TY - JOUR AB - Generally, the motion of fluids is smooth and laminar at low speeds but becomes highly disordered and turbulent as the velocity increases. The transition from laminar to turbulent flow can involve a sequence of instabilities in which the system realizes progressively more complicated states, or it can occur suddenly. Once the transition has taken place, it is generally assumed that, under steady conditions, the turbulent state will persist indefinitely. The flow of a fluid down a straight pipe provides a ubiquitous example of a shear flow undergoing a sudden transition from laminar to turbulent motion. Extensive calculations and experimental studies have shown that, at relatively low flow rates, turbulence in pipes is transient, and is characterized by an exponential distribution of lifetimes. They also suggest that for Reynolds numbers exceeding a critical value the lifetime diverges (that is, becomes infinitely large), marking a change from transient to persistent turbulence. Here we present experimental data and numerical calculations covering more than two decades of lifetimes, showing that the lifetime does not in fact diverge but rather increases exponentially with the Reynolds number. This implies that turbulence in pipes is only a transient event (contrary to the commonly accepted view), and that the turbulent and laminar states remain dynamically connected, suggesting avenues for turbulence control. AU - Björn Hof AU - Westerweel, Jerry AU - Schneider, Tobias M AU - Eckhardt, Bruno ID - 2791 IS - 7107 JF - Nature TI - Finite lifetime of turbulence in shear flows VL - 443 ER - TY - JOUR AB - Transition to turbulence in pipe flow has posed a riddle in fluid dynamics since the pioneering experiments of Reynolds[1]. Although the laminar flow is linearly stable for all flow rates, practical pipe flows become turbulent at large enough flow speeds. Turbulence arises suddenly and fully without distinct steps and without a clear critical point. The complexity of this problem has puzzled mathematicians, physicists and engineers for more than a century and no satisfactory explanation of this problem has been given. In a very recent theoretical approach it has been suggested that unstable solutions of the Navier Stokes equations may hold the key to understanding this problem. In numerical studies such unstable states have been identified as exact solutions for the idealized case of a pipe with periodic boundary conditions[2, 3]. These solutions have the form of waves extending through the entire pipe and travelling in the streamwise direction at a phase speed close to the bulk velocity of the fluid. With the aid of a recently developed high-speed stereoscopic Particle Image Velocimetry (PIV) system, we were able to observe transients of such unstable solutions in turbulent pipe flow[4]. AU - Björn Hof AU - van Doorne, Casimir W AU - Westerweel, Jerry AU - Nieuwstadt, Frans T ID - 2792 JF - Fluid Mechanics and its Applications TI - Observation of nonlinear travelling waves in turbulent pipe flow VL - 78 ER - TY - JOUR AB - IL-10 is a potent anti-inflammatory and immunomodulatory cytokine, exerting major effects in the degree and quality of the immune response. Using a newly generated IL-10 reporter mouse model, which easily allows the study of IL-10 expression from each allele in a single cell, we report here for the first time that IL-10 is predominantly monoallelic expressed in CD4+ T cells. Furthermore, we have compelling evidence that this expression pattern is not due to parental imprinting, allelic exclusion, or strong allelic bias. Instead, our results support a stochastic regulation mechanism, in which the probability to initiate allelic transcription depends on the strength of TCR signaling and subsequent capacity to overcome restrictions imposed by chromatin hypoacetylation. In vivo Ag-experienced T cells show a higher basal probability to transcribe IL-10 when compared with naive cells, yet still show mostly monoallelic IL-10 expression. Finally, statistical analysis on allelic expression data shows transcriptional independence between both alleles. We conclude that CD4+ T cells have a low probability for IL-10 allelic activation resulting in a predominantly monoallelic expression pattern, and that IL-10 expression appears to be stochastically regulated by controlling the frequency of expressing