We argue that while fluctuating fronts propagating into an unstable state should be in the standard Kardar-Parisi-Zhang (KPZ) universality class when they are pushed, they should not when they are... Show moreWe argue that while fluctuating fronts propagating into an unstable state should be in the standard Kardar-Parisi-Zhang (KPZ) universality class when they are pushed, they should not when they are pulled: The 1/t velocity relaxation of deterministic pulled fronts makes it unlikely that the KPZ equation is their proper effective long-wavelength low-frequency theory. Simulations in 2D confirm the proposed scenario, and yield exponents beta approximately 0.29+/-0.01, zeta approximately 0.40+/-0.02 for fluctuating pulled fronts, instead of the (1+1)D KPZ values beta = 1/3, zeta = 1/2. Our value of beta is consistent with an earlier result of Riordan et al., and with a recent conjecture that the exponents are the (2+1)D KPZ values. Show less
Rhizobia are soil bacteria that can engage in a symbiosis with leguminous plants that produces nitrogen-fixing root nodules. This symbiosis is based on specific recognition of signal molecules,... Show moreRhizobia are soil bacteria that can engage in a symbiosis with leguminous plants that produces nitrogen-fixing root nodules. This symbiosis is based on specific recognition of signal molecules, which are produced by both the bacterial and plant partners. In this review, recognition factors from the bacterial endosymbionts are discussed, with particular attention to secreted and cell surface glycans. Glycans that are discussed include the Nod factors, the extracellular polysaccharides, the lipopolysaccharides, the K-antigens, and the cyclic glucans. Recent advances in the understanding of the biosynthesis, secretion, and regulation of production of these glycans are reviewed, and their functions are compared with glycans produced by other bacteria, such as plant pathogens. Show less
Solitons are non-dissipative, nontrivial solutions of partial differential equations. In many cases their stability is well understood, e.g. there can be topological reasons that prevent a... Show moreSolitons are non-dissipative, nontrivial solutions of partial differential equations. In many cases their stability is well understood, e.g. there can be topological reasons that prevent a localised lump of energy to dissolve and become dissipative. However, there are very persistent, soliton-like objects even when there is no obvious conservation law that would guarantee stability and explain longevity. This thesis considers such solutions, called oscillons, that appear in variety of nonlinear scalar theories. In essence, they are persistent oscillations of the field around the (local) minimum of the potential. A numerical study of oscillons in two spatial dimensions is presented. Use of absorbing boundary conditions in the numerical grid enables the study of radiation losses over a long period of time and permits quantitative approach to the lifetime of oscillons. Furthermore, it is shown that oscillons are emitted by collapsing domains, which way they could come into being in nature, e.g. in the conditions met in the very early Universe. Show less
ENOD40, an early nodulin gene, has been postulated to play a significant role in legume root nodule ontogenesis, We have isolated two distinct ENOD40 genes from Lotus japonicus, The transcribed... Show moreENOD40, an early nodulin gene, has been postulated to play a significant role in legume root nodule ontogenesis, We have isolated two distinct ENOD40 genes from Lotus japonicus, The transcribed regions of the two ENOD40 genes share 65% homology, while the two promoters showed no significant homology, Both transcripts encode a putative dodecapeptide similar to that identified in other legumes forming determinate nodules, Both ENOD40 genes are coordinately expressed following inoculation of roots with Mesorhizobium loti or treatment with purified Nod factors. In the former case, mRNA accumulation could be detected up to 10 days following inoculation while in the latter case the accumulation was transient. High levels of both ENOD40 gene transcripts were found in nonsymbiotic tissues such as stems, fully developed flowers, green seed pods, and hypocotyls, A relatively lower level of both transcripts was observed in leaves, roots, and cotyledons. In situ hybridization studies revealed that, in mature nodules, transcripts of both ENOD40 genes accumulate in the nodule vascular system; additionally, in young seed pods strong signal is observed in the ovule, particularly In the phloem and epithelium, as well as in globular stage embryos. Show less
Decreased phosphorylation of focal adhesion kinase and paxillin is associated with loss of focal adhesions and stress fibers and precedes the onset of apoptosis (van de Water, B., Nagelkerke, J. F... Show moreDecreased phosphorylation of focal adhesion kinase and paxillin is associated with loss of focal adhesions and stress fibers and precedes the onset of apoptosis (van de Water, B., Nagelkerke, J. F., and Stevens, J. L. (1999) J. Biol. Chem. 274, 13328-13337). The cortical actin cytoskeletal network is also lost during apoptosis, yet little is known about the temporal relationship between altered phosphorylation of proteins that are critical in the regulation of this network and their potential cleavage by caspases during apoptosis. Adducins are central in the cortical actin network organization. Cisplatin caused apoptosis of renal proximal tubular epithelial cells, which was associated with the cleavage of alpha-adducin into a 74-kDa fragment; this was blocked by a general caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone (z-VAD-fmk). Hemagglutinin-tagged human alpha-adducin was cleaved into a similar 74-kDa fragment by caspase-3 in vitro but not by caspase-6 or -7. Asp-Arg-Val-Asp(29)-Glu, Asp-Ile-Val-Asp(208)-Arg, and Asp-Asp-Ser-Asp(633)-Ala were identified as the principal caspase-3 cleavage sites; Asp-Asp-Ser-Asp(633)-Ala was key in the formation of the 74-kDa fragment. Cisplatin also caused an increased phosphorylation of alpha-adducin and gamma-adducin in the MARCKS domain that preceded alpha-adducin cleavage and was associated with loss of adducins from adherens junctions; this was not affected by z-VAD-fmk. In conclusion, the data support a model in which increased phosphorylation of alpha-adducin due to cisplatin leads to dissociation from the cytoskeleton, a situation rendered irreversible by caspase-3-mediated cleavage of alpha-adducin at Asp-Asp-Ser-Asp(633)-Ala. Show less
