curvatures were regionalized within each muscle with the curvature facing the deeper aponeuroses, and this indicates a greater intramuscular pressure in the deeper layers of muscles. Muscle architectural measures may be in error when using 2D images for complex geometries such as the soleus. PMID:25324510

Toxicity of a polymer-graphene oxide composite against bacterial planktonic cells, biofilms, and mammalian cells

NASA Astrophysics Data System (ADS)

Mejías Carpio, Isis E.; Santos, Catherine M.; Wei, Xin; Rodrigues, Debora F.

2012-07-01

It is critical to develop highly effective antimicrobial agents that are not harmful to humans and do not present adverse effects on the environment. Although antimicrobial studies of graphene-based nanomaterials are still quite limited, some researchers have paid particular attention to such nanocomposites as promising candidates for the next generation of antimicrobial agents. The polyvinyl-N-carbazole (PVK)-graphene oxide (GO) nanocomposite (PVK-GO), which contains only 3 wt% of GO well-dispersed in a 97 wt% PVK matrix, presents excellent antibacterial properties without significant cytotoxicity to mammalian cells. The high polymer content in this nanocomposite makes future large-scale material manufacturing possible in a high-yield process of adiabatic bulk polymerization. In this study, the toxicity of PVK-GO was assessed with planktonic microbial cells, biofilms, and NIH 3T3 fibroblast cells. The antibacterial effects were evaluated against two Gram-negative bacteria: Escherichia coli and Cupriavidus metallidurans; and two Gram-positive bacteria: Bacillus subtilis and Rhodococcus opacus. The results show that the PVK-GO nanocomposite presents higher antimicrobial effects than the pristine GO. The effectiveness of the PVK-GO in solution was demonstrated as the nanocomposite ``encapsulated'' the bacterial cells, which led to reduced microbial metabolic activity and cell death. The fact that the PVK-GO did not present significant cytotoxicity to fibroblast cells offers a great opportunity for potential applications in important biomedical and industrial fields.It is critical to develop highly effective antimicrobial agents that are not harmful to humans and do not present adverse effects on the environment. Although antimicrobial studies of graphene-based nanomaterials are still quite limited, some researchers have paid particular attention to such nanocomposites as promising candidates for the next generation of antimicrobial agents. The polyvinyl

Dislocation-mediated growth of bacterial cell walls

PubMed Central

Amir, Ariel; Nelson, David R.

2012-01-01

Recent experiments have illuminated a remarkable growth mechanism of rod-shaped bacteria: proteins associated with cell wall extension move at constant velocity in circles oriented approximately along the cell circumference [Garner EC, et al., (2011) Science 333:222–225], [Domínguez-Escobar J, et al. (2011) Science 333:225–228], [van Teeffelen S, et al. (2011) PNAS 108:15822–15827]. We view these as dislocations in the partially ordered peptidoglycan structure, activated by glycan strand extension machinery, and study theoretically the dynamics of these interacting defects on the surface of a cylinder. Generation and motion of these interacting defects lead to surprising effects arising from the cylindrical geometry, with important implications for growth. We also discuss how long range elastic interactions and turgor pressure affect the dynamics of the fraction of actively moving dislocations in the bacterial cell wall. PMID:22660931

Curvature-induced stiffening of a fish fin.

PubMed

Nguyen, Khoi; Yu, Ning; Bandi, Mahesh M; Venkadesan, Madhusudhan; Mandre, Shreyas

2017-05-01

How fish modulate their fin stiffness during locomotive manoeuvres remains unknown. We show that changing the fin's curvature modulates its stiffness. Modelling the fin as bendable bony rays held together by a membrane, we deduce that fin curvature is manifested as a misalignment of the principal bending axes between neighbouring rays. An external force causes neighbouring rays to bend and splay apart, and thus stretches the membrane. This coupling between bending the rays and stretching the membrane underlies the increase in stiffness. Using three-dimensional reconstruction of a mackerel ( Scomber japonicus ) pectoral fin for illustration, we calculate the range of stiffnesses this fin is expected to span by changing curvature. The three-dimensional reconstruction shows that, even in its geometrically flat state, a functional curvature is embedded within the fin microstructure owing to the morphology of individual rays. As the ability of a propulsive surface to transmit force to the surrounding fluid is limited by its stiffness, the fin curvature controls the coupling between the fish and its surrounding fluid. Thereby, our results provide mechanical underpinnings and morphological predictions for the hypothesis that the spanned range of fin stiffnesses correlates with the behaviour and the ecological niche of the fish. © 2017 The Author(s).

Curvature-induced stiffening of a fish fin

PubMed Central

2017-01-01

How fish modulate their fin stiffness during locomotive manoeuvres remains unknown. We show that changing the fin's curvature modulates its stiffness. Modelling the fin as bendable bony rays held together by a membrane, we deduce that fin curvature is manifested as a misalignment of the principal bending axes between neighbouring rays. An external force causes neighbouring rays to bend and splay apart, and thus stretches the membrane. This coupling between bending the rays and stretching the membrane underlies the increase in stiffness. Using three-dimensional reconstruction of a mackerel (Scomber japonicus) pectoral fin for illustration, we calculate the range of stiffnesses this fin is expected to span by changing curvature. The three-dimensional reconstruction shows that, even in its geometrically flat state, a functional curvature is embedded within the fin microstructure owing to the morphology of individual rays. As the ability of a propulsive surface to transmit force to the surrounding fluid is limited by its stiffness, the fin curvature controls the coupling between the fish and its surrounding fluid. Thereby, our results provide mechanical underpinnings and morphological predictions for the hypothesis that the spanned range of fin stiffnesses correlates with the behaviour and the ecological niche of the fish. PMID:28566508

Towards understanding of Nipah virus attachment protein assembly and the role of protein affinity and crowding for membrane curvature events.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stachowiak, Jeanne C.; Hayden, Carl C.; Negrete, Oscar.

2013-10-01

Pathogenic viruses are a primary threat to our national security and to the health and economy of our world. Effective defense strategies to combat viral infection and spread require the development of understanding of the mechanisms that these pathogens use to invade the host cell. We present in this report results of our research into viral particle recognition and fusion to cell membranes and the role that protein affinity and confinement in lipid domains plays in membrane curvature in cellular fusion and fission events. Herein, we describe 1) the assembly of the G attachment protein of Nipah virus using pointmore » mutation studies to define its role in viral particle fusion to the cell membrane, 2) how lateral pressure of membrane bound proteins induce curvature in model membrane systems, and 3) the role of membrane curvature in the selective partitioning of molecular receptors and specific affinity of associated proteins.« less

Different Pattern of Inflammatory and Atrophic Changes in the Gastric Mucosa of the Greater and Lesser Curvature.

PubMed

Isajevs, Sergejs; Liepniece-Karele, Inta; Svirina, Darja; Santare, Daiga; Kaidaks, Sandris; Sivins, Armands; Vikmanis, Uldis; Leja, Marcis

2015-12-01

Appropriate biopsy sampling is important for the classification of gastritis, yet the extent of inflammation and atrophy of different regions of the stomach with chronic gastritis have been addressed only in a few studies. The aim of our study was to analyze the inflammatory, atrophic and metaplastic changes in the greater and lesser curvature of the antrum and corpus mucosa. 420 patients undergoing upper endoscopy were enrolled in the study. Four expert gastrointestinal pathologists graded biopsy specimens according to the updated Sydney classification. The obtained results showed that the mononuclear and granulocyte inflammatory cells were more prominent in the corpus lesser curvature compared to the corpus greater curvature (p=0.01 and p=0.0001, respectively). In addition, the extent and degree of atrophy and intestinal metaplasia were more prominent in the corpus lesser compared to the greater curvature (p=0.002 and p=0.0065, respectively). The frequency of distribution of H. pylori did not differ throughout both the corpus and antrum greater and lesser curvature. However, the degree of H. pylori colonization in the corpus was higher in the lesser than in the greater curvature. The interobserver agreement was significantly higher for corpus atrophy compared to antrum atrophy. These findings demonstrated that the more severe atrophic, metaplastic and inflammatory changes were observed in the lesser compared to the greater curvature of the stomach. In routine clinical settings, corpus and antral biopsies should be obtained from both lesser and greater curvature. Analysis of the incisura biopsy is also important.

Biological and cognitive correlates of cortical curvature in schizophrenia.

PubMed

Lubeiro, Alba; de Luis-García, Rodrigo; Rodríguez, Margarita; Álvarez, Aldara; de la Red, Henar; Molina, Vicente

2017-10-27

Mean cortical curvature may relate to cortico-cortical connections integrity. We explored the association between prefrontal (PFC) cortical curvature and fractional anisotropy (FA) values for tracts connecting PFC and relevant cortical regions. In schizophrenia Anatomical and diffusion magnetic resonance images were obtained from 34 patients (16 of them first-episodes) and 32 healthy controls. We calculated curvature at rostral lateral prefrontal (RLPF) and superior medial prefrontal (SMPF) areas and mean FA for the tracts respectively connecting RLPF and SMPF areas with anterior caudal cingulate (ACC), superior temporal gyrus (STG) and superior parietal SP regions. Cognitive and clinical data were collected, including baseline symptoms, Clinical Global Impression change scores from baseline to follow-up, illness duration and treatment dosage. Patients showed significantly lower FA values in the tracts linking right RLPF-ACC, right SMPF-SPG and bilaterally PFC-STG. FA values in short-range cortico-cortical connections (linking PFC and ACC) were inversely associated with PFC curvature. In patients, cognitive performance was negatively associated with PFC curvature. Larger curvature values were associated to lack of clinical improvement at follow-up. We conclude that cortical curvature is influenced by integrity in short-range cortico-cortical connections and relates to cognition and clinical outcome in schizophrenia patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial actin MreB assembles in complex with cell shape protein RodZ.

PubMed

van den Ent, Fusinita; Johnson, Christopher M; Persons, Logan; de Boer, Piet; Löwe, Jan

2010-03-17

Bacterial actin homologue MreB is required for cell shape maintenance in most non-spherical bacteria, where it assembles into helical structures just underneath the cytoplasmic membrane. Proper assembly of the actin cytoskeleton requires RodZ, a conserved, bitopic membrane protein that colocalises to MreB and is essential for cell shape determination. Here, we present the first crystal structure of bacterial actin engaged with a natural partner and provide a clear functional significance of the interaction. We show that the cytoplasmic helix-turn-helix motif of Thermotoga maritima RodZ directly interacts with monomeric as well as filamentous MreB and present the crystal structure of the complex. In vitro and in vivo analyses of mutant T. maritima and Escherichia coli RodZ validate the structure and reveal the importance of the MreB-RodZ interaction in the ability of cells to propagate as rods. Furthermore, the results elucidate how the bacterial actin cytoskeleton might be anchored to the membrane to help constrain peptidoglycan synthesis in the periplasm.

Curvature-induced domain wall pinning

NASA Astrophysics Data System (ADS)

Yershov, Kostiantyn V.; Kravchuk, Volodymyr P.; Sheka, Denis D.; Gaididei, Yuri

2015-09-01

It is shown that a local bend of a nanowire is a source of pinning potential for a transversal head-to-head (tail-to-tail) domain wall. Eigenfrequency of the domain wall free oscillations at the pinning potential and the effective friction are determined as functions of the curvature and domain wall width. The pinning potential originates from the effective curvature-induced Dzyaloshinsky-like term in the exchange energy. The theoretical results are verified by means of micromagnetic simulations for the case of parabolic shape of the wire bend.

Congenital penile curvature: update and management.

PubMed

Makovey, Iryna; Higuchi, Ty T; Montague, Drogo K; Angermeier, Kenneth W; Wood, Hadley M

2012-08-01

Congenital penile curvature results from disproportionate development of the tunica albuginea of the corporal bodies and is not associated with urethral malformation. Patients usually present after reaching puberty as the curvature becomes more apparent with erections, and severe curvature can make intercourse difficult or impossible, at which point surgical repair is recommended. Excellent outcomes can be expected with surgical intervention. The three most commonly used repair techniques are the original Nesbit procedure, modified Nesbit procedure, and plication. Nesbit and modified Nesbit techniques require that an incision is made in the tunica albuginea while plication techniques utilize plicating sutures without an incision. While Nesbit and modified Nesbit techniques are more complex operations, these generally result in less recurrences and more satisfactory outcomes as opposed to the quicker and simpler plication technique.

The interaction of bacterial magnetosomes and human liver cancer cells in vitro

NASA Astrophysics Data System (ADS)

Wang, Pingping; Chen, Chuanfang; Chen, Changyou; Li, Yue; Pan, Weidong; Song, Tao

2017-04-01

As the biogenic magnetic nanomaterial, bacterial magnetic nanoparticles, namely magnetosomes, provide many advantages for potential biomedical applications. As such, interactions among magnetosomes and target cells should be elucidated to develop their bioapplications and evaluate their biocompatibilities. In this study, the interaction of magnetosomes and human liver cancer HepG2 cells was examined. Prussian blue staining revealed numerous stained particles in or on the cells. Intracellular iron concentrations, measured through inductively coupled plasma optical emission spectroscopy, increased with the increasing concentration of the magnetosomes. Transmission electron microscopy images showed that magnetosomes could be internalized in cells, mainly encapsulated in membrane vesicles, such as endosomes and lysosomes, and partly found as free particles in the cytosol. Some of the magnetosomes on cellular surfaces were encapsulated through cell membrane ruffling, which is the initiating process of endocytosis. Applying low temperature treatment and using specific endocytic inhibitors, we validated that macropinocytosis and clathrin-mediated endocytosis were involved in magnetosome uptake by HepG2 cells. Consequently, we revealed the interaction and intrinsic endocytic mechanisms of magnetosomes and HepG2 cells. This study provides a basis for the further research on bacterial magnetosome applications in liver diseases.

One Bacterial Cell, One Complete Genome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos

2010-04-26

While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated frommore » the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.« less

The Disruptive Effect of Lysozyme on the Bacterial Cell Wall Explored by an "In-Silico" Structural Outlook

ERIC Educational Resources Information Center

Primo, Emiliano D.; Otero, Lisandro H.; Ruiz, Francisco; Klinke, Sebastián; Giordano, Walter

2018-01-01

The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall…

Aging and curvature discrimination from static and dynamic touch.

PubMed

Norman, J Farley; Kappers, Astrid M L; Cheeseman, Jacob R; Ronning, Cecilia; Thomason, Kelsey E; Baxter, Michael W; Calloway, Autum B; Lamirande, Davora N

2013-01-01

Two experiments evaluated the ability of 30 older and younger adults to discriminate the curvature of simple object surfaces from static and dynamic touch. The ages of the older adults ranged from 66 to 85 years, while those of the younger adults ranged from 20 to 29 years. For each participant in both experiments, the minimum curvature magnitude needed to reliably discriminate between convex and concave surfaces was determined. In Experiment 1, participants used static touch to make their judgments of curvature, while dynamic touch was used in Experiment 2. When static touch was used to discriminate curvature, a large effect of age occurred (the thresholds were 0.67 & 1.11/m for the younger and older participants, respectively). However, when participants used dynamic touch, there was no significant difference between the ability of younger and older participants to discriminate curvature (the thresholds were 0.58 & 0.59/m for the younger and older participants, respectively). The results of the current study demonstrate that while older adults can accurately discriminate surface curvature from dynamic touch, they possess significant impairments for static touch.

Trafficking and processing of bacterial proteins by mammalian cells: Insights from chondroitinase ABC.

PubMed

Muir, Elizabeth; Raza, Mansoor; Ellis, Clare; Burnside, Emily; Love, Fiona; Heller, Simon; Elliot, Matthew; Daniell, Esther; Dasgupta, Debayan; Alves, Nuno; Day, Priscilla; Fawcett, James; Keynes, Roger

2017-01-01

There is very little reported in the literature about the relationship between modifications of bacterial proteins and their secretion by mammalian cells that synthesize them. We previously reported that the secretion of the bacterial enzyme Chondroitinase ABC by mammalian cells requires the strategic removal of at least three N-glycosylation sites. The aim of this study was to determine if it is possible to enhance the efficacy of the enzyme as a treatment for spinal cord injury by increasing the quantity of enzyme secreted or by altering its cellular location. To determine if the efficiency of enzyme secretion could be further increased, cells were transfected with constructs encoding the gene for chondroitinase ABC modified for expression by mammalian cells; these contained additional modifications of strategic N-glycosylation sites or alternative signal sequences to direct secretion of the enzyme from the cells. We show that while removal of certain specific N-glycosylation sites enhances enzyme secretion, N-glycosylation of at least two other sites, N-856 and N-773, is essential for both production and secretion of active enzyme. Furthermore, we find that the signal sequence directing secretion also influences the quantity of enzyme secreted, and that this varies widely amongst the cell types tested. Last, we find that replacing the 3'UTR on the cDNA encoding Chondroitinase ABC with that of β-actin is sufficient to target the enzyme to the neuronal growth cone when transfected into neurons. This also enhances neurite outgrowth on an inhibitory substrate. Some intracellular trafficking pathways are adversely affected by cryptic signals present in the bacterial gene sequence, whilst unexpectedly others are required for efficient secretion of the enzyme. Furthermore, targeting chondroitinase to the neuronal growth cone promotes its ability to increase neurite outgrowth on an inhibitory substrate. These findings are timely in view of the renewed prospects for

Human Lung Fibroblasts Present Bacterial Antigens to Autologous Lung Th Cells.

PubMed

Hutton, Andrew J; Polak, Marta E; Spalluto, C Mirella; Wallington, Joshua C; Pickard, Chris; Staples, Karl J; Warner, Jane A; Wilkinson, Tom M A

2017-01-01

Lung fibroblasts are key structural cells that reside in the submucosa where they are in contact with large numbers of CD4 + Th cells. During severe viral infection and chronic inflammation, the submucosa is susceptible to bacterial invasion by lung microbiota such as nontypeable Haemophilus influenzae (NTHi). Given their proximity in tissue, we hypothesized that human lung fibroblasts play an important role in modulating Th cell responses to NTHi. We demonstrate that fibroblasts express the critical CD4 + T cell Ag-presentation molecule HLA-DR within the human lung, and that this expression can be recapitulated in vitro in response to IFN-γ. Furthermore, we observed that cultured lung fibroblasts could internalize live NTHi. Although unable to express CD80 and CD86 in response to stimulation, fibroblasts expressed the costimulatory molecules 4-1BBL, OX-40L, and CD70, all of which are related to memory T cell activation and maintenance. CD4 + T cells isolated from the lung were predominantly (mean 97.5%) CD45RO + memory cells. Finally, cultured fibroblasts activated IFN-γ and IL-17A cytokine production by autologous, NTHi-specific lung CD4 + T cells, and cytokine production was inhibited by a HLA-DR blocking Ab. These results indicate a novel role for human lung fibroblasts in contributing to responses against bacterial infection through activation of bacteria-specific CD4 + T cells. Copyright © 2016 by The American Association of Immunologists, Inc.

Curvature reduces bending strains in the quokka femur

PubMed Central

McCabe, Kyle; Henderson, Keith; Pantinople, Jess; Milne, Nick

2017-01-01

This study explores how curvature in the quokka femur may help to reduce bending strain during locomotion. The quokka is a small wallaby, but the curvature of the femur and the muscles active during stance phase are similar to most quadrupedal mammals. Our hypothesis is that the action of hip extensor and ankle plantarflexor muscles during stance phase place cranial bending strains that act to reduce the caudal curvature of the femur. Knee extensors and biarticular muscles that span the femur longitudinally create caudal bending strains in the caudally curved (concave caudal side) bone. These opposing strains can balance each other and result in less strain on the bone. We test this idea by comparing the performance of a normally curved finite element model of the quokka femur to a digitally straightened version of the same bone. The normally curved model is indeed less strained than the straightened version. To further examine the relationship between curvature and the strains in the femoral models, we also tested an extra-curved and a reverse-curved version with the same loads. There appears to be a linear relationship between the curvature and the strains experienced by the models. These results demonstrate that longitudinal curvature in bones may be a manipulable mechanism whereby bone can induce a strain gradient to oppose strains induced by habitual loading. PMID:28348929

Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing

NASA Astrophysics Data System (ADS)

Riba, J.; Gleichmann, T.; Zimmermann, S.; Zengerle, R.; Koltay, P.

2016-09-01

The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry.

Disformal invariance of curvature perturbation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Motohashi, Hayato; White, Jonathan, E-mail: motohashi@kicp.uchicago.edu, E-mail: jwhite@post.kek.jp

2016-02-01

We show that under a general disformal transformation the linear comoving curvature perturbation is not identically invariant, but is invariant on superhorizon scales for any theory that is disformally related to Horndeski's theory. The difference between disformally related curvature perturbations is found to be given in terms of the comoving density perturbation associated with a single canonical scalar field. In General Relativity it is well-known that this quantity vanishes on superhorizon scales through the Poisson equation that is obtained on combining the Hamiltonian and momentum constraints, and we confirm that a similar result holds for any theory that is disformallymore » related to Horndeski's scalar-tensor theory so long as the invertibility condition for the disformal transformation is satisfied. We also consider the curvature perturbation at full nonlinear order in the unitary gauge, and find that it is invariant under a general disformal transformation if we assume that an attractor regime has been reached. Finally, we also discuss the counting of degrees of freedom in theories disformally related to Horndeski's.« less

Sequence periodicity in nucleosomal DNA and intrinsic curvature.

PubMed

Nair, T Murlidharan

2010-05-17

Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.