cells, rather than absolute protein levels per cell. AU - Calado, Dinis P AU - Tiago Paixao AU - Holmberg, Dan AU - Haury, Matthias ID - 2894 IS - 8 JF - Journal of Immunology TI - Stochastic Monoallelic Expression of IL 10 in T Cells VL - 177 ER - TY - CHAP AB - Most binocular stereo algorithms assume that all scene elements are visible from both cameras. Scene elements that are visible from only one camera, known as occlusions, pose an important challenge for stereo. Occlusions are important for segmentation, because they appear near discontinuities. However, stereo algorithms tend to ignore occlusions because of their difficulty. One reason is that occlusions require the input images to be treated symmetrically, which complicates the problem formulation. Worse, certain depth maps imply physically impossible scene configurations, and must be excluded from the output. In this chapter we approach the problem of binocular stereo with occlusions from an energy minimization viewpoint. We begin by reviewing traditional stereo methods that do not handle occlusions. If occlusions are ignored, it is easy to formulate the stereo problem as a pixel labeling problem, which leads to an energy function that is common in early vision. This kind of energy function can he minimized using graph cuts, which is a combinatorial optimization technique that has proven to be very effective for low-level vision problems. Motivated by this, we have designed two graph cut stereo algorithms that are designed to handle occlusions. These algorithms produce promising experimental results on real data with ground truth. AU - Vladimir Kolmogorov AU - Zabih, Ramin ID - 2921 T2 - Handbook of Mathematical Models in Computer Vision TI - Graph cut algorithms for binocular stereo with occlusions ER - TY - CHAP AB - Arabidopsis thaliana is currently the most important model organism for basic molecular plant research. It is also a favourable model for developmental biology, as its embryogenesis follows a nearly invariant pattern of cell divisions and cell type specifications. Study of embryogenesis can involve genetic, physiological or biochemical approaches, but is always limited by the inaccessibility of the embryos which develop deep inside maternal tissue. Thus, for developmental studies, there is an increasing demand for methods which allow embryogenesis under artificial conditions, providing better accessibility to experimental manipulation. In this chapter, we address theoretical aspects of embryo culture, give some thoughts on which embryo culture system is suited best for which application and finally discuss three current methods which have been successfully used in Arabidopsis embryo culture. © 2006 Springer-Verlag Berlin Heidelberg. AU - Sauer, Michael AU - Jirí Friml ED - Mujib, Abdul ED - Šamaj, Jozef ID - 3002 T2 - Somatic Embryogenesis TI - In vitro culture of Arabidopsis embryos VL - 2 ER - TY - JOUR AB - Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux. AU - Petrášek, Jan AU - Mravec, Jozef AU - Bouchard, Rodolphe AU - Blakeslee, Joshua AU - Melinda Abas AU - Seifertová, Daniela AU - Wiśniewska, Justyna AU - Tadele, Zerihun AU - Kubeš, Martin AU - Čovanová, Milada AU - Dhonukshe, Pankaj AU - Skůpa, Petr AU - Eva Benková AU - Perry, Lucie AU - Křeček, Pavel AU - Lee, Ok Ran AU - Fink, Gerald R AU - Geisler, Markus AU - Murphy, Angus S AU - Luschnig, Christian AU - Zažímalová, Eva AU - Jirí Friml ID - 3012 IS - 5775 JF - Science TI - PIN proteins perform a rate-limiting function in cellular auxin efflux VL - 312 ER - TY - JOUR AB - The formation of the leaf vascular pattern has fascinated biologists for centuries. In the early leaf primordium, complex networks of procambial cells emerge from homogeneous subepidermal tissue. The molecular nature of the underlying positional information is unknown, but various lines of evidence implicate gradually restricted transport routes of the plant hormone auxin in defining sites of procambium formation. Here we show that a crucial member of the AtPIN family of auxin-efflux-associated proteins, AtPIN1, is expressed prior to pre-procambial and procambial cell fate markers in domains that become restricted toward sites of procambium formation. Subcellular AtPIN1 polarity indicates that auxin is directed to distinct "convergence points" in the epidermis, from where it defines the positions