Ovtsyna, A.O.; Schultze, M.; Tikhonovich, I.A.; Spaink, H.P.; Kondorosi, E.; Kondorosi, A.; Staehelin, C. 2000
Nod factors (NFs) are rhizobial lipo-chitooligosaccharide signals that trigger root nodule development in legumes. Modifications of NF structures influence their biological activity and affect... Show moreNod factors (NFs) are rhizobial lipo-chitooligosaccharide signals that trigger root nodule development in legumes. Modifications of NF structures influence their biological activity and affect their degradation by plant chitinases. Nodulation of certain pea cultivars by Rhizobium leguminosarum by. viciae requires modification of NFs at the reducing end by either an O-acetyl or a fucosyl group. Fucosylated NFs were produced by an in vitro reaction with NodZ fucosyltransferase and purified. Their biological activity on pea was tested by measuring their capacity to stimulate the activity of a hydrolase that cleaves NFs, Nonmodified and fucosylated NFs displayed this activity at nano- to picomolar concentrations, while a sulfated NF from Sinorhizobium meliloti was inactive. In an additional series of experiments, the stability of non-modified and fucosylated NFs in the presence of purified tobacco chitinases was compared. The presence of the fucosyl group affected the degradation rates and the accessibility of specific cleavage sites on the chitooligosaccharide backbone. These results suggest that the fucosyl group in NFs also weakens the interaction of NFs with certain chitinases or chitinase-related proteins in pea roots. Show less
Lipo-chitin oligosaecharides (LCOs) are usually produced and isolated for structural analysis from bacteria cultured under laboratory rather than field conditions. We have studied the influence of... Show moreLipo-chitin oligosaecharides (LCOs) are usually produced and isolated for structural analysis from bacteria cultured under laboratory rather than field conditions. We have studied the influence of bacterial growth temperature on the LCO structures produced by different Rhizobium leguminosarum strains, using thin-layer chromatographic, high-performance liquid chromatographic, and mass spectrometric analyses. Wild-type R, leguminosarum by. viciae Al was shown to produce larger relative amounts of nodX-mediated, acetylated LCOs at 12 degrees C than at 28 degrees C, indicating that the activity of nodX (a gene encoding an LCO O-acetyl transferase) is temperature dependent. Interestingly, symbiotic resistance genes sym1 and sym2 found in primitive pea cultivars are also temperature sensitive, only being active at low temperatures, at which they block nodulation by R. leguminosarum by. viciae strains lacking nodX: We therefore propose that the gene-for-gene relationship between plant and bacterium has a temperature-sensitive mechanism as an adaptation to environmental conditions. An R, leguminosarum by. trifolii strain was also shown to produce larger relative amounts of nodX-mediated, acetylated LCOs at 12 degrees C than at 28 degrees C. The major components synthesized by the two strains are produced at both temperatures but in different relative amounts, while some minor components are only produced at one of the two temperatures. Show less
We study the propagation of a "pulled" front with multiplicative noise that is created by a local perturbation of an unstable state. Unlike a front propagating into a metastable state, where a... Show moreWe study the propagation of a "pulled" front with multiplicative noise that is created by a local perturbation of an unstable state. Unlike a front propagating into a metastable state, where a separation of time scales for sufficiently large t creates a diffusive wandering of the front position about its mean, we predict that for so-called pulled fronts, the fluctuations are subdiffusive with root mean square wandering Delta(t) approximately t(1/4), not t(1/2). The subdiffusive behavior is confirmed by numerical simulations: For t600, these yield an effective exponent slightly larger than 1/4. Show less
A new method of computing using DNA plasmids is introduced and the potential advantages are listed. The new method is illustrated by reporting a laboratory computation of an instance of the NP... Show moreA new method of computing using DNA plasmids is introduced and the potential advantages are listed. The new method is illustrated by reporting a laboratory computation of an instance of the NP-complete algorithmic problem of computing the cardinal number of a maximal independent subset of the vertex set of a graph. A circular DNA plasmid, specifically designed for this method of molecular computing, was constructed. This computational plasmid contains a specially inserted series of DNA sequence segments, each of which is bordered by a characteristic pair of restriction enzyme sites. For the computation reported here, the DNA sequence segments of this series were used to represent the vertices of the graph being investigated. By applying a scheme of enzymatic treatments to the computational plasmids, modified plasmids were generated from which the solution of the computational problem was selected. This new method of computing is applicable to a wide variety of algorithmic problems. Further computations in this style are in progress. (C) 2000 Elsevier Science Ireland Ltd. All rights reserved. Show less
Storm, C.; Spruijt, W.; Ebert, U.; Saarloos, W. van 2000
We investigate the asymptotic relaxation of so-called pulled fronts propagating into an unstable state, and generalize the universal algebraic velocity relaxation of uniformly translating fronts to... Show moreWe investigate the asymptotic relaxation of so-called pulled fronts propagating into an unstable state, and generalize the universal algebraic velocity relaxation of uniformly translating fronts to fronts that generate periodic or even chaotic states. A surprising feature is that such fronts also exhibit a universal algebraic phase relaxation. For fronts that generate a periodic state, like those in the Swift-Hohenberg equation or in a Rayleigh-Benard experiment, this implies an algebraically slow relaxation of the pattern wavelength just behind the front, which should be experimentally testable. Show less