Sequence periodicity in nucleosomal DNA and intrinsic curvature

PubMed Central

2010-01-01

Background Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Results Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. Conclusions The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA. PMID:20487515

On 3-gauge transformations, 3-curvatures, and Gray-categories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Wei, E-mail: wwang@zju.edu.cn

In the 3-gauge theory, a 3-connection is given by a 1-form A valued in the Lie algebra g, a 2-form B valued in the Lie algebra h, and a 3-form C valued in the Lie algebra l, where (g,h,l) constitutes a differential 2-crossed module. We give the 3-gauge transformations from one 3-connection to another, and show the transformation formulae of the 1-curvature 2-form, the 2-curvature 3-form, and the 3-curvature 4-form. The gauge configurations can be interpreted as smooth Gray-functors between two Gray 3-groupoids: the path 3-groupoid P{sub 3}(X) and the 3-gauge group G{sup L} associated to the 2-crossed module L,more » whose differential is (g,h,l). The derivatives of Gray-functors are 3-connections, and the derivatives of lax-natural transformations between two such Gray-functors are 3-gauge transformations. We give the 3-dimensional holonomy, the lattice version of the 3-curvature, whose derivative gives the 3-curvature 4-form. The covariance of 3-curvatures easily follows from this construction. This Gray-categorical construction explains why 3-gauge transformations and 3-curvatures have the given forms. The interchanging 3-arrows are responsible for the appearance of terms with the Peiffer commutator (, )« less

Dynamic curvature sensing employing ionic-polymer-metal composite sensors

NASA Astrophysics Data System (ADS)

Bahramzadeh, Yousef; Shahinpoor, Mohsen

2011-09-01

A dynamic curvature sensor is presented based on ionic-polymer-metal composite (IPMC) for curvature monitoring of deployable/inflatable dynamic space structures. Monitoring the curvature variation is of high importance in various engineering structures including shape monitoring of deployable/inflatable space structures in which the structural boundaries undergo a dynamic deployment process. The high sensitivity of IPMCs to the applied deformations as well as its flexibility make IPMCs a promising candidate for sensing of dynamic curvature changes. Herein, we explore the dynamic response of an IPMC sensor strip with respect to controlled curvature deformations subjected to different forms of input functions. Using a specially designed experimental setup, the voltage recovery effect, phase delay, and rate dependency of the output voltage signal of an IPMC curvature sensor are analyzed. Experimental results show that the IPMC sensor maintains the linearity, sensitivity, and repeatability required for curvature sensing. Besides, in order to describe the dynamic phenomena such as the rate dependency of the IPMC sensor, a chemo-electro-mechanical model based on the Poisson-Nernst-Planck (PNP) equation for the kinetics of ion diffusion is presented. By solving the governing partial differential equations the frequency response of the IPMC sensor is derived. The physical model is able to describe the dynamic properties of the IPMC sensor and the dependency of the signal on rate of excitations.

Curvature and bow of bulk GaN substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foronda, Humberto M.; Young, Erin C.; Robertson, Christian A.

2016-07-21

We investigate the bow of free standing (0001) oriented hydride vapor phase epitaxy grown GaN substrates and demonstrate that their curvature is consistent with a compressive to tensile stress gradient (bottom to top) present in the substrates. The origin of the stress gradient and the curvature is attributed to the correlated inclination of edge threading dislocation (TD) lines away from the [0001] direction. A model is proposed and a relation is derived for bulk GaN substrate curvature dependence on the inclination angle and the density of TDs. The model is used to analyze the curvature for commercially available GaN substratesmore » as determined by high resolution x-ray diffraction. The results show a close correlation between the experimentally determined parameters and those predicted from theoretical model.« less

Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity.

PubMed

Binder, Dennis; Drepper, Thomas; Jaeger, Karl-Erich; Delvigne, Frank; Wiechert, Wolfgang; Kohlheyer, Dietrich; Grünberger, Alexander

2017-07-01

In natural habitats, microbes form multispecies communities that commonly face rapidly changing and highly competitive environments. Thus, phenotypic heterogeneity has evolved as an innate and important survival strategy to gain an overall fitness advantage over cohabiting competitors. However, in defined artificial environments such as monocultures in small- to large-scale bioreactors, cell-to-cell variations are presumed to cause reduced production yields as well as process instability. Hence, engineering microbial production toward phenotypic homogeneity is a highly promising approach for synthetic biology and bioprocess optimization. In this review, we discuss recent studies that have unraveled the cell-to-cell heterogeneity observed during bacterial gene expression and metabolite production as well as the molecular mechanisms involved. In addition, current single-cell technologies are briefly reviewed with respect to their applicability in exploring cell-to-cell variations. We highlight emerging strategies and tools to reduce phenotypic heterogeneity in biotechnological expression setups. Here, strain or inducer modifications are combined with cell physiology manipulations to achieve the ultimate goal of equalizing bacterial populations. In this way, the majority of cells can be forced into high productivity, thus reducing less productive subpopulations that tend to consume valuable resources during production. Modifications in uptake systems, inducer molecules or nutrients represent valuable tools for diminishing heterogeneity. Finally, we address the challenge of transferring homogeneously responding cells into large-scale bioprocesses. Environmental heterogeneity originating from extrinsic factors such as stirring speed and pH, oxygen, temperature or nutrient distribution can significantly influence cellular physiology. We conclude that engineering microbial populations toward phenotypic homogeneity is an increasingly important task to take biotechnological

Dysregulated luminal bacterial antigen-specific T-cell responses and antigen-presenting cell function in HLA-B27 transgenic rats with chronic colitis

PubMed Central

Qian, Bi-Feng; Tonkonogy, Susan L; Hoentjen, Frank; Dieleman, Levinus A; Sartor, R Balfour

2005-01-01

HLA-B27/β2 microglobulin transgenic (TG) rats spontaneously develop T-cell-mediated colitis when colonized with normal commensal bacteria, but remain disease-free under germ-free conditions. We investigated regulation of in vitro T-cell responses to enteric bacterial components. Bacterial lysates prepared from the caecal contents of specific pathogen-free (SPF) rats stimulated interferon-γ (IFN-γ) production by TG but not non-TG mesenteric lymph node (MLN) cells. In contrast, essentially equivalent amounts of interleukin-10 (IL-10) were produced by TG and non-TG cells. However, when cells from MLNs of non-TG rats were cocultured with TG MLN cells, no suppression of IFN-γ production was noted. Both non-TG and TG antigen-presenting cells (APC) pulsed with caecal bacterial lysate were able to induce IFN-γ production by TG CD4+ cells, although non-TG APC were more efficient than TG APC. Interestingly, the addition of exogenous IL-10 inhibited non-TG APC but not TG APC stimulation of IFN-γ production by cocultured TG CD4+ lymphocytes. Conversely, in the presence of exogenous IFN-γ, production of IL-10 was significantly lower in the supernatants of TG compared to non-TG APC cultures. We conclude that commensal luminal bacterial components induce exaggerated in vitro IFN-γ responses in HLA-B27 TG T cells, which may in turn inhibit the production of regulatory molecules, such as IL-10. Alterations in the production of IFN-γ, and in responses to this cytokine, as well as possible resistance of TG cells to suppressive regulation could together contribute to the development of chronic colitis in TG rats. PMID:16108823

Inequalities for scalar curvature of pseudo-Riemannian submanifolds

NASA Astrophysics Data System (ADS)

Tripathi, Mukut Mani; Gülbahar, Mehmet; Kılıç, Erol; Keleş, Sadık

2017-02-01

Some basic inequalities, involving the scalar curvature and the mean curvature, for a pseudo-Riemannian submanifold of a pseudo-Riemannian manifold are obtained. We also find inequalities for spacelike submanifolds. Equality cases are also discussed.

Enhanced Toxic Metal Accumulation in Engineered Bacterial Cells Expressing Arabidopsis thaliana Phytochelatin Synthase

PubMed Central

Sauge-Merle, Sandrine; Cuiné, Stéphan; Carrier, Patrick; Lecomte-Pradines, Catherine; Luu, Doan-Trung; Peltier, Gilles

2003-01-01

Phytochelatins (PCs) are metal-binding cysteine-rich peptides, enzymatically synthesized in plants and yeasts from glutathione in response to heavy metal stress by PC synthase (EC 2.3.2.15). In an attempt to increase the ability of bacterial cells to accumulate heavy metals, the Arabidopsis thaliana gene encoding PC synthase (AtPCS) was expressed in Escherichia coli. A marked accumulation of PCs was observed in vivo together with a decrease in the glutathione cellular content. When bacterial cells expressing AtPCS were placed in the presence of heavy metals such as cadmium or the metalloid arsenic, cellular metal contents were increased 20- and 50-fold, respectively. We discuss the possibility of using genes of the PC biosynthetic pathway to design bacterial strains or higher plants with increased abilities to accumulate toxic metals, and also arsenic, for use in bioremediation and/or phytoremediation processes. PMID:12514032

Chemical and Enzymatic Strategies for Bacterial and Mammalian Cell Surface Engineering.

PubMed

Bi, Xiaobao; Yin, Juan; Chen Guanbang, Ashley; Liu, Chuan-Fa

2018-06-07

The cell surface serves important functions such as the regulation of cell-cell and cell-environment interactions. The understanding and manipulation of the cell surface is important for a wide range of fundamental studies of cellular behavior and for biotechnological and medical applications. With the rapid advance of biology, chemistry and materials science, many strategies have been developed for the functionalization of bacterial and mammalian cell surfaces. Here, we review the recent development of chemical and enzymatic approaches to cell surface engineering with particular emphasis on discussing the advantages and limitations of each of these strategies. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Equal-Curvature X-Ray Telescopes

NASA Technical Reports Server (NTRS)

Saha, Timo T.; Zhang, William

2002-01-01

We introduce a new type of x-ray telescope design; an Equal-Curvature telescope. We simply add a second order axial sag to the base grazing incidence cone-cone telescope. The radius of curvature of the sag terms is the same on the primary surface and on the secondary surface. The design is optimized so that the on-axis image spot at the focal plane is minimized. The on-axis RMS (root mean square) spot diameter of two studied telescopes is less than 0.2 arc-seconds. The off-axis performance is comparable to equivalent Wolter type 1 telescopes.

Correlation between thoracolumbar curvatures and respiratory function in older adults.

PubMed

Rahman, Nor Najwatul Akmal Ab; Singh, Devinder Kaur Ajit; Lee, Raymond

2017-01-01

Aging is associated with alterations in thoracolumbar curvatures and respiratory function. Research information regarding the correlation between thoracolumbar curvatures and a comprehensive examination of respiratory function parameters in older adults is limited. The aim of the present study was to examine the correlation between thoracolumbar curvatures and respiratory function in community-dwelling older adults. Thoracolumbar curvatures (thoracic and lumbar) were measured using a motion tracker. Respiratory function parameters such as lung function, respiratory rate, respiratory muscle strength and respiratory muscle thickness (diaphragm and intercostal) were measured using a spirometer, triaxial accelerometer, respiratory pressure meter and ultrasound imaging, respectively. Sixty-eight community-dwelling older males and females from Kuala Lumpur, Malaysia, with mean (standard deviation) age of 66.63 (5.16) years participated in this cross-sectional study. The results showed that mean (standard deviation) thoracic curvature angle and lumbar curvature angles were -46.30° (14.66°) and 14.10° (10.58°), respectively. There was a significant negative correlation between thoracic curvature angle and lung function (forced expiratory volume in 1 second: r =-0.23, P <0.05; forced vital capacity: r =-0.32, P <0.05), quiet expiration intercostal thickness ( r =-0.22, P <0.05) and deep expiration diaphragm muscle thickness ( r =-0.21, P <0.05). The lumbar curvature angle had a significant negative correlation with respiratory muscle strength ( r =-0.29, P <0.05) and diaphragm muscle thickness at deep inspiration ( r =-0.22, P <0.05). However, respiratory rate was correlated neither with thoracic nor with lumbar curvatures. The findings of this study suggest that increase in both thoracic and lumbar curvatures is correlated with decrease in respiratory muscle strength, respiratory muscle thickness and some parameters of lung function. Clinically, both thoracic and

Aging and Curvature Discrimination from Static and Dynamic Touch

PubMed Central

Norman, J. Farley; Kappers, Astrid M. L.; Cheeseman, Jacob R.; Ronning, Cecilia; Thomason, Kelsey E.; Baxter, Michael W.; Calloway, Autum B.; Lamirande, Davora N.

2013-01-01

Two experiments evaluated the ability of 30 older and younger adults to discriminate the curvature of simple object surfaces from static and dynamic touch. The ages of the older adults ranged from 66 to 85 years, while those of the younger adults ranged from 20 to 29 years. For each participant in both experiments, the minimum curvature magnitude needed to reliably discriminate between convex and concave surfaces was determined. In Experiment 1, participants used static touch to make their judgments of curvature, while dynamic touch was used in Experiment 2. When static touch was used to discriminate curvature, a large effect of age occurred (the thresholds were 0.67 & 1.11/m for the younger and older participants, respectively). However, when participants used dynamic touch, there was no significant difference between the ability of younger and older participants to discriminate curvature (the thresholds were 0.58 & 0.59/m for the younger and older participants, respectively). The results of the current study demonstrate that while older adults can accurately discriminate surface curvature from dynamic touch, they possess significant impairments for static touch. PMID:23844224

An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1.

PubMed

Herlo, Rasmus; Lund, Viktor K; Lycas, Matthew D; Jansen, Anna M; Khelashvili, George; Andersen, Rita C; Bhatia, Vikram; Pedersen, Thomas S; Albornoz, Pedro B C; Johner, Niklaus; Ammendrup-Johnsen, Ina; Christensen, Nikolaj R; Erlendsson, Simon; Stoklund, Mikkel; Larsen, Jannik B; Weinstein, Harel; Kjærulff, Ole; Stamou, Dimitrios; Gether, Ulrik; Madsen, Kenneth L

2018-05-15

BAR domains are dimeric protein modules that sense, induce, and stabilize lipid membrane curvature. Here, we show that membrane curvature sensing (MCS) directs cellular localization and function of the BAR domain protein PICK1. In PICK1, and the homologous proteins ICA69 and arfaptin2, we identify an amphipathic helix N-terminal to the BAR domain that mediates MCS. Mutational disruption of the helix in PICK1 impaired MCS without affecting membrane binding per se. In insulin-producing INS-1E cells, super-resolution microscopy revealed that disruption of the helix selectively compromised PICK1 density on insulin granules of high curvature during their maturation. This was accompanied by reduced hormone storage in the INS-1E cells. In Drosophila, disruption of the helix compromised growth regulation. By demonstrating size-dependent binding on insulin granules, our finding highlights the function of MCS for BAR domain proteins in a biological context distinct from their function, e.g., at the plasma membrane during endocytosis. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

A simple and novel modification of comet assay for determination of bacteriophage mediated bacterial cell lysis.

PubMed

Khairnar, Krishna; Sanmukh, Swapnil; Chandekar, Rajshree; Paunikar, Waman

2014-07-01

The comet assay is the widely used method for in vitro toxicity testing which is also an alternative to the use of animal models for in vivo testing. Since, its inception in 1984 by Ostling and Johansson, it is being modified frequently for a wide range of application. In spite of its wide applicability, unfortunately there is no report of its application in bacteriophages research. In this study, a novel application of comet assay for the detection of bacteriophage mediated bacterial cell lysis was described. The conventional methods in bacteriophage research for studying bacterial lysis by bacteriophages are plaque assay method. It is time consuming, laborious and costly. The lytic activity of bacteriophage devours the bacterial cell which results in the release of bacterial genomic material that gets detected by ethidium bromide staining method by the comet assay protocol. The objective of this study was to compare efficacy of comet assay with different assay used to study phage mediated bacterial lysis. The assay was performed on culture isolates (N=80 studies), modified comet assay appear to have relatively higher sensitivity and specificity than other assay. The results of the study showed that the application of comet assay can be an economical, time saving and less laborious alternative to conventional plaque assay for the detection of bacteriophage mediated bacterial cell lysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Spinal curvature measurement by tracked ultrasound snapshots.

PubMed

Ungi, Tamas; King, Franklin; Kempston, Michael; Keri, Zsuzsanna; Lasso, Andras; Mousavi, Parvin; Rudan, John; Borschneck, Daniel P; Fichtinger, Gabor

2014-02-01

Monitoring spinal curvature in adolescent kyphoscoliosis requires regular radiographic examinations; however, the applied ionizing radiation increases the risk of cancer. Ultrasound imaging is favored over radiography because it does not emit ionizing radiation. Therefore, we tested an ultrasound system for spinal curvature measurement, with the help of spatial tracking of the ultrasound transducer. Tracked ultrasound was used to localize vertebral transverse processes as landmarks along the spine to measure curvature angles. The method was tested in two scoliotic spine models by localizing the same landmarks using both ultrasound and radiographic imaging and comparing the angles obtained. A close correlation was found between tracked ultrasound and radiographic curvature measurements. Differences between results of the two methods were 1.27 ± 0.84° (average ± SD) in an adult model and 0.96 ± 0.87° in a pediatric model. Our results suggest that tracked ultrasound may become a more tolerable and more accessible alternative to radiographic spine monitoring in adolescent kyphoscoliosis. Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Influence of Coanda surface curvature on performance of bladeless fan

NASA Astrophysics Data System (ADS)

Li, Guoqi; Hu, Yongjun; Jin, Yingzi; Setoguchi, Toshiaki; Kim, Heuy Dong

2014-10-01

The unique Coanda surface has a great influence on the performance of bladeless fan. However, there is few studies to explain the relationship between the performance and Coanda surface curvature at present. In order to gain a qualitative understanding of effect of the curvature on the performance of bladeless fan, numerical studies are performed in this paper. Firstly, three-dimensional numerical simulation is done by Fluent software. For the purpose to obtain detailed information of the flow field around the Coanda surface, two-dimensional numerical simulation is also conducted. Five types of Coanda surfaces with different curvature are designed, and the flow behaviour and the performance of them are analyzed and compared with those of the prototype. The analysis indicates that the curvature of Coanda surface is strongly related to blowing performance, It is found that there is an optimal curvature of Coanda surfaces among the studied models. Simulation result shows that there is a special low pressure region. With increasing curvature in Y direction, several low pressure regions gradually enlarged, then begin to merge slowly, and finally form a large area of low pressure. From the analyses of streamlines and velocity angle, it is found that the magnitude of the curvature affects the flow direction and reasonable curvature can induce fluid flow close to the wall. Thus, it leads to that the curvature of the streamlines is consistent with that of Coanda surface. Meanwhile, it also causes the fluid movement towards the most suitable direction. This study will provide useful information to performance improvements of bladeless fans.

Nastic curvatures of wheat coleoptiles that develop in true microgravity

NASA Technical Reports Server (NTRS)

Heathcote, D. G.; Chapman, D. K.; Brown, A. H.

1995-01-01

Dark-grown wheat coleoptiles developed strong curvatures within 5 h of being transferred in orbit from a 1 g centrifuge to microgravity during an experiment flown on the IML-1 shuttle mission. The curving tendency was strongest in seedlings that were immature, with coleoptiles shorter than 10 mm at the time of transfer. The curvature direction was non-random, and directed away from the caryopsis (the coleptile face adjacent to the caryopsis becoming convex). The curvatures were most marked in the basal third of the coleoptiles, contrasting with phototropic responses, which occur in the apical third. We interpret these curvatures as being nastic, and related to the curvatures commonly reported to occur during clinostat rotation treatments.

Comparative analysis of two discretizations of Ricci curvature for complex networks.

PubMed

Samal, Areejit; Sreejith, R P; Gu, Jiao; Liu, Shiping; Saucan, Emil; Jost, Jürgen

2018-06-05

We have performed an empirical comparison of two distinct notions of discrete Ricci curvature for graphs or networks, namely, the Forman-Ricci curvature and Ollivier-Ricci curvature. Importantly, these two discretizations of the Ricci curvature were developed based on different properties of the classical smooth notion, and thus, the two notions shed light on different aspects of network structure and behavior. Nevertheless, our extensive computational analysis in a wide range of both model and real-world networks shows that the two discretizations of Ricci curvature are highly correlated in many networks. Moreover, we show that if one considers the augmented Forman-Ricci curvature which also accounts for the two-dimensional simplicial complexes arising in graphs, the observed correlation between the two discretizations is even higher, especially, in real networks. Besides the potential theoretical implications of these observations, the close relationship between the two discretizations has practical implications whereby Forman-Ricci curvature can be employed in place of Ollivier-Ricci curvature for faster computation in larger real-world networks whenever coarse analysis suffices.

Radion stabilization in higher curvature warped spacetime

NASA Astrophysics Data System (ADS)

Das, Ashmita; Mukherjee, Hiya; Paul, Tanmoy; SenGupta, Soumitra

2018-02-01

We consider a five dimensional AdS spacetime in presence of higher curvature term like F(R) = R + α R^2 in the bulk. In this model, we examine the possibility of modulus stabilization from the scalar degrees of freedom of higher curvature gravity free of ghosts. Our result reveals that the model stabilizes itself and the mechanism of modulus stabilization can be argued from a geometric point of view. We determine the region of the parametric space for which the modulus (or radion) can to be stabilized. We also show how the mass and coupling parameters of radion field are modified due to higher curvature term leading to modifications of its phenomenological implications on the visible 3-brane.

Effect of Plate Curvature on Blast Response of Structural Steel Plates

NASA Astrophysics Data System (ADS)

Veeredhi, Lakshmi Shireen Banu; Ramana Rao, N. V.; Veeredhi, Vasudeva Rao

2018-04-01

In the present work an attempt is made, through simulation studies, to determine the effect of plate curvature on the blast response of a door structure made of ASTM A515 grade 50 steel plates. A door structure with dimensions of 5.142 m × 2.56 m × 10 mm having six different radii of curvatures is analyzed which is subjected to blast load. The radii of curvature investigated are infinity (flat plate), 16.63, 10.81, 8.26, 6.61 and 5.56 m. In the present study, a stand-off distance of 11 m is considered for all the cases. Results showed that the door structure with smallest radius of curvature experienced least plastic deformation and yielding when compared to a door with larger radius of curvature with same projected area. From the present Investigation, it is observed that, as the radius of curvature of the plate increases, the deformation mode gradually shifts from indentation mode to flexural mode. The plates with infinity and 16.63 m radius of curvature have undergone flexural mode of deformation and plates with 6.61 and 5.56 m radius of curvature undergo indentation mode of deformation. Whereas, mixed mode of deformation that consists of both flexural and indentation mode of deformations are seen in the plates with radius of curvature 10.81 and 8.26 m. As the radius of curvature of the plate decreases the ability of the plate to mitigate the effect the blast loads increased. It is observed that the plate with smaller radius of curvature deflects most of the blast energy and results in least indentation mode of deformation. The most significant observation made in the present investigation is that the strain energy absorbed by the steel plate gets reduced to 1/3 rd when the radius of curvature is approximately equal to the stand-off distance which could be the critical radius of curvature.