of major veins. Integrated polarities in all emerging veins indicate auxin drainage toward pre-existing veins, but veins display divergent polarities as they become connected at both ends. Auxin application and transport inhibition reveal that convergence point positioning and AtPIN1 expression domain dynamics are self-organizing, auxin-transport-dependent processes. We derive a model for self-regulated, reiterative patterning of all vein orders and postulate at its onset a common epidermal auxin-focusing mechanism for major-vein positioning and phyllotactic patterning. AU - Scarpella, Enrico AU - Marcos, Danielle AU - Jirí Friml AU - Berleth, Thomas ID - 3010 IS - 8 JF - Genes and Development TI - Control of leaf vascular patterning by polar auxin transport VL - 20 ER - TY - JOUR AB - Root gravitropism describes the orientation of root growth along the gravity vector and is mediated by differential cell elongation in the root meristem. This response requires the coordinated, asymmetric distribution of the phytohormone auxin within the root meristem, and depends on the concerted activities of PIN proteins and AUX1 - members of the auxin transport pathway. Here, we show that intracellular trafficking and proteasome activity combine to control PIN2 degradation during root gravitropism. Following gravi-stimulation, proteasome-dependent variations in PIN2 localization and degradation at the upper and lower sides of the root result in asymmetric distribution of PIN2. Ubiquitination of PIN2 occurs in a proteasome-dependent manner, indicating that the proteasome is involved in the control of PIN2 turnover. Stabilization of PIN2 affects its abundance and distribution, and leads to defects in auxin distribution and gravitropic responses. We describe the effects of auxin on PIN2 localization and protein levels, indicating that redistribution of auxin during the gravitropic response may be involved in the regulation of PIN2 protein. AU - Abas, Lindy AU - Benjamins, René AU - Malenica, Nenad AU - Paciorek, Tomasz AU - Wiśniewska, Justyna AU - Moulinier-Anzola, Jeanette C AU - Sieberer, Tobias AU - Jirí Friml AU - Luschnig, Christian ID - 3007 IS - 3 JF - Nature Cell Biology TI - Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism VL - 8 ER - TY - JOUR AB - Dividing plant cells perform a remarkable task of building a new cell wall within the cytoplasm in a few minutes. A long-standing paradigm claims that this primordial cell wall, known as the cell plate, is generated by delivery of newly synthesized material from Golgi apparatus-originated secretory vesicles. Here, we show that, in diverse plant species, cell surface material, including plasma membrane proteins, cell wall components, and exogenously applied endocytic tracers, is rapidly delivered to the forming cell plate. Importantly, this occurs even when de novo protein synthesis is blocked. In addition, cytokinesis-specific syntaxin KNOLLE as well as plasma membrane (PM) resident proteins localize to endosomes that fuse to initiate the cell plate. The rate of endocytosis is strongly enhanced during cell plate formation, and its genetic or pharmacological inhibition leads to cytokinesis defects. Our results reveal that endocytic delivery of cell surface material significantly contributes to cell plate formation during plant cytokinesis. AU - Dhonukshe, Pankaj AU - Baluška, František AU - Schlicht, Markus AU - Hlavacka, Andrej AU - Šamaj, Jozef AU - Jirí Friml AU - Gadella, Theodorus W ID - 3006 IS - 1 JF - Developmental Cell TI - Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis VL - 10 ER - TY - JOUR AB - Polar flow of the phytohormone auxin requires plasma membrane‐associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed the importance of PIN polar positions for directional auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity signals directly demonstrates that PIN polarity is a primary factor in determining the direction of auxin flow in meristematic tissues. This finding provides a crucial piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN polarity. AU - Wiśniewska, Justyna AU - Xu, Jian AU - Seifertová, Daniela AU - Brewer, Philip B AU - Růžička, Kamil AU - Blilou, Ikram AU - Rouquié, David AU - Eva Benková AU - Scheres, Ben AU - Jirí Friml ID - 3011 IS - 5775 JF - Science TI - Polar PIN localization directs auxin flow in plants VL - 312 ER -