Curvature of Double-Membrane Organelles Generated by Changes in Membrane Size and Composition

PubMed Central

Knorr, Roland L.; Dimova, Rumiana; Lipowsky, Reinhard

2012-01-01

Transient double-membrane organelles are key players in cellular processes such as autophagy, reproduction, and viral infection. These organelles are formed by the bending and closure of flat, double-membrane sheets. Proteins are believed to be important in these morphological transitions but the underlying mechanism of curvature generation is poorly understood. Here, we describe a novel mechanism for this curvature generation which depends primarily on three membrane properties: the lateral size of the double-membrane sheets, the molecular composition of their highly curved rims, and a possible asymmetry between the two flat faces of the sheets. This mechanism is evolutionary advantageous since it does not require active processes and is readily available even when resources within the cell are restricted as during starvation, which can induce autophagy and sporulation. We identify pathways for protein-assisted regulation of curvature generation, organelle size, direction of bending, and morphology. Our theory also provides a mechanism for the stabilization of large double-membrane sheet-like structures found in the endoplasmic reticulum and in the Golgi cisternae. PMID:22427874

Controllable curvature from planar polymer sheets in response to light.

PubMed

Hubbard, Amber M; Mailen, Russell W; Zikry, Mohammed A; Dickey, Michael D; Genzer, Jan

2017-03-22

The ability to change shape and control curvature in 3D structures starting from planar sheets can aid in assembly and add functionality to an object. Herein, we convert planar sheets of shape memory polymers (SMPs) into 3D objects with controllable curvature by dictating where the sheets shrink. Ink patterned on the surface of the sheet absorbs infrared (IR) light, resulting in localized heating, and the material shrinks locally wherever the temperature exceeds the activation temperature, T a . We introduce two different mechanisms for controlling curvature within SMP sheets. The 'direct' mechanism uses localized shrinkage to induce curvature only in regions patterned with ink. The 'indirect' mechanism uses localized shrinkage in regions patterned with ink to induce curvature in neighboring regions without ink through a balance of internal stresses. Finite element analysis predicts the final shape of the polymer sheets with excellent qualitative agreement with experimental studies. Results from this study show that curvature can be controlled by the distribution and darkness of the ink pattern on the polymer sheet. Additionally, we utilize the direct and indirect curvature mechanisms to demonstrate the formation and actuation of gripper devices, which represent the potential utility of this approach.

Periodic growth of bacterial colonies

NASA Astrophysics Data System (ADS)

Yamazaki, Yoshihiro; Ikeda, Takemasa; Shimada, Hirotoshi; Hiramatsu, Fumiko; Kobayashi, Naoki; Wakita, Jun-ichi; Itoh, Hiroto; Kurosu, Sayuri; Nakatsuchi, Michio; Matsuyama, Tohey; Matsushita, Mitsugu

2005-06-01

The formation of concentric ring colonies by bacterial species Bacillus subtilis and Proteus mirabilis has been investigated experimentally, focusing our attention on the dependence of local cell density upon the bacterial motility. It has been confirmed that these concentric ring colonies reflect the periodic change of the bacterial motility between motile cell state and immotile cell state. We conclude that this periodic change is macroscopically determined neither by biological factors (i.e., biological clock) nor by chemical factors (chemotaxis as inhibitor). And our experimental results strongly suggest that the essential factor for the change of the bacterial motility during concentric ring formation is the local cell density.

Burkholderia Type VI Secretion Systems Have Distinct Roles in Eukaryotic and Bacterial Cell Interactions

PubMed Central

Schwarz, Sandra; West, T. Eoin; Boyer, Frédéric; Chiang, Wen-Chi; Carl, Mike A.; Hood, Rachel D.; Rohmer, Laurence; Tolker-Nielsen, Tim; Skerrett, Shawn J.; Mougous, Joseph D.

2010-01-01

Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs) of Burkholderia thailandensis (B. thai) in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ΔT6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans—leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections. PMID:20865170

The compensation of Gaussian curvature in developable cones is local

NASA Astrophysics Data System (ADS)

Wang, Jin; Witten, Thomas

2009-03-01

We use the angular deficit scheme[1] to determine numerically the distribution of Gaussian curvature in developable cones(d-cones)[2] formed by forcing a flat elastic sheet into a circular container so that the sheet buckles. This provides a new way to confirm the vanishing of mean-curvature[3] at the rim where the sheet touches the container. This angular deficit scheme also allows us to explore the potential role of the Gauss-Bonnet theorem in explaining the mean-curvature vanishing phenomenon. The theorem's global constraint on curvature resembles the global conditions observed to be relevant for vanishing mean curvature. However, our result suggests that the Gauss-Bonnet theorem does not explain the vanishing of mean-curvature. [1] V. Borrelli, F. Cazals, and J.-M. Morvan, Computer Aided Geometric Design 20, 319 (2003). [2] E. Cerda, S. Chaieb, F. Melo, and L. Mahadevan, Nature 401, 46 (1999). [3] T. Liang and T. A. Witten, Phys. Rev. E 73, 046604 (2006).

The acoustic sensor for rapid analysis of bacterial cells in the conductive suspensions.

PubMed

Borodina, I A; Zaitsev, B D; Guliy, O; Teplykh, A A; Shikhabudinov, A M

2017-11-01

The possibility of using the acoustic sensor on the basis of a two-channel delay line for rapid analysis of bacterial cells in the conductive suspensions was investigated. The dependencies of change in phase and insertion loss of output signal of the sensor on conductivity of buffer solution with various concentrations of cells due to a specific interaction "bacterial cells - mini-antibodies" for electrically open and electrically shorted channels of delay line were measured. It has been found that these changes have the most values for the electrically open channel. It has been also shown that the sensor rapidly responds to the specific interaction and the time stabilization of the phase and insertion loss of output signal is less than 10min. Copyright © 2017 Elsevier B.V. All rights reserved.

Internal curvature signal and noise in low- and high-level vision

PubMed Central

Grabowecky, Marcia; Kim, Yee Joon; Suzuki, Satoru

2011-01-01

How does internal processing contribute to visual pattern perception? By modeling visual search performance, we estimated internal signal and noise relevant to perception of curvature, a basic feature important for encoding of three-dimensional surfaces and objects. We used isolated, sparse, crowded, and face contexts to determine how internal curvature signal and noise depended on image crowding, lateral feature interactions, and level of pattern processing. Observers reported the curvature of a briefly flashed segment, which was presented alone (without lateral interaction) or among multiple straight segments (with lateral interaction). Each segment was presented with no context (engaging low-to-intermediate-level curvature processing), embedded within a face context as the mouth (engaging high-level face processing), or embedded within an inverted-scrambled-face context as a control for crowding. Using a simple, biologically plausible model of curvature perception, we estimated internal curvature signal and noise as the mean and standard deviation, respectively, of the Gaussian-distributed population activity of local curvature-tuned channels that best simulated behavioral curvature responses. Internal noise was increased by crowding but not by face context (irrespective of lateral interactions), suggesting prevention of noise accumulation in high-level pattern processing. In contrast, internal curvature signal was unaffected by crowding but modulated by lateral interactions. Lateral interactions (with straight segments) increased curvature signal when no contextual elements were added, but equivalent interactions reduced curvature signal when each segment was presented within a face. These opposing effects of lateral interactions are consistent with the phenomena of local-feature contrast in low-level processing and global-feature averaging in high-level processing. PMID:21209356

Diethylaminoethyl-cellulose-bacterial cell immunoadsorbent columns: preparation of serotype-specific globulin and immunofluorescent conjugates for Streptococcus mutans serotypes a and d.

PubMed

McKinney, R M; Thacker, L

1976-04-01

Diethylaminoethyl (DEAE)-cellulose was used as a support material for preparing bacterial cell columns. Pretreatment of the bacterial cells with formalin was essential in obtaining satisfactory adherence of the cells to DEAE-cellulose. Cross-reacting antibodies were removed from antibody preparations against strains of Streptococcus mutans serotypes a and d by adsorption on appropriate bacterial cell columns. S. mutans serotype d was further divided into two subtypes on the basis of immunofluorescent staining with conjugates of immunospecifically adsorbed immunoglobulin G. The DEAE-cellulose-bacterial cell columns were regenerated after use by desorbing the cross-reacting antibodies with low-pH buffer and were used repeatedly over and 18-month period with no detectable loss in effectiveness.

Observer variation in the assessment of root canal curvature.

PubMed

Faraj, S; Boutsioukis, C

2017-02-01

To evaluate the inter- and intra-observer agreement between training/trained endodontists regarding the ex vivo classification of root canal curvature into three categories and its measurement using three quantitative methods. Periapical radiographs of seven extracted human posterior teeth with varying degrees of curvature were exposed ex vivo. Twenty training/trained endodontists were asked to classify the root canal curvature into three categories (<10°, 10-30°, >30°), to measure the curvature using three quantitative methods (Schneider, Weine, Pruett) and to draw angles of 10° or 30°, as a control experiment. The procedure was repeated after six weeks. Inter- and intra-observer agreement was evaluated by the intraclass correlation coefficient and weighted kappa. The inter-observer agreement on the visual classification of root canal curvature was substantial (ICC = 0.65, P < 0.018), but a trend towards underestimation of the angle was evident. Participants modified their classifications both within and between the two sessions. Median angles drawn as a control experiment were not significantly different from the target values (P > 0.10), but the results of individual participants varied. When quantitative methods were used, the inter- and intra-observer agreement on the angle measurements was considerably better (ICC = 0.76-0.82, P < 0.001) than on the radius measurements (ICC = 0.16-0.19, P > 0.895). Visual estimation of root canal curvature was not reliable. The use of computer-based quantitative methods is recommended. The measurement of radius of curvature was more subjective than angle measurement. Endodontic Associations need to provide specific guidelines on how to estimate root canal curvature in case difficulty assessment forms. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

A novel curvature-controllable steerable needle for percutaneous intervention.

PubMed

Bui, Van Khuyen; Park, Sukho; Park, Jong-Oh; Ko, Seong Young

2016-08-01

Over the last few decades, flexible steerable robotic needles for percutaneous intervention have been the subject of significant interest. However, there still remain issues related to (a) steering the needle's direction with less damage to surrounding tissues and (b) increasing the needle's maximum curvature for better controllability. One widely used approach is to control the fixed-angled bevel-tip needle using a "duty-cycle" algorithm. While this algorithm has shown its applicability, it can potentially damage surrounding tissue, which has prevented the widespread adoption of this technology. This situation has motivated the development of a new steerable flexible needle that can change its curvature without axial rotation, while at the same time producing a larger curvature. In this article, we propose a novel curvature-controllable steerable needle. The proposed robotic needle consists of two parts: a cannula and a stylet with a bevel-tip. The curvature of the needle's path is controlled by a control offset, defined by the offset between the bevel-tip and the cannula. As a result, the necessity of rotating the whole needle's body is decreased. The duty-cycle algorithm is utilized to a limited degree to obtain a larger radius of curvature, which is similar to a straight path. The first prototype of 0.46 mm (outer diameter) was fabricated and tested with both in vitro gelatin phantom and ex vivo cow liver tissue. The maximum curvatures measured 0.008 mm(-1) in 6 wt% gelatin phantom, 0.0139 mm(-1) in 10 wt% gelatin phantom, and 0.0038 mm(-1) in cow liver. The experimental results show a linear relationship between the curvature and the control offset, which can be utilized for future implementation of this control algorithm. © IMechE 2016.

Revealing the Effects of Nanoscale Membrane Curvature on Lipid Mobility.

PubMed

Kabbani, Abir Maarouf; Woodward, Xinxin; Kelly, Christopher V

2017-10-18

Recent advances in nanoengineering and super-resolution microscopy have enabled new capabilities for creating and observing membrane curvature. However, the effects of curvature on single-lipid diffusion have yet to be revealed. The simulations presented here describe the capabilities of varying experimental methods for revealing the effects of nanoscale curvature on single-molecule mobility. Traditionally, lipid mobility is revealed through fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), and single particle tracking (SPT). However, these techniques vary greatly in their ability to detect the effects of nanoscale curvature on lipid behavior. Traditionally, FRAP and FCS depend on diffraction-limited illumination and detection. A simulation of FRAP shows minimal effects on lipids diffusion due to a 50 nm radius membrane bud. Throughout the stages of the budding process, FRAP detected minimal changes in lipid recovery time due to the curvature versus flat membrane. Simulated FCS demonstrated small effects due to a 50 nm radius membrane bud that was more apparent with curvature-dependent lipid mobility changes. However, SPT achieves a sub-diffraction-limited resolution of membrane budding and lipid mobility through the identification of the single-lipid positions with ≤15 nm spatial and ≤20 ms temporal resolution. By mapping the single-lipid step lengths to locations on the membrane, the effects of membrane topography and curvature could be correlated to the effective membrane viscosity. Single-fluorophore localization techniques, such SPT, can detect membrane curvature and its effects on lipid behavior. These simulations and discussion provide a guideline for optimizing the experimental procedures in revealing the effects of curvature on lipid mobility and effective local membrane viscosity.

Revealing the Effects of Nanoscale Membrane Curvature on Lipid Mobility

PubMed Central

Kabbani, Abir Maarouf; Woodward, Xinxin

2017-01-01

Recent advances in nanoengineering and super-resolution microscopy have enabled new capabilities for creating and observing membrane curvature. However, the effects of curvature on single-lipid diffusion have yet to be revealed. The simulations presented here describe the capabilities of varying experimental methods for revealing the effects of nanoscale curvature on single-molecule mobility. Traditionally, lipid mobility is revealed through fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), and single particle tracking (SPT). However, these techniques vary greatly in their ability to detect the effects of nanoscale curvature on lipid behavior. Traditionally, FRAP and FCS depend on diffraction-limited illumination and detection. A simulation of FRAP shows minimal effects on lipids diffusion due to a 50 nm radius membrane bud. Throughout the stages of the budding process, FRAP detected minimal changes in lipid recovery time due to the curvature versus flat membrane. Simulated FCS demonstrated small effects due to a 50 nm radius membrane bud that was more apparent with curvature-dependent lipid mobility changes. However, SPT achieves a sub-diffraction-limited resolution of membrane budding and lipid mobility through the identification of the single-lipid positions with ≤15 nm spatial and ≤20 ms temporal resolution. By mapping the single-lipid step lengths to locations on the membrane, the effects of membrane topography and curvature could be correlated to the effective membrane viscosity. Single-fluorophore localization techniques, such SPT, can detect membrane curvature and its effects on lipid behavior. These simulations and discussion provide a guideline for optimizing the experimental procedures in revealing the effects of curvature on lipid mobility and effective local membrane viscosity. PMID:29057801

Sorting of amphiphile membrane components in curvature and composition gradients

NASA Astrophysics Data System (ADS)

Tian, Aiwei

Phase and shape heterogeneities in biomembranes are of functional importance. However, it is difficult to elucidate the roles membrane heterogeneities play in maintaining cellular function due to the complexity of biomembranes. Therefore, investigations of phase behavior and composition/curvature coupling in lipid and polymer model membranes offer some advantages. In this thesis, phase properties in lipid and polymer giant vesicles were studied. Line tension at the fluid/fluid phase boundary of giant lipid unilamellar vesicles was determined directly by micropipette aspiration, and found to be composition-dependent. Dynamics of calcium-induced domains within polyanionic vesicles subject to chemical stimuli were investigated, which revealed the strength of molecular interaction and suggested applications in triggered delivery. In addition, curvature sorting of lipids and proteins was examined. Lipid membrane tethers were pulled from giant unilamellar vesicles using two micropipettes and a bead. Tether radius can be controlled and measured in this system. By examining fluorescence intensity of labeled molecules as a function of curvature, we found that DiI dyes (lipid analogues with spontaneous curvatures) had no curvature preference down to radii of 10 nm. Theoretical calculation predicted that the distribution of small lipids was dominated by entropy instead of bending energy. However protein Cholera toxin subunit B was efficiently sorted away from the high positive curvature due to its negative spontaneous curvature. Bending stiffness was determined to decrease as curvature increased in homogeneous membranes with ternary lipid mixtures near a critical consulate point, revealing the strong preferential intermolecular interactions of such mixtures. In addition, diffusion controlled domain growth was observed in tethers pulled from phase-separated vesicles, which provides a new dynamic sorting principle for lipids and proteins in curvature gradients.

Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations

PubMed Central

Schreiber, Frank; Dal Co, Alma; Kiviet, Daniel J.; Littmann, Sten

2017-01-01

While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed. PMID:29253903

Microelectrofluidic lens for variable curvature

NASA Astrophysics Data System (ADS)

Chang, Jong-hyeon; Lee, Eunsung; Jung, Kyu-Dong; Lee, Seungwan; Choi, Minseog; Kim, Woonbae

2012-10-01

This paper presents a tunable liquid lens based on microelectrofluidic technology which integrates electrowetting and microfluidics. In the novel microelectrofluidic lens (MEFL), electrowetting in the hydrophobic surface channel induces the Laplace pressure difference between two fluidic interfaces on the lens aperture and the surface channel. Then, the pressure difference makes the lens curvature tunable. The previous electrowetting lens in which the contact angle changes at the side wall has a certain limitation of the curvature variation because of the contact angle saturation. Although the contact angle saturation also appears in the surface channel of the MEFL, the low surface channel increases the Laplace pressure and it makes the MEFL to have full variation of the optical power possible. The magnitude of the applied voltage determines the lens curvature in the analog mode MEFL as well as the electrowetting lens. Digital operation is also possible when the control electrodes of the MEFL are patterned to have an array. It is expected that the proposed MEFL is able to be widely used because of its full variation of the optical power without the use of oil and digital operation with fast response.

Adjusting Curvatures Of Large Mirrors And Lenses

NASA Technical Reports Server (NTRS)

Birnbaum, Morris M.

1992-01-01

Actuators apply stresses to generate distortions counteracting undesired distortions in technique for adjusting curvature of large focusing mirror or lens. Motor-and-gear assemblies under remote control vary squeeze of ring clamp and push or pull of hollow shaft to make fine adjustments in curvature of mirror. Applicable to large astronomical-telescope mirrors with diameters of 60 cm or more.

Heterologous Expression of Toxins from Bacterial Toxin-Antitoxin Systems in Eukaryotic Cells: Strategies and Applications

PubMed Central

Yeo, Chew Chieng; Abu Bakar, Fauziah; Chan, Wai Ting; Espinosa, Manuel; Harikrishna, Jennifer Ann

2016-01-01

Toxin-antitoxin (TA) systems are found in nearly all prokaryotic genomes and usually consist of a pair of co-transcribed genes, one of which encodes a stable toxin and the other, its cognate labile antitoxin. Certain environmental and physiological cues trigger the degradation of the antitoxin, causing activation of the toxin, leading either to the death or stasis of the host cell. TA systems have a variety of functions in the bacterial cell, including acting as mediators of programmed cell death, the induction of a dormant state known as persistence and the stable maintenance of plasmids and other mobile genetic elements. Some bacterial TA systems are functional when expressed in eukaryotic cells and this has led to several innovative applications, which are the subject of this review. Here, we look at how bacterial TA systems have been utilized for the genetic manipulation of yeasts and other eukaryotes, for the containment of genetically modified organisms, and for the engineering of high expression eukaryotic cell lines. We also examine how TA systems have been adopted as an important tool in developmental biology research for the ablation of specific cells and the potential for utility of TA systems in antiviral and anticancer gene therapies. PMID:26907343

On the role of tip curvature on flapping plates.

PubMed

Martin, Nathan; Gharib, Morteza

2018-01-09

During the flapping motion of a fish's tail, the caudal fin exhibits antero-posterior bending and dorso-ventral bending, the latter of which is referred to as chord-wise bending herein. The impact of chord-wise tip curvature on the hydrodynamic forces for flapping plates is investigated to explore potential mechanisms to improve the maneuverability or the performance of autonomous underwater vehicles. First, actuated chord-wise tip curvature is explored. Comparison of rigid curved geometries to a rigid flat plate as a baseline suggests that an increased curvature decreases the generated forces. An actuated plate with a dynamic tip curvature is created to illustrate a modulation of this decrease in forces. Second, the impact of curvature is isolated using curved plates with an identical planform area. Comparison of rigid curved geometries as a baseline corroborates the result that an increased curvature decreases the generated forces, with the exception that presenting a concave geometry into the flow increases the thrust and the efficiency. A passively-actuated plate is designed to capitalize on this effect by presenting a concave geometry into the flow throughout the cycle. The dynamically and passively actuated plates show potential to improve the maneuverability and the efficiency of autonomous underwater vehicles, respectively.

Lipopolysaccharide structure impacts the entry kinetics of bacterial outer membrane vesicles into host cells

PubMed Central

Hadis, Mohammed; Alderwick, Luke

2017-01-01

Outer membrane vesicles are nano-sized microvesicles shed from the outer membrane of Gram-negative bacteria and play important roles in immune priming and disease pathogenesis. However, our current mechanistic understanding of vesicle-host cell interactions is limited by a lack of methods to study the rapid kinetics of vesicle entry and cargo delivery to host cells. Here, we describe a highly sensitive method to study the kinetics of vesicle entry into host cells in real-time using a genetically encoded, vesicle-targeted probe. We found that the route of vesicular uptake, and thus entry kinetics and efficiency, are shaped by bacterial cell wall composition. The presence of lipopolysaccharide O antigen enables vesicles to bypass clathrin-mediated endocytosis, which enhances both their entry rate and efficiency into host cells. Collectively, our findings highlight the composition of the bacterial cell wall as a major determinant of secretion-independent delivery of virulence factors during Gram-negative infections. PMID:29186191

Isoprenoid Biosynthesis Inhibitors Targeting Bacterial Cell Growth.

PubMed

Desai, Janish; Wang, Yang; Wang, Ke; Malwal, Satish R; Oldfield, Eric

2016-10-06

We synthesized potential inhibitors of farnesyl diphosphate synthase (FPPS), undecaprenyl diphosphate synthase (UPPS), or undecaprenyl diphosphate phosphatase (UPPP), and tested them in bacterial cell growth and enzyme inhibition assays. The most active compounds were found to be bisphosphonates with electron-withdrawing aryl-alkyl side chains which inhibited the growth of Gram-negative bacteria (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa) at ∼1-4 μg mL -1 levels. They were found to be potent inhibitors of FPPS; cell growth was partially "rescued" by the addition of farnesol or overexpression of FPPS, and there was synergistic activity with known isoprenoid biosynthesis pathway inhibitors. Lipophilic hydroxyalkyl phosphonic acids inhibited UPPS and UPPP at micromolar levels; they were active (∼2-6 μg mL -1 ) against Gram-positive but not Gram-negative organisms, and again exhibited synergistic activity with cell wall biosynthesis inhibitors, but only indifferent effects with other inhibitors. The results are of interest because they describe novel inhibitors of FPPS, UPPS, and UPPP with cell growth inhibitory activities as low as ∼1-2 μg mL -1 . © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cosmic curvature from de Sitter equilibrium cosmology.

PubMed

Albrecht, Andreas

2011-10-07

I show that the de Sitter equilibrium cosmology generically predicts observable levels of curvature in the Universe today. The predicted value of the curvature, Ω(k), depends only on the ratio of the density of nonrelativistic matter to cosmological constant density ρ(m)(0)/ρ(Λ) and the value of the curvature from the initial bubble that starts the inflation, Ω(k)(B). The result is independent of the scale of inflation, the shape of the potential during inflation, and many other details of the cosmology. Future cosmological measurements of ρ(m)(0)/ρ(Λ) and Ω(k) will open up a window on the very beginning of our Universe and offer an opportunity to support or falsify the de Sitter equilibrium cosmology.

Curvature controlled wetting in two dimensions

NASA Astrophysics Data System (ADS)

Gil, Tamir; Mikheev, Lev V.

1995-07-01

A complete wetting transition at vanishing curvature of the substrate in two-dimensional circular geometry is studied by the transfer matrix method. We find an exact formal mapping of the partition function of the problem onto that of a (1+1)-dimensional wetting problem in planar geometry. As the radius of the substrate r0-->∞, the leading effect of the curvature is adding the Laplace pressure ΠL~r-10 to the pressure balance in the film. At temperatures and pressures under which the wetting is complete in planar geometry, Laplace pressure suppresses divergence of the mean thickness of the wetting layer lW, leading to a power law lW~r1/30. At a critical wetting transition of a planar substrate, curvature adds a relevant field; the corresponding multiscaling forms are readily available. The method allows for the systematic evaluation of corrections to the leading behavior; the next to the leading term reduces the thickness by the amount proportional to r-1/30

The physical boundaries of public goods cooperation between surface-attached bacterial cells

PubMed Central

Weigert, Michael; Kümmerli, Rolf

2017-01-01

Bacteria secrete a variety of compounds important for nutrient scavenging, competition mediation and infection establishment. While there is a general consensus that secreted compounds can be shared and therefore have social consequences for the bacterial collective, we know little about the physical limits of such bacterial social interactions. Here, we address this issue by studying the sharing of iron-scavenging siderophores between surface-attached microcolonies of the bacterium Pseudomonas aeruginosa. Using single-cell fluorescent microscopy, we show that siderophores, secreted by producers, quickly reach non-producers within a range of 100 µm, and significantly boost their fitness. Producers in turn respond to variation in sharing efficiency by adjusting their pyoverdine investment levels. These social effects wane with larger cell-to-cell distances and on hard surfaces. Thus, our findings reveal the boundaries of compound sharing, and show that sharing is particularly relevant between nearby yet physically separated bacteria on soft surfaces, matching realistic natural conditions such as those encountered in soft tissue infections. PMID:28701557

Analysis of gene expression levels in individual bacterial cells without image segmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwak, In Hae; Son, Minjun; Hagen, Stephen J., E-mail: sjhagen@ufl.edu

2012-05-11

Highlights: Black-Right-Pointing-Pointer We present a method for extracting gene expression data from images of bacterial cells. Black-Right-Pointing-Pointer The method does not employ cell segmentation and does not require high magnification. Black-Right-Pointing-Pointer Fluorescence and phase contrast images of the cells are correlated through the physics of phase contrast. Black-Right-Pointing-Pointer We demonstrate the method by characterizing noisy expression of comX in Streptococcus mutans. -- Abstract: Studies of stochasticity in gene expression typically make use of fluorescent protein reporters, which permit the measurement of expression levels within individual cells by fluorescence microscopy. Analysis of such microscopy images is almost invariably based on amore » segmentation algorithm, where the image of a cell or cluster is analyzed mathematically to delineate individual cell boundaries. However segmentation can be ineffective for studying bacterial cells or clusters, especially at lower magnification, where outlines of individual cells are poorly resolved. Here we demonstrate an alternative method for analyzing such images without segmentation. The method employs a comparison between the pixel brightness in phase contrast vs fluorescence microscopy images. By fitting the correlation between phase contrast and fluorescence intensity to a physical model, we obtain well-defined estimates for the different levels of gene expression that are present in the cell or cluster. The method reveals the boundaries of the individual cells, even if the source images lack the resolution to show these boundaries clearly.« less

Cellular damage in bacterial meningitis: an interplay of bacterial and host driven toxicity.

PubMed

Weber, Joerg R; Tuomanen, Elaine I

2007-03-01

Bacterial meningitis is still an important infectious disease causing death and disability. Invasive bacterial infections of the CNS generate some of the most powerful inflammatory responses known in medicine. Although the components of bacterial cell surfaces are now chemically defined in exquisite detail and the interaction with several receptor pathways has been discovered, it is only very recently that studies combining these advanced biochemical and cell biological tools have been done. Additional to the immunological response direct bacterial toxicity has been identified as an important contributor to neuronal damage. A detailed understanding of the complex interaction of bacterial toxicity and host response may generate opportunities for innovative and specific neuroprotective therapies.

Clinical workflow for spinal curvature measurement with portable ultrasound

NASA Astrophysics Data System (ADS)

Tabanfar, Reza; Yan, Christina; Kempston, Michael; Borschneck, Daniel; Ungi, Tamas; Fichtinger, Gabor

2016-03-01

PURPOSE: Spinal curvature monitoring is essential in making treatment decisions in scoliosis. Monitoring entails radiographic examinations, however repeated ionizing radiation exposure has been shown to increase cancer risk. Ultrasound does not emit ionizing radiation and is safer for spinal curvature monitoring. We investigated a clinical sonography protocol and challenges associated with position-tracked ultrasound in spinal curvature measurement in scoliosis. METHODS: Transverse processes were landmarked along each vertebra using tracked ultrasound snapshots. The transverse process angle was used to determine the orientation of each vertebra. We tested our methodology on five patients in a local pediatric scoliosis clinic, comparing ultrasound to radiographic curvature measurements. RESULTS: Despite strong correlation between radiographic and ultrasound curvature angles in phantom studies, we encountered new challenges in the clinical setting. Our main challenge was differentiating transverse processes from ribs and other structures during landmarking. We observed up to 13° angle variability for a single vertebra and a 9.85° +/- 10.81° difference between ultrasound and radiographic Cobb angles for thoracic curvatures. Additionally, we were unable to visualize anatomical landmarks in the lumbar region where soft tissue depth was 25-35mm. In volunteers with large Cobb angles (greater than 40° thoracic and 60° lumbar), we observed spinal protrusions resulting in incomplete probe-skin contact and partial ultrasound images not suitable for landmarking. CONCLUSION: Spinal curvature measurement using tracked ultrasound is viable on phantom spine models. In the clinic, new challenges were encountered which must be resolved before a universal sonography protocol can be developed.

Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations.

PubMed

Ghosh, Anirban; Baltekin, Özden; Wäneskog, Marcus; Elkhalifa, Dina; Hammarlöf, Disa L; Elf, Johan; Koskiniemi, Sanna

2018-05-02

Bacterial populations can use bet-hedging strategies to cope with rapidly changing environments. One example is non-growing cells in clonal bacterial populations that are able to persist antibiotic treatment. Previous studies suggest that persisters arise in bacterial populations either stochastically through variation in levels of global signalling molecules between individual cells, or in response to various stresses. Here, we show that toxins used in contact-dependent growth inhibition (CDI) create persisters upon direct contact with cells lacking sufficient levels of CdiI immunity protein, which would otherwise bind to and neutralize toxin activity. CDI-mediated persisters form through a feedforward cycle where the toxic activity of the CdiA toxin increases cellular (p)ppGpp levels, which results in Lon-mediated degradation of the immunity protein and more free toxin. Thus, CDI systems mediate a population density-dependent bet-hedging strategy, where the fraction of non-growing cells is increased only when there are many cells of the same genotype. This may be one of the mechanisms of how CDI systems increase the fitness of their hosts. © 2018 The Authors.

Membrane curvature and its generation by BAR proteins

PubMed Central

Mim, Carsten; Unger, Vinzenz M

2012-01-01

Membranes are flexible barriers that surround the cell and its compartments. To execute vital functions such as locomotion or receptor turnover, cells need to control the shapes of their membranes. In part, this control is achieved through membrane-bending proteins, such as the bin/amphiphysin/rvs domain (BAR) proteins. Many open questions remain about the mechanisms by which membrane-bending proteins function. Addressing this shortfall, recent structures of BAR protein:membrane complexes support existing mechanistic models, but also produced novel insights into how BAR-domain proteins sense, stabilize and generate curvature. Here we review these recent findings, focusing on how BAR proteins interact with the membrane, and how the resulting scaffold structures might aid the recruitment of other proteins to the sites where membranes are bent. PMID:23058040

Curvature-driven capillary migration and assembly of rod-like particles

PubMed Central

Cavallaro, Marcello; Botto, Lorenzo; Lewandowski, Eric P.; Wang, Marisa; Stebe, Kathleen J.

2011-01-01

Capillarity can be used to direct anisotropic colloidal particles to precise locations and to orient them by using interface curvature as an applied field. We show this in experiments in which the shape of the interface is molded by pinning to vertical pillars of different cross-sections. These interfaces present well-defined curvature fields that orient and steer particles along complex trajectories. Trajectories and orientations are predicted by a theoretical model in which capillary forces and torques are related to Gaussian curvature gradients and angular deviations from principal directions of curvature. Interface curvature diverges near sharp boundaries, similar to an electric field near a pointed conductor. We exploit this feature to induce migration and assembly at preferred locations, and to create complex structures. We also report a repulsive interaction, in which microparticles move away from planar bounding walls along curvature gradient contours. These phenomena should be widely useful in the directed assembly of micro- and nanoparticles with potential application in the fabrication of materials with tunable mechanical or electronic properties, in emulsion production, and in encapsulation. PMID:22184218

Wall extensibility and gravitropic curvature of sunflower hypocotyls: correlation between timing of curvature and changes in extensibility

NASA Technical Reports Server (NTRS)

Bagshaw, S. L.; Cleland, R. E.

1990-01-01

Gravitropic curvature results from unequal growth rates on the upper and lower sides of horizontal stems. These unequal growth rates could be due to differences in wall extensibility between the two sides. To test this, the time course of curvature of horizontal sunflower (Helianthus annuus L.) hypocotyls was determined and compared with the time courses of changes in Instron-measured wall extensibility (PEx) of the upper and lower epidermal layers. As gravicurvature developed, so did the difference in PEx between the upper and lower epidermis. The enhanced growth rate on the lower side during the period of maximum increase in curvature was matched by PEx values greater than those of the vertical control, while the inhibited growth rate on the upper side was accompanied by PEx values below that of the control. The close correlation between changes in growth rates and alterations in PEx demonstrates that changes in wall extensibility play a major role in controlling gravicurvature.

Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions.

PubMed

Hesketh, Andy; Vergnano, Marta; Wan, Chris; Oliver, Stephen G

2017-07-25

We have engineered Saccharomyces cerevisiae to inducibly synthesize the prokaryotic signaling nucleotides cyclic di-GMP (cdiGMP), cdiAMP, and ppGpp in order to characterize the range of effects these nucleotides exert on eukaryotic cell function during bacterial pathogenesis. Synthetic genetic array (SGA) and transcriptome analyses indicated that, while these compounds elicit some common reactions in yeast, there are also complex and distinctive responses to each of the three nucleotides. All three are capable of inhibiting eukaryotic cell growth, with the guanine nucleotides exhibiting stronger effects than cdiAMP. Mutations compromising mitochondrial function and chromatin remodeling show negative epistatic interactions with all three nucleotides. In contrast, certain mutations that cause defects in chromatin modification and ribosomal protein function show positive epistasis, alleviating growth inhibition by at least two of the three nucleotides. Uniquely, cdiGMP is lethal both to cells growing by respiration on acetate and to obligately fermentative petite mutants. cdiGMP is also synthetically lethal with the ribonucleotide reductase (RNR) inhibitor hydroxyurea. Heterologous expression of the human ppGpp hydrolase Mesh1p prevented the accumulation of ppGpp in the engineered yeast and restored cell growth. Extensive in vivo interactions between bacterial signaling molecules and eukaryotic gene function occur, resulting in outcomes ranging from growth inhibition to death. cdiGMP functions through a mechanism that must be compensated by unhindered RNR activity or by functionally competent mitochondria. Mesh1p may be required for abrogating the damaging effects of ppGpp in human cells subjected to bacterial infection. IMPORTANCE During infections, pathogenic bacteria can release nucleotides into the cells of their eukaryotic hosts. These nucleotides are recognized as signals that contribute to the initiation of defensive immune responses that help the infected

Global Curvature Buckling and Snapping of Spherical Shells.

NASA Astrophysics Data System (ADS)

Pezzulla, Matteo; Stoop, Norbert; Steranka, Mark; Bade, Abdikhalaq; Trejo, Miguel; Holmes, Douglas

A spherical shell under external pressure will eventually buckle locally through the development of a dimple. However, when a free spherical shell is subject to variations in natural curvature, it will either buckle globally or snap towards a buckled configuration. We study the similarities and differences between pressure and curvature instabilities in spherical shells. We show how the critical buckling natural curvature is largely independent of the thinness and half-angle of the shell, while the critical snapping natural curvature grows linearly with the half-angle. As a result, we demonstrate how a critical half-angle, depending only on the thinness of the shell, sets the threshold between two different kinds of snapping: as a rule of thumb, shallow shells snap into everted shells, while deep shells snap into buckled shells. As the developed models are purely geometrical, the results are applicable to a large variety of stimuli and scales. NSF CAREER CMMI-1454153.

Flow derivatives and curvatures for a normal shock

NASA Astrophysics Data System (ADS)

Emanuel, G.

2018-03-01

A detached bow shock wave is strongest where it is normal to the upstream velocity. While the jump conditions across the shock are straightforward, many properties, such as the shock's curvatures and derivatives of the pressure, along and normal to a normal shock, are indeterminate. A novel procedure is introduced for resolving the indeterminacy when the unsteady flow is three-dimensional and the upstream velocity may be nonuniform. Utilizing this procedure, normal shock relations are provided for the nonunique orientation of the flow plane and the corresponding shock's curvatures and, e.g., the downstream normal derivatives of the pressure and the velocity components. These algebraic relations explicitly show the dependence of these parameters on the shock's shape and the upstream velocity gradient. A simple relation, valid only for a normal shock, is obtained for the average curvatures. Results are also obtained when the shock is an elliptic paraboloid shock. These derivatives are both simple and proportional to the average curvature.

Bacterial reduction by cell salvage washing and leukocyte depletion filtration.

PubMed

Waters, Jonathan H; Tuohy, Marion J; Hobson, Donna F; Procop, Gary

2003-09-01

Blood conservation techniques are being increasingly used because of the increased cost and lack of availability of allogeneic blood. Cell salvage offers great blood savings opportunities but is thought to be contraindicated in a number of areas (e.g., blood contaminated with bacteria). Several outcome studies have suggested the safety of this technique in trauma and colorectal surgery, but many practitioners are still hesitant to apply cell salvage in the face of frank bacterial contamination. This study was undertaken to assess the efficacy of bacterial removal when cell salvage was combined with leukocyte depletion filtration. Expired packed erythrocytes were obtained and inoculated with a fixed amount of a stock bacteria (Escherichia coli American Type Culture Collections [ATCC] 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 29213, or Bacteroides fragilis ATCC 25285) in amounts ranging from 2,000 to 4,000 colony forming units/ml. The blood was processed via a cell salvage machine. The washed blood was then filtered using a leukocyte reduction filter. The results for blood taken during each step of processing were compared using a repeated-measures design. Fifteen units of blood were contaminated with each of the stock bacteria. From the prewash sample to the postfiltration sample, 99.0%, 99.6%, 100%, and 97.6% of E. coli, S. aureus, P. aeruginosa, and B. fragilis were removed, respectively. Significant but not complete removal of contaminating bacteria was seen. An increased level of patient safety may be added to cell salvage by including a leukocyte depletion filter when salvaging blood that might be grossly contaminated with bacteria.

Measuring masses of single bacterial whole cells with a quadrupole ion trap.

PubMed

Peng, Wen-Ping; Yang, Yi-Chang; Kang, Ming-Wei; Lee, Yuan T; Chang, Huan-Cheng

2004-09-29

A novel method has been developed to precisely measure the masses of single bacterial whole cells using a quadrupole ion trap as an electrodynamic balance. The bacterial cells were introduced into the ion trap by matrix-assisted laser desorption/ionization, confined in space by audio frequency ac fields, and detected by elastic light scattering. Mass measurement accuracy approaching 0.1% was achieved for Escherichia coli K-12 with a mass distribution of +/-3% from 60 repetitive measurements of the particles and their clusters. This is the first high-precision mass measurement reported for any intact microorganisms with masses greater than 1 x 1010 Da. The method opens new avenues for high-precision mass measurement of single microbial particles and offers an alternative approach for rapid identification of microorganisms by mass spectrometry.

Exploring bacterial infections: theoretical and experimental studies of the bacterial population dynamics and antibiotic treatment

NASA Astrophysics Data System (ADS)

Shao, Xinxian

Bacterial infections are very common in human society. Thus extensive research has been conducted to reveal the molecular mechanisms of the pathogenesis and to evaluate the antibiotics' efficacy against bacteria. Little is known, however, about the population dynamics of bacterial populations and their interactions with the host's immune system. In this dissertation, a stochatic model is developed featuring stochastic phenotypic switching of bacterial individuals to explain the single-variant bottleneck discovered in multi strain bacterial infections. I explored early events in a bacterial infection establishment using classical experiments of Moxon and Murphy on neonatal rats. I showed that the minimal model and its simple variants do not work. I proposed modifications to the model that could explain the data quantitatively. The bacterial infections are also commonly established in physical structures, as biofilms or 3-d colonies. In contrast, most research on antibiotic treatment of bacterial infections has been conducted in well-mixed liquid cultures. I explored the efficacy of antibiotics to treat such bacterial colonies, a broadly applicable method is designed and evaluated where discrete bacterial colonies on 2-d surfaces were exposed to antibiotics. I discuss possible explanations and hypotheses for the experimental results. To verify these hypotheses, we investigated the dynamics of bacterial population as 3-d colonies. We showed that a minimal mathematical model of bacterial colony growth in 3-d was able to account for the experimentally observed presence of a diffusion-limited regime. The model further revealed highly loose packing of the cells in 3-d colonies and smaller cell sizes in colonies than plancktonic cells in corresponding liquid culture. Further experimental tests of the model predictions have revealed that the ratio of the cell size in liquid culture to that in colony cultures was consistent with the model prediction, that the dead cells

The speed-curvature power law of movements: a reappraisal.

PubMed

Zago, Myrka; Matic, Adam; Flash, Tamar; Gomez-Marin, Alex; Lacquaniti, Francesco

2018-01-01

Several types of curvilinear movements obey approximately the so called 2/3 power law, according to which the angular speed varies proportionally to the 2/3 power of the curvature. The origin of the law is debated but it is generally thought to depend on physiological mechanisms. However, a recent paper (Marken and Shaffer, Exp Brain Res 88:685-690, 2017) claims that this power law is simply a statistical artifact, being a mathematical consequence of the way speed and curvature are calculated. Here we reject this hypothesis by showing that the speed-curvature power law of biological movements is non-trivial. First, we confirm that the power exponent varies with the shape of human drawing movements and with environmental factors. Second, we report experimental data from Drosophila larvae demonstrating that the power law does not depend on how curvature is calculated. Third, we prove that the law can be violated by means of several mathematical and physical examples. Finally, we discuss biological constraints that may underlie speed-curvature power laws discovered in empirical studies.

Temperate bacterial viruses as double-edged swords in bacterial warfare.

PubMed

Gama, João Alves; Reis, Ana Maria; Domingues, Iolanda; Mendes-Soares, Helena; Matos, Ana Margarida; Dionisio, Francisco

2013-01-01

It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a "replicating toxin". However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails.

Temperate Bacterial Viruses as Double-Edged Swords in Bacterial Warfare

PubMed Central

Gama, João Alves; Reis, Ana Maria; Domingues, Iolanda; Mendes-Soares, Helena; Matos, Ana Margarida; Dionisio, Francisco

2013-01-01

It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a “replicating toxin”. However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails. PMID:23536852

Role of Sulfhydryl Sites on Bacterial Cell Walls in the Biosorption, Mobility and Bioavailability of Mercury and Uranium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Myneni, Satish C.; Mishra, Bhoopesh; Fein, Jeremy

2009-04-01

The goal of this exploratory study is to provide a quantitative and mechanistic understanding of the impact of bacterial sulfhydryl groups on the bacterial uptake, speciation, methylation and bioavailability of Hg and redox changes of uranium. The relative concentration and reactivity of different functional groups present on bacterial surfaces will be determined, enabling quantitative predictions of the role of biosorption of Hg under the physicochemical conditions found at contaminated DOE sites.The hypotheses we propose to test in this investigation are as follows- 1) Sulfhydryl groups on bacterial cell surfaces modify Hg speciation and solubility, and play an important role, specificallymore » in the sub-micromolar concentration ranges of metals in the natural and contaminated systems. 2) Sulfhydryl binding of Hg on bacterial surfaces significantly influences Hg transport into the cell and the methylation rates by the bacteria. 3) Sulfhydryls on cell membranes can interact with hexavalent uranium and convert to insoluble tetravalent species. 4) Bacterial sulfhydryl surface groups are inducible by the presence of metals during cell growth. Our studies focused on the first hypothesis, and we examined the nature of sulfhydryl sites on three representative bacterial species: Bacillus subtilis, a common gram-positive aerobic soil species; Shewanella oneidensis, a facultative gram-negative surface water species; and Geobacter sulfurreducens, an anaerobic iron-reducing gram-negative species that is capable of Hg methylation; and at a range of Hg concentration (and Hg:bacterial concentration ratio) in which these sites become important. A summary of our findings is as follows- Hg adsorbs more extensively to bacteria than other metals. Hg adsorption also varies strongly with pH and chloride concentration, with maximum adsorption occurring under circumneutral pH conditions for both Cl-bearing and Cl-free systems. Under these conditions, all bacterial species tested

A novel setup for wafer curvature measurement at very high heating rates.

PubMed

Islam, T; Zechner, J; Bernardoni, M; Nelhiebel, M; Pippan, R

2017-02-01

The curvature evolution of a thin film layer stack containing a top Al layer is measured during temperature cycles with very high heating rates. The temperature cycles are generated by means of programmable electrical power pulses applied to miniaturized polysilicon heater systems embedded inside a semiconductor chip and the curvature is measured by a fast wafer curvature measurement setup. Fast temperature cycles with heating duration of 100 ms are created to heat the specimen up to 270 °C providing an average heating rate of 2500 K/s. As a second approach, curvature measurement utilizing laser scanning Doppler vibrometry is also demonstrated which verifies the results obtained from the fast wafer curvature measurement setup. Film stresses calculated from the measured curvature values compare well to literature results, indicating that the new method can be used to measure curvature during fast temperature cycling.

Positive spatial curvature does not falsify the landscape

NASA Astrophysics Data System (ADS)

Horn, B.

2017-12-01

We present a simple cosmological model where the quantum tunneling of a scalar field rearranges the energetics of the matter sector, sending a stable static ancestor vacuum with positive spatial curvature into an inating solution with positive curvature. This serves as a proof of principle that an observation of positive spatial curvature does not falsify the hypothesis that our current observer patch originated from false vacuum tunneling in a string or field theoretic landscape. This poster submission is a summary of the work, and was presented at the 3rd annual ICPPA held in Moscow from October 2 to 5, 2017, by Prof. Rostislav Konoplich on behalf of the author.

Curvature perturbation and waterfall dynamics in hybrid inflation

NASA Astrophysics Data System (ADS)

Akbar Abolhasani, Ali; Firouzjahi, Hassan; Sasaki, Misao

2011-10-01

We investigate the parameter spaces of hybrid inflation model with special attention paid to the dynamics of waterfall field and curvature perturbations induced from its quantum fluctuations. Depending on the inflaton field value at the time of phase transition and the sharpness of the phase transition inflation can have multiple extended stages. We find that for models with mild phase transition the induced curvature perturbation from the waterfall field is too large to satisfy the COBE normalization. We investigate the model parameter space where the curvature perturbations from the waterfall quantum fluctuations vary between the results of standard hybrid inflation and the results obtained here.

Discrimination of curvature from motion during smooth pursuit eye movements and fixation.

PubMed

Ross, Nicholas M; Goettker, Alexander; Schütz, Alexander C; Braun, Doris I; Gegenfurtner, Karl R

2017-09-01

Smooth pursuit and motion perception have mainly been investigated with stimuli moving along linear trajectories. Here we studied the quality of pursuit movements to curved motion trajectories in human observers and examined whether the pursuit responses would be sensitive enough to discriminate various degrees of curvature. In a two-interval forced-choice task subjects pursued a Gaussian blob moving along a curved trajectory and then indicated in which interval the curve was flatter. We also measured discrimination thresholds for the same curvatures during fixation. Motion curvature had some specific effects on smooth pursuit properties: trajectories with larger amounts of curvature elicited lower open-loop acceleration, lower pursuit gain, and larger catch-up saccades compared with less curved trajectories. Initially, target motion curvatures were underestimated; however, ∼300 ms after pursuit onset pursuit responses closely matched the actual curved trajectory. We calculated perceptual thresholds for curvature discrimination, which were on the order of 1.5 degrees of visual angle (°) for a 7.9° curvature standard. Oculometric sensitivity to curvature discrimination based on the whole pursuit trajectory was quite similar to perceptual performance. Oculometric thresholds based on smaller time windows were higher. Thus smooth pursuit can quite accurately follow moving targets with curved trajectories, but temporal integration over longer periods is necessary to reach perceptual thresholds for curvature discrimination. NEW & NOTEWORTHY Even though motion trajectories in the real world are frequently curved, most studies of smooth pursuit and motion perception have investigated linear motion. We show that pursuit initially underestimates the curvature of target motion and is able to reproduce the target curvature ∼300 ms after pursuit onset. Temporal integration of target motion over longer periods is necessary for pursuit to reach the level of precision found

Seasonal and spatial distribution of bacterial biomass and the percentage of viable cells in a reservoir of Alabama

USGS Publications Warehouse

Tietjen, T.E.; Wetzel, R.G.

2003-01-01

Spatial community dynamics of bacterioplankton were evaluated along the length of the former stream channel of Elledge Lake, a small reservoir in western Alabama. The reservoir was strongly stratified from April to October with up to a 10??C temperature difference across the 1 m deep metalimnion. Bacterial biomass was highest during late summer, with a general pattern of increasing abundance from the inflowing river (???10 ??g C l-1) to the dam (???20-30 ??g C l-1). Bacterial numbers also increased following a >10-fold increase in turbidity associated with a major precipitation event, although only ???10% of these cells were viable. The percentage of viable cells generally increased through the stratified period with 50-70% viable cells in late summer. Overall, an average of 38% of bacterial cells were viable, with a range from <20 to 70%. Although these values were similar to those found by others, additional patterns were identified that have not been previously observed: a marked decline in viable cells was found following turbid storm inflows and increases in the percentage of viable cells occurred during spring warming and following autumnal mixing events. Although a modest increase in abundance occurred along the gradient from inflow down-reservoir to the dam, bacterial abundance did not increase near the dam in a pattern coincident with the commonly observed increased algal biomass in the lacustrine portion of reservoir ecosystems. The increases observed in bacterial viability moving from the inflowing rivers towards the dam and later in stratified periods stress the importance of differences in environmental conditions in time and space in regulating bacterial biomass and development, as well as of shifts that would be anticipated accompanying altered hydrological regimes under climatic change.

Femoral condyle curvature is correlated with knee walking kinematics in ungulates.

PubMed

Sylvester, Adam D

2015-12-01

The knee has been the focus of many studies linking mammalian postcranial form with locomotor behaviors and animal ecology. A more difficult task has been linking joint morphology with joint kinematics during locomotor tasks. Joint curvature represents one opportunity to link postcranial morphology with walking kinematics because joint curvature develops in response to mechanical loading. As an initial examination of mammalian knee joint curvature, the curvature of the medial femoral condyle was measured on femora representing 11 ungulate species. The position of a region of low curvature was measured using a metric termed the "angle to low curvature". This low-curvature region is important because it provides the greatest contact area between femoral and tibial condyles. Kinematic knee angles during walking were derived from the literature and kinematic knee angles across the gait cycle were correlated with angle to low curvature values. The highest correlation between kinematic knee angle and the angle to low curvature metric occurred at 20% of the walking gait cycle. This early portion of the walking gait cycle is associated with a peak in the vertical ground reaction force for some mammals. The chondral modeling theory predicts that frequent and heavy loading of particular regions of a joint surface during ontogeny will result in these regions being flatter than the surrounding joint surface. The locations of flatter regions of the femoral condyles of ungulates, and their association with knee angles used during the early stance phase of walking provides support for the chondral modeling theory. © 2015 Wiley Periodicals, Inc.

Symmetry and scale orient Min protein patterns in shaped bacterial sculptures

NASA Astrophysics Data System (ADS)

Wu, Fabai; van Schie, Bas G. C.; Keymer, Juan E.; Dekker, Cees

2015-08-01

The boundary of a cell defines the shape and scale of its subcellular organization. However, the effects of the cell's spatial boundaries as well as the geometry sensing and scale adaptation of intracellular molecular networks remain largely unexplored. Here, we show that living bacterial cells can be ‘sculpted’ into defined shapes, such as squares and rectangles, which are used to explore the spatial adaptation of Min proteins that oscillate pole-to-pole in rod-shaped Escherichia coli to assist cell division. In a wide geometric parameter space, ranging from 2 × 1 × 1 to 11 × 6 × 1 μm3, Min proteins exhibit versatile oscillation patterns, sustaining rotational, longitudinal, diagonal, stripe and even transversal modes. These patterns are found to directly capture the symmetry and scale of the cell boundary, and the Min concentration gradients scale with the cell size within a characteristic length range of 3-6 μm. Numerical simulations reveal that local microscopic Turing kinetics of Min proteins can yield global symmetry selection, gradient scaling and an adaptive range, when and only when facilitated by the three-dimensional confinement of the cell boundary. These findings cannot be explained by previous geometry-sensing models based on the longest distance, membrane area or curvature, and reveal that spatial boundaries can facilitate simple molecular interactions to result in far more versatile functions than previously understood.

Advanced Curvature Deformable Mirrors

DTIC Science & Technology

2010-09-01

ORGANIZATION NAME(S) AND ADDRESS(ES) University of Hawaii ,Institute for Astronomy,640 North A‘ohoku Place, #209 , Hilo ,HI,96720-2700 8. PERFORMING...Advanced Curvature Deformable Mirrors Christ Ftaclas1,2, Aglae Kellerer2 and Mark Chun2 Institute for Astronomy, University of Hawaii

Model-independent Constraints on Cosmic Curvature and Opacity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Guo-Jian; Li, Zheng-Xiang; Xia, Jun-Qing

2017-09-20

In this paper, we propose to estimate the spatial curvature of the universe and the cosmic opacity in a model-independent way with expansion rate measurements, H ( z ), and type Ia supernova (SNe Ia). On the one hand, using a nonparametric smoothing method Gaussian process, we reconstruct a function H ( z ) from opacity-free expansion rate measurements. Then, we integrate the H ( z ) to obtain distance modulus μ {sub H}, which is dependent on the cosmic curvature. On the other hand, distances of SNe Ia can be determined by their photometric observations and thus are opacity-dependent.more » In our analysis, by confronting distance moduli μ {sub H} with those obtained from SNe Ia, we achieve estimations for both the spatial curvature and the cosmic opacity without any assumptions for the cosmological model. Here, it should be noted that light curve fitting parameters, accounting for the distance estimation of SNe Ia, are determined in a global fit together with the cosmic opacity and spatial curvature to get rid of the dependence of these parameters on cosmology. In addition, we also investigate whether the inclusion of different priors for the present expansion rate ( H {sub 0}: global estimation, 67.74 ± 0.46 km s{sup −1} Mpc{sup −1}, and local measurement, 73.24 ± 1.74 km s{sup −1} Mpc{sup −1}) exert influence on the reconstructed H ( z ) and the following estimations of the spatial curvature and cosmic opacity. Results show that, in general, a spatially flat and transparent universe is preferred by the observations. Moreover, it is suggested that priors for H {sub 0} matter a lot. Finally, we find that there is a strong degeneracy between the curvature and the opacity.« less

Long-term Results of Ventral Penile Curvature Repair in Childhood.

PubMed

Golomb, Dor; Sivan, Bezalel; Livne, Pinhas M; Nevo, Amihay; Ben-Meir, David

2018-02-01

To assess the postpubertal outcome of ventral penile curvature repaired in infancy in terms of recurrence and aesthetics. Postpubertal patients treated for hypospadias and ventral penile curvature in infancy at a tertiary medical center were invited to undergo assessment of the quality of the repair. Findings were compared between patients with a straight penis after skin release and patients who required dorsal plication. The cohort included 27 patients of mean age 16.5 years who were reported with straight penis after surgery. Postpubertal curvature was found in 6 of 14 patients (43%) successfully treated by skin release and 10 of 13 patients (77%) who underwent dorsal plication (P = .087). Significant curvature (≥30 degrees) was found in 1 of 14 patients in the skin-release group and 4 of 13 in the dorsal plication group (P = .16). Rates of redo urethroplasty were 2 of 14 (14%) and 5 of 10 (50%), respectively. Patient satisfaction with the appearance of the penis did not differ significantly. Ventral penile curvature repaired in infancy often recurs after puberty. The need for dorsal plication has a trend-level association with recurrence of penile curvature in puberty. It might also be related to the degree of postpubertal penile curvature and the need for redo urethroplasty. Procedure type does not affect patient satisfaction with the postpubertal appearance of the penis. Copyright © 2017 Elsevier Inc. All rights reserved.

Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems?

PubMed

Lebaron, P; Servais, P; Agogué, H; Courties, C; Joux, F

2001-04-01

The nucleic acid contents of individual bacterial cells as determined with three different nucleic acid-specific fluorescent dyes (SYBR I, SYBR II, and SYTO 13) and flow cytometry were compared for different seawater samples. Similar fluorescence patterns were observed, and bacteria with high apparent nucleic acid contents (HNA) could be discriminated from bacteria with low nucleic acid contents (LNA). The best discrimination between HNA and LNA cells was found when cells were stained with SYBR II. Bacteria in different water samples collected from seven freshwater, brackish water, and seawater ecosystems were prelabeled with tritiated leucine and then stained with SYBR II. After labeling and staining, HNA, LNA, and total cells were sorted by flow cytometry, and the specific activity of each cellular category was determined from leucine incorporation rates. The HNA cells were responsible for most of the total bacterial production, and the specific activities of cells in the HNA population varied between samples by a factor of seven. We suggest that nucleic acid content alone can be a better indicator of the fraction of growing cells than total counts and that this approach should be combined with other fluorescent physiological probes to improve detection of the most active cells in aquatic systems.

Does the High Nucleic Acid Content of Individual Bacterial Cells Allow Us To Discriminate between Active Cells and Inactive Cells in Aquatic Systems?

PubMed Central

Lebaron, Philippe; Servais, Pierre; Agogué, Helene; Courties, Claude; Joux, Fabien

2001-01-01

The nucleic acid contents of individual bacterial cells as determined with three different nucleic acid-specific fluorescent dyes (SYBR I, SYBR II, and SYTO 13) and flow cytometry were compared for different seawater samples. Similar fluorescence patterns were observed, and bacteria with high apparent nucleic acid contents (HNA) could be discriminated from bacteria with low nucleic acid contents (LNA). The best discrimination between HNA and LNA cells was found when cells were stained with SYBR II. Bacteria in different water samples collected from seven freshwater, brackish water, and seawater ecosystems were prelabeled with tritiated leucine and then stained with SYBR II. After labeling and staining, HNA, LNA, and total cells were sorted by flow cytometry, and the specific activity of each cellular category was determined from leucine incorporation rates. The HNA cells were responsible for most of the total bacterial production, and the specific activities of cells in the HNA population varied between samples by a factor of seven. We suggest that nucleic acid content alone can be a better indicator of the fraction of growing cells than total counts and that this approach should be combined with other fluorescent physiological probes to improve detection of the most active cells in aquatic systems. PMID:11282632

Intensity-Curvature Measurement Approaches for the Diagnosis of Magnetic Resonance Imaging Brain Tumors.

PubMed

Ciulla, Carlo; Veljanovski, Dimitar; Rechkoska Shikoska, Ustijana; Risteski, Filip A

2015-11-01

This research presents signal-image post-processing techniques called Intensity-Curvature Measurement Approaches with application to the diagnosis of human brain tumors detected through Magnetic Resonance Imaging (MRI). Post-processing of the MRI of the human brain encompasses the following model functions: (i) bivariate cubic polynomial, (ii) bivariate cubic Lagrange polynomial, (iii) monovariate sinc, and (iv) bivariate linear. The following Intensity-Curvature Measurement Approaches were used: (i) classic-curvature, (ii) signal resilient to interpolation, (iii) intensity-curvature measure and (iv) intensity-curvature functional. The results revealed that the classic-curvature, the signal resilient to interpolation and the intensity-curvature functional are able to add additional information useful to the diagnosis carried out with MRI. The contribution to the MRI diagnosis of our study are: (i) the enhanced gray level scale of the tumor mass and the well-behaved representation of the tumor provided through the signal resilient to interpolation, and (ii) the visually perceptible third dimension perpendicular to the image plane provided through the classic-curvature and the intensity-curvature functional.

Intensity-Curvature Measurement Approaches for the Diagnosis of Magnetic Resonance Imaging Brain Tumors

PubMed Central

Ciulla, Carlo; Veljanovski, Dimitar; Rechkoska Shikoska, Ustijana; Risteski, Filip A.

2015-01-01

This research presents signal-image post-processing techniques called Intensity-Curvature Measurement Approaches with application to the diagnosis of human brain tumors detected through Magnetic Resonance Imaging (MRI). Post-processing of the MRI of the human brain encompasses the following model functions: (i) bivariate cubic polynomial, (ii) bivariate cubic Lagrange polynomial, (iii) monovariate sinc, and (iv) bivariate linear. The following Intensity-Curvature Measurement Approaches were used: (i) classic-curvature, (ii) signal resilient to interpolation, (iii) intensity-curvature measure and (iv) intensity-curvature functional. The results revealed that the classic-curvature, the signal resilient to interpolation and the intensity-curvature functional are able to add additional information useful to the diagnosis carried out with MRI. The contribution to the MRI diagnosis of our study are: (i) the enhanced gray level scale of the tumor mass and the well-behaved representation of the tumor provided through the signal resilient to interpolation, and (ii) the visually perceptible third dimension perpendicular to the image plane provided through the classic-curvature and the intensity-curvature functional. PMID:26644943

3D geometrical assessment of femoral curvature: a reverse engineering technique.

PubMed

Chantarapanich, Nattapon; Sitthiseripratip, Kriskrai; Mahaisavariya, Banchong; Wongcumchang, Marut; Siribodhi, Pongwit

2008-09-01

Investigate the 2D/3D geometry of femoral curvature and femoral length using the advanced technique of computerized tomography combined with reverse engineering techniques. The present study was performed using reverse engineering technique based on CT data of 99 cadaveric femora. The femur was divided into three segments, proximal, mid-shaft, and distal regions by defining 35% and 65% of the femoral total length as a boundary of each region. The intramedullary canal in the mid-shaft region was mainly extracted to determine the set of circular center, which could consequence to approximate the 3D femoral radius of curvature using the 3D least square best fit. The 3D femoral curvature was then projected into A-P and M-L directions to investigate the correlation of 2D/3D femoral curvature as normal radiographic images. It was found that the average 3D Thai femoral curvature was 895.46-mm (SD = 238.06) and the average femoral total length is 421.96-mm (SD = 27.61). In addition, the 2D femoral curvature derived from sagittal radiographic image can be used to determine the 3D femoral curvature with this equation: R3D = RSagittal + 3.67 with r = 0.987. This described technique is a non-destructive method that can effectively assess the internal/ external 3D geometric data of the femur The obtained data is useful to develop a proper design of prosthesis that required inserting into the intramedullary canal. From the present study, it can be concluded that the 2DSagittal femoral curvature derived from standard radiographic image can be represented for the 3D femoral curvature.

Influence of implant rod curvature on sagittal correction of scoliosis deformity.

PubMed

Salmingo, Remel Alingalan; Tadano, Shigeru; Abe, Yuichiro; Ito, Manabu

2014-08-01

Deformation of in vivo-implanted rods could alter the scoliosis sagittal correction. To our knowledge, no previous authors have investigated the influence of implanted-rod deformation on the sagittal deformity correction during scoliosis surgery. To analyze the changes of the implant rod's angle of curvature during surgery and establish its influence on sagittal correction of scoliosis deformity. A retrospective analysis of the preoperative and postoperative implant rod geometry and angle of curvature was conducted. Twenty adolescent idiopathic scoliosis patients underwent surgery. Average age at the time of operation was 14 years. The preoperative and postoperative implant rod angle of curvature expressed in degrees was obtained for each patient. Two implant rods were attached to the concave and convex side of the spinal deformity. The preoperative implant rod geometry was measured before surgical implantation. The postoperative implant rod geometry after surgery was measured by computed tomography. The implant rod angle of curvature at the sagittal plane was obtained from the implant rod geometry. The angle of curvature between the implant rod extreme ends was measured before implantation and after surgery. The sagittal curvature between the corresponding spinal levels of healthy adolescents obtained by previous studies was compared with the implant rod angle of curvature to evaluate the sagittal curve correction. The difference between the postoperative implant rod angle of curvature and normal spine sagittal curvature of the corresponding instrumented level was used to evaluate over or under correction of the sagittal deformity. The implant rods at the concave side of deformity of all patients were significantly deformed after surgery. The average degree of rod deformation Δθ at the concave and convex sides was 15.8° and 1.6°, respectively. The average preoperative and postoperative implant rod angle of curvature at the concave side was 33.6° and 17.8�

Ultraviolet micro-Raman spectrograph for the detection of small numbers of bacterial cells

NASA Astrophysics Data System (ADS)

Chadha, S.; Nelson, W. H.; Sperry, J. F.

1993-11-01

The construction of a practical UV micro-Raman spectrograph capable of selective excitation of bacterial cells and other microscopic samples has been described. A reflective objective is used to focus cw laser light on a sample and at the same time collect the scattered light at 180°. With the aid of a quartz lens the image produced is focused on the slits of a spectrograph equipped with a single 2400 grooves/mm grating optimized for 250 nm. Spectra were detected by means of a blue-intensified diode array detector. Resonance Raman spectra of Bacillus subtilis and Flavobacterium capsulatum excited by the 257.2 nm output of a cw laser were recorded in the 900-1800 cm-1 region. Bacterial cells were immobilized on a quartz plate by means of polylysine and were counted visually. Cooling was required to retard sample degradation. Sample sizes ranged from 1 to 50 cells with excitation times varying from 15 to 180 s. Excellent spectra have been obtained from 20 cells in 15 s using a spectrograph having only 3% throughput.

Image processing via level set curvature flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malladi, R.; Sethian, J.A.

We present a controlled image smoothing and enhancement method based on a curvature flow interpretation of the geometric heat equation. Compared to existing techniques, the model has several distinct advantages. (i) It contains just one enhancement parameter. (ii) The scheme naturally inherits a stopping criterion from the image; continued application of the scheme produces no further change. (iii) The method is one of the fastest possible schemes based on a curvature-controlled approach. 15 ref., 6 figs.

Role of facet curvature for accurate vertebral facet load analysis.

PubMed

Holzapfel, Gerhard A; Stadler, Michael

2006-06-01

The curvature of vertebral facet joints may play an important role in the study of load-bearing characteristics and clinical interventions such as graded facetectomy. In previously-published finite element simulations of this procedure, the curvature was either neglected or approximated with a varying degree of accuracy. Here we study the effect of the curvature in three different load situations by using a numerical model which is able to represent the actual curvature without any loss of accuracy. The results show that previously-used approximations of the curvature lead to good results in the analysis of sagittal moment/rotation. However, for sagittal shear-force/displacement and for the contact stress distribution, previous results deviate significantly from our results. These findings are supported through related convergence studies. Hence we can conclude that in order to obtain reliable results for the analysis of sagittal shear-force/displacement and the contact stress distribution in the facet joint, the curvature must not be neglected. This is of particular importance for the numerical simulation of the spine, which may lead to improved diagnostics, effective surgical planning and intervention. The proposed method may represent a more reliable basis for optimizing the biomedical engineering design for tissue engineering or, for example, for spinal implants.

Foveal Curvature and Asymmetry Assessed Using Optical Coherence Tomography.

PubMed

VanNasdale, Dean A; Eilerman, Amanda; Zimmerman, Aaron; Lai, Nicky; Ramsey, Keith; Sinnott, Loraine T

2017-06-01

The aims of this study were to use cross-sectional optical coherence tomography imaging and custom curve fitting software to evaluate and model the foveal curvature as a spherical surface and to compare the radius of curvature in the horizontal and vertical meridians and test the sensitivity of this technique to anticipated meridional differences. Six 30-degree foveal-centered radial optical coherence tomography cross-section scans were acquired in the right eye of 20 clinically normal subjects. Cross sections were manually segmented, and custom curve fitting software was used to determine foveal pit radius of curvature using the central 500, 1000, and 1500 μm of the foveal contour. Radius of curvature was compared across different fitting distances. Root mean square error was used to determine goodness of fit. The radius of curvature was compared between the horizontal and vertical meridians for each fitting distance. There radius of curvature was significantly different when comparing each of the three fitting distances (P < .01 for each comparison). The average radii of curvature were 970 μm (95% confidence interval [CI], 913 to 1028 μm), 1386 μm (95% CI, 1339 to 1439 μm), and 2121 μm (95% CI, 2066 to 2183) for the 500-, 1000-, and 1500-μm fitting distances, respectively. Root mean square error was also significantly different when comparing each fitting distance (P < .01 for each comparison). The average root mean square errors were 2.48 μm (95% CI, 2.41 to 2.53 μm), 6.22 μm (95% CI, 5.77 to 6.60 μm), and 13.82 μm (95% CI, 12.93 to 14.58 μm) for the 500-, 1000-, and 1500-μm fitting distances, respectively. The radius of curvature between the horizontal and vertical meridian radii was statistically different only in the 1000- and 1500-μm fitting distances (P < .01 for each), with the horizontal meridian being flatter than the vertical. The foveal contour can be modeled as a sphere with low curve fitting error over a limited distance and capable of

Higher Curvature Gravity from Entanglement in Conformal Field Theories.

PubMed

Haehl, Felix M; Hijano, Eliot; Parrikar, Onkar; Rabideau, Charles

2018-05-18

By generalizing different recent works to the context of higher curvature gravity, we provide a unifying framework for three related results: (i) If an asymptotically anti-de Sitter (AdS) spacetime computes the entanglement entropies of ball-shaped regions in a conformal field theory using a generalized Ryu-Takayanagi formula up to second order in state deformations around the vacuum, then the spacetime satisfies the correct gravitational equations of motion up to second order around the AdS background. (ii) The holographic dual of entanglement entropy in higher curvature theories of gravity is given by the Wald entropy plus a particular correction term involving extrinsic curvatures. (iii) Conformal field theory relative entropy is dual to gravitational canonical energy (also in higher curvature theories of gravity). Especially for the second point, our novel derivation of this previously known statement does not involve the Euclidean replica trick.

Higher Curvature Gravity from Entanglement in Conformal Field Theories

NASA Astrophysics Data System (ADS)

Haehl, Felix M.; Hijano, Eliot; Parrikar, Onkar; Rabideau, Charles

2018-05-01

By generalizing different recent works to the context of higher curvature gravity, we provide a unifying framework for three related results: (i) If an asymptotically anti-de Sitter (AdS) spacetime computes the entanglement entropies of ball-shaped regions in a conformal field theory using a generalized Ryu-Takayanagi formula up to second order in state deformations around the vacuum, then the spacetime satisfies the correct gravitational equations of motion up to second order around the AdS background. (ii) The holographic dual of entanglement entropy in higher curvature theories of gravity is given by the Wald entropy plus a particular correction term involving extrinsic curvatures. (iii) Conformal field theory relative entropy is dual to gravitational canonical energy (also in higher curvature theories of gravity). Especially for the second point, our novel derivation of this previously known statement does not involve the Euclidean replica trick.

Classification of Hamilton-Jacobi separation in orthogonal coordinates with diagonal curvature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajaratnam, Krishan, E-mail: k2rajara@uwaterloo.ca; McLenaghan, Raymond G., E-mail: rgmclenaghan@uwaterloo.ca

2014-08-15

We find all orthogonal metrics where the geodesic Hamilton-Jacobi equation separates and the Riemann curvature tensor satisfies a certain equation (called the diagonal curvature condition). All orthogonal metrics of constant curvature satisfy the diagonal curvature condition. The metrics we find either correspond to a Benenti system or are warped product metrics where the induced metric on the base manifold corresponds to a Benenti system. Furthermore, we show that most metrics we find are characterized by concircular tensors; these metrics, called Kalnins-Eisenhart-Miller metrics, have an intrinsic characterization which can be used to obtain them on a given space. In conjunction withmore » other results, we show that the metrics we found constitute all separable metrics for Riemannian spaces of constant curvature and de Sitter space.« less

Quantifying the Relationship between Curvature and Electric Potential in Lipid Bilayers.

PubMed

Bruhn, Dennis S; Lomholt, Michael A; Khandelia, Himanshu

2016-06-02

Cellular membranes mediate vital cellular processes by being subject to curvature and transmembrane electrical potentials. Here we build upon the existing theory for flexoelectricity in liquid crystals to quantify the coupling between lipid bilayer curvature and membrane potentials. Using molecular dynamics simulations, we show that headgroup dipole moments, the lateral pressure profile across the bilayer, and spontaneous curvature all systematically change with increasing membrane potentials. In particular, there is a linear dependence between the bending moment (the product of bending rigidity and spontaneous curvature) and the applied membrane potentials. We show that biologically relevant membrane potentials can induce biologically relevant curvatures corresponding to radii of around 500 nm. The implications of flexoelectricity in lipid bilayers are thus likely to be of considerable consequence both in biology and in model lipid bilayer systems.

The domain organization of the bacterial intermediate filament-like protein crescentin is important for assembly and function

PubMed Central

Cabeen, Matthew T; Herrmann, Harald; Jacobs-Wagner, Christine

2011-01-01

Crescentin is a bacterial filament-forming protein that exhibits domain organization features found in metazoan intermediate filament (IF) proteins. Structure-function studies of eukaryotic IFs have been hindered by a lack of simple genetic systems and easily quantifiable phenotypes. Here we exploit the characteristic localization of the crescentin structure along the inner curvature of Caulobacter crescentus cells and the loss of cell curvature associated with impaired crescentin function to analyze the importance of the domain organization of crescentin. By combining biochemistry and ultrastructural analysis in vitro with cellular localization and functional studies, we show that crescentin requires its distinctive domain organization, and furthermore that different structural elements have distinct structural and functional contributions. The head domain can be functionally subdivided into two subdomains; the first (amino-terminal) is required for function but not assembly, while the second is necessary for structure assembly. The rod domain is similarly required for structure assembly, and the linker L1 appears important to prevent runaway assembly into nonfunctional aggregates. The data also suggest that the stutter and the tail domain have critical functional roles in stabilizing crescentin structures against disassembly by monovalent cations in the cytoplasm. This study suggests that the IF-like behavior of crescentin is a consequence of its domain organization, implying that the IF protein layout is an adaptable cytoskeletal motif, much like the actin and tubulin folds, that is broadly exploited for various functions throughout life from bacteria to humans. © 2011 Wiley-Liss, Inc. PMID:21360832

Turning maneuvers in sharks: Predicting body curvature from axial morphology.

PubMed

Porter, Marianne E; Roque, Cassandra M; Long, John H

2009-08-01

Given the diversity of vertebral morphologies among fishes, it is tempting to propose causal links between axial morphology and body curvature. We propose that shape and size of the vertebrae, intervertebral joints, and the body will more accurately predict differences in body curvature during swimming rather than a single meristic such as total vertebral number alone. We examined the correlation between morphological features and maximum body curvature seen during routine turns in five species of shark: Triakis semifasciata, Heterodontus francisci, Chiloscyllium plagiosum, Chiloscyllium punctatum, and Hemiscyllium ocellatum. We quantified overall body curvature using three different metrics. From a separate group of size-matched individuals, we measured 16 morphological features from precaudal vertebrae and the body. As predicted, a larger pool of morphological features yielded a more robust prediction of maximal body curvature than vertebral number alone. Stepwise linear regression showed that up to 11 features were significant predictors of the three measures of body curvature, yielding highly significant multiple regressions with r(2) values of 0.523, 0.537, and 0.584. The second moment of area of the centrum was always the best predictor, followed by either centrum length or transverse height. Ranking as the fifth most important variable in three different models, the body's total length, fineness ratio, and width were the most important non-vertebral morphologies. Without considering the effects of muscle activity, these correlations suggest a dominant role for the vertebral column in providing the passive mechanical properties of the body that control, in part, body curvature during swimming. (c) 2009 Wiley-Liss, Inc.

Positive and negative tropic curvature induced by microbeam irradiation of protonemal tip cells of the moss Ceratodon purpureus.

PubMed

Lamparter, T; Kagawa, T; Brücker, G; Wada, M

2004-01-01

The photoreceptor phytochrome mediates tropic responses in protonemata of the moss Ceratodon purpureus. Under standard conditions the tip cells grow towards unilateral red light, or perpendicular to the electrical vector of polarized light. In this study the response of tip cells to partial irradiation of the apical region was analysed using a microbeam apparatus. The fluence response curve gave an unexpected pattern: whereas a 15-min microbeam with light intensities around 3 micro mol m (-2) s (-1) induced a growth curvature towards the irradiated side, higher light intensities around 100 micro mol m (-2) s (-1) caused a negative response, the cells grew away from the irradiated side. This avoidance response is explained by two effects: the light intensity is high enough to induce photoconversion into the active Pfr form of phytochrome, not only on the irradiated but also on the non-irradiated side by stray light. At the same time, the strong light on the irradiated side acts antagonistically to Pfr. As a result of this inhibition, the growth direction is moved to the light-avoiding side. Such a Pfr-independent mechanism might be important for the phototropic response to distinguish between the light-directed and light-avoiding side under unilateral light.

Lipopolysaccharide Clearance, Bacterial Clearance, and Systemic Inflammatory Responses Are Regulated by Cell Type–Specific Functions of TLR4 during Sepsis

PubMed Central

Deng, Meihong; Loughran, Patricia; Gibson, Gregory; Sodhi, Chhinder; Watkins, Simon; Hackam, David

2013-01-01

The morbidity associated with bacterial sepsis is the result of host immune responses to pathogens, which are dependent on pathogen recognition by pattern recognition receptors, such as TLR4. TLR4 is expressed on a range of cell types, yet the mechanisms by which cell-specific functions of TLR4 lead to an integrated sepsis response are poorly understood. To address this, we generated mice in which TLR4 was specifically deleted from myeloid cells (LysMTLR4KO) or hepatocytes (HCTLR4KO) and then determined survival, bacterial counts, host inflammatory responses, and organ injury in a model of cecal ligation and puncture (CLP), with or without antibiotics. LysM-TLR4 was required for phagocytosis and efficient bacterial clearance in the absence of antibiotics. Survival, the magnitude of the systemic and local inflammatory responses, and liver damage were associated with bacterial levels. HCTLR4 was required for efficient LPS clearance from the circulation, and deletion of HCTLR4 was associated with enhanced macrophage phagocytosis, lower bacterial levels, and improved survival in CLP without antibiotics. Antibiotic administration during CLP revealed an important role for hepatocyte LPS clearance in limiting sepsis-induced inflammation and organ injury. Our work defines cell type–selective roles for TLR4 in coordinating complex immune responses to bacterial sepsis and suggests that future strategies for modulating microbial molecule recognition should account for varying roles of pattern recognition receptors in multiple cell populations. PMID:23562812

Living Toroids - Cells on Toroidal Surfaces

NASA Astrophysics Data System (ADS)

Chang, Ya-Wen; Angelini, Thomas; Marquez, Samantha; Kim, Harold; Fernandez-Nieves, Alberto

2014-03-01

Cellular environment influences a multitude of cellular functions by providing chemical and physical signals that modulate cell behavior, dynamics, development, and eventually survival. Substrate mechanics has been recognized as one of the important physical cues that governs cell behavior at single cell level as well as in collective cell motion. Past research has suggested several contact-guided behaviors to be the result of surface curvature. However, studies on the effect of curvature are relatively scarce likely due to the difficulty in generating substrates with well-defined curvature. Here we describe the generation of toroidal droplets, which unlike spherical droplets, have regions of both positive and negative Gaussian curvature. Additionally, the range of curvatures can be controlled by varying the size and aspect ratio of the torus. Cells are either encapsulated inside toroidal droplets or located on toroidal hydrogel surfaces. Preliminary studies use B. Subtilis to study the organization of bacteria biofilms. When confined in droplets surrounded by yield-stress fluid, bacteria self-organize into heterogeneous biofilm at fluid- substrate interface. It is found that the surface curvature in the sub-millimeter scale has little effect on biofilm architecture.

Representation of tactile curvature in macaque somatosensory area 2

PubMed Central

Connor, Charles E.; Hsiao, Steven S.

2013-01-01

Tactile shape information is elaborated in a cortical hierarchy spanning primary (SI) and secondary somatosensory cortex (SII). Indeed, SI neurons in areas 3b and 1 encode simple contour features such as small oriented bars and edges, whereas higher order SII neurons represent large curved contour features such as angles and arcs. However, neural coding of these contour features has not been systematically characterized in area 2, the most caudal SI subdivision in the postcentral gyrus. In the present study, we analyzed area 2 neural responses to embossed oriented bars and curved contour fragments to establish whether curvature representations are generated in the postcentral gyrus. We found that many area 2 neurons (26 of 112) exhibit clear curvature tuning, preferring contours pointing in a particular direction. Fewer area 2 neurons (15 of 112) show preferences for oriented bars. Because area 2 response patterns closely resembled SII patterns, we also compared area 2 and SII response time courses to characterize the temporal dynamics of curvature synthesis in the somatosensory system. We found that curvature representations develop and peak concurrently in area 2 and SII. These results reveal that transitions from orientation tuning to curvature selectivity in the somatosensory cortical hierarchy occur within SI rather than between SI and SII. PMID:23536717

Synthetic inhibitors of bacterial cell division targeting the GTP-binding site of FtsZ.

PubMed

Ruiz-Avila, Laura B; Huecas, Sonia; Artola, Marta; Vergoñós, Albert; Ramírez-Aportela, Erney; Cercenado, Emilia; Barasoain, Isabel; Vázquez-Villa, Henar; Martín-Fontecha, Mar; Chacón, Pablo; López-Rodríguez, María L; Andreu, José M

2013-09-20

Cell division protein FtsZ is the organizer of the cytokinetic Z-ring in most bacteria and a target for new antibiotics. FtsZ assembles with GTP into filaments that hydrolyze the nucleotide at the association interface between monomers and then disassemble. We have replaced FtsZ's GTP with non-nucleotide synthetic inhibitors of bacterial division. We searched for these small molecules among compounds from the literature, from virtual screening (VS), and from our in-house synthetic library (UCM), employing a fluorescence anisotropy primary assay. From these screens we have identified the polyhydroxy aromatic compound UCM05 and its simplified analogue UCM44 that specifically bind to Bacillus subtilis FtsZ monomers with micromolar affinities and perturb normal assembly, as examined with light scattering, polymer sedimentation, and negative stain electron microscopy. On the other hand, these ligands induce the cooperative assembly of nucleotide-devoid archaeal FtsZ into distinct well-ordered polymers, different from GTP-induced filaments. These FtsZ inhibitors impair localization of FtsZ into the Z-ring and inhibit bacterial cell division. The chlorinated analogue UCM53 inhibits the growth of clinical isolates of antibiotic-resistant Staphylococcus aureus and Enterococcus faecalis. We suggest that these interfacial inhibitors recapitulate binding and some assembly-inducing effects of GTP but impair the correct structural dynamics of FtsZ filaments and thus inhibit bacterial division, possibly by binding to a small fraction of the FtsZ molecules in a bacterial cell, which opens a new approach to FtsZ-based antibacterial drug discovery.

Curvature tensors unified field equations on SEXn

NASA Astrophysics Data System (ADS)

Chung, Kyung Tae; Lee, Il Young

1988-09-01

We study the curvature tensors and field equations in the n-dimensional SE manifold SEXn. We obtain several basic properties of the vectors S λ and U λ and then of the SE curvature tensor and its contractions, such as a generalized Ricci identity, a generalized Bianchi identity, and two variations of the Bianchi identity satisfied by the SE Einstein tensor. Finally, a system of field equations is discussed in SEXn and one of its particular solutions is constructed and displayed.

Interaction of Bacterial Phenazines with Colistimethate in Bronchial Epithelial Cells.

PubMed

Mossine, Valeri V; Chance, Deborah L; Waters, James K; Mawhinney, Thomas P

2018-05-21

Multidrug-resistant bacterial infections are being increasingly treated in clinics with polymyxins, a class of antibiotics associated with adverse effects in the kidney, nervous system, or airways of a significant proportion of human and animal patients. Although many of the resistant pathogens display enhanced virulence, a hazard of cytotoxic interactions between polymyxin antibiotics and bacterial virulence factors (VFs) has not been assessed, to date. We report here on testing paired combinations of four Pseudomonas aeruginosa VF phenazine toxins, pyocyanin (PYO), 1-hydroxyphenazine (1-HP), phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), and two commonly prescribed polymyxin drugs, colistimethate (CMS)/colistin and polymyxin B, in three human airway cell lines, BEAS-2B, HBE-1, and CFT-1. Cytotoxicities of individual antibiotics, toxins, and their combinations were evaluated by simultaneous measurement of mitochondrial metabolic, total transcriptional/translational, and the Nrf2 stress response regulator activities in treated cells. Two phenazines, PYO and 1-HP, were cytotoxic at clinically relevant concentrations (100-150 μM) and prompted a significant increase in the oxidative stress-induced transcriptional activity in surviving cells. The polymyxin antibiotics arrested the cell proliferation at clinically achievable (< 1 mM) concentrations, as well, with CMS displaying a surprisingly high cytotoxicity (ED 50 = 180 μM) in BEAS-2B. The dose-response curves were probed by the median-effect analysis which established a synergistically enhanced cytotoxicity of the PYO/CMS combination in all three airway cell lines; a particularly strong effect was observed in the BEAS-2B cells, with the combination index (CI) = 0.27 at ED 50 PCA, PCN, and 1-HP potentiated CMS cytotoxicity to a smaller extent. The cytotoxicity of CMS could be reduced with 10 mM N -acetyl-cysteine. Iron chelators, while ineffective against the polymyxins, could rescue all three

Directable weathering of concave rock using curvature estimation.

PubMed

Jones, Michael D; Farley, McKay; Butler, Joseph; Beardall, Matthew

2010-01-01

We address the problem of directable weathering of exposed concave rock for use in computer-generated animation or games. Previous weathering models that admit concave surfaces are computationally inefficient and difficult to control. In nature, the spheroidal and cavernous weathering rates depend on the surface curvature. Spheroidal weathering is fastest in areas with large positive mean curvature and cavernous weathering is fastest in areas with large negative mean curvature. We simulate both processes using an approximation of mean curvature on a voxel grid. Both weathering rates are also influenced by rock durability. The user controls rock durability by editing a durability graph before and during weathering simulation. Simulations of rockfall and colluvium deposition further improve realism. The profile of the final weathered rock matches the shape of the durability graph up to the effects of weathering and colluvium deposition. We demonstrate the top-down directability and visual plausibility of the resulting model through a series of screenshots and rendered images. The results include the weathering of a cube into a sphere and of a sheltered inside corner into a cavern as predicted by the underlying geomorphological models.

Effects of wall curvature on turbulence statistics

NASA Technical Reports Server (NTRS)

Moser, R. D.; Moin, P.

1985-01-01

A three-dimensional, time-dependent, direct numerical simulation of low-Reynolds number turbulent flow in a mildly curved channel was performed, and the results examined to determine the mechanism by which curvature affects wall-bounded turbulent shear flows. A spectral numerical method with about one-million modes was employed, and no explicit subgrid scale model was used. The effects of curvature on this flow were determined by comparing the concave and convex sides of the channel. The observed effects are consistent with experimental observations for mild curvature. The most significant difference in the turbulence statistics between the concave and convex sides is in the Reynolds shear stress. This is accompanied by significant differences in the terms of the Reynolds shear stress balance equations. In addition, it was found that stationary Taylor-Goertler vortices were present and that they had a significant effect on the flow by contributing to the mean Reynolds shear stress, and by enhancing the difference between the wall shear stresses.

CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE*

PubMed Central

MIKUCKI, MICHAEL; ZHOU, Y. C.

2017-01-01

This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization. PMID:29056778

Scalar curvature in conformal geometry of Connes-Landi noncommutative manifolds

NASA Astrophysics Data System (ADS)

Liu, Yang

2017-11-01

We first propose a conformal geometry for Connes-Landi noncommutative manifolds and study the associated scalar curvature. The new scalar curvature contains its Riemannian counterpart as the commutative limit. Similar to the results on noncommutative two tori, the quantum part of the curvature consists of actions of the modular derivation through two local curvature functions. Explicit expressions for those functions are obtained for all even dimensions (greater than two). In dimension four, the one variable function shows striking similarity to the analytic functions of the characteristic classes appeared in the Atiyah-Singer local index formula, namely, it is roughly a product of the j-function (which defines the A ˆ -class of a manifold) and an exponential function (which defines the Chern character of a bundle). By performing two different computations for the variation of the Einstein-Hilbert action, we obtain deep internal relations between two local curvature functions. Straightforward verification for those relations gives a strong conceptual confirmation for the whole computational machinery we have developed so far, especially the Mathematica code hidden behind the paper.

Curvature of blended rolled edge reflectors at the shadow boundary contour

NASA Technical Reports Server (NTRS)

Ellingson, S. W.

1988-01-01

A technique is advanced for computing the radius of curvature of blended rolled edge reflector surfaces at the shadow boundary, in the plane perpendicular to the shadow boundary contour. This curvature must be known in order to compute the spurious endpoint contributions in the physical optics (PO) solution for the scattering from reflectors with rolled edges. The technique is applicable to reflectors with radially-defined rim-shapes and rolled edge terminations. The radius of curvature for several basic reflector systems is computed, and it is shown that this curvature can vary greatly along the shadow boundary contour. Finally, the total PO field in the target zone of a sample compact range system is computed and corrected using the shadow boundary radius of curvature, obtained using the technique. It is shown that the fields obtained are a better approximation to the true scattered fields.

Curvature effects on activation speed and repolarization in an ionic model of cardiac myocytes

NASA Astrophysics Data System (ADS)

Comtois, P.; Vinet, A.

1999-10-01

Reentry is a major mechanism underlying the initiation and perpetuation of many cardiac arrhythmias 12345. Stimulated ventricular myocytes give action potential characterized by a fast upstroke, a long-lasting plateau, and a late repolarization phase. The plateau phase determines the action potential duration (APD) during which the system remains refractory, a property essential to the synchronization of the heart cycle. The APD varies much with prematurity and this change has been shown to be the main determinant of the dynamics in models of paced cells and cable, and during reentry in the one-dimensional loop. Curvature has also been shown to be an important factor for propagation in experimental and theoretical cardiac extended tissue. The objective of this paper is to combine both curvature and prematurity effects in a kinematical model of propagation in cardiac tissue. First, an approximation of the ionic model is used to obtain the effects of curvature and prematurity on the speed of propagation, the APD, and the absolute refractory period. Two versions of the ionic model are studied that differ in their rate of excitability recovery. The functions are used in a kinematical model describing the propagation of period-1 solutions around an annulus.

End-Stopping Predicts Curvature Tuning along the Ventral Stream

PubMed Central

Hartmann, Till S.; Livingstone, Margaret S.

2017-01-01

Neurons in primate inferotemporal cortex (IT) are clustered into patches of shared image preferences. Functional imaging has shown that these patches are activated by natural categories (e.g., faces, body parts, and places), artificial categories (numerals, words) and geometric features (curvature and real-world size). These domains develop in the same cortical locations across monkeys and humans, which raises the possibility of common innate mechanisms. Although these commonalities could be high-level template-based categories, it is alternatively possible that the domain locations are constrained by low-level properties such as end-stopping, eccentricity, and the shape of the preferred images. To explore this, we looked for correlations among curvature preference, receptive field (RF) end-stopping, and RF eccentricity in the ventral stream. We recorded from sites in V1, V4, and posterior IT (PIT) from six monkeys using microelectrode arrays. Across all visual areas, we found a tendency for end-stopped sites to prefer curved over straight contours. Further, we found a progression in population curvature preferences along the visual hierarchy, where, on average, V1 sites preferred straight Gabors, V4 sites preferred curved stimuli, and many PIT sites showed a preference for curvature that was concave relative to fixation. Our results provide evidence that high-level functional domains may be mapped according to early rudimentary properties of the visual system. SIGNIFICANCE STATEMENT The macaque occipitotemporal cortex contains clusters of neurons with preferences for categories such as faces, body parts, and places. One common question is how these clusters (or “domains”) acquire their cortical position along the ventral stream. We and other investigators previously established an fMRI-level correlation among these category domains, retinotopy, and curvature preferences: for example, in inferotemporal cortex, face- and curvature-preferring domains show a

Surface nanoporosity has a greater influence on osteogenic and bacterial cell adhesion than crystallinity and wettability

NASA Astrophysics Data System (ADS)

Rodriguez-Contreras, Alejandra; Guadarrama Bello, Dainelys; Nanci, Antonio

2018-07-01

There has been much emphasis on the influence of crystallinity and wettability for modulating cell activity, particularly for bone biomaterials. In this context, we have generated titanium oxide layers with similar mesoporous topography and surface roughness but with amorphous or crystalline oxide layers and differential wettability. We then investigated their influence on the behavior of MC3T3 osteoblastic and bacterial cells. There was no difference in cell adhesion, spreading and growth on amorphous and crystalline surfaces. The number of focal adhesions was similar, however, cells on the amorphous surface exhibited a higher frequency of mature adhesions. The crystallinity of the surface layers also had no bearing on bacterial adhesion. While it cannot be excluded that surface crystallinity, roughness and wettability contribute to some degree to determining cell behavior, our data suggest that physical characteristics of surfaces represent the major determinant.

Effect of Gaussian curvature modulus on the shape of deformed hollow spherical objects.

PubMed

Quilliet, C; Farutin, A; Marmottant, P

2016-06-01

A popular description of soft membranes uses the surface curvature energy introduced by Helfrich, which includes a spontaneous curvature parameter. In this paper we show how the Helfrich formula can also be of interest for a wider class of spherical elastic surfaces, namely with shear elasticity, and likely to model other deformable hollow objects. The key point is that when a stress-free state with spherical symmetry exists before subsequent deformation, its straightforwardly determined curvature ("geometrical spontaneous curvature") differs most of the time from the Helfrich spontaneous curvature parameter that should be considered in order to have the model being correctly used. Using the geometrical curvature in a set of independent parameters unveils the role of the Gaussian curvature modulus, which appears to play on the shape of an elastic surface even though this latter is closed, contrary to what happens for surfaces without spontaneous curvature. In appendices, clues are given to apply this alternative and convenient formulation of the elastic surface model to the particular case of thin spherical shells of isotropic material (TSSIMs).

The effects of streamline curvature and swirl on turbulent flows in curved ducts

NASA Technical Reports Server (NTRS)

Cheng, Chih-Hsiung; Farokhi, Saeed

1990-01-01

A technique for improving the numerical predictions of turbulent flows with the effect of streamline curvature is developed. Separated flows, the flow in a curved duct, and swirling flows are examples of flow fields where streamline curvature plays a dominant role. A comprehensive literature review on the effect of streamline curvature was conducted. New algebraic formulations for the eddy viscosity incorporating the kappa-epsilon turbulence model are proposed to account for various effects of streamline curvature. The loci of flow reversal of the separated flows over various backward-facing steps are employed to test the capability of the proposed turbulence model in capturing the effect of local curvature. The inclusion of the effect of longitudinal curvature in the proposed turbulence model is validated by predicting the distributions of the static pressure coefficients in an S-bend duct and in 180 degree turn-around ducts. The proposed turbulence model embedded with transverse curvature modification is substantiated by predicting the decay of the axial velocities in the confined swirling flows. The numerical predictions of different curvature effects by the proposed turbulence models are also reported.

Identification of Apical and Cervical Curvature Radius of Human Molars.

PubMed

Estrela, Carlos; Bueno, Mike R; Barletta, Fernando B; Guedes, Orlando A; Porto, Olavo C; Estrela, Cyntia R A; Pécora, Jesus Djalma

2015-01-01

To determine the frequency of apical and cervical curvatures in human molars using the radius method and cone-beam computed tomography (CBCT) images. Four hundred images of mandibular and maxillary first and second molars were selected from a database of CBCT exams. The radius of curvature of curved root canals was measured using a circumcenter based on three mathematical points. Radii were classified according to the following scores: 0 - straight line; 1 - large radius (r > 8 mm, mild curvature); 2 - intermediate radius (r > 4 and r < 8 mm, moderate curvature); and 3 - small radius (r ≤ 4 mm, severe curvature). The frequency of curved root canals was analyzed according to root canal, root thirds, and coronal and sagittal planes, and assessed using the chi-square test (significance at α = 0.05). Of the 1,200 evaluated root canals, 92.75% presented curved root canals in the apical third and 73.25% in the cervical third on coronal plane images; sagittal plane analysis yielded 89.75% of curved canals in the apical third and 77% in the cervical third. Root canals with a large radius were significantly more frequent when compared with the other categories, regardless of root third or plane. Most root canals of maxillary and mandibular first and second molars showed some degree of curvature in the apical and cervical thirds, regardless of the analyzed plane (coronal or sagittal).

Measurement of sternal curvature angle on patients with pectus excavatum.

PubMed

Lee, Cory; Zavala-Garcia, Abraham; Teekappanavar, Neha; Lee, Catherine; Idowu, Olajire; Kim, Sunghoon

2017-01-01

Pectus excavatum (PE) is a chest deformity characterized by marked sternal depression. The objective of this study was to quantify the sternal curvature observed in patients diagnosed with PE using the sternal curvature angle (SCA). A retrospective review of lateral chest X-rays of patients with PE from 2006 to 2013 was performed. The SCA was measured in a manner similar to the method of Cobb's angle is used to measure spinal curvature. SCA and Haller index were calculated from the chest X-rays for all patients. Lateral chest X-rays of 202 PE and 196 normal control patients were analyzed. The mean SCA ± SD of PE patients was 40.56° ± 12.88° compared to 22.02° ± 7.65° for normal patients. The difference was statistically significant with a p value of <0.0001. No significant concordance between SCA and Haller index measurements in the PE group was found (Kendall τ = -0.00015, p value = 0.9975). The difference in sternal curvature as measured by the sternal curvature angle between the pectus excavatum and normal patients was statistically significant. Our data suggest that sternal depression evident in PE patients is not a simple linear depression of the sternum but due to curvature in the sternal body.

Manipulating lipid membrane architecture by liquid crystal-analog curvature elasticity (Presentation Recording)

NASA Astrophysics Data System (ADS)

Lee, Sin-Doo

2015-10-01

Soft matters such as liquid crystals and biological molecules exhibit a variety of interesting physical phenomena as well as new applications. Recently, in mimicking biological systems that have the ability to sense, regulate, grow, react, and regenerate in a highly responsive and self-adaptive manner, the significance of the liquid crystal order in living organisms, for example, a biological membrane possessing the lamellar order, is widely recognized from the viewpoints of physics and chemistry of interfaces and membrane biophysics. Lipid bilayers, resembling cell membranes, provide primary functions for the transport of biological components of ions and molecules in various cellular activities, including vesicle budding and membrane fusion, through lateral organization of the membrane components such as proteins. In this lecture, I will describe how the liquid crystal-analog curvature elasticity of a lipid bilayer plays a critical role in developing a new platform for understanding diverse biological functions at a cellular level. The key concept is to manipulate the local curvature at an interface between a solid substrate and a model membrane. Two representative examples will be demonstrated: one of them is the topographic control of lipid rafts in a combinatorial array where the ligand-receptor binding event occurs and the other concerns the reconstitution of a ring-type lipid raft in bud-mimicking architecture within the framework of the curvature elasticity.

Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations.

PubMed

Logsdon, Michelle M; Aldridge, Bree B

2018-01-01

Model bacteria, such as E. coli and B. subtilis , tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity.

Bacterial Cell Enlargement Requires Control of Cell Wall Stiffness Mediated by Peptidoglycan Hydrolases

PubMed Central

Wheeler, Richard; Turner, Robert D.; Bailey, Richard G.; Salamaga, Bartłomiej; Mesnage, Stéphane; Mohamad, Sharifah A. S.; Hayhurst, Emma J.; Horsburgh, Malcolm; Hobbs, Jamie K.

2015-01-01

ABSTRACT Most bacterial cells are enclosed in a single macromolecule of the cell wall polymer, peptidoglycan, which is required for shape determination and maintenance of viability, while peptidoglycan biosynthesis is an important antibiotic target. It is hypothesized that cellular enlargement requires regional expansion of the cell wall through coordinated insertion and hydrolysis of peptidoglycan. Here, a group of (apparent glucosaminidase) peptidoglycan hydrolases are identified that are together required for cell enlargement and correct cellular morphology of Staphylococcus aureus, demonstrating the overall importance of this enzyme activity. These are Atl, SagA, ScaH, and SagB. The major advance here is the explanation of the observed morphological defects in terms of the mechanical and biochemical properties of peptidoglycan. It was shown that cells lacking groups of these hydrolases have increased surface stiffness and, in the absence of SagB, substantially increased glycan chain length. This indicates that, beyond their established roles (for example in cell separation), some hydrolases enable cellular enlargement by making peptidoglycan easier to stretch, providing the first direct evidence demonstrating that cellular enlargement occurs via modulation of the mechanical properties of peptidoglycan. PMID:26220963

Holographic helical superconductor with higher curvature corrections

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Subir; Paul, Chandrima

2018-01-01

We study SU(2) × U(1) gauge theory with Chern-Simons term, coupled to scalar field in adjoint, in Einstein-Gauss-Bonnet gravity. We explore phases of holographic superconductor in terms of the condensates and free energies in the background of AdS black hole and AdS soliton. In the case of black hole, we find with increasing strength of higher curvature terms, transition temperature decreases. For AdS soliton, the critical value of chemical potential increases as the higher curvature terms dominate.

Optical fiber curvature sensor based on MMF-SCF-MMF structure

NASA Astrophysics Data System (ADS)

Wang, Qi; Liu, Yu

2018-07-01

A sensitive curvature sensor based on MMF-SCF-MMF (MMF: multimode fiber; SCF: seven core fiber) structure is proposed. The multimode fiber (MMF) are used to improve the light coupling efficiency between the input singlemode fiber (SMF) and the seven-core fiber (SCF), and the seven-core fiber is used as the main element for curvature measurement. Experimental results show that the best curvature sensitivity reaches 41.46453 nm/m-1 in the range of 0.094 m-1-0.567 m-1. The temperature sensitivity is up to 59.02 pm/°C in the range of 20 °C-55 °C. The optical curvature sensors are widely used for buildings structure health monitoring and mechanical engineering due to the advantages of compact structure, anti-electromagnetic interference, and low cost.

Humidity-dependent bacterial cells functional morphometry investigations using atomic force microscope.

PubMed

Nikiyan, Hike; Vasilchenko, Alexey; Deryabin, Dmitry

2010-01-01

The effect of a relative humidity (RH) in a range of 93-65% on morphological and elastic properties of Bacillus cereus and Escherichia coli cells was evaluated using atomic force microscopy. It is shown that gradual dehumidification of bacteria environment has no significant effect on cell dimensional features and considerably decreases them only at 65% RH. The increasing of the bacteria cell wall roughness and elasticity occurs at the same time. Observed changes indicate that morphological properties of B. cereus are rather stable in wide range of relative humidity, whereas E. coli are more sensitive to drying, significantly increasing roughness and stiffness parameters at RH cell wall structure of gram-positive and gram-negative bacterial cells.

Humidity-Dependent Bacterial Cells Functional Morphometry Investigations Using Atomic Force Microscope

PubMed Central

Nikiyan, Hike; Vasilchenko, Alexey; Deryabin, Dmitry

2010-01-01

The effect of a relative humidity (RH) in a range of 93–65% on morphological and elastic properties of Bacillus cereus and Escherichia coli cells was evaluated using atomic force microscopy. It is shown that gradual dehumidification of bacteria environment has no significant effect on cell dimensional features and considerably decreases them only at 65% RH. The increasing of the bacteria cell wall roughness and elasticity occurs at the same time. Observed changes indicate that morphological properties of B. cereus are rather stable in wide range of relative humidity, whereas E. coli are more sensitive to drying, significantly increasing roughness and stiffness parameters at RH ≤ 84% RH. It is discussed the dependence of the response features on differences in cell wall structure of gram-positive and gram-negative bacterial cells. PMID:20652040

Measurement of the gravity-field curvature by atom interferometry.

PubMed

Rosi, G; Cacciapuoti, L; Sorrentino, F; Menchetti, M; Prevedelli, M; Tino, G M

2015-01-09

We present the first direct measurement of the gravity-field curvature based on three conjugated atom interferometers. Three atomic clouds launched in the vertical direction are simultaneously interrogated by the same atom interferometry sequence and used to probe the gravity field at three equally spaced positions. The vertical component of the gravity-field curvature generated by nearby source masses is measured from the difference between adjacent gravity gradient values. Curvature measurements are of interest in geodesy studies and for the validation of gravitational models of the surrounding environment. The possibility of using such a scheme for a new determination of the Newtonian constant of gravity is also discussed.

Dynamic Curvature Steering Control for Autonomous Vehicle: Performance Analysis

NASA Astrophysics Data System (ADS)

Aizzat Zakaria, Muhammad; Zamzuri, Hairi; Amri Mazlan, Saiful

2016-02-01

This paper discusses the design of dynamic curvature steering control for autonomous vehicle. The lateral control and longitudinal control are discussed in this paper. The controller is designed based on the dynamic curvature calculation to estimate the path condition and modify the vehicle speed and steering wheel angle accordingly. In this paper, the simulation results are presented to show the capability of the controller to track the reference path. The controller is able to predict the path and modify the vehicle speed to suit the path condition. The effectiveness of the controller is shown in this paper whereby identical performance is achieved with the benchmark but with extra curvature adaptation capabilites.

Principal curvatures and area ratio of propagating surfaces in isotropic turbulence

NASA Astrophysics Data System (ADS)

Zheng, Tianhang; You, Jiaping; Yang, Yue

2017-10-01

We study the statistics of principal curvatures and the surface area ratio of propagating surfaces with a constant or nonconstant propagating velocity in isotropic turbulence using direct numerical simulation. Propagating surface elements initially constitute a plane to model a planar premixed flame front. When the statistics of evolving propagating surfaces reach the stationary stage, the statistical profiles of principal curvatures scaled by the Kolmogorov length scale versus the constant displacement speed scaled by the Kolmogorov velocity scale collapse at different Reynolds numbers. The magnitude of averaged principal curvatures and the number of surviving surface elements without cusp formation decrease with increasing displacement speed. In addition, the effect of surface stretch on the nonconstant displacement speed inhibits the cusp formation on surface elements at negative Markstein numbers. In order to characterize the wrinkling process of the global propagating surface, we develop a model to demonstrate that the increase of the surface area ratio is primarily due to positive Lagrangian time integrations of the area-weighted averaged tangential strain-rate term and propagation-curvature term. The difference between the negative averaged mean curvature and the positive area-weighted averaged mean curvature characterizes the cellular geometry of the global propagating surface.

Bone marrow-derived cells participate in stromal remodeling of the lung following acute bacterial pneumonia in mice.

PubMed

Serikov, Vladimir B; Mikhaylov, Viatcheslav M; Krasnodembskay, Anna D; Matthay, Michael A

2008-01-01

Bone marrow-derived cells (BMDC) have been shown to graft injured tissues, differentiate in specialized cells, and participate in repair. The importance of these processes in acute lung bacterial inflammation and development of fibrosis is unknown. The goal of this study was to investigate the temporal sequence and lineage commitment of BMDC in mouse lungs injured by bacterial pneumonia. We transplanted GFP-tagged BMDC into 5-Gy-irradiated C57BL/6 mice. After 3 months of recovery, mice were subjected to LD(50) intratracheal instillation of live E. coli (controls received saline) which produced pneumonia and subsequent areas of fibrosis. Lungs were investigated by immunohistology for up to 6 months. At the peak of lung inflammation, the predominant influx of BMDC were GFP(+) leukocytes. Postinflammatory foci of lung fibrosis were evident after 1-2 months. The fibrotic foci in lung stroma contained clusters of GFP(+) CD45(+) cells, GFP(+) vimentin-positive cells, and GFP(+) collagen I-positive fibroblasts. GFP(+) endothelial or epithelial cells were not identified. These data suggest that following 5-Gy irradiation and acute bacterial pneumonia, BMDC may temporarily participate in lung postinflammatory repair and stromal remodeling without long-term engraftment as specialized endothelial or epithelial cells.

Riemann curvature of a boosted spacetime geometry

NASA Astrophysics Data System (ADS)

Battista, Emmanuele; Esposito, Giampiero; Scudellaro, Paolo; Tramontano, Francesco

2016-10-01

The ultrarelativistic boosting procedure had been applied in the literature to map the metric of Schwarzschild-de Sitter spacetime into a metric describing de Sitter spacetime plus a shock-wave singularity located on a null hypersurface. This paper evaluates the Riemann curvature tensor of the boosted Schwarzschild-de Sitter metric by means of numerical calculations, which make it possible to reach the ultrarelativistic regime gradually by letting the boost velocity approach the speed of light. Thus, for the first time in the literature, the singular limit of curvature, through Dirac’s δ distribution and its derivatives, is numerically evaluated for this class of spacetimes. Moreover, the analysis of the Kretschmann invariant and the geodesic equation shows that the spacetime possesses a “scalar curvature singularity” within a 3-sphere and it is possible to define what we here call “boosted horizon”, a sort of elastic wall where all particles are surprisingly pushed away, as numerical analysis demonstrates. This seems to suggest that such “boosted geometries” are ruled by a sort of “antigravity effect” since all geodesics seem to refuse to enter the “boosted horizon” and are “reflected” by it, even though their initial conditions are aimed at driving the particles toward the “boosted horizon” itself. Eventually, the equivalence with the coordinate shift method is invoked in order to demonstrate that all δ2 terms appearing in the Riemann curvature tensor give vanishing contribution in distributional sense.

Curvature-induced capillary interaction of spherical particles at a liquid interface.

PubMed

Würger, Alois

2006-10-01

We consider a liquid interface with different principal curvatures +/-c and find that the mere presence of a spherical particle leads to a deformation field of quadrupolar symmetry; the corresponding "capillary quadrupole moment" is given by the ratio of the particle size and the curvature radius. The resulting pair interaction of nearby particles is anisotropic and favors the formation of aggregates of cubic symmetry. Since the single-particle trapping energy depends quadratically on curvature with a negative prefactor, a curvature gradient induces a lateral force that pushes the particles towards strongly curved regions of the interface. As an illustration we discuss the effects occurring on a catenoid.

An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.

2015-02-09

Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has beenmore » observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.« less

An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

NASA Astrophysics Data System (ADS)

Song, Zhen; Kenney, Janice P. L.; Fein, Jeremy B.; Bunker, Bruce A.

2012-06-01

Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

Effect of Micro- and Nanoscale Topography on the Adhesion of Bacterial Cells to Solid Surfaces

PubMed Central

Hsu, Lillian C.; Fang, Jean; Borca-Tasciuc, Diana A.; Worobo, Randy W.

2013-01-01

Attachment and biofilm formation by bacterial pathogens on surfaces in natural, industrial, and hospital settings lead to infections and illnesses and even death. Minimizing bacterial attachment to surfaces using controlled topography could reduce the spreading of pathogens and, thus, the incidence of illnesses and subsequent human and financial losses. In this context, the attachment of key microorganisms, including Escherichia coli, Listeria innocua, and Pseudomonas fluorescens, to silica and alumina surfaces with micron and nanoscale topography was investigated. The results suggest that orientation of the attached cells occurs preferentially such as to maximize their contact area with the surface. Moreover, the bacterial cells exhibited different morphologies, including different number and size of cellular appendages, depending on the topographical details of the surface to which they attached. This suggests that bacteria may utilize different mechanisms of attachment in response to surface topography. These results are important for the design of novel microbe-repellant materials. PMID:23416997

An experimental study of Au removal from solution by non-metabolizing bacterial cells and their exudates

NASA Astrophysics Data System (ADS)

Kenney, Janice P. L.; Song, Zhen; Bunker, Bruce A.; Fein, Jeremy B.

2012-06-01

In this study, we examine the initial interactions between aqueous Au(III)-hydroxide-chloride aqueous complexes and bacteria by measuring the effects of non-metabolizing cells on the speciation and distribution of Au. We conducted batch Au(III) removal experiments, measuring the kinetics and pH dependence of Au removal, and tracking valence state transformations and binding environments using XANES spectroscopy. These experiments were conducted using non-metabolizing cells of Bacillus subtilis or Pseudomonas putida suspended in a 5 ppm Au(III)-(hydroxide)-chloride starting solution of 0.1 M NaClO4 to buffer ionic strength. Both bacterial species removed greater than 85% of the Au from solution after 2 h of exposure time below approximately pH 5. Above pH 5, the extent of Au removed from solution decreased with increasing pH, with less than approximately 10% removal of Au from solution above pH 7.5. Kinetics experiments indicated that the Au removal with both bacterial species was rapid at pH 3, and slowed with increasing pH. Reversibility experiments demonstrated that (1) once the Au was removed from solution, adjusting 35 the pH alone did not remobilize the Au into solution and (2) the presence of cysteine in solution in the reversibility experiments caused Au to desorb, suggesting that the Au was not internalized within the bacterial cells. Our results suggest that Au removal occurs as a two-step pH-dependent adsorption reduction process. The speciation of the aqueous Au and the bacterial surface appears to control the rate of Au removal from solution. Under low pH conditions, the cell walls are only weakly negatively charged and aqueous Au complexes adsorb readily and rapidly. With increasing pH, the cell wall becomes more negatively charged, slowing adsorption significantly. The XANES data demonstrate that the reduction of Au(III) by bacterial exudates is slower and less extensive than the reduction observed in the bacteria-bearing systems, and we conclude that

Bacterial interactions in dental biofilm development.

PubMed

Hojo, K; Nagaoka, S; Ohshima, T; Maeda, N

2009-11-01

Recent analyses with ribosomal RNA-based technologies have revealed the diversity of bacterial populations within dental biofilms, and have highlighted their important contributions to oral health and disease. Dental biofilms are exceedingly complex and multispecies ecosystems, where oral bacteria interact cooperatively or competitively with other members. Bacterial interactions that influence dental biofilm communities include various different mechanisms. During the early stage of biofilm formation, it is known that planktonic bacterial cells directly attach to surfaces of the oral cavity or indirectly bind to other bacterial cells that have already colonized. Adherence through co-aggregation may be critical for the temporary retention of bacteria on dental surfaces, and may facilitate eventual bacterial colonization. It is likely that metabolic communication, genetic exchange, production of inhibitory factors (e.g., bacteriocins, hydrogen peroxide, etc.), and quorum-sensing are pivotal regulatory factors that determine the bacterial composition and/or metabolism. Since each bacterium can easily access a neighboring bacterial cell and its metabolites, genetic exchanges and metabolic communication may occur frequently in dental biofilms. Quorum-sensing is defined as gene regulation in response to cell density, which influences various functions, e.g., virulence and bacteriocin production. In this review, we discuss these important interactions among oral bacteria within the dental biofilm communities.

Berry Curvature in Magnon-Phonon Hybrid Systems.

PubMed

Takahashi, Ryuji; Nagaosa, Naoto

2016-11-18

We study theoretically the Berry curvature of the magnon induced by the hybridization with the acoustic phonons via the spin-orbit and dipolar interactions. We first discuss the magnon-phonon hybridization via the dipolar interaction, and show that the dispersions have gapless points in momentum space, some of which form a loop. Next, when both spin-orbit and dipolar interactions are considered, we show anisotropic texture of the Berry curvature and its divergence with and without gap closing. Realistic evaluation of the consequent anomalous velocity is given for yttrium iron garnet.

Dissecting Bacterial Cell Wall Entry and Signaling in Eukaryotic Cells: an Actin-Dependent Pathway Parallels Platelet-Activating Factor Receptor-Mediated Endocytosis.

PubMed

Loh, Lip Nam; Gao, Geli; Tuomanen, Elaine I

2017-01-03

The Gram-positive bacterial cell wall (CW) peptidoglycan-teichoic acid complex is released into the host environment during bacterial metabolism or death. It is a highly inflammatory Toll-like receptor 2 (TLR2) ligand, and previous in vivo studies have demonstrated its ability to recapitulate pathological features of pneumonia and meningitis. We report that an actin-dependent pathway is involved in the internalization of the CW by epithelial and endothelial cells, in addition to the previously described platelet-activating factor receptor (PAFr)-dependent uptake pathway. Unlike the PAFr-dependent pathway, which is mediated by clathrin and dynamin and does not lead to signaling, the alternative pathway is sensitive to 5-(N-ethyl-N-isopropyl) amiloride (EIPA) and engenders Rac1, Cdc42, and phosphatidylinositol 3-kinase (PI3K) signaling. Upon internalization by this macropinocytosis-like pathway, CW is trafficked to lysosomes. Intracellular CW trafficking is more complex than previously recognized and suggests multiple points of interaction with and without innate immune signaling. Streptococcus pneumoniae is a major human pathogen infecting the respiratory tract and brain. It is an established model organism for understanding how infection injures the host. During infection or bacterial growth, bacteria shed their cell wall (CW) into the host environment and trigger inflammation. A previous study has shown that CW enters and crosses cell barriers by interacting with a receptor on the surfaces of host cells, termed platelet-activating factor receptor (PAFr). In the present study, by using cells that are depleted of PAFr, we identified a second pathway with features of macropinocytosis, which is a receptor-independent fluid uptake mechanism by cells. Each pathway contributes approximately the same amount of cell wall trafficking, but the PAFr pathway is silent, while the new pathway appears to contribute to the host inflammatory response to CW insult. Copyright © 2017

Patient satisfaction with correction of congenital penile curvature.

PubMed

Mayer, M; Rey Valzacchi, G; Silva Garretón, A; Layus, O; Gueglio, G

2017-12-29

Congenital penile curvature is a relatively rare disease, resulting from a deviation of the penis from the body's straight axis when erect. The prevalence is difficult to determine. Although it has been suggested that the condition could affect up to 10% of the male population, most of these deviations are minor, with no clinical or psychological importance, which leads to its underdiagnosis. Effective correction of the deviation can markedly improve the quality of life of adolescents with this condition. To assess the quality of the sex life of patients diagnosed with congenital penile curvature who underwent surgical correction. Design Retrospective, observational cohort study. Data was collected from the medical records of patients who underwent surgical correction of congenital penile curvature from June 2004 to August 2016. The patients completed the following self-administered questionnaires: Sexual Quality of Life Questionnaire-Male (SQOL-M), International Index of Erectile Function 5 (IIEF 5) and "How satisfied are you with the results of the surgery? From 0 to 10". Twenty-two corporoplasties were performed to correct the patients' congenital penile curvature. The patients' average age was 23.4 years (range, 17-35). The mean deviation prior to surgery was 47.9° (range, 20°-90°). The average score on the SQOL-M was 52 points (range, 6-66). The average score on the IIEF 5 was 22.4 points. Congenital penile curvature profoundly decreases quality of life, and early surgery is fundamental for repairing the anatomical deformation and thereby significantly restores the patients' psychosocial and sexual wellbeing. Copyright © 2017 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors.

PubMed

Brutesco, Catherine; Prévéral, Sandra; Escoffier, Camille; Descamps, Elodie C T; Prudent, Elsa; Cayron, Julien; Dumas, Louis; Ricquebourg, Manon; Adryanczyk-Perrier, Géraldine; de Groot, Arjan; Garcia, Daniel; Rodrigue, Agnès; Pignol, David; Ginet, Nicolas

2017-01-01

Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible P ars promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction. We also investigated the bioluminescence reporter gene system transferred into Deinococcus deserti, an environmental, desiccation- and radiation-tolerant bacterium that would reduce the manufacturing costs of bacterial biosensors for commercial water analyzers and open the field of biodetection in radioactive environments. We thus successfully obtained a cell survival biosensor and a metal biosensor able to detect a concentration as low as 100 nM of arsenite in D. deserti. We demonstrated that the arsenite biosensor resisted desiccation and remained functional after 7 days stored in air-dried D. deserti cells. We also report here the use of a new near-infrared (NIR) fluorescent reporter candidate, a bacteriophytochrome from the magnetotactic bacterium Magnetospirillum magneticum AMB-1, which showed a NIR fluorescent signal that remained optimal despite increasing sample turbidity, while in similar conditions, a drastic loss of the lux-based biosensors signal was observed.

Conformally Invariant Powers of the Laplacian, Q-Curvature, and Tractor Calculus

NASA Astrophysics Data System (ADS)

Gover, A. Rod; Peterson, Lawrence J.

We describe an elementary algorithm for expressing, as explicit formulae in tractor calculus, the conformally invariant GJMS operators due to C.R. Graham et alia. These differential operators have leading part a power of the Laplacian. Conformal tractor calculus is the natural induced bundle calculus associated to the conformal Cartan connection. Applications discussed include standard formulae for these operators in terms of the Levi-Civita connection and its curvature and a direct definition and formula for T. Branson's so-called Q-curvature (which integrates to a global conformal invariant) as well as generalisations of the operators and the Q-curvature. Among examples, the operators of order 4, 6 and 8 and the related Q-curvatures are treated explicitly. The algorithm exploits the ambient metric construction of Fefferman and Graham and includes a procedure for converting the ambient curvature and its covariant derivatives into tractor calculus expressions. This is partly based on [12], where the relationship of the normal standard tractor bundle to the ambient construction is described.

Charge modeling of ionic polymer-metal composites for dynamic curvature sensing

NASA Astrophysics Data System (ADS)

Bahramzadeh, Yousef; Shahinpoor, Mohsen

2011-04-01

A curvature sensor based on Ionic Polymer-Metal Composite (IPMC) is proposed and characterized for sensing of curvature variation in structures such as inflatable space structures in which using low power and flexible curvature sensor is of high importance for dynamic monitoring of shape at desired points. The linearity of output signal of sensor for calibration, effect of deflection rate at low frequencies and the phase delay between the output signal and the input deformation of IPMC curvature sensor is investigated. An analytical chemo-electro-mechanical model for charge dynamic of IPMC sensor is presented based on Nernst-Planck partial differential equation which can be used to explain the phenomena observed in experiments. The rate dependency of output signal and phase delay between the applied deformation and sensor signal is studied using the proposed model. The model provides a background for predicting the general characteristics of IPMC sensor. It is shown that IPMC sensor exhibits good linearity, sensitivity, and repeatability for dynamic curvature sensing of inflatable structures.

Association of microRNAs with Types of Leaf Curvature in Brassica rapa.

PubMed

Ren, Wenqing; Wang, Han; Bai, Jinjuan; Wu, Feijie; He, Yuke

2018-01-01

Many vegetable crops of Brassica rapa are characterized by their typical types of leaf curvature. Leaf curvature in the right direction and to the proper degree is important for the yield and quality of green vegetable products, when cultivated under stress conditions. Recent research has unveiled some of the roles of miRNAs in Brassica crops such as how they regulate the timing of leafy head initiation and shape of the leafy head. However, the molecular mechanism underlying the variability in leaf curvature in B. rapa remains unclear. We tested the hypothesis that the leaf curvature of B. rapa is affected by miRNA levels. On the basis of leaf phenotyping, 56 B. rapa accessions were classified into five leaf curvature types, some of which were comparable to miRNA mutants of Arabidopsis thaliana in phenotype. Higher levels of miR166 and miR319a expression were associated with downward curvature and wavy margins, respectively. Overexpression of the Brp - MIR166g-1 gene caused rosette leaves to change from flat to downward curving and folding leaves to change from upward curving to flat, leading to the decrease in the number of incurved leaves and size of the leafy head. Our results reveal that miRNAs affect the types of leaf curvature in B. rapa . These findings provide insight into the relationship between miRNAs and variation in leaf curvature.

Association of microRNAs with Types of Leaf Curvature in Brassica rapa

PubMed Central

Ren, Wenqing; Wang, Han; Bai, Jinjuan; Wu, Feijie; He, Yuke

2018-01-01

Many vegetable crops of Brassica rapa are characterized by their typical types of leaf curvature. Leaf curvature in the right direction and to the proper degree is important for the yield and quality of green vegetable products, when cultivated under stress conditions. Recent research has unveiled some of the roles of miRNAs in Brassica crops such as how they regulate the timing of leafy head initiation and shape of the leafy head. However, the molecular mechanism underlying the variability in leaf curvature in B. rapa remains unclear. We tested the hypothesis that the leaf curvature of B. rapa is affected by miRNA levels. On the basis of leaf phenotyping, 56 B. rapa accessions were classified into five leaf curvature types, some of which were comparable to miRNA mutants of Arabidopsis thaliana in phenotype. Higher levels of miR166 and miR319a expression were associated with downward curvature and wavy margins, respectively. Overexpression of the Brp-MIR166g-1 gene caused rosette leaves to change from flat to downward curving and folding leaves to change from upward curving to flat, leading to the decrease in the number of incurved leaves and size of the leafy head. Our results reveal that miRNAs affect the types of leaf curvature in B. rapa. These findings provide insight into the relationship between miRNAs and variation in leaf curvature. PMID:29467771

Intramanual and intermanual transfer of the curvature aftereffect

PubMed Central

Duijndam, Maarten J. A.; Ketels, Myrna F. M.; Wilbers, Martine T. J. M.; Zwijsen, Sandra A.; Kappers, Astrid M. L.

2008-01-01

The existence and transfer of a haptic curvature aftereffect was investigated to obtain a greater insight into neural representation of shape. The haptic curvature aftereffect is the phenomenon whereby a flat surface is judged concave if the preceding touched stimulus was convex and vice versa. Single fingers were used to touch the subsequently presented stimuli. A substantial aftereffect was found when the adaptation surface and the test surface were touched by the same finger. Furthermore, a partial, but significant transfer of the aftereffect was demonstrated between fingers of the same hand and between fingers of both the hands. These results provide evidence that curvature information is not only represented at a level that is directly connected to the mechanoreceptors of individual fingers but is also represented at a stage in the somatosensory cortex shared by the fingers of both the hands. PMID:18438649

Interaction of Uranium with Bacterial Cell Surfaces: Inferences from Phosphatase-Mediated Uranium Precipitation.

PubMed

Kulkarni, Sayali; Misra, Chitra Seetharam; Gupta, Alka; Ballal, Anand; Apte, Shree Kumar

2016-08-15

Deinococcus radiodurans and Escherichia coli expressing either PhoN, a periplasmic acid phosphatase, or PhoK, an extracellular alkaline phosphatase, were evaluated for uranium (U) bioprecipitation under two specific geochemical conditions (GCs): (i) a carbonate-deficient condition at near-neutral pH (GC1), and (ii) a carbonate-abundant condition at alkaline pH (GC2). Transmission electron microscopy revealed that recombinant cells expressing PhoN/PhoK formed cell-associated uranyl phosphate precipitate under GC1, whereas the same cells displayed extracellular precipitation under GC2. These results implied that the cell-bound or extracellular location of the precipitate was governed by the uranyl species prevalent at that particular GC, rather than the location of phosphatase. MINTEQ modeling predicted the formation of predominantly positively charged uranium hydroxide ions under GC1 and negatively charged uranyl carbonate-hydroxide complexes under GC2. Both microbes adsorbed 6- to 10-fold more U under GC1 than under GC2, suggesting that higher biosorption of U to the bacterial cell surface under GC1 may lead to cell-associated U precipitation. In contrast, at alkaline pH and in the presence of excess carbonate under GC2, poor biosorption of negatively charged uranyl carbonate complexes on the cell surface might have resulted in extracellular precipitation. The toxicity of U observed under GC1 being higher than that under GC2 could also be attributed to the preferential adsorption of U on cell surfaces under GC1. This work provides a vivid description of the interaction of U complexes with bacterial cells. The findings have implications for the toxicity of various U species and for developing biological aqueous effluent waste treatment strategies. The present study provides illustrative insights into the interaction of uranium (U) complexes with recombinant bacterial cells overexpressing phosphatases. This work demonstrates the effects of aqueous speciation of U on

Interaction of Uranium with Bacterial Cell Surfaces: Inferences from Phosphatase-Mediated Uranium Precipitation

PubMed Central

Kulkarni, Sayali; Misra, Chitra Seetharam; Gupta, Alka; Ballal, Anand

2016-01-01

ABSTRACT Deinococcus radiodurans and Escherichia coli expressing either PhoN, a periplasmic acid phosphatase, or PhoK, an extracellular alkaline phosphatase, were evaluated for uranium (U) bioprecipitation under two specific geochemical conditions (GCs): (i) a carbonate-deficient condition at near-neutral pH (GC1), and (ii) a carbonate-abundant condition at alkaline pH (GC2). Transmission electron microscopy revealed that recombinant cells expressing PhoN/PhoK formed cell-associated uranyl phosphate precipitate under GC1, whereas the same cells displayed extracellular precipitation under GC2. These results implied that the cell-bound or extracellular location of the precipitate was governed by the uranyl species prevalent at that particular GC, rather than the location of phosphatase. MINTEQ modeling predicted the formation of predominantly positively charged uranium hydroxide ions under GC1 and negatively charged uranyl carbonate-hydroxide complexes under GC2. Both microbes adsorbed 6- to 10-fold more U under GC1 than under GC2, suggesting that higher biosorption of U to the bacterial cell surface under GC1 may lead to cell-associated U precipitation. In contrast, at alkaline pH and in the presence of excess carbonate under GC2, poor biosorption of negatively charged uranyl carbonate complexes on the cell surface might have resulted in extracellular precipitation. The toxicity of U observed under GC1 being higher than that under GC2 could also be attributed to the preferential adsorption of U on cell surfaces under GC1. This work provides a vivid description of the interaction of U complexes with bacterial cells. The findings have implications for the toxicity of various U species and for developing biological aqueous effluent waste treatment strategies. IMPORTANCE The present study provides illustrative insights into the interaction of uranium (U) complexes with recombinant bacterial cells overexpressing phosphatases. This work demonstrates the effects of aqueous

Topology of codimension-one foliations of nonnegative curvature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolotov, Dmitry V

We show that a transversely oriented C{sup 2}-foliation of codimension one with nonnegative Ricci curvature on a closed orientable manifold is a foliation with almost no holonomy. This allows us to decompose the manifold into blocks on which this foliation has a simple structure. We also show that a manifold homeomorphic to a 5-dimensional sphere does not admit a codimension-one C{sup 2}-foliation with nonnegative sectional curvature. Bibliography: 29 titles.

BT-benzo-29 inhibits bacterial cell proliferation by perturbing FtsZ assembly.

PubMed

Ray, Shashikant; Jindal, Bhavya; Kunal, Kishore; Surolia, Avadhesha; Panda, Dulal

2015-10-01

We have identified a potent antibacterial agent N-(4-sec-butylphenyl)-2-(thiophen-2-yl)-1H-benzo[d]imidazole-4-carboxamide (BT-benzo-29) from a library of benzimidazole derivatives that stalled bacterial division by inhibiting FtsZ assembly. A short (5 min) exposure of BT-benzo-29 disassembled the cytokinetic Z-ring in Bacillus subtilis cells without affecting the cell length and nucleoids. BT-benzo-29 also perturbed the localization of early and late division proteins such as FtsA, ZapA and SepF at the mid-cell. Further, BT-benzo-29 bound to FtsZ with a dissociation constant of 24 ± 3 μm and inhibited the assembly and GTPase activity of purified FtsZ. A docking analysis suggested that BT-benzo-29 may bind to FtsZ at the C-terminal domain near the T7 loop. BT-benzo-29 displayed significantly weaker inhibitory effects on the assembly and GTPase activity of two mutants (L272A and V275A) of FtsZ supporting the prediction of the docking analysis. Further, BT-benzo-29 did not appear to inhibit DNA duplication and nucleoid segregation and it did not perturb the membrane potential of B. subtilis cells. The results suggested that BT-benzo-29 exerts its potent antibacterial activity by inhibiting FtsZ assembly. Interestingly, BT-benzo-29 did not affect the membrane integrity of mammalian red blood cells. BT-benzo-29 bound to tubulin with a much weaker affinity than FtsZ and exerted significantly weaker effects on mammalian cells than on the bacterial cells indicating that the compound may have a strong antibacterial potential. © 2015 FEBS.